Publications by the Center’s Members

2024

• Pawar, K, Kawamura, T, Kirino, Y. The tRNA^Val half: A strong endogenous Toll-like receptor 7 ligand with a 5′-terminal universal sequence signature. Proc Natl Acad Sci U S A. 2024;121 (19):e2319569121. doi: 10.1073/pnas.2319569121. PubMed PMID:38683985.
• Gumas, J, Kawamura, T, Shigematsu, M, Kirino, Y. Immunostimulatory short non-coding RNAs in the circulation of patients with tuberculosis infection. Mol Ther Nucleic Acids. 2024;35 (1):102156. doi: 10.1016/j.omtn.2024.102156. PubMed PMID:38481936 PubMed Central PMC10933579.

2023

• Akins, RB, Ostberg, K, Cherlin, T, Tsiouplis, NJ, Loher, P, Rigoutsos, I. The Typical tRNA Co-Expresses Multiple 5′ tRNA Halves Whose Sequences and Abundances Depend on Isodecoder and Isoacceptor and Change with Tissue Type, Cell Type, and Disease. Noncoding RNA. 2023;9 (6):. doi: 10.3390/ncrna9060069. PubMed PMID:37987365 PubMed Central PMC10660753.
• Pliatsika, V, Cherlin, T, Loher, P, Vlantis, P, Nagarkar, P, Nersisyan, S, Rigoutsos, I. MINRbase: a comprehensive database of nuclear- and mitochondrial-ribosomal-RNA-derived fragments (rRFs). Nucleic Acids Res. 2023; :. doi: 10.1093/nar/gkad833. PubMed PMID:37843123.
• Nersisyan, S, Montenont, E, Loher, P, Middleton, EA, Campbell, R, Bray, P, Rigoutsos, I. Characterization of all small RNAs in and comparisons across cultured megakaryocytes and platelets of healthy individuals and COVID-19 patients. J Thromb Haemost. 2023;21 (11):3252-3267. doi: 10.1016/j.jtha.2023.07.028. PubMed PMID:37558133 .
• Zebrowski, AM, Loher, P, Buckler, DG, Rigoutsos, I, Carr, BG, Wiebe, DJ. Using medicare claims to estimate risk-adjusted performance of Pennsylvania trauma centers. PLOS Digit Health. 2023;2 (6):e0000263. doi: 10.1371/journal.pdig.0000263. PubMed PMID:37267229 PubMed Central PMC10237397.

2022

• Karathanasis N, Hwang D, Heng V, Abhimannyu R, Slogoff-Sevilla P, Buchel G, Frisbie V, Li P, Kryoneriti D, Rigoutsos I. Reproducibility efforts as a teaching tool: A pilot study. PLoS Comput Biol. 2022 Nov 10;18(11):e1010615. doi: 10.1371/journal.pcbi.1010615. PubMed PMID: 36355750 PubMed Central PMCID: PMC9648701.
• Welch DR, Foster C, Rigoutsos I. Roles of mitochondrial genetics in cancer metastasis. Trends Cancer. 2022 Jul 29;S2405-8033(22)00157-1. doi: 10.1016/j.trecan.2022.07.004. PubMed PMID:35915015.
• Hope, JL, Zhao, M, Stairiker, CJ, Kiernan, CH, Carey, AJ, Mueller, YM, van Meurs, M, Brouwers-Haspels, I, Otero, DC, Bae, EA, Faso, HA, Maas, A, de Looper, H, Fortina, PM, Rigoutsos, I, Bradley, LM, Erkeland, SJ, Katsikis, PD. MicroRNA-139 Expression Is Dispensable for the Generation of Influenza-Specific CD8⁺ T Cell Responses. J Immunol. 2022;208 (3):603-617. doi: 10.4049/jimmunol.2000621. PubMed PMID:35022277 PubMed Central PMC10118001.
• Bhatlekar S, Jacob S, Tugolukova E, Manne BK, Kosaka Y, Loher P, O’Connell RM, Planelles V, Rondina MT, Rigoutsos I, Bray PF. Interferon α-induced SAMHD1 regulates human cultured megakaryocyte apoptosis and proplatelet formation. Haematologica. 2022 Feb 1;107(2):558-561. doi: 10.3324/haematol.2021.279864. PubMed PMID:34758609 PubMed Central PMCID:PMC8804568.
• Clemente, P, Calvo-Garrido, J, Pearce, SF, Schober, FA, Shigematsu, M, Siira, SJ, Laine, I, Spåhr, H, Steinmetzger, C, Petzold, K, Kirino, Y, Wibom, R, Rackham, O, Filipovska, A, Rorbach, J, Freyer, C, Wredenberg, A. ANGEL2 phosphatase activity is required for non-canonical mitochondrial RNA processing. Nat Commun. 2022;13 (1):5750. doi: 10.1038/s41467-022-33368-9. PubMed PMID:36180430 PubMed Central PMC9525292.
• Shigematsu, M, Kirino, Y. Making Invisible RNA Visible: Discriminative Sequencing Methods for RNA Molecules with Specific Terminal Formations. Biomolecules. 2022;12 (5):. doi: 10.3390/biom12050611. PubMed PMID:35625540 PubMed Central PMC9138997.

2021

• Bhatlekar, S, Jacob, S, Manne, BK, Guo, L, Denorme, F, Tugolukova, EA, Cody, MJ, Kosaka, Y, Rigoutsos, I, Campbell, RA, Rowley, JW, O’Connell, RM, Bray, PF. Megakaryocyte-specific knockout of the Mir-99b/let7e/125a cluster lowers platelet count without altering platelet function. Blood Cells Mol Dis. 2021;92 :102624. doi: 10.1016/j.bcmd.2021.102624. PubMed PMID:34775219 PubMed Central PMC8682963.
• Tanaka, R, Terai, M, Londin, E, Sato, T. The Role of HGF/MET Signaling in Metastatic Uveal Melanoma. Cancers (Basel). 2021;13 (21):. doi: 10.3390/cancers13215457. PubMed PMID:34771620 PubMed Central PMC8582360.
• Broseghini, E, Dika, E, Londin, E, Ferracin, M. MicroRNA Isoforms Contribution to Melanoma Pathogenesis. Noncoding RNA. 2021;7 (4):. doi: 10.3390/ncrna7040063. PubMed PMID:34698264 PubMed Central PMC8544706.
• Zingone A, Sinha S, Ante M, Nguyen C, Daujotyte D, Bowman ED, Sinha N, Mitchell KA, Chen Q, Yan C, Loher P, Meerzaman D, Ruppin E, Ryan BM. A comprehensive map of alternative polyadenylation in African American and European American lung cancer patients. Nat Commun. 2021 Sep 23;12(1):5605. doi: 10.1038/s41467-021-25763-5. PubMed PMID:34556645.
• Shigematsu M, Kawamura T, Morichika K, Izumi N, Kiuchi T, Honda S, Pliatsika V, Matsubara R, Rigoutsos I, Katsuma S, Tomari Y, Kirino Y. RNase κ promotes robust piRNA production by generating 2′,3′-cyclic phosphate-containing precursors. Nat Commun. 2021 Jul 23;12(1):4498. doi: 10.1038/s41467-021-24681-w. PubMed PMID:34301931.
• Kaufman EJ, Zebrowski AM, Holena DN, Loher P, Wiebe DJ, Carr BG. The Short and the Long of it: Timing of Mortality for Older Adults in a State Trauma System. J Surg Res. 2021 Jul 16;268:17-24. doi: 10.1016/j.jss.2021.06.042. Epub ahead of print. PubMed PMID:34280661.
• Xu, J, Crossley, E, Wagenfuehr, J, Mitui, M, Londin, E, Patel, K, Park, JY. Control Charting Genomic Data. J Appl Lab Med. 2021;6 (4):892-901. doi: 10.1093/jalm/jfaa201. PubMed PMID:33319223 .
• Dika E, Broseghini E, Porcellini E, Lambertini M, Riefolo M, Durante G, Loher P, Roncarati R, Bassi C, Misciali C, Negrini M, Rigoutsos I, Londin E, Patrizi A, Ferracin M. Unraveling the role of microRNA/isomiR network in multiple primary melanoma pathogenesis. Cell Death Dis. 2021 May 12;12(5):473. doi: 10.1038/s41419-021-03764-y. PubMed PMID:33980826.
• Kawamura T, Shigematsu M, Kirino Y. In vitro production and multiplex quantification of 2′,3′-cyclic phosphate-containing 5′-tRNA half molecules. Methods. 2021 May 4:S1046-2023(21)00124-9. doi: 10.1016/j.ymeth.2021.04.024. Epub ahead of print. PubMed PMID:33962012.
• Telonis AG, Rigoutsos I. The transcriptional trajectories of pluripotency and differentiation comprise genes with antithetical architecture and repetitive-element content. BMC Biol. 2021 Mar 25;19(1):60. doi: 10.1186/s12915-020-00928-8. PubMed PMID:33765992.
• Loher P, Karathanasis N. Machine Learning Approaches Identify Genes Containing Spatial Information From Single-Cell Transcriptomics Data. Front Genet. 2021 Feb 1;11:612840. doi: 10.3389/fgene.2020.612840. PubMed PMID:33633771 PubMed Central PMCID:PMC7902049.
• Loher P, Karathanasis N, Londin E, Bray P, Pliatsika V, Telonis AG, Rigoutsos I. IsoMiRmap-fast, deterministic, and exhaustive mining of isomiRs from short RNA-seq datasets. Bioinformatics. 2021 Jan 20:btab016. doi: 10.1093/bioinformatics/btab016. Epub ahead of print. PubMed PMID:33471076.

2020

• Giuliani, A, Londin, E, Ferracin, M, Mensà, E, Prattichizzo, F, Ramini, D, Marcheselli, F, Recchioni, R, Rippo, MR, Bonafè, M, Rigoutsos, I, Olivieri, F, Sabbatinelli, J. Long-term exposure of human endothelial cells to metformin modulates miRNAs and isomiRs. Sci Rep. 2020;10 (1):21782. doi: 10.1038/s41598-020-78871-5. PubMed PMID:33311640 PubMed Central PMC7732983.
• Vrettos N, Maragkakis M, Alexiou P, Sgourdou P, Ibrahim F, Palmieri D, Kirino Y, Mourelatos Z. Modulation of Aub-TDRD interactions elucidates piRNA amplification and germplasm formation. Life Sci Alliance. 2020 Dec 29;4(3):e202000912. doi: 10.26508/lsa.202000912. PubMed PMID:33376130 PubMed Central PMCID:PMC7772777.
• Pawar K, Shigematsu M, Sharbati S, Kirino Y. Infection-induced 5′-half molecules of tRNAHisGUG activate Toll-like receptor 7. PLoS Biol. 2020 Dec 17;18(12):e3000982. doi: 10.1371/journal.pbio.3000982. PubMed PMID:33332353.
• Tanevski, J, Nguyen, T, Truong, B, Karaiskos, N, Ahsen, ME, Zhang, X, Shu, C, Xu, K, Liang, X, Hu, Y, Pham, HV, Xiaomei, L, Le, TD, Tarca, AL, Bhatti, G, Romero, R, Karathanasis, N, Loher, P, Chen, Y, Ouyang, Z, Mao, D, Zhang, Y, Zand, M, Ruan, J, Hafemeister, C, Qiu, P, Tran, D, Nguyen, T, Gabor, A, Yu, T, Guinney, J, Glaab, E, Krause, R, Banda, P; DREAM SCTC Consortium, Stolovitzky, G, Rajewsky, N, Saez-Rodriguez, J, Meyer, P. Gene selection for optimal prediction of cell position in tissues from single-cell transcriptomics data. Life Sci Alliance. 2020 Sep 24;3(11):e202000867. doi: 10.26508/lsa.202000867. PubMed PMID:32972997.
• Magee, R, Rigoutsos, I. On the expanding roles of tRNA fragments in modulating cell behavior. Nucleic Acids Res. 2020 Sep 25;48(17):9433-9448. doi: 10.1093/nar/gkaa657. PubMed PMID:32890397.
• Suzuki T, Yashiro Y, Kikuchi I, Ishigami Y, Saito H, Matsuzawa I, Okada S, Mito M, Iwasaki S, Ma D, Zhao X, Asano K, Lin H, Kirino Y, Sakaguchi Y, Suzuki T. Complete chemical structures of human mitochondrial tRNAs. Nat Commun. 2020 Aug 28;11(1):4269. doi: 10.1038/s41467-020-18068-6. PubMed PMID:32859890 PubMed Central PMC7455718.
• Shigematsu, M, Kirino, Y. Oxidative stress enhances the expression of 2′,3′-cyclic phosphate-containing RNAs. RNA Biol. 2020. doi: 10.1080/15476286.2020.1766861. PubMed PMID:32397797.
• Charalambidis, A, Chatziagapis, G, Rondogiannis, P. A fixed point theorem on lexicographic lattice structures. LICS ’20: 35th annual ACM/IEEE symposium on logic in computer science, Saarbrücken, Germany, July 8-11, 2020 [Internet]. ACM 2020;301–11. doi: 10.1145/3373718.3394797
• Cherlin, T, Magee, R, Jing, Y, Pliatsika, V, Loher, P, Rigoutsos, I. Ribosomal RNA fragmentation into short RNAs (rRFs) is modulated in a sex- and population of origin-specific manner. BMC Biol 18, 38 (2020). doi: 10.1186/s12915-020-0763-0. PubMed PMID:32279660.
• Pichler, M, Rodriguez-Aguayo, C, Nam, SY, Dragomir, MP, Bayraktar, R, Anfossi, S, Knutsen, E, Ivan, C, Fuentes-Mattei, E, Lee, SK, Ling, H, Catela Ivkovic, T, Huang, G, Huang, L, Okugawa, Y, Katayama, H, Taguchi, A, Bayraktar, E, Bhattacharya, R, Amero, P, He, WR, Tran, AM, Vychytilova-Faltejskova, P, Klec, C, Bonilla, DL, Zhang, X, Kapitanovic, S, Loncar, B, Gafà, R, Wang, Z, Cristini, V, Hanash, SM, Bar-Eli, M, Lanza, G, Slaby, O, Goel, A, Rigoutsos, I, Lopez-Berestein, G, Calin, GA. Therapeutic potential of FLANC, a novel primate-specific long non-coding RNA in colorectal cancer. Gut Published Online First: 27 January 2020. doi: 10.1136/gutjnl-2019-318903. PubMed PMID:31988194
• Salcedo, A, Tarabichi, M, Espiritu, SMG, Deshwar, AG, David, M, Wilson, NM, Dentro, S, Wintersinger, JA, Liu, LY, Ko, M, Sivanandan, S, Zhang, H, Zhu, K, Ou Yang, TH, Chilton, JM, Buchanan, A, Lalansingh, CM, P’ng, C, Anghel, CV, Umar, I, Lo, B, Zou, W; DREAM SMC-Het Participants, Simpson, JT, Stuart, JM, Anastassiou, D, Guan, Y, Ewing, AD, Ellrott, K, Wedge, DC, Morris, Q, Van Loo, P, Boutros, PC. A community effort to create standards for evaluating tumor subclonal reconstruction. Nat Biotechnol. 2020;38(1):97–107. doi: 10.1038/s41587-019-0364-z. PubMed PMID:31919445.
• Terai, M, Londin, E, Rochani, A, Link, E, Lam, B, Kaushal, G, Bhushan, A, Orloff, M, Sato, T. Expression of Tryptophan 2,3-Dioxygenase in Metastatic Uveal Melanoma. Cancers (Basel). 2020;12 (2):. doi: 10.3390/cancers12020405. PubMed PMID:32050636 PubMed Central PMC7072257.

2019

• Simonneau C, Yang J, Kong X, Kilker R, Edelstein L, Fortina P, Londin E, Horowitz A. Validation of a Miniaturized Permeability Assay Compatible with CRISPR-Mediated Genome-Wide Screen. Sci Rep. 2019 Oct 2;9(1):14238. doi: 10.1038/s41598-019-50588-0. PubMed PMID: 31578372 PubMed Central PMCID: PMC6775082.
• Shigematsu, M, Morichika, K, Kawamura, T, Honda, S, Kirino, Y. Genome-wide identification of short 2′,3′-cyclic phosphate-containing RNAs and their regulation in aging. PLoS Genet. 2019 Nov 13;15(11):e1008469. doi: 10.1371/journal.pgen.1008469. PubMed PMID:31721758.
• Parasido, E, Avetian, GS, Naeem, A, Graham, G, Pishvaian, M, Glasgow, E, Mudambi, S, Lee, Y, Ihemelandu, C, Choudhry, M, Peran, I, Banerjee, PP, Avantaggiati, ML, Bryant, K, Baldelli, E, Pierobon, M, Liotta, L, Petricoin, E, Fricke, ST, Sebastian, A, Cozzitorto, J, Loots, GG, Kumar, D, Byers, S, Londin, E, DiFeo, A, Narla, G, Winter, J, Brody, JR, Rodriguez, O, Albanese, C. The Sustained Induction of c-MYC Drives Nab-Paclitaxel Resistance in Primary Pancreatic Ductal Carcinoma Cells. Mol Cancer Res. 2019;17 (9):1815-1827. doi: 10.1158/1541-7786.MCR-19-0191. PubMed PMID:31164413 PubMed Central PMC6726538.
• Pawar, K, Shigematsu, M, Loher, P, Honda, S, Rigoutsos, I, Kirino, Y. Exploration of CCA-added RNAs revealed the expression of mitochondrial non-coding RNAs regulated by CCA-adding enzyme. RNA Biol. 2019 Sep 12:1-9. doi: 10.1080/15476286.2019.1664885. PubMed PMID:31512554.
• Desvignes, T, Loher, P, Eilbeck, K, Ma, J, Urgese, G, Fromm, B, Sydes, J, Aparicio-Puerta, E, Barrera, V, Espín, R, Thibord, F, Ros, XB, Londin, E, Telonis, AG, Ficarra, E, Friedländer, MR, Postlethwait, JH, Rigoutsos, I, Hackenberg, M, Vlachos, IS, Halushka, MK, Pantano, L. Unification of miRNA and isomiR research: the mirGFF3 format and the mirtop API. Bioinformatics. 2019 Aug 29. doi: 10.1093/bioinformatics/btz675. PubMed PMID:31504201.
• Rigoutsos, I, Londin, E, Kirino, Y. Short RNA regulators: the past, the present, the future, and implications for precision medicine and health disparities. Curr Opin Biotechnol. 2019 Aug;58:202-210. doi: 10.1016/j.copbio.2019.05.014. PubMed PMID:31323485.
• Fernandes, SJ, Morikawa, H, Ewing, E, Ruhrmann, S, Joshi, RN, Lagani, V, Karathanasis, N, Khademi, M, Planell, N, Schmidt, A, Tsamardinos, I, Olsson, T, Piehl, F, Kockum, I, Jagodic, M, Tegnér, J, Gomez-Cabrero, D. Non-parametric combination analysis of multiple data types enables detection of novel regulatory mechanisms in T cells of multiple sclerosis patients. Sci Rep. 2019 Aug 19;9(1):11996. doi: 10.1038/s41598-019-48493-7. PubMed PMID:31427643.
• Londin, E, Magee, R, Shields, CL, Lally, SE, Sato, T, Rigoutsos, I. IsomiRs and tRNA-derived Fragments are Associated with Metastasis and Patient Survival in Uveal Melanoma. Pigment Cell Melanoma Res. 2019; :. doi: 10.1111/pcmr.12810. PubMed PMID:31283110.
• Magee, R, Londin, E, Rigoutsos, I. tRNA-derived fragments as sex-dependent circulating candidate biomarkers for Parkinson’s disease. Parkinsonism Relat Disor Aug 2019 May 25;65:203-209. doi: 10.1016/j.parkreldis.2019.05.035. PubMed PMID:31402278.
• Ewing, E, Kular, L, Fernandes, SJ, Karathanasis, N, Lagani, V, Ruhrmann, S, Tsamardinos, I, Tegner, J, Piehl, F, Gomez-Cabrero, D, Maja Jagodic, M. Combining evidence from four immune cell types identifies DNA methylation patterns that implicate functionally distinct pathways during Multiple Sclerosis progression. EBioMedicine 2019 Apr 30. doi: 10.1016/j.ebiom.2019.04.042. PubMed PMID:31053557.
• Telonis, AG, Loher, P, Magee, R, Pliatsika, V, Londin, E, Kirino, Y, Rigoutsos, I. tRNA Fragments Show Intertwining with mRNAs of Specific Repeat Content and Have Links to Disparities. Cancer Res. 2019 Apr 17. doi: 10.1158/0008-5472.CAN-19-0789. PubMed PMID:30996049.
• Srinivasan, S, Yeri, A, Cheah, PS, Chung, A, Danielson, K, De, Hoff, P, Filant, J, Laurent, CD, Laurent, LD, Magee, R, Moeller, C, Murthy, VL, Nejad, P, Paul, A, Rigoutsos, I, Rodosthenous, R, Shah, RV, Simonson, B, To, C, Wong, D, Yan, IK, Zhang, X, Balaj, L, Breakefield, XO, Daaboul, G, Gandhi, R, Lapidus, J, Londin, E, Patel, T, Raffai, RL, Sood, AK, Alexander, RP, Das, S, Laurent, LC. Small RNA Sequencing across Diverse Biofluids Identifies Optimal Methods for exRNA Isolation. Cell. 2019 Apr 4;177(2):446-462.e16. doi: 10.1016/j.cell.2019.03.024. PubMed PMID:30951671.
• Paolillo, C, Londin, E, Fortina, P. Single-Cell Genomics. Clin Chem. 2019;65 (8):972-985. doi: 10.1373/clinchem.2017.283895. PubMed PMID:30872376 .
• Youssefian, L, Vahidnezhad, H, Saeidian, AH, Touati, A, Sotoudeh, S, Mahmoudi, H, Mansouri, P, Daneshpazhooh, M, Aghazadeh, N, Hesari, KK, Basiri, M, Londin, E, Kumar, G, Zeinali, S, Fortina, P, Uitto, J. Autosomal recessive congenital ichthyosis: Genomic landscape and phenotypic spectrum in a cohort of 125 consanguineous families. Hum Mutat. 2019;40 (3):288-298. doi: 10.1002/humu.23695. PubMed PMID:30578701 .
• Yang, J, Simonneau, C, Kilker, R, Oakley, L, Byrne, MD, Nichtova, Z, Stefanescu, I, Pardeep-Kumar, F, Tripathi, S, Londin, E, Saugier-Veber, P, Willard, B, Thakur, M, Pickup, S, Ishikawa, H, Schroten, H, Smeyne, R, Horowitz, A. Murine MPDZ-linked hydrocephalus is caused by hyperpermeability of the choroid plexus. EMBO Mol Med. 2019;11 (1):. doi: 10.15252/emmm.201809540. PubMed PMID:30518636 PubMed Central PMC6328942.
• Jain, A, Brown, SZ, Thomsett, HL, Londin, E, Brody, JR. Evaluation of Post-transcriptional Gene Regulation in Pancreatic Cancer Cells: Studying RNA Binding Proteins and Their mRNA Targets. Methods Mol Biol. 2019;1882 :239-252. doi: 10.1007/978-1-4939-8879-2_22. PubMed PMID:30378060 .
• Nevler, A, Muller, AJ, Sutanto-Ward, E, DuHadaway, JB, Nagatomo, K, Londin, E, O’Hayer, K, Cozzitorto, JA, Lavu, H, Yeo, TP, Curtis, M, Villatoro, T, Leiby, BE, Mandik-Nayak, L, Winter, JM, Yeo, CJ, Prendergast, GC, Brody, JR. Host IDO2 Gene Status Influences Tumor Progression and Radiotherapy Response in KRAS-Driven Sporadic Pancreatic Cancers. Clin Cancer Res. 2019;25 (2):724-734. doi: 10.1158/1078-0432.CCR-18-0814. PubMed PMID:30266763 PubMed Central PMC6335160.

2018

• Shigematsu, M, Kawamura, T, Kirino, Y. Generation of 2′,3′-Cyclic Phosphate-Containing RNAs as a Hidden Layer of the Transcriptome. Front Genet. 2018;9 :562. doi: 10.3389/fgene.2018.00562. PubMed PMID:30538719 PubMed Central PMC6277466.
• Magee, RG, Telonis, AG, Loher, P, Londin, E, Rigoutsos, I. Profiles of miRNA Isoforms and tRNA Fragments in Prostate Cancer. Sci Rep. 2018;8 (1):5314. doi: 10.1038/s41598-018-22488-2. PubMed PMID:29593348 PubMed Central PMC5871839.
• Telonis, AG, Rigoutsos, I. Race Disparities in the Contribution of miRNA Isoforms and tRNA-Derived Fragments to Triple-Negative Breast Cancer. Cancer Res. 2018;78 (5):1140-1154. doi: 10.1158/0008-5472.CAN-17-1947. PubMed PMID:29229607 PubMed Central PMC5935570.
• Sponziello, M, Benvenuti, S, Gentile, A, Pecce, V, Rosignolo, F, Virzì, AR, Milan, M, Comoglio, PM, Londin, E, Fortina, P, Barnabei, A, Appetecchia, M, Marandino, F, Russo, D, Filetti, S, Durante, C, Verrienti, A. Whole exome sequencing identifies a germline MET mutation in two siblings with hereditary wild-type RET medullary thyroid cancer. Hum. Mutat. 2018;39 (3):371-377. doi: 10.1002/humu.23378. PubMed PMID:29219214 .
• Pliatsika, V, Loher, P, Magee, R, Telonis, AG, Londin, E, Shigematsu, M, Kirino, Y, Rigoutsos, I. MINTbase v2.0: a comprehensive database for tRNA-derived fragments that includes nuclear and mitochondrial fragments from all The Cancer Genome Atlas projects. Nucleic Acids Res. 2018;46 (D1):D152-D159. doi: 10.1093/nar/gkx1075. PubMed PMID:29186503 PubMed Central PMC5753276.
• Vahidnezhad, H, Youssefian, L, Saeidian, AH, Mahmoudi, H, Touati, A, Abiri, M, Kajbafzadeh, AM, Aristodemou, S, Liu, L, McGrath, JA, Ertel, A, Londin, E, Kariminejad, A, Zeinali, S, Fortina, P, Uitto, J. Recessive mutation in tetraspanin CD151 causes Kindler syndrome-like epidermolysis bullosa with multi-systemic manifestations including nephropathy. Matrix Biol. 2018;66 :22-33. doi: 10.1016/j.matbio.2017.11.003. PubMed PMID:29138120 .
• Loher, P, Telonis, AG, Rigoutsos, I. Accurate Profiling and Quantification of tRNA Fragments from RNA-Seq Data: A Vade Mecum for MINTmap. Methods Mol. Biol. 2018;1680 :237-255. doi: 10.1007/978-1-4939-7339-2_16. PubMed PMID:29030853 .
• Shigematsu, M, Honda, S, Kirino, Y. Dumbbell-PCR for Discriminative Quantification of a Small RNA Variant. Methods Mol. Biol. 2018;1680 :65-73. doi: 10.1007/978-1-4939-7339-2_4. PubMed PMID:29030841 .
• Andrabi, SBA, Tahara, M, Matsubara, R, Toyama, T, Aonuma, H, Sakakibara, H, Suematsu, M, Tanabe, K, Nozaki, T, Nagamune, K. Plant hormone cytokinins control cell cycle progression and plastid replication in apicomplexan parasites. Parasitol. Int. 2018;67 (1):47-58. doi: 10.1016/j.parint.2017.03.003. PubMed PMID:28344153 .
• Shigematsu, M, Kirino, Y. 5′-Terminal nucleotide variations in human cytoplasmic tRNAHisGUG and its 5′-halves. RNA. 2017;23 (2):161-168. doi: 10.1261/rna.058024.116. PubMed PMID:27879434 PubMed Central PMC5238791.

2017

• Yao, B, Mandrà, S, Curry, JO, Shaikhutdinov, S, Freund, HJ, Schrier, J. Gas Separation through Bilayer Silica, the Thinnest Possible Silica Membrane. ACS Appl Mater Interfaces. 2017;9 (49):43061-43071. doi: 10.1021/acsami.7b13302. PubMed PMID:29156127 .
• Cancer Genome Atlas Research Network. Electronic address: andrew_aguirre@dfci.harvard.edu, Cancer Genome Atlas Research Network. Integrated Genomic Characterization of Pancreatic Ductal Adenocarcinoma. Cancer Cell. 2017;32 (2):185-203.e13. doi: 10.1016/j.ccell.2017.07.007. PubMed PMID:28810144 PubMed Central PMC5964983.
• Magee, R, Telonis, AG, Cherlin, T, Rigoutsos, I, Londin, E. Assessment of isomiR Discrimination Using Commercial qPCR Methods. Noncoding RNA. 2017;3 (2):. doi: 10.3390/ncrna3020018. PubMed PMID:28730153 PubMed Central PMC5514785.
• Chand, SN, Zarei, M, Schiewer, MJ, Kamath, AR, Romeo, C, Lal, S, Cozzitorto, JA, Nevler, A, Scolaro, L, Londin, E, Jiang, W, Meisner-Kober, N, Pishvaian, MJ, Knudsen, KE, Yeo, CJ, Pascal, JM, Winter, JM, Brody, JR. Posttranscriptional Regulation of PARG mRNA by HuR Facilitates DNA Repair and Resistance to PARP Inhibitors. Cancer Res. 2017;77 (18):5011-5025. doi: 10.1158/0008-5472.CAN-16-2704. PubMed PMID:28687616 PubMed Central PMC5663502.
• Zarei, M, Lal, S, Parker, SJ, Nevler, A, Vaziri-Gohar, A, Dukleska, K, Mambelli-Lisboa, NC, Moffat, C, Blanco, FF, Chand, SN, Jimbo, M, Cozzitorto, JA, Jiang, W, Yeo, CJ, Londin, ER, Seifert, EL, Metallo, CM, Brody, JR, Winter, JM. Posttranscriptional Upregulation of IDH1 by HuR Establishes a Powerful Survival Phenotype in Pancreatic Cancer Cells. Cancer Res. 2017;77 (16):4460-4471. doi: 10.1158/0008-5472.CAN-17-0015. PubMed PMID:28652247 PubMed Central PMC5922269.
• Honda, S, Loher, P, Morichika, K, Shigematsu, M, Kawamura, T, Kirino, Y, Rigoutsos, I, Kirino, Y. Increasing cell density globally enhances the biogenesis of Piwi-interacting RNAs in Bombyx mori germ cells. Sci Rep. 2017;7 (1):4110. doi: 10.1038/s41598-017-04429-7. PubMed PMID:28646211 PubMed Central PMC5482885.
• Honda, S, Kawamura, T, Loher, P, Morichika, K, Rigoutsos, I, Kirino, Y. The biogenesis pathway of tRNA-derived piRNAs in Bombyx germ cells. Nucleic Acids Res. 2017;45 (15):9108-9120. doi: 10.1093/nar/gkx537. PubMed PMID:28645172 PubMed Central PMC5587776.
• Hou, YM, Matsubara, R, Takase, R, Masuda, I, Sulkowska, JI. TrmD: A Methyl Transferase for tRNA Methylation With m¹G37. Enzymes. 2017;41 :89-115. doi: 10.1016/bs.enz.2017.03.003. PubMed PMID:28601227 PubMed Central PMC6054489.
• Rigoutsos, I, Lee, SK, Nam, SY, Anfossi, S, Pasculli, B, Pichler, M, Jing, Y, Rodriguez-Aguayo, C, Telonis, AG, Rossi, S, Ivan, C, Catela Ivkovic, T, Fabris, L, Clark, PM, Ling, H, Shimizu, M, Redis, RS, Shah, MY, Zhang, X, Okugawa, Y, Jung, EJ, Tsirigos, A, Huang, L, Ferdin, J, Gafà, R, Spizzo, R, Nicoloso, MS, Paranjape, AN, Shariati, M, Tiron, A, Yeh, JJ, Teruel-Montoya, R, Xiao, L, Melo, SA, Menter, D, Jiang, ZQ, Flores, ER, Negrini, M, Goel, A, Bar-Eli, M, Mani, SA, Liu, CG, Lopez-Berestein, G, Berindan-Neagoe, I, Esteller, M, Kopetz, S, Lanza, G, Calin, GA. N-BLR, a primate-specific non-coding transcript leads to colorectal cancer invasion and migration. Genome Biol. 2017;18 (1):98. doi: 10.1186/s13059-017-1224-0. PubMed PMID:28535802 PubMed Central PMC5442648.
• Matsubara, R, Fukuda, Y, Murakoshi, F, Nomura, O, Suzuki, T, Tada, C, Nakai, Y. Detection and molecular status of Isospora sp. from the domestic pigeon (Columba livia domestica). Parasitol. Int. 2017;66 (5):588-592. doi: 10.1016/j.parint.2017.05.004. PubMed PMID:28495225 .
• Lal, S, Cheung, EC, Zarei, M, Preet, R, Chand, SN, Mambelli-Lisboa, NC, Romeo, C, Stout, MC, Londin, E, Goetz, A, Lowder, CY, Nevler, A, Yeo, CJ, Campbell, PM, Winter, JM, Dixon, DA, Brody, JR. CRISPR Knockout of the HuR Gene Causes a Xenograft Lethal Phenotype. Mol. Cancer Res. 2017;15 (6):696-707. doi: 10.1158/1541-7786.MCR-16-0361. PubMed PMID:28242812 PubMed Central PMC5466444.
• Loher, P, Telonis, AG, Rigoutsos, I. MINTmap: fast and exhaustive profiling of nuclear and mitochondrial tRNA fragments from short RNA-seq data. Sci Rep. 2017;7 :41184. doi: 10.1038/srep41184. PubMed PMID:28220888 PubMed Central PMC5318995.
• Telonis, AG, Magee, R, Loher, P, Chervoneva, I, Londin, E, Rigoutsos, I. Knowledge about the presence or absence of miRNA isoforms (isomiRs) can successfully discriminate amongst 32 TCGA cancer types. Nucleic Acids Res. 2017;45 (6):2973-2985. doi: 10.1093/nar/gkx082. PubMed PMID:28206648 PubMed Central PMC5389567.
• Magee, R, Loher, P, Londin, E, Rigoutsos, I. Threshold-seq: a tool for determining the threshold in short RNA-seq datasets. Bioinformatics. 2017;33 (13):2034-2036. doi: 10.1093/bioinformatics/btx073. PubMed PMID:28203700 PubMed Central PMC5870860.
• Shigematsu, M, Honda, S, Loher, P, Telonis, AG, Rigoutsos, I, Kirino, Y. YAMAT-seq: an efficient method for high-throughput sequencing of mature transfer RNAs. Nucleic Acids Res. 2017;45 (9):e70. doi: 10.1093/nar/gkx005. PubMed PMID:28108659 PubMed Central PMC5605243.

2016

• Karathanasis, N, Tsamardinos, I, Lagani, V. omicsNPC: Applying the Non-Parametric Combination Methodology to the Integrative Analysis of Heterogeneous Omics Data. PLoS ONE. 2016;11 (11):e0165545. doi: 10.1371/journal.pone.0165545. PubMed PMID:27812137 PubMed Central PMC5094732.
• Singh, J, Boopathi, E, Addya, S, Phillips, B, Rigoutsos, I, Penn, RB, Rattan, S. Aging-associated changes in microRNA expression profile of internal anal sphincter smooth muscle: Role of microRNA-133a. Am. J. Physiol. Gastrointest. Liver Physiol. 2016;311 (5):G964-G973. doi: 10.1152/ajpgi.00290.2016. PubMed PMID:27634012 PubMed Central PMC5130548.
• Mogilyansky, E, Clark, P, Quann, K, Zhou, H, Londin, E, Jing, Y, Rigoutsos, I. Post-transcriptional Regulation of BRCA2 through Interactions with miR-19a and miR-19b. Front Genet. 2016;7 :143. doi: 10.3389/fgene.2016.00143. PubMed PMID:27630665 PubMed Central PMC5005319.
• Oran, AR, Adams, CM, Zhang, XY, Gennaro, VJ, Pfeiffer, HK, Mellert, HS, Seidel, HE, Mascioli, K, Kaplan, J, Gaballa, MR, Shen, C, Rigoutsos, I, King, MP, Cotney, JL, Arnold, JJ, Sharma, SD, Martinez-Outschoorn, UE, Vakoc, CR, Chodosh, LA, Thompson, JE, Bradner, JE, Cameron, CE, Shadel, GS, Eischen, CM, McMahon, SB. Multi-focal control of mitochondrial gene expression by oncogenic MYC provides potential therapeutic targets in cancer. Oncotarget. 2016;7 (45):72395-72414. doi: 10.18632/oncotarget.11718. PubMed PMID:27590350 PubMed Central PMC5340124.
• Paolillo, C, Londin, E, Fortina, P. Next generation sequencing in cancer: opportunities and challenges for precision cancer medicine. Scand. J. Clin. Lab. Invest. Suppl. 2016;245 :S84-91. doi: 10.1080/00365513.2016.1210331. PubMed PMID:27542004 .
• Zhou, H, Telonis, AG, Jing, Y, Xia, NL, Biederman, L, Jimbo, M, Blanco, F, Londin, E, Brody, JR, Rigoutsos, I. GPRC5A is a potential oncogene in pancreatic ductal adenocarcinoma cells that is upregulated by gemcitabine with help from HuR. Cell Death Dis. 2016;7 :e2294. doi: 10.1038/cddis.2016.169. PubMed PMID:27415424 PubMed Central PMC4973341.
• Farooqi, MS, Mitui, M, Londin, ER, Park, JY. High Concentration Capture Probes Enhance Massively Parallel Sequencing Assays. Clin. Chem. 2016;62 (7):1032-4. doi: 10.1373/clinchem.2016.255026. PubMed PMID:27217445 .
• Tahara, M, Andrabi, SB, Matsubara, R, Aonuma, H, Nagamune, K. A host cell membrane microdomain is a critical factor for organelle discharge by Toxoplasma gondii. Parasitol. Int. 2016;65 (5 Pt A):378-88. doi: 10.1016/j.parint.2016.05.012. PubMed PMID:27217289 .
• Pliatsika, V, Loher, P, Telonis, AG, Rigoutsos, I. MINTbase: a framework for the interactive exploration of mitochondrial and nuclear tRNA fragments. Bioinformatics. 2016;32 (16):2481-9. doi: 10.1093/bioinformatics/btw194. PubMed PMID:27153631 PubMed Central PMC4978933.
• Simon, LM, Chen, ES, Edelstein, LC, Kong, X, Bhatlekar, S, Rigoutsos, I, Bray, PF, Shaw, CA. Integrative Multi-omic Analysis of Human Platelet eQTLs Reveals Alternative Start Site in Mitofusin 2. Am. J. Hum. Genet. 2016;98 (5):883-897. doi: 10.1016/j.ajhg.2016.03.007. PubMed PMID:27132591 PubMed Central PMC4863560.
• Velmurugu, Y, Chen, X, Slogoff Sevilla, P, Min, JH, Ansari, A. Twist-open mechanism of DNA damage recognition by the Rad4/XPC nucleotide excision repair complex. Proc. Natl. Acad. Sci. U.S.A. 2016;E2296-E2305. doi: 10.1073/pnas.1514666113. PubMed PMID:27035942. PubMed Central PMC4843471.
• Ybañez, RH, Leesombun, A, Nishimura, M, Matsubara, R, Kojima, M, Sakakibara, H, Nagamune, K, Nishikawa, Y. In vitro and in vivo effects of the phytohormone inhibitor fluridone against Neospora caninum infection. Parasitol. Int. 2016;65 (4):319-22. doi: 10.1016/j.parint.2016.03.009. PubMed PMID:27021922 .
• Pawar, K, Sharbati, J, Einspanier, R, Sharbati, S. Mycobacterium bovis BCG Interferes with miR-3619-5p Control of Cathepsin S in the Process of Autophagy. Front Cell Infect Microbiol. 2016;6 :27. doi: 10.3389/fcimb.2016.00027. PubMed PMID:27014637 PubMed Central PMC4783571.
• Telonis, AG, Loher, P, Kirino, Y, Rigoutsos, I. Consequential considerations when mapping tRNA fragments. BMC Bioinformatics. 2016;17 :123. doi: 10.1186/s12859-016-0921-0. PubMed PMID:26961774 PubMed Central PMC4785646.
• Izumi, N, Shoji, K, Sakaguchi, Y, Honda, S, Kirino, Y, Suzuki, T, Katsuma, S, Tomari, Y. Identification and Functional Analysis of the Pre-piRNA 3′ Trimmer in Silkworms. Cell. 2016;164 (5):962-73. doi: 10.1016/j.cell.2016.01.008. PubMed PMID:26919431 PubMed Central PMC4856147.
• Honda, S, Morichika, K, Kirino, Y. Selective amplification and sequencing of cyclic phosphate-containing RNAs by the cP-RNA-seq method. Nat Protoc. 2016;11 (3):476-89. doi: 10.1038/nprot.2016.025. PubMed PMID:26866791 PubMed Central PMC4852555.
• Pawar, K, Hanisch, C, Palma Vera, SE, Einspanier, R, Sharbati, S. Down regulated lncRNA MEG3 eliminates mycobacteria in macrophages via autophagy. Sci Rep. 2016;6 :19416. doi: 10.1038/srep19416. PubMed PMID:26757825 PubMed Central PMC4725832.
• Kawamura, T, Hirata, A, Ohno, S, Nomura, Y, Nagano, T, Nameki, N, Yokogawa, T, Hori, H. Multisite-specific archaeosine tRNA-guanine transglycosylase (ArcTGT) from Thermoplasma acidophilum, a thermo-acidophilic archaeon. Nucleic Acids Res. 2016;44 (4):1894-908. doi: 10.1093/nar/gkv1522. PubMed PMID:26721388 PubMed Central PMC4770233.
• Blanco, FF, Jimbo, M, Wulfkuhle, J, Gallagher, I, Deng, J, Enyenihi, L, Meisner-Kober, N, Londin, E, Rigoutsos, I, Sawicki, JA, Risbud, MV, Witkiewicz, AK, McCue, PA, Jiang, W, Rui, H, Yeo, CJ, Petricoin, E, Winter, JM, Brody, JR. The mRNA-binding protein HuR promotes hypoxia-induced chemoresistance through posttranscriptional regulation of the proto-oncogene PIM1 in pancreatic cancer cells. Oncogene. 2016;35 (19):2529-41. doi: 10.1038/onc.2015.325. PubMed PMID:26387536 .
• Sakai, H, Kirino, Y, Kastuma, S, Aoki, F, Suzuki, MG. Morphological and histomorphological structures of testes and ovaries in early developmental stages of the silkworm, Bombyx mori. Journal of Insect Biotechnology and Sericology 2016; 85: 15-20

2015

• Londin, ER, Barash, CI. What is translational bioinformatics?. Appl Transl Genom. 2015;6 :1-2. doi: 10.1016/j.atg.2015.08.003. PubMed PMID:27054069 PubMed Central PMC4803779.
• Matsubara, R, Aonuma, H, Kojima, M, Tahara, M, Andrabi, SB, Sakakibara, H, Nagamune, K. Plant Hormone Salicylic Acid Produced by a Malaria Parasite Controls Host Immunity and Cerebral Malaria Outcome. PLoS ONE. 2015;10 (10):e0140559. doi: 10.1371/journal.pone.0140559. PubMed PMID:26466097 PubMed Central PMC4605785.
• Shigematsu, M, Kirino, Y. tRNA-Derived Short Non-coding RNA as Interacting Partners of Argonaute Proteins. Gene Regul Syst Bio. 2015;9 :27-33. doi: 10.4137/GRSB.S29411. PubMed PMID:26401098 PubMed Central PMC4567038.
• Telonis, AG, Loher, P, Jing, Y, Londin, E, Rigoutsos, I. Beyond the one-locus-one-miRNA paradigm: microRNA isoforms enable deeper insights into breast cancer heterogeneity. Nucleic Acids Res. 2015;43 (19):9158-75. doi: 10.1093/nar/gkv922. PubMed PMID:26400174 PubMed Central PMC4627084.
• Telonis, AG, Loher, P, Honda, S, Jing, Y, Palazzo, J, Kirino, Y, Rigoutsos, I. Dissecting tRNA-derived fragment complexities using personalized transcriptomes reveals novel fragment classes and unexpected dependencies. Oncotarget. 2015;6 (28):24797-822. doi: 10.18632/oncotarget.4695. PubMed PMID:26325506 PubMed Central PMC4694795.
• Liu, J, Cao, S, Chen, Z, Raine, A, Hanlon, A, Ai, Y, Zhou, G, Yan, C, Leung, PW, McCauley, L, Pinto-Martin, J, Jintan Cohort Study Group. Cohort Profile Update: The China Jintan Child Cohort Study. Int J Epidemiol. 2015;44 (5):1548, 1548a-1548al. doi: 10.1093/ije/dyv119. PubMed PMID:26323725 PubMed Central PMC4707195.
• Jimbo, M, Blanco, FF, Huang, YH, Telonis, AG, Screnci, BA, Cosma, GL, Alexeev, V, Gonye, GE, Yeo, CJ, Sawicki, JA, Winter, JM, Brody, JR. Targeting the mRNA-binding protein HuR impairs malignant characteristics of pancreatic ductal adenocarcinoma cells. Oncotarget. 2015;6 (29):27312-31. doi: 10.18632/oncotarget.4743. PubMed PMID:26314962 PubMed Central PMC4694992.
• Papoudou-Bai, A, Hatzimichael, E, Kyriazopoulou, L, Briasoulis, E, Kanavaros, P. Rare variants in the spectrum of human herpesvirus 8/Epstein-Barr virus-copositive lymphoproliferations. Hum. Pathol. 2015;46 (10):1566-71. doi: 10.1016/j.humpath.2015.06.020. PubMed PMID:26299509 .
• Quann, K, Jing, Y, Rigoutsos, I. Post-transcriptional regulation of BRCA1 through its coding sequence by the miR-15/107 group of miRNAs. Front Genet. 2015;6 :242. doi: 10.3389/fgene.2015.00242. PubMed PMID:26257769 PubMed Central PMC4513244.
• Honda, S, Loher, P, Shigematsu, M, Palazzo, JP, Suzuki, R, Imoto, I, Rigoutsos, I, Kirino, Y. Sex hormone-dependent tRNA halves enhance cell proliferation in breast and prostate cancers. Proc. Natl. Acad. Sci. U.S.A. 2015;112 (29):E3816-25. doi: 10.1073/pnas.1510077112. PubMed PMID:26124144 PubMed Central PMC4517238.
• Telonis, AG, Margarity, M. Phobos: A novel software for recording rodents’ behavior during the thigmotaxis and the elevated plus-maze test. Neurosci. Lett. 2015;599 :81-5. doi: 10.1016/j.neulet.2015.05.045. PubMed PMID:26007702 .
• Kouno, T, Luengas, EM, Shigematsu, M, Shandilya, SM, Zhang, J, Chen, L, Hara, M, Schiffer, CA, Harris, RS, Matsuo, H. Structure of the Vif-binding domain of the antiviral enzyme APOBEC3G. Nat. Struct. Mol. Biol. 2015;22 (6):485-91. doi: 10.1038/nsmb.3033. PubMed PMID:25984970 PubMed Central PMC4456288.
• Londin, E, Loher, P, Rigoutsos, I. Reply to Backes and Keller: Identification of novel tissue-specific and primate-specific human microRNAs. Proc. Natl. Acad. Sci. U.S.A. 2015;112 (22):E2851. doi: 10.1073/pnas.1505397112. PubMed PMID:25979943 PubMed Central PMC4460515.
• Karathanasis, N, Tsamardinos, I, Poirazi, P. MiRduplexSVM: A High-Performing MiRNA-Duplex Prediction and Evaluation Methodology. PLoS ONE. 2015;10 (5):e0126151. doi: 10.1371/journal.pone.0126151. PubMed PMID:25961860 PubMed Central PMC4427487.
• Telonis, AG, Kirino, Y, Rigoutsos, I. Mitochondrial tRNA-lookalikes in nuclear chromosomes: could they be functional?. RNA Biol. 2015;12 (4):375-80. doi: 10.1080/15476286.2015.1017239. PubMed PMID:25849196 PubMed Central PMC4615777.
• Honda, S, Shigematsu, M, Morichika, K, Telonis, AG, Kirino, Y. Four-leaf clover qRT-PCR: A convenient method for selective quantification of mature tRNA. RNA Biol. 2015;12 (5):501-8. doi: 10.1080/15476286.2015.1031951. PubMed PMID:25833336 PubMed Central PMC4615770.
• Simons, C, Griffin, LB, Helman, G, Golas, G, Pizzino, A, Bloom, M, Murphy, JL, Crawford, J, Evans, SH, Topper, S, Whitehead, MT, Schreiber, JM, Chapman, KA, Tifft, C, Lu, KB, Gamper, H, Shigematsu, M, Taft, RJ, Antonellis, A, Hou, YM, Vanderver, A. Loss-of-function alanyl-tRNA synthetase mutations cause an autosomal-recessive early-onset epileptic encephalopathy with persistent myelination defect. Am. J. Hum. Genet. 2015;96 (4):675-81. doi: 10.1016/j.ajhg.2015.02.012. PubMed PMID:25817015 PubMed Central PMC4385183.
• Honda, S, Kirino, Y. Dumbbell-PCR: a method to quantify specific small RNA variants with a single nucleotide resolution at terminal sequences. Nucleic Acids Res. 2015;43 (12):e77. doi: 10.1093/nar/gkv218. PubMed PMID:25779041 PubMed Central PMC4499115.
• Londin, E, Loher, P, Telonis, AG, Quann, K, Clark, P, Jing, Y, Hatzimichael, E, Kirino, Y, Honda, S, Lally, M, Ramratnam, B, Comstock, CE, Knudsen, KE, Gomella, L, Spaeth, GL, Hark, L, Katz, LJ, Witkiewicz, A, Rostami, A, Jimenez, SA, Hollingsworth, MA, Yeh, JJ, Shaw, CA, McKenzie, SE, Bray, P, Nelson, PT, Zupo, S, Van Roosbroeck, K, Keating, MJ, Calin, GA, Yeo, C, Jimbo, M, Cozzitorto, J, Brody, JR, Delgrosso, K, Mattick, JS, Fortina, P, Rigoutsos, I. Analysis of 13 cell types reveals evidence for the expression of numerous novel primate- and tissue-specific microRNAs. Proc. Natl. Acad. Sci. U.S.A. 2015;112 (10):E1106-15. doi: 10.1073/pnas.1420955112. PubMed PMID:25713380 PubMed Central PMC4364231.
• Pliatsika, V, Rigoutsos, I. “Off-Spotter”: very fast and exhaustive enumeration of genomic lookalikes for designing CRISPR/Cas guide RNAs. Biol. Direct. 2015;10 :4. doi: 10.1186/s13062-015-0035-z. PubMed PMID:25630343 PubMed Central PMC4326336.
• Oulas A, Karathanasis N, Louloupi A, Pavlopoulos GA, Poirazi P, Kalantidis K, Iliopoulos I. Prediction of miRNA targets. Methods Mol Biol. 2015;1269:207-29. doi: 10.1007/978-1-4939-2291-8_13. PubMed PMID:25577381.
• Park JY, Clark P, Londin E, Sponziello M, Kricka LJ, Fortina P. Clinical exome performance for reporting secondary genetic findings. Clin Chem. 2015 Jan;61(1):213-20. doi: 10.1373/clinchem.2014.231456. PubMed PMID:25414276 PubMed Central PMC4404496.
• Honda, S, Kirino, Y. SHOT-RNAs: a novel class of tRNA-derived functional RNAs expressed in hormone-dependent cancers. Molecular & Cellular Oncology. 2015;3:2. doi: 10.1080/23723556.2015.1079672.

2014

• Zhou, H, Rigoutsos, I. The emerging roles of GPRC5A in diseases. Oncoscience. 2014;1 (12):765-76. doi: 10.18632/oncoscience.104. PubMed PMID:25621293 PubMed Central PMC4303886.
• Kawamura, T, Anraku, R, Hasegawa, T, Tomikawa, C, Hori, H. Transfer RNA methyltransferases from Thermoplasma acidophilum, a thermoacidophilic archaeon. Int J Mol Sci. 2014;16 (1):91-113. doi: 10.3390/ijms16010091. PubMed PMID:25546389 PubMed Central PMC4307237.
• Telonis, AG, Loher, P, Kirino, Y, Rigoutsos, I. Nuclear and mitochondrial tRNA-lookalikes in the human genome. Front Genet. 2014;5 :344. doi: 10.3389/fgene.2014.00344. PubMed PMID:25339973 PubMed Central PMC4189335.
• Loher, P, Londin, ER, Rigoutsos, I. IsomiR expression profiles in human lymphoblastoid cell lines exhibit population and gender dependencies. Oncotarget. 2014;5 (18):8790-802. doi: 10.18632/oncotarget.2405. PubMed PMID:25229428 PubMed Central PMC4226722.
• Primikyri, A, Chatziathanasiadou, MV, Karali, E, Kostaras, E, Mantzaris, MD, Hatzimichael, E, Shin, JS, Chi, SW, Briasoulis, E, Kolettas, E, Gerothanassis, IP, Tzakos, AG. Direct binding of Bcl-2 family proteins by quercetin triggers its pro-apoptotic activity. ACS Chem. Biol. 2014;9 (12):2737-41. doi: 10.1021/cb500259e. PubMed PMID:25211642 .
• Hatzimichael, E, Tsolas, E, Briasoulis, E. Profile of pacritinib and its potential in the treatment of hematologic disorders. J Blood Med. 2014;5 :143-52. doi: 10.2147/JBM.S51253. PubMed PMID:25170285 PubMed Central PMC4145824.
• Park, JY, Kricka, LJ, Clark, P, Londin, E, Fortina, P. Clinical genomics: when whole genome sequencing is like a whole-body CT scan. Clin. Chem. 2014;60 (11):1390-2. doi: 10.1373/clinchem.2014.230276. PubMed PMID:25114273 PubMed Central PMC4396804.
• Clark, PM, Loher, P, Quann, K, Brody, J, Londin, ER, Rigoutsos, I. Argonaute CLIP-Seq reveals miRNA targetome diversity across tissue types. Sci Rep. 2014;4 :5947. doi: 10.1038/srep05947. PubMed PMID:25103560 PubMed Central PMC4894423.
• Benetatos, L, Vartholomatos, G, Hatzimichael, E. DLK1-DIO3 imprinted cluster in induced pluripotency: landscape in the mist. Cell. Mol. Life Sci. 2014;71 (22):4421-30. doi: 10.1007/s00018-014-1698-9. PubMed PMID:25098353 .
• Hatzimichael, E, Syed, N, Lo Nigro, C, Crook, T. A blood test to identify when melanoma metastasizes: a reality for melanoma management?. Melanoma Manag. 2014;1 (1):11-14. doi: 10.2217/mmt.14.11. PubMed PMID:30190804 PubMed Central PMC6094697.
• Benetatos, L, Hatzimichael, E. Delta-like homologue 1 and its role in the bone marrow niche and hematologic malignancies. Clin Lymphoma Myeloma Leuk. 2014;14 (6):451-5. doi: 10.1016/j.clml.2014.06.019. PubMed PMID:25066037 .
• Zhou, H, Rigoutsos, I. MiR-103a-3p targets the 5′ UTR of GPRC5A in pancreatic cells. RNA. 2014;20 (9):1431-9. doi: 10.1261/rna.045757.114. PubMed PMID:24984703 PubMed Central PMC4138326.
• Hatzimichael, E, Syed, N, Lo Nigro, C, Rao, B, Crook, T. How detection of epigenetic alterations of blood-borne DNA could improve melanoma diagnosis. Expert Rev. Mol. Diagn. 2014;14 (6):639-42. doi: 10.1586/14737159.2014.928204. PubMed PMID:24926921 .
• Swarup, A, Lu, J, DeWoody, KC, Antoniewicz, MR. Metabolic network reconstruction, growth characterization and 13C-metabolic flux analysis of the extremophile Thermus thermophilus HB8. Metab. Eng. 2014;24 :173-80. doi: 10.1016/j.ymben.2014.05.013. PubMed PMID:24909362 .
• Londin, ER, Adijanto, J, Philp, N, Novelli, A, Vitale, E, Perria, C, Serra, G, Alesi, V, Surrey, S, Fortina, P. Donor splice-site mutation in CUL4B is likely cause of X-linked intellectual disability. Am. J. Med. Genet. A. 2014;164A (9):2294-9. doi: 10.1002/ajmg.a.36629. PubMed PMID:24898194 PubMed Central PMC4404493.
• Ho, VM, Dallalzadeh, LO, Karathanasis, N, Keles, MF, Vangala, S, Grogan, T, Poirazi, P, Martin, KC. GluA2 mRNA distribution and regulation by miR-124 in hippocampal neurons. Mol. Cell. Neurosci. 2014;61 :1-12. doi: 10.1016/j.mcn.2014.04.006. PubMed PMID:24784359 PubMed Central PMC4134974.
• Correnti, JM, Juskeviciute, E, Swarup, A, Hoek, JB. Pharmacological ceramide reduction alleviates alcohol-induced steatosis and hepatomegaly in adiponectin knockout mice. Am. J. Physiol. Gastrointest. Liver Physiol. 2014;306 (11):G959-73. doi: 10.1152/ajpgi.00395.2013. PubMed PMID:24742988 PubMed Central PMC4042116.
• Gkourogianni, A, Kosteria, I, Telonis, AG, Margeli, A, Mantzou, E, Konsta, M, Loutradis, D, Mastorakos, G, Papassotiriou, I, Klapa, MI, Kanaka-Gantenbein, C, Chrousos, GP. Plasma metabolomic profiling suggests early indications for predisposition to latent insulin resistance in children conceived by ICSI. PLoS ONE. 2014;9 (4):e94001. doi: 10.1371/journal.pone.0094001. PubMed PMID:24728198 PubMed Central PMC3984097.
• Kastritis, E, Zagouri, F, Symeonidis, A, Roussou, M, Sioni, A, Pouli, A, Delimpasi, S, Katodritou, E, Michalis, E, Michael, M, Hatzimichael, E, Vassou, A, Repousis, P, Christophoridou, A, Kartasis, Z, Stefanoudaki, E, Megalakaki, C, Giannouli, S, Kyrtsonis, MC, Konstantopoulos, K, Spyroupoulou-Vlachou, M, Terpos, E, Dimopoulos, MA, Greek Myeloma Study Group. Preserved levels of uninvolved immunoglobulins are independently associated with favorable outcome in patients with symptomatic multiple myeloma. Leukemia. 2014;28 (10):2075-9. doi: 10.1038/leu.2014.110. PubMed PMID:24637336 .
• Mercier, I, Gonzales, DM, Quann, K, Pestell, TG, Molchansky, A, Sotgia, F, Hulit, J, Gandara, R, Wang, C, Pestell, RG, Lisanti, MP, Jasmin, JF. CAPER, a novel regulator of human breast cancer progression. Cell Cycle. 2014;13 (8):1256-64. doi: 10.4161/cc.28156. PubMed PMID:24621503 PubMed Central PMC4049962.
• Karathanasis, N, Tsamardinos, I, Poirazi, P. Don’t use a cannon to kill the .. miRNA mosquito. Bioinformatics. 2014;30 (7):1047-8. doi: 10.1093/bioinformatics/btu100. PubMed PMID:24618472 .
• Lal, S, Burkhart, RA, Beeharry, N, Bhattacharjee, V, Londin, ER, Cozzitorto, JA, Romeo, C, Jimbo, M, Norris, ZA, Yeo, CJ, Sawicki, JA, Winter, JM, Rigoutsos, I, Yen, TJ, Brody, JR. HuR posttranscriptionally regulates WEE1: implications for the DNA damage response in pancreatic cancer cells. Cancer Res. 2014;74 (4):1128-40. doi: 10.1158/0008-5472.CAN-13-1915. PubMed PMID:24536047 PubMed Central PMC4353573.
• Londin, ER, Hatzimichael, E, Loher, P, Edelstein, L, Shaw, C, Delgrosso, K, Fortina, P, Bray, PF, McKenzie, SE, Rigoutsos, I. The human platelet: strong transcriptome correlations among individuals associate weakly with the platelet proteome. Biol. Direct. 2014;9 :3. doi: 10.1186/1745-6150-9-3. PubMed PMID:24524654 PubMed Central PMC3937023.
• Hatzimichael, E, Lagos, K, Sim, VR, Briasoulis, E, Crook, T. Epigenetics in diagnosis, prognostic assessment and treatment of cancer: an update. EXCLI J. 2014;13 :954-76. . PubMed PMID:26417314 PubMed Central PMC4464089.
• Honda, S, Kirino, Y, Kirino, Y. Analysis of sDMA modifications of PIWI proteins. Methods Mol. Biol. 2014;1093 :137-48. doi: 10.1007/978-1-62703-694-8_11. PubMed PMID:24178562 PubMed Central PMC4376280.
• Benetatos, L, Vartholomatos, G, Hatzimichael, E. Polycomb group proteins and MYC: the cancer connection. Cell. Mol. Life Sci. 2014;71 (2):257-69. doi: 10.1007/s00018-013-1426-x. PubMed PMID:23897499 .
• Katodritou, E, Vadikolia, C, Lalagianni, C, Kotsopoulou, M, Papageorgiou, G, Kyrtsonis, MC, Matsouka, P, Giannakoulas, N, Kyriakou, D, Karras, G, Anagnostopoulos, N, Michali, E, Briasoulis, E, Hatzimichael, E, Spanoudakis, E, Zikos, P, Tsakiridou, A, Tsionos, K, Anargyrou, K, Symeonidis, A, Maniatis, A, Terpos, E. “Real-world” data on the efficacy and safety of lenalidomide and dexamethasone in patients with relapsed/refractory multiple myeloma who were treated according to the standard clinical practice: a study of the Greek Myeloma Study Group. Ann. Hematol. 2014;93 (1):129-39. doi: 10.1007/s00277-013-1841-y. PubMed PMID:23892921 .
• Morichika, K, Sugimoto, M, Yasuda, K, Kinoshita, T. Possible regulation of Oct60 transcription by a positive feedback loop in Xenopus oocytes. Zygote. 2014;22 (2):266-74. doi: 10.1017/S0967199412000536. PubMed PMID:23186935 .
• Pawar, K, Kaul, G. Toxicity of titanium oxide nanoparticles causes functionality and DNA damage in buffalo (Bubalus bubalis) sperm in vitro. Toxicol Ind Health. 2014;30 (6):520-33. doi: 10.1177/0748233712462475. PubMed PMID:23064765 .
• Shigematsu, M, Honda, S, Kirino, Y (2014) “Transfer RNA as a Source of Small Functional RNA”J Mol Biol & Mol Imaging 1(2): 8 doi: Download

2013

• Mogilyansky, E, Rigoutsos, I. The miR-17/92 cluster: a comprehensive update on its genomics, genetics, functions and increasingly important and numerous roles in health and disease. Cell Death Differ. 2013;20 (12):1603-14. doi: 10.1038/cdd.2013.125. PubMed PMID:24212931 PubMed Central PMC3824591.
• Fedan, JS, Thompson, JA, Ismailoglu, UB, Jing, Y. Tracheal epithelium cell volume responses to hyperosmolar, isosmolar and hypoosmolar solutions: relation to epithelium-derived relaxing factor (EpDRF) effects. Front Physiol. 2013;4 :287. doi: 10.3389/fphys.2013.00287. PubMed PMID:24130533 PubMed Central PMC3795350.
• Tomikawa, C, Ohira, T, Inoue, Y, Kawamura, T, Yamagishi, A, Suzuki, T, Hori, H. Distinct tRNA modifications in the thermo-acidophilic archaeon, Thermoplasma acidophilum. FEBS Lett. 2013;587 (21):3575-80. doi: 10.1016/j.febslet.2013.09.021. PubMed PMID:24076028 .
• Shigematsu, M, Ogawa, T, Tanaka, W, Takahashi, K, Kitamoto, HK, Hidaka, M, Masaki, H. Evidence for DNA cleavage caused directly by a transfer RNA-targeting toxin. PLoS ONE. 2013;8 (9):e75512. doi: 10.1371/journal.pone.0075512. PubMed PMID:24069426 PubMed Central PMC3775755.
• Honda, S, Kirino, Y, Maragkakis, M, Alexiou, P, Ohtaki, A, Murali, R, Mourelatos, Z, Kirino, Y. Mitochondrial protein BmPAPI modulates the length of mature piRNAs. RNA. 2013;19 (10):1405-18. doi: 10.1261/rna.040428.113. PubMed PMID:23970546 PubMed Central PMC3854531.
• Hoeke, L, Sharbati, J, Pawar, K, Keller, A, Einspanier, R, Sharbati, S. Intestinal Salmonella typhimurium infection leads to miR-29a induced caveolin 2 regulation. PLoS ONE. 2013;8 (6):e67300. doi: 10.1371/journal.pone.0067300. PubMed PMID:23826261 PubMed Central PMC3691122.
• Londin, E, Yadav, P, Surrey, S, Kricka, LJ, Fortina, P. Use of linkage analysis, genome-wide association studies, and next-generation sequencing in the identification of disease-causing mutations. Methods Mol. Biol. 2013;1015 :127-46. doi: 10.1007/978-1-62703-435-7_8. PubMed PMID:23824853 .
• Burkhart, RA, Pineda, DM, Chand, SN, Romeo, C, Londin, ER, Karoly, ED, Cozzitorto, JA, Rigoutsos, I, Yeo, CJ, Brody, JR, Winter, JM. HuR is a post-transcriptional regulator of core metabolic enzymes in pancreatic cancer. RNA Biol. 2013;10 (8):1312-23. doi: 10.4161/rna.25274. PubMed PMID:23807417 PubMed Central PMC3817153.
• Hatzimichael, E, Murray, S, Briasoulis, E. Absence of BRAF exon 15 mutations in multiple myeloma and Waldenström’s macroglobulinemia questions its validity as a therapeutic target in plasma cell neoplasias. Am J Blood Res. 2013;3 (2):181-5. . PubMed PMID:23675568 PubMed Central PMC3649814.
• Murakoshi, F, Fukuda, Y, Matsubara, R, Kato, Y, Sato, R, Sasaki, T, Tada, C, Nakai, Y. Detection and genotyping of Cryptosporidium spp. in large Japanese field mice, Apodemus speciosus. Vet. Parasitol. 2013;196 (1-2):184-8. doi: 10.1016/j.vetpar.2013.02.011. PubMed PMID:23601844 .
• Quann, K, Gonzales, DM, Mercier, I, Wang, C, Sotgia, F, Pestell, RG, Lisanti, MP, Jasmin, JF. Caveolin-1 is a negative regulator of tumor growth in glioblastoma and modulates chemosensitivity to temozolomide. Cell Cycle. 2013;12 (10):1510-20. doi: 10.4161/cc.24497. PubMed PMID:23598719 PubMed Central PMC3680531.
• Hatzimichael, E, Crook, T. Cancer epigenetics: new therapies and new challenges. J Drug Deliv. 2013;2013 :529312. doi: 10.1155/2013/529312. PubMed PMID:23533770 PubMed Central PMC3600296.
• He, J, Jing, Y, Li, W, Qian, X, Xu, Q, Li, FS, Liu, LZ, Jiang, BH, Jiang, Y. Roles and mechanism of miR-199a and miR-125b in tumor angiogenesis. PLoS ONE. 2013;8 (2):e56647. doi: 10.1371/journal.pone.0056647. PubMed PMID:23437196 PubMed Central PMC3577861.
• Bray, PF, McKenzie, SE, Edelstein, LC, Nagalla, S, Delgrosso, K, Ertel, A, Kupper, J, Jing, Y, Londin, E, Loher, P, Chen, HW, Fortina, P, Rigoutsos, I. The complex transcriptional landscape of the anucleate human platelet. BMC Genomics. 2013;14 :1. doi: 10.1186/1471-2164-14-1. PubMed PMID:23323973 PubMed Central PMC3722126.
• Terayama, K, Kataoka, K, Morichika, K, Orii, H, Watanabe, K, Mochii, M. Developmental regulation of locomotive activity in Xenopus primordial germ cells. Dev. Growth Differ. 2013;55 (2):217-28. doi: 10.1111/dgd.12018. PubMed PMID:23278717 .
• Xu, Q, Jiang, Y, Yin, Y, Li, Q, He, J, Jing, Y, Qi, YT, Xu, Q, Li, W, Lu, B, Peiper, SS, Jiang, BH, Liu, LZ. A regulatory circuit of miR-148a/152 and DNMT1 in modulating cell transformation and tumor angiogenesis through IGF-IR and IRS1. J Mol Cell Biol. 2013;5 (1):3-13. doi: 10.1093/jmcb/mjs049. PubMed PMID:22935141 PubMed Central PMC3570052.
• Benetatos, L, Hatzimichael, E, Londin, E, Vartholomatos, G, Loher, P, Rigoutsos, I, Briasoulis, E. The microRNAs within the DLK1-DIO3 genomic region: involvement in disease pathogenesis. Cell. Mol. Life Sci. 2013;70 (5):795-814. doi: 10.1007/s00018-012-1080-8. PubMed PMID:22825660 .
• Mercier, I, Camacho, J, Titchen, K, Gonzales, DM, Quann, K, Bryant, KG, Molchansky, A, Milliman, JN, Whitaker-Menezes, D, Sotgia, F, Jasmin, JF, Schwarting, R, Pestell, RG, Blagosklonny, MV, Lisanti, MP. Caveolin-1 and accelerated host aging in the breast tumor microenvironment: chemoprevention with rapamycin, an mTOR inhibitor and anti-aging drug. Am. J. Pathol. 2012;181 (1):278-93. doi: 10.1016/j.ajpath.2012.03.017. PubMed PMID:22698676 PubMed Central PMC3388151.
• Rahman, S, Quann, K, Pandya, D, Singh, S, Khan, ZK, Jain, P. HTLV-1 Tax mediated downregulation of miRNAs associated with chromatin remodeling factors in T cells with stably integrated viral promoter. PLoS ONE. 2012;7 (4):e34490. doi: 10.1371/journal.pone.0034490. PubMed PMID:22496815 PubMed Central PMC3319589.
• Loher, P, Vasilakis, N, Malamon, J, Chen, HW and Rigoutsos, I (2013) “HandsFree – Next Generation Sequence Processing, Mapping and Analysis Made Easy” Proceedings DILS2013 doi: DILS-SYS-EC-paper4
• Honda, S and Kirino, Y (2013) “PIWIL1 (piwi-like RNA-mediated gene silencing 1)” Atlas Genet Cytogenet Oncol Haematol. 17(12):833-836. doi: Genes/PIWIL1ID46561ch12q24
• Pawar K, Kaul G. Toxicity of Europium Oxide Nanoparticles on the Buffalo (Bubalus bubalis) Spermatozoa DNA Damage. Advanced Science, Engineering and Medicine. 5(1):11-17. DOI: https://doi.org/10.1166/asem.2013.1230
• Kyan, Y, Matsubara, R, Nagamune, K. Toxoplasma gondii and Its Prevalence in Okinawa Prefecture. J Antibacterial Antifungal Agents 2013, 41(1), 19-28; (in Japanese)
• Karathanasis, N, Tsamardinos, I, Poirazi, P. A bioinformatics approach for investigating the determinants of Drosha processing. IEEE 13th International Conference on Bioinformatics & Bioengineering, 2013. doi: 10.1109/BIBE.2013.6701569

2012

• Rossi, S, Di Narzo, AF, Mestdagh, P, Jacobs, B, Bosman, FT, Gustavsson, B, Majoie, B, Roth, A, Vandesompele, J, Rigoutsos, I, Delorenzi, M, Tejpar, S. microRNAs in colon cancer: a roadmap for discovery. FEBS Lett. 2012;586 (19):3000-7. . PubMed PMID:23166923 .
• He, J, Xu, Q, Jing, Y, Agani, F, Qian, X, Carpenter, R, Li, Q, Wang, XR, Peiper, SS, Lu, Z, Liu, LZ, Jiang, BH. Reactive oxygen species regulate ERBB2 and ERBB3 expression via miR-199a/125b and DNA methylation. EMBO Rep. 2012;13 (12):1116-22. doi: 10.1038/embor.2012.162. PubMed PMID:23146892 PubMed Central PMC3512405.
• Suzuki, R, Honda, S, Kirino, Y. PIWI Expression and Function in Cancer. Front Genet. 2012;3 :204. doi: 10.3389/fgene.2012.00204. PubMed PMID:23087701 PubMed Central PMC3472457.
• Loher, P, Rigoutsos, I. Interactive exploration of RNA22 microRNA target predictions. Bioinformatics. 2012;28 (24):3322-3. doi: 10.1093/bioinformatics/bts615. PubMed PMID:23074262 .
• Hatzimichael, E, Lo Nigro, C, Lattanzio, L, Syed, N, Shah, R, Dasoula, A, Janczar, K, Vivenza, D, Monteverde, M, Merlano, M, Papoudou-Bai, A, Bai, M, Schmid, P, Stebbing, J, Bower, M, Dyer, MJ, Karran, LE, ElguetaKarstegl, C, Farrell, PJ, Thompson, A, Briasoulis, E, Crook, T. The collagen prolyl hydroxylases are novel transcriptionally silenced genes in lymphoma. Br. J. Cancer. 2012;107 (8):1423-32. doi: 10.1038/bjc.2012.380. PubMed PMID:22955849 PubMed Central PMC3494450.
• Oulas, A, Karathanasis, N, Louloupi, A, Iliopoulos, I, Kalantidis, K, Poirazi, P. A new microRNA target prediction tool identifies a novel interaction of a putative miRNA with CCND2. RNA Biol. 2012;9 (9):1196-207. doi: 10.4161/rna.21725. PubMed PMID:22954617 PubMed Central PMC3579887.
• Hirata, A, Fujishima, K, Yamagami, R, Kawamura, T, Banfield, JF, Kanai, A, Hori, H. X-ray structure of the fourth type of archaeal tRNA splicing endonuclease: insights into the evolution of a novel three-unit composition and a unique loop involved in broad substrate specificity. Nucleic Acids Res. 2012;40 (20):10554-66. doi: 10.1093/nar/gks826. PubMed PMID:22941657 PubMed Central PMC3488258.
• Xia, Z, Clark, P, Huynh, T, Loher, P, Zhao, Y, Chen, HW, Ren, P, Rigoutsos, I, Zhou, R. Molecular dynamics simulations of Ago silencing complexes reveal a large repertoire of admissible ‘seed-less’ targets. Sci Rep. 2012;2 :569. doi: 10.1038/srep00569. PubMed PMID:22888400 PubMed Central PMC3415692.
• Vourekas, A, Zheng, Q, Alexiou, P, Maragkakis, M, Kirino, Y, Gregory, BD, Mourelatos, Z. Mili and Miwi target RNA repertoire reveals piRNA biogenesis and function of Miwi in spermiogenesis. Nat. Struct. Mol. Biol. 2012;19 (8):773-81. doi: 10.1038/nsmb.2347. PubMed PMID:22842725 PubMed Central PMC3414646.
• Pineda, DM, Rittenhouse, DW, Valley, CC, Cozzitorto, JA, Burkhart, RA, Leiby, B, Winter, JM, Weber, MC, Londin, ER, Rigoutsos, I, Yeo, CJ, Gorospe, M, Witkiewicz, AK, Sachs, JN, Brody, JR. HuR’s post-transcriptional regulation of Death Receptor 5 in pancreatic cancer cells. Cancer Biol. Ther. 2012;13 (10):946-55. doi: 10.4161/cbt.20952. PubMed PMID:22785201 PubMed Central PMC3414415.
• Delage, B, Luong, P, Maharaj, L, O’Riain, C, Syed, N, Crook, T, Hatzimichael, E, Papoudou-Bai, A, Mitchell, TJ, Whittaker, SJ, Cerio, R, Gribben, J, Lemoine, N, Bomalaski, J, Li, CF, Joel, S, Fitzgibbon, J, Chen, LT, Szlosarek, PW. Promoter methylation of argininosuccinate synthetase-1 sensitises lymphomas to arginine deiminase treatment, autophagy and caspase-dependent apoptosis. Cell Death Dis. 2012;3 :e342. doi: 10.1038/cddis.2012.83. PubMed PMID:22764101 PubMed Central PMC3406582.
• Lo Nigro, C, Monteverde, M, Lee, S, Lattanzio, L, Vivenza, D, Comino, A, Syed, N, McHugh, A, Wang, H, Proby, C, Garrone, O, Merlano, M, Hatzimichael, E, Briasoulis, E, Gojis, O, Palmieri, C, Jordan, L, Quinlan, P, Thompson, A, Crook, T. NT5E CpG island methylation is a favourable breast cancer biomarker. Br. J. Cancer. 2012;107 (1):75-83. doi: 10.1038/bjc.2012.212. PubMed PMID:22653144 PubMed Central PMC3389412.
• Dranitsaris, G, Hatzimichael, E. Interpreting results from oncology clinical trials: a comparison of denosumab to zoledronic acid for the prevention of skeletal-related events in cancer patients. Support Care Cancer. 2012;20 (7):1353-60. doi: 10.1007/s00520-012-1461-4. PubMed PMID:22539050 PubMed Central PMC3360851.
• Honda, S, Hayashi, S, Nakane, T, Imoto, I, Kurosawa, K, Mizuno, S, Okamoto, N, Kato, M, Yoshihashi, H, Kubota, T, Nakagawa, E, Goto, Y, Inazawa, J. The incidence of hypoplasia of the corpus callosum in patients with dup (X)(q28) involving MECP2 is associated with the location of distal breakpoints. Am. J. Med. Genet. A. 2012;158A (6):1292-303. doi: 10.1002/ajmg.a.35321. PubMed PMID:22528406 .
• Dimopoulos, MA, Kastritis, E, Delimpasi, S, Katodritou, E, Hatzimichael, E, Kyrtsonis, MC, Repousis, P, Tsirogianni, M, Kartasis, Z, Parcharidou, A, Michael, M, Michalis, E, Tsatalas, C, Stefanoudaki, E, Hatjiharissi, E, Gika, D, Symeonidis, A, Terpos, E, Zervas, K, Greek Myeloma Study Group. Multiple myeloma in octogenarians: clinical features and outcome in the novel agent era. Eur. J. Haematol. 2012;89 (1):10-5. doi: 10.1111/j.1600-0609.2012.01784.x. PubMed PMID:22469521 .
• Wang, H, Lee, S, Nigro, CL, Lattanzio, L, Merlano, M, Monteverde, M, Matin, R, Purdie, K, Mladkova, N, Bergamaschi, D, Harwood, C, Syed, N, Szlosarek, P, Briasoulis, E, McHugh, A, Thompson, A, Evans, A, Leigh, I, Fleming, C, Inman, GJ, Hatzimichael, E, Proby, C, Crook, T. NT5E (CD73) is epigenetically regulated in malignant melanoma and associated with metastatic site specificity. Br. J. Cancer. 2012;106 (8):1446-52. doi: 10.1038/bjc.2012.95. PubMed PMID:22454080 PubMed Central PMC3326678.
• Shigematsu, M, Ogawa, T, Kitamoto, HK, Hidaka, M, Masaki, H. Specific phase arrest of cell cycle restores cell viability against tRNA cleavage by killer toxin. Biochem. Biophys. Res. Commun. 2012;420 (4):750-4. doi: 10.1016/j.bbrc.2012.03.061. PubMed PMID:22450321 .
• Coley, HM, Hatzimichael, E, Blagden, S, McNeish, I, Thompson, A, Crook, T, Syed, N. Polo Like Kinase 2 Tumour Suppressor and cancer biomarker: new perspectives on drug sensitivity/resistance in ovarian cancer. Oncotarget. 2012;3 (1):78-83. doi: 10.18632/oncotarget.332. PubMed PMID:22289679 PubMed Central PMC3292894.
• Hatzimichael, E, Dasoula, A, Kounnis, V, Benetatos, L, Lo Nigro, C, Lattanzio, L, Papoudou-Bai, A, Dranitsaris, G, Briasoulis, E, Crook, T. Bcl2-interacting killer CpG methylation in multiple myeloma: a potential predictor of relapsed/refractory disease with therapeutic implications. Leuk. Lymphoma. 2012;53 (9):1709-13. doi: 10.3109/10428194.2012.661854. PubMed PMID:22288719 .
• Murakoshi, F, Xiao, L, Matsubara, R, Sato, R, Kato, Y, Sasaki, T, Fukuda, Y, Tada, C, Nakai, Y. Molecular characterization of Cryptosporidium spp. in grazing beef cattle in Japan. Vet. Parasitol. 2012;187 (1-2):123-8. doi: 10.1016/j.vetpar.2011.12.011. PubMed PMID:22265080 .
• Honda, S, Satomura, S, Hayashi, S, Imoto, I, Nakagawa, E, Goto, Y, Inazawa, J, Japanese Mental Retardation Consortium. Concomitant microduplications of MECP2 and ATRX in male patients with severe mental retardation. J. Hum. Genet. 2012;57 (1):73-7. doi: 10.1038/jhg.2011.131. PubMed PMID:22129561 .
• Jing, Y, Liu, LZ, Jiang, Y, Zhu, Y, Guo, NL, Barnett, J, Rojanasakul, Y, Agani, F, Jiang, BH. Cadmium increases HIF-1 and VEGF expression through ROS, ERK, and AKT signaling pathways and induces malignant transformation of human bronchial epithelial cells. Toxicol. Sci. 2012;125 (1):10-9. doi: 10.1093/toxsci/kfr256. PubMed PMID:21984483 PubMed Central PMC3243743.
• Karathanasis, N, Angelos, A, Tsamardinos, I, Poirazi, P. SVM-based miRNA:MiRNA*duplex prediction. IEEE 12th International Conference on Bioinformatics & Bioengineering, 2012. doi: 10.1109/BIBE.2012.6399670

2011

• Tay, Y, Kats, L, Salmena, L, Weiss, D, Tan, SM, Ala, U, Karreth, F, Poliseno, L, Provero, P, Di Cunto, F, Lieberman, J, Rigoutsos, I, Pandolfi, PP. Coding-independent regulation of the tumor suppressor PTEN by competing endogenous mRNAs. Cell. 2011;147 (2):344-57. doi: 10.1016/j.cell.2011.09.029. PubMed PMID:22000013 PubMed Central PMC3235920.
• Zhang, XY, Pfeiffer, HK, Mellert, HS, Stanek, TJ, Sussman, RT, Kumari, A, Yu, D, Rigoutsos, I, Thomas-Tikhonenko, A, Seidel, HE, Chodosh, LA, Packham, G, Baserga, R, McMahon, SB. Inhibition of the single downstream target BAG1 activates the latent apoptotic potential of MYC. Mol. Cell. Biol. 2011;31 (24):5037-45. doi: 10.1128/MCB.06297-11. PubMed PMID:21986497 PubMed Central PMC3233020.
• Carpenter, RL, Jiang, Y, Jing, Y, He, J, Rojanasakul, Y, Liu, LZ, Jiang, BH. Arsenite induces cell transformation by reactive oxygen species, AKT, ERK1/2, and p70S6K1. Biochem. Biophys. Res. Commun. 2011;414 (3):533-8. doi: 10.1016/j.bbrc.2011.09.102. PubMed PMID:21971544 .
• Londin, ER, Keller, MA, D’Andrea, MR, Delgrosso, K, Ertel, A, Surrey, S, Fortina, P. Whole-exome sequencing of DNA from peripheral blood mononuclear cells (PBMC) and EBV-transformed lymphocytes from the same donor. BMC Genomics. 2011;12 :464. doi: 10.1186/1471-2164-12-464. PubMed PMID:21943378 PubMed Central PMC3203102.
• Haiminen, N, Kuhn, DN, Parida, L, Rigoutsos, I. Evaluation of methods for de novo genome assembly from high-throughput sequencing reads reveals dependencies that affect the quality of the results. PLoS ONE. 2011;6 (9):e24182. doi: 10.1371/journal.pone.0024182. PubMed PMID:21915294 PubMed Central PMC3168497.
• Liu, LZ, Jing, Y, Jiang, LL, Jiang, XE, Jiang, Y, Rojanasakul, Y, Jiang, BH. Acacetin inhibits VEGF expression, tumor angiogenesis and growth through AKT/HIF-1α pathway. Biochem. Biophys. Res. Commun. 2011;413 (2):299-305. doi: 10.1016/j.bbrc.2011.08.091. PubMed PMID:21893035 PubMed Central PMC3224790.
• Liu, LZ, Jiang, Y, Carpenter, RL, Jing, Y, Peiper, SC, Jiang, BH. Role and mechanism of arsenic in regulating angiogenesis. PLoS ONE. 2011;6 (6):e20858. doi: 10.1371/journal.pone.0020858. PubMed PMID:21687637 PubMed Central PMC3110823.
• Kirino, Y. [Role of arginine methylation in the Piwi-interacting RNA pathway]. Seikagaku. 2011;83 (4):312-6. . PubMed PMID:21626884 .
• Tzakos, AG, Fokas, D, Johannes, C, Moussis, V, Hatzimichael, E, Briasoulis, E. Targeting oncogenic protein-protein interactions by diversity oriented synthesis and combinatorial chemistry approaches. Molecules. 2011;16 (6):4408-27. doi: 10.3390/molecules16064408. PubMed PMID:21623312 .
• Oulas, A, Karathanasis, N, Louloupi, A, Poirazi, P. Finding cancer-associated miRNAs: methods and tools. Mol. Biotechnol. 2011;49 (1):97-107. doi: 10.1007/s12033-011-9416-4. PubMed PMID:21607762 .
• Liu, LZ, Li, C, Chen, Q, Jing, Y, Carpenter, R, Jiang, Y, Kung, HF, Lai, L, Jiang, BH. MiR-21 induced angiogenesis through AKT and ERK activation and HIF-1α expression. PLoS ONE. 2011;6 (4):e19139. doi: 10.1371/journal.pone.0019139. PubMed PMID:21544242 PubMed Central PMC3081346.
• Kirino, Y, Vourekas, A, Khandros, E, Mourelatos, Z. Immunoprecipitation of piRNPs and directional, next generation sequencing of piRNAs. Methods Mol. Biol. 2011;725 :281-93. doi: 10.1007/978-1-61779-046-1_18. PubMed PMID:21528460 .
• Syed, N, Coley, HM, Sehouli, J, Koensgen, D, Mustea, A, Szlosarek, P, McNeish, I, Blagden, SP, Schmid, P, Lovell, DP, Hatzimichael, E, Crook, T. Polo-like kinase Plk2 is an epigenetic determinant of chemosensitivity and clinical outcomes in ovarian cancer. Cancer Res. 2011;71 (9):3317-27. doi: 10.1158/0008-5472.CAN-10-2048. PubMed PMID:21402713 .
• Benetatos, L, Vartholomatos, G, Hatzimichael, E. MEG3 imprinted gene contribution in tumorigenesis. Int. J. Cancer. 2011;129 (4):773-9. doi: 10.1002/ijc.26052. PubMed PMID:21400503 .
• Pawar, K, Kaul, G. Assessment of buffalo (Bubalus bubalis) sperm DNA fragmentation using a sperm chromatin dispersion test. Reprod. Domest. Anim. 2011;46 (6):964-9. doi: 10.1111/j.1439-0531.2011.01766.x. PubMed PMID:21382103 .
• Benetatos, L, Dasoula, A, Hatzimichael, E, Syed, N, Voukelatou, M, Dranitsaris, G, Bourantas, KL, Crook, T. Polo-like kinase 2 (SNK/PLK2) is a novel epigenetically regulated gene in acute myeloid leukemia and myelodysplastic syndromes: genetic and epigenetic interactions. Ann. Hematol. 2011;90 (9):1037-45. doi: 10.1007/s00277-011-1193-4. PubMed PMID:21340720 .
• Jasmin, JF, Rengo, G, Lymperopoulos, A, Gupta, R, Eaton, GJ, Quann, K, Gonzales, DM, Mercier, I, Koch, WJ, Lisanti, MP. Caveolin-1 deficiency exacerbates cardiac dysfunction and reduces survival in mice with myocardial infarction. Am. J. Physiol. Heart Circ. Physiol. 2011;300 (4):H1274-81. doi: 10.1152/ajpheart.01173.2010. PubMed PMID:21297026 PubMed Central PMC3075024.
• Gao, JS, Zhang, Y, Tang, X, Tucker, LD, Tarwater, PM, Quesenberry, PJ, Rigoutsos, I, Ramratnam, B. The Evi1, microRNA-143, K-Ras axis in colon cancer. FEBS Lett. 2011;585 (4):693-9. doi: 10.1016/j.febslet.2011.01.033. PubMed PMID:21276449 PubMed Central PMC3440864.
• Kogo, N, Tazaki, A, Kashino, Y, Morichika, K, Orii, H, Mochii, M, Watanabe, K. Germ-line mitochondria exhibit suppressed respiratory activity to support their accurate transmission to the next generation. Dev. Biol. 2011;349 (2):462-9. doi: 10.1016/j.ydbio.2010.11.021. PubMed PMID:21112323 .
• Hayashi, S, Imoto, I, Aizu, Y, Okamoto, N, Mizuno, S, Kurosawa, K, Okamoto, N, Honda, S, Araki, S, Mizutani, S, Numabe, H, Saitoh, S, Kosho, T, Fukushima, Y, Mitsubuchi, H, Endo, F, Chinen, Y, Kosaki, R, Okuyama, T, Ohki, H, Yoshihashi, H, Ono, M, Takada, F, Ono, H, Yagi, M, Matsumoto, H, Makita, Y, Hata, A, Inazawa, J. Clinical application of array-based comparative genomic hybridization by two-stage screening for 536 patients with mental retardation and multiple congenital anomalies. J. Hum. Genet. 2011;56 (2):110-24. doi: 10.1038/jhg.2010.129. PubMed PMID:20981036 .
• Rossi, S, Tsirigos, A, Amoroso, A, Mascellani, N, Rigoutsos, I, Calin, GA, Volinia, S. OMiR: Identification of associations between OMIM diseases and microRNAs. Genomics. 2011;97 (2):71-6. doi: 10.1016/j.ygeno.2010.10.004. PubMed PMID:20974243.
• Oulas, A, Karathanasis, N, Poirazi, P. Computational identification of miRNAs involved in cancer. Methods Mol. Biol. 2011;676 :23-41. doi: 10.1007/978-1-60761-863-8_2. PubMed PMID:20931387.

2010

• Mimaki, M, Hatakeyama, H, Komaki, H, Yokoyama, M, Arai, H, Kirino, Y, Suzuki, T, Nishino, I, Nonaka, I, Goto, Y. Reversible infantile respiratory chain deficiency: a clinical and molecular study. Ann. Neurol. 2010;68 (6):845-54. doi: 10.1002/ana.22111. PubMed PMID:21194154 .
• Hatzimichael, E, Dasoula, A, Benetatos, L, Syed, N, Dranitsaris, G, Crook, T, Bourantas, K. Study of specific genetic and epigenetic variables in multiple myeloma. Leuk. Lymphoma. 2010;51 (12):2270-4. doi: 10.3109/10428194.2010.528095. PubMed PMID:21067440 .
• Chaliasos, N, Challa, A, Hatzimichael, E, Koutsouka, F, Bourantas, DK, Vlahos, AP, Siamopoulou, A, Bourantas, KL, Makis, A. Serum adipocytokine and vascular inflammation marker levels in Beta-thalassaemia major patients. Acta Haematol. 2010;124 (4):191-6. doi: 10.1159/000320274. PubMed PMID:21042009 .
• Londin, ER, Keller, MA, Maista, C, Smith, G, Mamounas, LA, Zhang, R, Madore, SJ, Gwinn, K, Corriveau, RA. CoAIMs: a cost-effective panel of ancestry informative markers for determining continental origins. PLoS ONE. 2010;5 (10):e13443. doi: 10.1371/journal.pone.0013443. PubMed PMID:20976178 PubMed Central PMC2955551.
• Vourekas, A, Kirino, Y, Mourelatos, Z. Elective affinities: a Tudor-Aubergine tale of germline partnership. Genes Dev. 2010;24 (18):1963-6. doi: 10.1101/gad.1977010. PubMed PMID:20844011 PubMed Central PMC2939360.
• Amer, S, Matsubara, R, Murakoshi, F, Nakai, Y. Molecular analysis of Cryptosporidium parvum HNJ-1 isolated in Japan. J. Vet. Med. Sci. 2010;72 (12):1647-9. . PubMed PMID:20689224 .
• Makis, A, Shipway, D, Hatzimichael, E, Galanakis, E, Pshezhetskiy, D, Chaliasos, N, Stebbing, J, Siamopoulou, A. Cytokine and adhesion molecule expression evolves between the neutrophilic and lymphocytic phases of viral meningitis. J. Interferon Cytokine Res. 2010;30 (9):661-5. doi: 10.1089/jir.2009.0113. PubMed PMID:20626298 .
• Honda, S, Hayashi, S, Imoto, I, Toyama, J, Okazawa, H, Nakagawa, E, Goto, Y, Inazawa, J. Copy-number variations on the X chromosome in Japanese patients with mental retardation detected by array-based comparative genomic hybridization analysis. J. Hum. Genet. 2010;55 (9):590-9. doi: 10.1038/jhg.2010.74. PubMed PMID:20613765 .
• Rigoutsos, I, Furnari, F. Gene-expression forum: Decoy for microRNAs. Nature. 2010;465 (7301):1016-7. doi: 10.1038/4651016a. PubMed PMID:20577197 .
• Lee, S, Syed, N, Taylor, J, Smith, P, Griffin, B, Baens, M, Bai, M, Bourantas, K, Stebbing, J, Naresh, K, Nelson, M, Tuthill, M, Bower, M, Hatzimichael, E, Crook, T. DUSP16 is an epigenetically regulated determinant of JNK signalling in Burkitt’s lymphoma. Br. J. Cancer. 2010;103 (2):265-74. doi: 10.1038/sj.bjc.6605711. PubMed PMID:20551953 PubMed Central PMC2906728.
• Honda, S, Orii, KO, Kobayashi, J, Hayashi, S, Imamura, A, Imoto, I, Nakagawa, E, Goto, Y, Inazawa, J. Novel deletion at Xq24 including the UBE2A gene in a patient with X-linked mental retardation. J. Hum. Genet. 2010;55 (4):244-7. doi: 10.1038/jhg.2010.14. PubMed PMID:20339384 .
• Morichika, K, Kataoka, K, Terayama, K, Tazaki, A, Kinoshita, T, Watanabe, K, Mochii, M. Perturbation of Notch/Suppressor of Hairless pathway disturbs migration of primordial germ cells in Xenopus embryo. Dev. Growth Differ. 2010;52 (2):235-44. doi: 10.1111/j.1440-169X.2009.01164.x. PubMed PMID:20151992 .
• Rigoutsos, I. Short RNAs: how big is this iceberg?. Curr. Biol. 2010;20 (3):R110-3. doi: 10.1016/j.cub.2009.12.036. PubMed PMID:20144771 .
• Laurent, L, Wong, E, Li, G, Huynh, T, Tsirigos, A, Ong, CT, Low, HM, Kin Sung, KW, Rigoutsos, I, Loring, J, Wei, CL. Dynamic changes in the human methylome during differentiation. Genome Res. 2010;20 (3):320-31. doi: 10.1101/gr.101907.109. PubMed PMID:20133333 PubMed Central PMC2840979.
• Song Gao, J, Zhang, Y, Li, M, Tucker, LD, Machan, JT, Quesenberry, P, Rigoutsos, I, Ramratnam, B. Atypical transcription of microRNA gene fragments. Nucleic Acids Res. 2010;38 (9):2775-87. doi: 10.1093/nar/gkp1242. PubMed PMID:20097657 PubMed Central PMC2875006.
• Kirino, Y, Vourekas, A, Kim, N, de Lima Alves, F, Rappsilber, J, Klein, PS, Jongens, TA, Mourelatos, Z. Arginine methylation of vasa protein is conserved across phyla. J. Biol. Chem. 2010;285 (11):8148-54. doi: 10.1074/jbc.M109.089821. PubMed PMID:20080973 PubMed Central PMC2832966.
• Hatzimichael, E, Tuthill, M. Hematopoietic stem cell transplantation. Stem Cells Cloning. 2010;3 :105-17. doi: 10.2147/SCCAA.S6815. PubMed PMID:24198516 PubMed Central PMC3781735.
• Kirino, Y, Vourekas, A, Sayed, N, de Lima Alves, F, Thomson, T, Lasko, P, Rappsilber, J, Jongens, TA, Mourelatos, Z. Arginine methylation of Aubergine mediates Tudor binding and germ plasm localization. RNA. 2010;16 (1):70-8. doi: 10.1261/rna.1869710. PubMed PMID:19926723 PubMed Central PMC2802038.
• Ximeri, M, Galanopoulos, A, Klaus, M, Parcharidou, A, Giannikou, K, Psyllaki, M, Symeonidis, A, Pappa, V, Kartasis, Z, Liapi, D, Hatzimichael, E, Kokoris, S, Korkolopoulou, P, Sambani, C, Pontikoglou, C, Papadaki, HA, Hellenic MDS Study Group. Effect of lenalidomide therapy on hematopoiesis of patients with myelodysplastic syndrome associated with chromosome 5q deletion. Haematologica. 2010;95 (3):406-14. doi: 10.3324/haematol.2009.010876. PubMed PMID:19773257 PubMed Central PMC2833070.
• Hatzimichael, E, Dasoula, A, Shah, R, Syed, N, Papoudou-Bai, A, Coley, HM, Dranitsaris, G, Bourantas, KL, Stebbing, J, Crook, T. The prolyl-hydroxylase EGLN3 and not EGLN1 is inactivated by methylation in plasma cell neoplasia. Eur. J. Haematol. 2010;84 (1):47-51. doi: 10.1111/j.1600-0609.2009.01344.x. PubMed PMID:19737309 .
• Benetatos L, Hatzimichael E, Dasoula A, Dranitsaris G, Tsiara S, Syrrou M, Georgiou I, Bourantas KL. CpG methylation analysis of the MEG3 and SNRPN imprinted genes in acute myeloid leukemia and myelodysplastic syndromes. Leuk Res. 2010 Feb;34(2):148-53. doi: 10.1016/j.leukres.2009.06.019. PubMed PMID:19595458.
• Huynh, T., M. Vlachos and I. Rigoutsos. (2010) “Anchoring millions of distinct reads on the human genome within seconds” Proceedings 13th International Conference on Extending Database Technology (EDBT), Lausanne, Switzerland.

2009

• Tay, Y, Peter, S, Rigoutsos, I, Barahona, P, Ahmed, S, Dröge, P. Insights into the regulation of a common variant of HMGA2 associated with human height during embryonic development. Stem Cell Rev. 2009;5 (4):328-33. doi: 10.1007/s12015-009-9095-8. PubMed PMID:20058197 .
• Tsirigos, A, Rigoutsos, I. Alu and b1 repeats have been selectively retained in the upstream and intronic regions of genes of specific functional classes. PLoS Comput. Biol. 2009;5 (12):e1000610. doi: 10.1371/journal.pcbi.1000610. PubMed PMID:20019790 PubMed Central PMC2784220.
• Shigematsu, M, Ogawa, T, Kido, A, Kitamoto, HK, Hidaka, M, Masaki, H. Cellular and transcriptional responses of yeast to the cleavage of cytosolic tRNAs induced by colicin D. Yeast. 2009;26 (12):663-73. doi: 10.1002/yea.1725. PubMed PMID:19877125 .
• Zhang, Y, Gao, JS, Tang, X, Tucker, LD, Quesenberry, P, Rigoutsos, I, Ramratnam, B. MicroRNA 125a and its regulation of the p53 tumor suppressor gene. FEBS Lett. 2009;583 (22):3725-30. doi: 10.1016/j.febslet.2009.10.002. PubMed PMID:19818772 PubMed Central PMC3594778.
• Jain, P, Manuel, SL, Khan, ZK, Ahuja, J, Quann, K, Wigdahl, B. DC-SIGN mediates cell-free infection and transmission of human T-cell lymphotropic virus type 1 by dendritic cells. J. Virol. 2009;83 (21):10908-21. doi: 10.1128/JVI.01054-09. PubMed PMID:19692463 PubMed Central PMC2772783.
• Navarro, F, Gutman, D, Meire, E, Cáceres, M, Rigoutsos, I, Bentwich, Z, Lieberman, J. miR-34a contributes to megakaryocytic differentiation of K562 cells independently of p53. Blood. 2009;114 (10):2181-92. doi: 10.1182/blood-2009-02-205062. PubMed PMID:19584398 .
• Suriyawong, A, Magee, R, Peebles, K, Biswas, P. Energy recycling by co-combustion of coal and recovered paint solids from automobile paint operations. J Air Waste Manag Assoc. 2009;59 (5):560-7. . PubMed PMID:19583156 .
• Hatzimichael, E, Dranitsaris, G, Dasoula, A, Benetatos, L, Stebbing, J, Crook, T, Bourantas, KL. Von Hippel-Lindau methylation status in patients with multiple myeloma: a potential predictive factor for the development of bone disease. Clin Lymphoma Myeloma. 2009;9 (3):239-42. doi: 10.3816/CLM.2009.n.047. PubMed PMID:19525194 .
• Hatzimichael, E, Benetatos, L, Dasoula, A, Dranitsaris, G, Tsiara, S, Georgiou, I, Syrrou, M, Stebbing, J, Coley, HM, Crook, T, Bourantas, KL. Absence of methylation-dependent transcriptional silencing in TP73 irrespective of the methylation status of the CDKN2A CpG island in plasma cell neoplasia. Leuk. Res. 2009;33 (9):1272-5. doi: 10.1016/j.leukres.2009.04.009. PubMed PMID:19423161 .
• Kirino, Y, Kim, N, de Planell-Saguer, M, Khandros, E, Chiorean, S, Klein, PS, Rigoutsos, I, Jongens, TA, Mourelatos, Z. Arginine methylation of Piwi proteins catalysed by dPRMT5 is required for Ago3 and Aub stability. Nat. Cell Biol. 2009;11 (5):652-8. doi: 10.1038/ncb1872. PubMed PMID:19377467 PubMed Central PMC2746449.
• Rigoutsos, I. New tricks for animal microRNAS: targeting of amino acid coding regions at conserved and nonconserved sites. Cancer Res. 2009;69 (8):3245-8. doi: 10.1158/0008-5472.CAN-09-0352. PubMed PMID:19351814 .
• Lepoutre, V, Jain, P, Quann, K, Wigdahl, B, Khan, ZK. Role of resident CNS cell populations in HTLV-1-associated neuroinflammatory disease. Front Biosci (Landmark Ed). 2009;14 :1152-68. . PubMed PMID:19273122 PubMed Central PMC2739244.
• Powles, T, Stebbing, J, Bazeos, A, Hatzimichael, E, Mandalia, S, Nelson, M, Gazzard, B, Bower, M. The role of immune suppression and HHV-8 in the increasing incidence of HIV-associated multicentric Castleman’s disease. Ann. Oncol. 2009;20 (4):775-9. doi: 10.1093/annonc/mdn697. PubMed PMID:19179554 .

2008

• Descamps, M, Hatzimichael, E, Bhuva, N, Stebbing, J. Radiological imaging in the context of HIV infection: size of the lesion is not everything. J HIV Ther. 2008;13 (3):47-8. . PubMed PMID:19039294 .
• Jing, Y, Dowdy, JA, Van Scott, MR, Fedan, JS. Simultaneous measurement of mechanical responses and transepithelial potential difference and resistance, in guinea-pig isolated, perfused trachea using a novel apparatus: pharmacological characterization. Eur. J. Pharmacol. 2008;598 (1-3):98-103. doi: 10.1016/j.ejphar.2008.09.009. PubMed PMID:18835555 .
• Tay, Y, Zhang, J, Thomson, AM, Lim, B, Rigoutsos, I. MicroRNAs to Nanog, Oct4 and Sox2 coding regions modulate embryonic stem cell differentiation. Nature. 2008;455 (7216):1124-8. doi: 10.1038/nature07299. PubMed PMID:18806776 .
• Kirino, Y, Mourelatos, Z. Site-specific crosslinking of human microRNPs to RNA targets. RNA. 2008;14 (10):2254-9. doi: 10.1261/rna.1133808. PubMed PMID:18719246 PubMed Central PMC2553735.
• Kalyuzhnaya, MG, Lapidus, A, Ivanova, N, Copeland, AC, McHardy, AC, Szeto, E, Salamov, A, Grigoriev, IV, Suciu, D, Levine, SR, Markowitz, VM, Rigoutsos, I, Tringe, SG, Bruce, DC, Richardson, PM, Lidstrom, ME, Chistoserdova, L. High-resolution metagenomics targets specific functional types in complex microbial communities. Nat. Biotechnol. 2008;26 (9):1029-34. doi: 10.1038/nbt.1488. PubMed PMID:18711340 .
• Benetatos, L, Dasoula, A, Hatzimichael, E, Georgiou, I, Syrrou, M, Bourantas, KL. Promoter hypermethylation of the MEG3 (DLK1/MEG3) imprinted gene in multiple myeloma. Clin Lymphoma Myeloma. 2008;8 (3):171-5. doi: 10.3816/CLM.2008.n.021. PubMed PMID:18650181 .
• Holland, LZ, Albalat, R, Azumi, K, Benito-Gutiérrez, E, Blow, MJ, Bronner-Fraser, M, Brunet, F, Butts, T, Candiani, S, Dishaw, LJ, Ferrier, DE, Garcia-Fernàndez, J, Gibson-Brown, JJ, Gissi, C, Godzik, A, Hallböök, F, Hirose, D, Hosomichi, K, Ikuta, T, Inoko, H, Kasahara, M, Kasamatsu, J, Kawashima, T, Kimura, A, Kobayashi, M, Kozmik, Z, Kubokawa, K, Laudet, V, Litman, GW, McHardy, AC, Meulemans, D, Nonaka, M, Olinski, RP, Pancer, Z, Pennacchio, LA, Pestarino, M, Rast, JP, Rigoutsos, I, Robinson-Rechavi, M, Roch, G, Saiga, H, Sasakura, Y, Satake, M, Satou, Y, Schubert, M, Sherwood, N, Shiina, T, Takatori, N, Tello, J, Vopalensky, P, Wada, S, Xu, A, Ye, Y, Yoshida, K, Yoshizaki, F, Yu, JK, Zhang, Q, Zmasek, CM, de Jong, PJ, Osoegawa, K, Putnam, NH, Rokhsar, DS, Satoh, N, Holland, PW. The amphioxus genome illuminates vertebrate origins and cephalochordate biology. Genome Res. 2008;18 (7):1100-11. doi: 10.1101/gr.073676.107. PubMed PMID:18562680 PubMed Central PMC2493399.
• Kurata, S, Weixlbaumer, A, Ohtsuki, T, Shimazaki, T, Wada, T, Kirino, Y, Takai, K, Watanabe, K, Ramakrishnan, V, Suzuki, T. Modified uridines with C5-methylene substituents at the first position of the tRNA anticodon stabilize U.G wobble pairing during decoding. J. Biol. Chem. 2008;283 (27):18801-11. doi: 10.1074/jbc.M800233200. PubMed PMID:18456657 .
• Tsirigos, A, Rigoutsos, I. Human and mouse introns are linked to the same processes and functions through each genome’s most frequent non-conserved motifs. Nucleic Acids Res. 2008;36 (10):3484-93. doi: 10.1093/nar/gkn155. PubMed PMID:18450818 PubMed Central PMC2425492.
• Jing, Y, Dowdy, JA, Van Scott, MR, Fedan, JS. Hyperosmolarity-induced dilation and epithelial bioelectric responses of guinea pig trachea in vitro: role of kinase signaling. J. Pharmacol. Exp. Ther. 2008;326 (1):186-95. doi: 10.1124/jpet.107.135871. PubMed PMID:18413857 .
• Hatzimichael, E, Dasoula, A, Benetatos, L, Makis, A, Stebbing, J, Crook, T, Syrrou, M, Bourantas, KL. The absence of CDKN1C (p57KIP2) promoter methylation in myeloid malignancies also characterizes plasma cell neoplasms. Br. J. Haematol. 2008;141 (4):557-8. doi: 10.1111/j.1365-2141.2008.07034.x. PubMed PMID:18371112 .
• Styczynski, MP, Jensen, KL, Rigoutsos, I, Stephanopoulos, G. BLOSUM62 miscalculations improve search performance. Nat. Biotechnol. 2008;26 (3):274-5. doi: 10.1038/nbt0308-274. PubMed PMID:18327232 .
• Wang, WX, Rajeev, BW, Stromberg, AJ, Ren, N, Tang, G, Huang, Q, Rigoutsos, I, Nelson, PT. The expression of microRNA miR-107 decreases early in Alzheimer’s disease and may accelerate disease progression through regulation of beta-site amyloid precursor protein-cleaving enzyme 1. J. Neurosci. 2008;28 (5):1213-23. doi: 10.1523/JNEUROSCI.5065-07.2008. PubMed PMID:18234899 PubMed Central PMC2837363.
• Benetatos, L, Dasoula, A, Syed, N, Hatzimichael, E, Crook, T, Bourantas, KL. Methylation analysis of the von Hippel-Lindau gene in acute myeloid leukaemia and myelodysplastic syndromes. Leukemia. 2008;22 (6):1293-5. doi: 10.1038/sj.leu.2405053. PubMed PMID:18094722 .

2007

• Warnecke, F, Luginbühl, P, Ivanova, N, Ghassemian, M, Richardson, TH, Stege, JT, Cayouette, M, McHardy, AC, Djordjevic, G, Aboushadi, N, Sorek, R, Tringe, SG, Podar, M, Martin, HG, Kunin, V, Dalevi, D, Madejska, J, Kirton, E, Platt, D, Szeto, E, Salamov, A, Barry, K, Mikhailova, N, Kyrpides, NC, Matson, EG, Ottesen, EA, Zhang, X, Hernández, M, Murillo, C, Acosta, LG, Rigoutsos, I, Tamayo, G, Green, BD, Chang, C, Rubin, EM, Mathur, EJ, Robertson, DE, Hugenholtz, P, Leadbetter, JR. Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature. 2007;450 (7169):560-5. doi: 10.1038/nature06269. PubMed PMID:18033299 .
• Kirino, Y, Mourelatos, Z. 2′-O-methyl modification in mouse piRNAs and its methylase. Nucleic Acids Symp Ser (Oxf). 2007; (51):417-8. doi: 10.1093/nass/nrm209. PubMed PMID:18029764 .
• Londin, ER, Mentzer, L, Sirotkin, HI. Churchill regulates cell movement and mesoderm specification by repressing Nodal signaling. BMC Dev. Biol. 2007;7 :120. doi: 10.1186/1471-213X-7-120. PubMed PMID:17980025 PubMed Central PMC2180179.
• McHardy, AC, Rigoutsos, I. What’s in the mix: phylogenetic classification of metagenome sequence samples. Curr. Opin. Microbiol. 2007;10 (5):499-503. doi: 10.1016/j.mib.2007.08.004. PubMed PMID:17933580 .
• Tay, YM, Tam, WL, Ang, YS, Gaughwin, PM, Yang, H, Wang, W, Liu, R, George, J, Ng, HH, Perera, RJ, Lufkin, T, Rigoutsos, I, Thomson, AM, Lim, B. MicroRNA-134 modulates the differentiation of mouse embryonic stem cells, where it causes post-transcriptional attenuation of Nanog and LRH1. Stem Cells. 2008;26 (1):17-29. doi: 10.1634/stemcells.2007-0295. PubMed PMID:17916804 .
• Panteli, K, Bai, M, Hatzimichael, E, Zagorianakou, N, Agnantis, NJ, Bourantas, K. Serum levels, and bone marrow immunohistochemical expression of, vascular endothelial growth factor in patients with chronic myeloproliferative diseases. Hematology. 2007;12 (6):481-6. doi: 10.1080/10245330701554664. PubMed PMID:17852434 .
• Kirino, Y, Mourelatos, Z. The mouse homolog of HEN1 is a potential methylase for Piwi-interacting RNAs. RNA. 2007;13 (9):1397-401. doi: 10.1261/rna.659307. PubMed PMID:17652135 PubMed Central PMC1950760.
• Londin, ER, Mentzer, L, Gates, KP, Sirotkin, HI. Expression and regulation of the zinc finger transcription factor Churchill during zebrafish development. Gene Expr. Patterns. 2007;7 (6):645-50. doi: 10.1016/j.modgep.2007.04.002. PubMed PMID:17521969 PubMed Central PMC1976285.
• Mavromatis, K, Ivanova, N, Barry, K, Shapiro, H, Goltsman, E, McHardy, AC, Rigoutsos, I, Salamov, A, Korzeniewski, F, Land, M, Lapidus, A, Grigoriev, I, Richardson, P, Hugenholtz, P, Kyrpides, NC. Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nat. Methods. 2007;4 (6):495-500. doi: 10.1038/nmeth1043. PubMed PMID:17468765 .
• Hayashi, S, Honda, S, Minaguchi, M, Makita, Y, Okamoto, N, Kosaki, R, Okuyama, T, Imoto, I, Mizutani, S, Inazawa, J. Construction of a high-density and high-resolution human chromosome X array for comparative genomic hybridization analysis. J. Hum. Genet. 2007;52 (5):397-405. doi: 10.1007/s10038-007-0127-4. PubMed PMID:17406783 .
• Kirino, Y, Mourelatos, Z. Mouse Piwi-interacting RNAs are 2′-O-methylated at their 3′ termini. Nat. Struct. Mol. Biol. 2007;14 (4):347-8. doi: 10.1038/nsmb1218. PubMed PMID:17384647 .
• Honda, S, Hayashi, S, Kato, M, Niida, Y, Hayasaka, K, Okuyama, T, Imoto, I, Mizutani, S, Inazawa, J. Clinical and molecular cytogenetic characterization of two patients with non-mutational aberrations of the FMR2 gene. Am. J. Med. Genet. A. 2007;143A (7):687-93. doi: 10.1002/ajmg.a.31638. PubMed PMID:17343270 .
• Kampani, K, Quann, K, Ahuja, J, Wigdahl, B, Khan, ZK, Jain, P. A novel high throughput quantum dot-based fluorescence assay for quantitation of virus binding and attachment. J. Virol. Methods. 2007;141 (2):125-32. doi: 10.1016/j.jviromet.2006.11.043. PubMed PMID:17204339 PubMed Central PMC1975807.
• McHardy, AC, Martín, HG, Tsirigos, A, Hugenholtz, P, Rigoutsos, I. Accurate phylogenetic classification of variable-length DNA fragments. Nat. Methods. 2007;4 (1):63-72. doi: 10.1038/nmeth976. PubMed PMID:17179938 .
• Benetatos, L, Hatzimichael, E, Vassou, A, Bourantas, KL. Cryptococcus lung infection complicating fludarabine treatment in a chronic lymphocytic leukemia patient. Leuk. Res. 2007;31 (1):119-20. doi: 10.1016/j.leukres.2006.03.008. PubMed PMID:16620969 .

2006

• Winston, A, Hatzimichael, E, Marvin, V, Stebbing, J, Bower, M. Host pharmacogenetics in the treatment of HIV and cancer. Curr Drug Saf. 2006;1 (1):107-16. . PubMed PMID:18690920 .
• Hatzimichael, E, Benetatos, L, Stebbing, J, Kapsali, E, Panayiotopoulou, S, Bourantas, KL. Spontaneous splenic haematoma in a multiple myeloma patient receiving pegfilgrastim support. Clin Lab Haematol. 2006;28 (6):416-8. doi: 10.1111/j.1365-2257.2006.00819.x. PubMed PMID:17105496 .
• Loose, C, Jensen, K, Rigoutsos, I, Stephanopoulos, G. A linguistic model for the rational design of antimicrobial peptides. Nature. 2006;443 (7113):867-9. doi: 10.1038/nature05233. PubMed PMID:17051220 .
• García Martín, H, Ivanova, N, Kunin, V, Warnecke, F, Barry, KW, McHardy, AC, Yeates, C, He, S, Salamov, AA, Szeto, E, Dalin, E, Putnam, NH, Shapiro, HJ, Pangilinan, JL, Rigoutsos, I, Kyrpides, NC, Blackall, LL, McMahon, KD, Hugenholtz, P. Metagenomic analysis of two enhanced biological phosphorus removal (EBPR) sludge communities. Nat. Biotechnol. 2006;24 (10):1263-9. doi: 10.1038/nbt1247. PubMed PMID:16998472 .
• Miranda, KC, Huynh, T, Tay, Y, Ang, YS, Tam, WL, Thomson, AM, Lim, B, Rigoutsos, I. A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes. Cell. 2006;126 (6):1203-17. doi: 10.1016/j.cell.2006.07.031. PubMed PMID:16990141 .
• Makis, AC, Hatzimichael, EC, Stebbing, J. The genomics of new drugs in sickle cell disease. Pharmacogenomics. 2006;7 (6):909-17. doi: 10.2217/14622416.7.6.909. PubMed PMID:16981849 .
• Noma, A, Kirino, Y, Ikeuchi, Y, Suzuki, T. Biosynthesis of wybutosine, a hyper-modified nucleoside in eukaryotic phenylalanine tRNA. EMBO J. 2006;25 (10):2142-54. doi: 10.1038/sj.emboj.7601105. PubMed PMID:16642040 PubMed Central PMC1462984.
• Rigoutsos, I, Huynh, T, Miranda, K, Tsirigos, A, McHardy, A, Platt, D. Short blocks from the noncoding parts of the human genome have instances within nearly all known genes and relate to biological processes. Proc. Natl. Acad. Sci. U.S.A. 2006;103 (17):6605-10. doi: 10.1073/pnas.0601688103. PubMed PMID:16636294 PubMed Central PMC1447521.
• Makis, AC, Hatzimichael, EC, Stebbing, J, Bourantas, KL. C-reactive protein and vascular cell adhesion molecule-1 as markers of severity in sickle cell disease. Arch. Intern. Med. 2006;166 (3):366-8. doi: 10.1001/archinte.166.3.366. PubMed PMID:16476879 .
• Kirino, Y, Yasukawa, T, Marjavaara, SK, Jacobs, HT, Holt, IJ, Watanabe, K, Suzuki, T. Acquisition of the wobble modification in mitochondrial tRNALeu(CUN) bearing the G12300A mutation suppresses the MELAS molecular defect. Hum. Mol. Genet. 2006;15 (6):897-904. doi: 10.1093/hmg/ddl007. PubMed PMID:16446307 .
• Höhl, M, Rigoutsos, I, Ragan, MA. Pattern-based phylogenetic distance estimation and tree reconstruction. Evol. Bioinform. Online. 2007;2 :359-75. . PubMed PMID:19455227 PubMed Central PMC2674673.
• Mullins, IM, Siadaty, MS, Lyman, J, Scully, K, Garrett, CT, Miller, WG, Muller, R, Robson, B, Apte, C, Weiss, S, Rigoutsos, I, Platt, D, Cohen, S, Knaus, WA. Data mining and clinical data repositories: Insights from a 667,000 patient data set. Comput. Biol. Med. 2006;36 (12):1351-77. doi: 10.1016/j.compbiomed.2005.08.003. PubMed PMID:16375883 .
• Stebbing, J, Mazhar, D, Lewis, R, Palmieri, C, Hatzimichael, E, Nelson, M, Gazzard, B, Bower, M. The presentation and survival of patients with non-cutaneous AIDS-associated Kaposi’s sarcoma. Ann. Oncol. 2006;17 (3):503-6. doi: 10.1093/annonc/mdj091. PubMed PMID:16311274 .
• Jensen, KL, Styczynski, MP, Rigoutsos, I, Stephanopoulos, GN. A generic motif discovery algorithm for sequential data. Bioinformatics. 2006;22 (1):21-8. doi: 10.1093/bioinformatics/bti745. PubMed PMID:16257985 .

2005

• Kirino, Y, Suzuki, T. Human mitochondrial diseases associated with tRNA wobble modification deficiency. RNA Biol. 2005;2 (2):41-4. . PubMed PMID:17132941 .
• Stebbing, J, Hatzimichael, E, Bower, M, Winston, A. The rationale and development of new drugs to treat HIV infection. Med Chem. 2005;1 (6):635-42. . PubMed PMID:16787347 .
• Makis, AC, Galanakis, E, Hatzimichael, EC, Papadopoulou, ZL, Siamopoulou, A, Bourantas, KL. Serum levels of soluble interleukin-2 receptor alpha (sIL-2Ralpha) as a predictor of outcome in brucellosis. J. Infect. 2005;51 (3):206-10. doi: 10.1016/j.jinf.2004.10.013. PubMed PMID:16230217 .
• Darzentas, N, Rigoutsos, I, Ouzounis, CA. Sensitive detection of sequence similarity using combinatorial pattern discovery: a challenging study of two distantly related protein families. Proteins. 2005;61 (4):926-37. doi: 10.1002/prot.20608. PubMed PMID:16224785 .
• Panteli, KE, Hatzimichael, EC, Bouranta, PK, Katsaraki, A, Seferiadis, K, Stebbing, J, Bourantas, KL. Serum interleukin (IL)-1, IL-2, sIL-2Ra, IL-6 and thrombopoietin levels in patients with chronic myeloproliferative diseases. Br. J. Haematol. 2005;130 (5):709-15. doi: 10.1111/j.1365-2141.2005.05674.x. PubMed PMID:16115126 .
• Tsirigos, A, Rigoutsos, I. A sensitive, support-vector-machine method for the detection of horizontal gene transfers in viral, archaeal and bacterial genomes. Nucleic Acids Res. 2005;33 (12):3699-707. doi: 10.1093/nar/gki660. PubMed PMID:16006619 PubMed Central PMC1174904.
• Sfagos, C, Makis, AC, Chaidos, A, Hatzimichael, EC, Dalamaga, A, Kosma, K, Bourantas, KL. Serum ferritin, transferrin and soluble transferrin receptor levels in multiple sclerosis patients. Mult. Scler. 2005;11 (3):272-5. doi: 10.1191/1352458505ms1171oa. PubMed PMID:15957506 .
• Yasukawa, T, Kirino, Y, Ishii, N, Holt, IJ, Jacobs, HT, Makifuchi, T, Fukuhara, N, Ohta, S, Suzuki, T, Watanabe, K. Wobble modification deficiency in mutant tRNAs in patients with mitochondrial diseases. FEBS Lett. 2005;579 (13):2948-52. doi: 10.1016/j.febslet.2005.04.038. PubMed PMID:15893315 .
• Kirino, Y, Goto, Y, Campos, Y, Arenas, J, Suzuki, T. Specific correlation between the wobble modification deficiency in mutant tRNAs and the clinical features of a human mitochondrial disease. Proc. Natl. Acad. Sci. U.S.A. 2005;102 (20):7127-32. doi: 10.1073/pnas.0500563102. PubMed PMID:15870203 PubMed Central PMC1129107.
• Wouters, MA, Rigoutsos, I, Chu, CK, Feng, LL, Sparrow, DB, Dunwoodie, SL. Evolution of distinct EGF domains with specific functions. Protein Sci. 2005;14 (4):1091-103. doi: 10.1110/ps.041207005. PubMed PMID:15772310 PubMed Central PMC2253431.
• Tsirigos, A, Rigoutsos, I. A new computational method for the detection of horizontal gene transfer events. Nucleic Acids Res. 2005;33 (3):922-33. doi: 10.1093/nar/gki187. PubMed PMID:15716310 PubMed Central PMC549390.
• Londin, ER, Niemiec, J, Sirotkin, HI. Chordin, FGF signaling, and mesodermal factors cooperate in zebrafish neural induction. Dev. Biol. 2005;279 (1):1-19. doi: 10.1016/j.ydbio.2004.11.016. PubMed PMID:15708554 .
• Kirino, Y. and Suzuki, T (2005) “MELAS A3243G mutation and tRNA modification disorder” Rinsyoukensa 49: 89-95

2004

• Styczynski, MP, Jensen, KL, Rigoutsos, I, Stephanopoulos, GN. An extension and novel solution to the (l,d)-motif challenge problem. Genome Inform. 2004;15 (2):63-71. . PubMed PMID:15706492 .
• Kirino, Y, Yasukawa, T, Ohta, S, Akira, S, Ishihara, K, Watanabe, K, Suzuki, T. Codon-specific translational defect caused by a wobble modification deficiency in mutant tRNA from a human mitochondrial disease. Proc. Natl. Acad. Sci. U.S.A. 2004;101 (42):15070-5. doi: 10.1073/pnas.0405173101. PubMed PMID:15477592 PubMed Central PMC524061.
• Mogilyansky, E, Loa, CC, Adelson, ME, Mordechai, E, Tilton, RC. Comparison of Western immunoblotting and the C6 Lyme antibody test for laboratory detection of Lyme disease. Clin. Diagn. Lab. Immunol. 2004;11 (5):924-9. doi: 10.1128/CDLI.11.5.924-929.2004. PubMed PMID:15358654 PubMed Central PMC515278.
• Meşe, G, Londin, E, Mui, R, Brink, PR, White, TW. Altered gating properties of functional Cx26 mutants associated with recessive non-syndromic hearing loss. Hum. Genet. 2004;115 (3):191-9. doi: 10.1007/s00439-004-1142-6. PubMed PMID:15241677 .
• Huynh, T, Rigoutsos, I. The web server of IBM’s Bioinformatics and Pattern Discovery group: 2004 update. Nucleic Acids Res. 2004;32 (Web Server issue):W10-5. doi: 10.1093/nar/gkh367. PubMed PMID:15215340 PubMed Central PMC441505.
• Chaidos, A, Makis, A, Hatzimichael, E, Tsiara, S, Gouva, M, Tzouvara, E, Bourantas, KL. Treatment of beta-thalassemia patients with recombinant human erythropoietin: effect on transfusion requirements and soluble adhesion molecules. Acta Haematol. 2004;111 (4):189-95. doi: 10.1159/000077551. PubMed PMID:15153710 .
• Limongelli, A, Schaefer, J, Jackson, S, Invernizzi, F, Kirino, Y, Suzuki, T, Reichmann, H, Zeviani, M. Variable penetrance of a familial progressive necrotising encephalopathy due to a novel tRNA(Ile) homoplasmic mutation in the mitochondrial genome. J. Med. Genet. 2004;41 (5):342-9. . PubMed PMID:15121771 PubMed Central PMC1735786.
• Paredes, CJ, Rigoutsos, I, Papoutsakis, ET. Transcriptional organization of the Clostridium acetobutylicum genome. Nucleic Acids Res. 2004;32 (6):1973-81. doi: 10.1093/nar/gkh509. PubMed PMID:15060177 PubMed Central PMC390361.
• Makis, AC, Hatzimichael, EC, Kolios, G, Bourantas, KL. Circulating endothelin-3 levels in patients with sickle cell disease during hydroxyurea treatment. Haematologica. 2004;89 (3):360-1. . PubMed PMID:15020278 .
• Wong, MS, Raab, RM, Rigoutsos, I, Stephanopoulos, GN, Kelleher, JK. Metabolic and transcriptional patterns accompanying glutamine depletion and repletion in mouse hepatoma cells: a model for physiological regulatory networks. Physiol. Genomics. 2004;16 (2):247-55. doi: 10.1152/physiolgenomics.00088.2003. PubMed PMID:14612591 .
• Rigoutsos, I. and T. Huynh “Chung-Kwei: a pattern-discovery-based system for the automatic identification of unsolicited e-mail messages (SPAM)” First Conference on Email and Anti-Spam (CEAS2004), Mountain View, CA, July 2004
• Moxley, J., G. Stephanopoulos and I. Rigoutsos “Systems biology: using systems approaches to manage biological complexity” Foundations of Computer Aided Process Design Conference on Discovery though Product and Process Design (FOCAPD 2004), Princeton University, Princeton, NJ, July 2004

2003

• Murphy, E, Rigoutsos, I, Shibuya, T, Shenk, TE. Reevaluation of human cytomegalovirus coding potential. Proc. Natl. Acad. Sci. U.S.A. 2003;100 (23):13585-90. doi: 10.1073/pnas.1735466100. PubMed PMID:14593199 PubMed Central PMC263857.
• Azumi, K, De Santis, R, De Tomaso, A, Rigoutsos, I, Yoshizaki, F, Pinto, MR, Marino, R, Shida, K, Ikeda, M, Ikeda, M, Arai, M, Inoue, Y, Shimizu, T, Satoh, N, Rokhsar, DS, Du Pasquier, L, Kasahara, M, Satake, M, Nonaka, M. Genomic analysis of immunity in a Urochordate and the emergence of the vertebrate immune system: “waiting for Godot”. Immunogenetics. 2003;55 (8):570-81. doi: 10.1007/s00251-003-0606-5. PubMed PMID:14530883 .
• Platt, DE, Guerra, C, Zanotti, G, Rigoutsos, I. Global secondary structure packing angle bias in proteins. Proteins. 2003;53 (2):252-61. doi: 10.1002/prot.10448. PubMed PMID:14517976 .
• Kurata, S, Ohtsuki, T, Wada, T, Kirino, Y, Takai, K, Saigo, K, Watanabe, K, Suzuki, T. Decoding property of C5 uridine modification at the wobble position of tRNA anticodon. Nucleic Acids Res. Suppl. 2003; (3):245-6. . PubMed PMID:14510472 .
• Rigoutsos, I, Riek, P, Graham, RM, Novotny, J. Structural details (kinks and non-alpha conformations) in transmembrane helices are intrahelically determined and can be predicted by sequence pattern descriptors. Nucleic Acids Res. 2003;31 (15):4625-31. . PubMed PMID:12888523 PubMed Central PMC169910.
• Londin, ER, Meng, H, Gruen, JR. A transcription map of the 6p22.3 reading disability locus identifying candidate genes. BMC Genomics. 2003;4 (1):25. doi: 10.1186/1471-2164-4-25. PubMed PMID:12834540 PubMed Central PMC166143.
• Huynh, T, Rigoutsos, I, Parida, L, Platt, D, Shibuya, T. The web server of IBM’s Bioinformatics and Pattern Discovery group. Nucleic Acids Res. 2003;31 (13):3645-50. . PubMed PMID:12824385 PubMed Central PMC169027.
• Iliopoulos, I, Tsoka, S, Andrade, MA, Enright, AJ, Carroll, M, Poullet, P, Promponas, V, Liakopoulos, T, Palaios, G, Pasquier, C, Hamodrakas, S, Tamames, J, Yagnik, AT, Tramontano, A, Devos, D, Blaschke, C, Valencia, A, Brett, D, Martin, D, Leroy, C, Rigoutsos, I, Sander, C, Ouzounis, CA. Evaluation of annotation strategies using an entire genome sequence. Bioinformatics. 2003;19 (6):717-26. . PubMed PMID:12691983 .
• Rigoutsos, I, Novotny, J, Huynh, T, Chin-Bow, ST, Parida, L, Platt, D, Coleman, D, Shenk, T. In silico pattern-based analysis of the human cytomegalovirus genome. J. Virol. 2003;77 (7):4326-44. . PubMed PMID:12634390 PubMed Central PMC150618.

2002

• Dehal, P, Satou, Y, Campbell, RK, Chapman, J, Degnan, B, De Tomaso, A, Davidson, B, Di Gregorio, A, Gelpke, M, Goodstein, DM, Harafuji, N, Hastings, KE, Ho, I, Hotta, K, Huang, W, Kawashima, T, Lemaire, P, Martinez, D, Meinertzhagen, IA, Necula, S, Nonaka, M, Putnam, N, Rash, S, Saiga, H, Satake, M, Terry, A, Yamada, L, Wang, HG, Awazu, S, Azumi, K, Boore, J, Branno, M, Chin-Bow, S, DeSantis, R, Doyle, S, Francino, P, Keys, DN, Haga, S, Hayashi, H, Hino, K, Imai, KS, Inaba, K, Kano, S, Kobayashi, K, Kobayashi, M, Lee, BI, Makabe, KW, Manohar, C, Matassi, G, Medina, M, Mochizuki, Y, Mount, S, Morishita, T, Miura, S, Nakayama, A, Nishizaka, S, Nomoto, H, Ohta, F, Oishi, K, Rigoutsos, I, Sano, M, Sasaki, A, Sasakura, Y, Shoguchi, E, Shin-i, T, Spagnuolo, A, Stainier, D, Suzuki, MM, Tassy, O, Takatori, N, Tokuoka, M, Yagi, K, Yoshizaki, F, Wada, S, Zhang, C, Hyatt, PD, Larimer, F, Detter, C, Doggett, N, Glavina, T, Hawkins, T, Richardson, P, Lucas, S, Kohara, Y, Levine, M, Satoh, N, Rokhsar, DS. The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins. Science. 2002;298 (5601):2157-67. doi: 10.1126/science.1080049. PubMed PMID:12481130 .
• Ahn, J, Won, TW, Kaplan, DE, Londin, ER, Kuzmic, P, Gelernter, J, Gruen, JR. A detailed physical map of the 6p reading disability locus, including new markers and confirmation of recombination suppression. Hum. Genet. 2002;111 (4-5):339-49. doi: 10.1007/s00439-002-0771-x. PubMed PMID:12384775 .
• Rigoutsos, I, Huynh, T, Floratos, A, Parida, L, Platt, D. Dictionary-driven protein annotation. Nucleic Acids Res. 2002;30 (17):3901-16. . PubMed PMID:12202776 PubMed Central PMC137405.
• Shibuya, T, Rigoutsos, I. Dictionary-driven prokaryotic gene finding. Nucleic Acids Res. 2002;30 (12):2710-25. . PubMed PMID:12060689 PubMed Central PMC117281.
• Wang, X., J. T.L. Wang, D. Shasha, B. A. Shapiro, I. Rigoutsos and K. Zhang “Finding patterns in three dimensional graphs: algorithms and applications to scientific data mining” IEEE Transactions on Data and Knowledge Engineering 14(4):731-749, July/August 2002

2001

• Gu, Y, Jing, Y, Kumar, A, Sharma, Y, Fujioka, H, Singh, N. Isolation of human neuronal cells resistant to toxicity by the prion protein peptide 106-126. J. Alzheimers Dis. 2001;3 (2):169-180. . PubMed PMID:12214058 .
• Makis, AC, Chaliasos, N, Hatzimichael, EC, Bourantas, KL. Recombinant human erythropoietin therapy in a transfusion-dependent beta-thalassemia major patient. Ann. Hematol. 2001;80 (8):492-5. . PubMed PMID:11563599 .
• Christou, L, Hatzimichael, E, Chaidos, A, Tsiara, S, Bourantas, KL. Treatment of plasma cell leukemia with vincristine, liposomal doxorubicin and dexamethasone. Eur. J. Haematol. 2001;67 (1):51-3. . PubMed PMID:11553267 .
• Novotny, J, Rigoutsos, I, Coleman, D, Shenk, T. In silico structural and functional analysis of the human cytomegalovirus (HHV5) genome. J. Mol. Biol. 2001;310 (5):1151-66. doi: 10.1006/jmbi.2001.4798. PubMed PMID:11502002 .
• Riek, RP, Rigoutsos, I, Novotny, J, Graham, RM. Non-alpha-helical elements modulate polytopic membrane protein architecture. J. Mol. Biol. 2001;306 (2):349-62. doi: 10.1006/jmbi.2000.4402. PubMed PMID:11237604 .
• Voulgari, PV, Hatzimichael, EC, Tsiara, S, Tzallas, C, Drosos, AA, Bourantas, KL. Investigation for the presence of anti-erythropoietin antibodies in patients with myelodysplastic syndromes. Eur. J. Haematol. 2001;66 (1):31-6. . PubMed PMID:11168505 .
• Hatzimichael, EC, Christou, L, Bai, M, Kolios, G, Kefala, L, Bourantas, KL. Serum levels of IL-6 and its soluble receptor (sIL-6R) in Waldenström’s macroglobulinemia. Eur. J. Haematol. 2001;66 (1):1-6. . PubMed PMID:11168500 .
• Platt, D. E., L. Parida, Y. Gao, A. Floratos and I. Rigoutsos “QSAR in grossly underdetermined systems: opportunities and issues” IBM Journal of Research and Development 45(3/4):533-544, May/July 2001
• Floratos, A., I. Rigoutsos, L. Parida and Y. Gao “DELPHI: a pattern-based method for detecting sequence similarity” IBM Journal of Research and Development 45(3/4):455-474, May/July 2001
• Parida, L., I. Rigoutsos and D. E. Platt “An output-sensitive flexible pattern discovery algorithm” Proceedings 12th Annual Symposium on Combinatorial Pattern Matching (CPM 2001) pp. 131-142, Jerusalem, Israel, July 2001

Before 2000

• Makis, AC, Hatzimichael, EC, Mavridis, A, Bourantas, KL. Alpha-2-macroglobulin and interleukin-6 levels in steady-state sickle cell disease patients. Acta Haematol. 2000;104 (4):164-8. doi: 10.1159/000046509. PubMed PMID:11279305 .
• Parida, L, Floratos, A, Rigoutsos, I I. MUSCA: An Algorithm for Constrained Alignment of Multiple Data Sequences. Genome Inform Ser Workshop Genome Inform. 1998;9 :112-119. . PubMed PMID:11072327 .
• Rigoutsos, I, Floratos, A, Parida, L, Gao, Y, Platt, D. The emergence of pattern discovery techniques in computational biology. Metab. Eng. 2000;2 (3):159-77. doi: 10.1006/mben.2000.0151. PubMed PMID:11056059 .
• Makis, AC, Hatzimichael, EC, Bourantas, KL. The role of cytokines in sickle cell disease. Ann. Hematol. 2000;79 (8):407-13. . PubMed PMID:10985359 .
• Bourantas, KL, Hatzimichael, EC, Makis, AC, Kapsali, E, Tsiara, S, Christou, L, Seferiadis, K. Prolonged interferon-alpha-2b treatment of hairy cell leukemia patients. Eur. J. Haematol. 2000;64 (5):350-1. . PubMed PMID:10863983 .
• Rigoutsos, I, Gao, Y, Floratos, A, Parida, L. Building dictionaries of 1D and 3D motifs by mining the Unaligned 1D sequences of 17 archaeal and bacterial genomes. Proc Int Conf Intell Syst Mol Biol. 1999; :223-33. . PubMed PMID:10786305 .
• Bourantas, KL, Xenakis, TA, Hatzimichael, EC, Kontogeorgakos, V, Beris, AE. Peri-operative use of recombinant human erythropoietin in Jehovah’s Witnesses. Haematologica. 2000;85 (4):444-5. . PubMed PMID:10756382 .
• Rigoutsos, I, Floratos, A, Ouzounis, C, Gao, Y, Parida, L. Dictionary building via unsupervised hierarchical motif discovery in the sequence space of natural proteins. Proteins. 1999;37 (2):264-77. . PubMed PMID:10584071 .
• Zanusso, G, Petersen, RB, Jin, T, Jing, Y, Kanoush, R, Ferrari, S, Gambetti, P, Singh, N. Proteasomal degradation and N-terminal protease resistance of the codon 145 mutant prion protein. J. Biol. Chem. 1999;274 (33):23396-404. . PubMed PMID:10438517 .
• Christou, L, Hatzimichael, EC, Sotsiou-Candila, F, Siamopoulos, K, Bourantas, KL. A patient with multiple myeloma, amyloidosis and light-chain deposition disease in kidneys with a long survival. Acta Haematol. 1999;101 (4):202-5. doi: 10.1159/000040954. PubMed PMID:10436302 .
• Bourantas, KL, Hatzimichael, EC, Makis, AC, Chaidos, A, Kapsali, ED, Tsiara, S, Mavridis, A. Serum beta-2-microglobulin, TNF-alpha and interleukins in myeloproliferative disorders. Eur. J. Haematol. 1999;63 (1):19-25. . PubMed PMID:10414450 .
• Silverman, BD, Pitman, MC, Platt, DE, Rigoutsos, I. Molecular moment similarity between clozapine and substituted [(4-phenylpiperazinyl)-methyl] benzamides: selective dopamine D4 agonists. J. Comput. Aided Mol. Des. 1998;12 (6):525-32. . PubMed PMID:9879500 .
• Rigoutsos, I, Floratos, A. Combinatorial pattern discovery in biological sequences: The TEIRESIAS algorithm. Bioinformatics. 1998;14 (1):55-67. . PubMed PMID:9520502 .
• Califano, A, Rigoutsos, I. FLASH: a fast look-up algorithm for string homology. Proc Int Conf Intell Syst Mol Biol. 1993;1 :56-64. . PubMed PMID:7584371 .
• Parida, L., I. Rigoutsos, A. Floratos, D. Platt, and Y. Gao “Pattern discovery on character sets and real valued data: linear bound on irredundant motifs and an efficient polynomial time algorithm” Proceedings 11th Annual ACM/SIAM Symposium on Discrete Algorithms (SODA ’00), pp. 297-308, San Francisco, CA, January 2000
• Floratos, A., I. Rigoutsos, L. Parida, G. Stolovitzky and Y. Gao “Sequence homology detection through large-scale pattern discovery” Proceedings 3rd Annual ACM International Conference on Computational Molecular Biology (RECOMB ’99) pp. 164-173, Lyon, France, April 1999
• Parida, L., A. Floratos and I. Rigoutsos “An approximation algorithm for alignment of multiple sequences using motif discovery” Journal of Combinatorial Optimization 3(2/3):247-275, July 1999
• Rigoutsos, I., A. Floratos, C. Ouzounis and Y. Gao “From motif discovery to functional characterization and structure prediction: a feasible journey” Proceedings 2nd Annual TIGR Conference on Computational Genomics Reston, VA. November 1998
• Rigoutsos, I. and A. Delis “Managing statistical behavior of large data sets in networked architectures” IEEE Transactions on Parallel and Distributed Systems 9(11):1073-1087, November 1998
• Rigoutsos, I. and A. Floratos “Motif discovery without alignment or enumeration” Proceedings 2nd Annual ACM International Conference on Computational Molecular Biology (RECOMB ’98) pp. 221-227, New York, NY, March 1998
• Rigoutsos, I “Well-behaved, tunable 3D affine invariants” Proceedings IEEE Conference on Computer Vision and Pattern Recognition (CVPR ’98) Santa Barbara, CA. June 1998
• Rigoutsos, I “2D affine-invariants that distribute uniformly and can be tuned to any convex feature domain” Proceedings International Conference on Computer Vision (ICCV ’98) Bombay, India, January 1998
• Wang X., J. Wang, D. Shasha, B. Shapiro, S. Dikshitulu, I. Rigoutsos and K. Zhang “Automated discovery of active motifs in three dimensional molecules” Proceedings 3rd International Conference On Knowledge Discovery And Data Mining (KDD-97) Newport Beach, CA, August 1997
• Wolfson, H. and I. Rigoutsos “Geometric Hashing: an overview” IEEE Computational Science & Engineering 4(4):10-21, October-December 1997
• Rigoutsos, I. and A. Delis “The impact of hashing function choice on the load balancing in very large datasets” Proceedings 8th International Conference on Software Engineering and Knowledge Engineering (SEKE ’96) Lake Tahoe, NE. June 1996
• Rigoutsos, I. and R. Hummel “A Bayesian approach to model matching with geometric hashing” Computer Vision and Image Understanding 62(1):11-26, July 1995
• Rigoutsos, I. and A. Califano “dFLASH: a distributed fast look-up algorithm for string homology” Proceedings Conference on Parallel Computation and Problem Solving Environments Dartmouth Institute for Advanced Graduate Studies, Hanover, NH, July 1994
• Rigoutsos I. and A. Califano “Searching in parallel for similar strings” IEEE Computational Science and Engineering 1(2):60-75, Summer 1994
• Rigoutsos, I. and R. Hummel “Distributed Bayesian object recognition” Proceedings IEEE Conference on Computer Vision and Pattern Recognition (CVPR ’93) New York, NY, June 1993
• Califano, A. and I. Rigoutsos “FLASH: a fast look-up algorithm for string homology” Proceedings IEEE Conference on Computer Vision and Pattern Recognition (CVPR ’93) New York, NY. June 1993
• Rigoutsos, I. and R. Hummel “Massively parallel model matching: geometric hashing on the connection machine” IEEE Computer: Special Issue on Parallel Processing for Computer Vision and Image Understanding 25(2):33-42, February 1992
• Berger, M. and I. Rigoutsos “An algorithm for point clustering and grid generation” IEEE Transactions on Systems, Man and Cybernetics 21(5):1278-1286, September/October 1991
• Rigoutsos, I. and R. Hummel “Several results on affine geometric hashing” Proceedings 8th Israeli Conference on Artificial Intelligence and Computer Vision Tel Aviv, Israel. December 1991
• Rigoutsos, I. and R. Hummel “Robust similarity invariant matching in the presence of noise” Proceedings 8th Israeli Conference on Artificial Intelligence and Computer Vision Tel Aviv, Israel. December 1991
• Rigoutsos, I “Visuo-tactual coarseness estimation tasks: 1: experiments, 2: modeling” Proceedings Vision Interface ’91, Calgary, Canada, June 1991
• Rigoutsos, I. and R. Hummel “Implementation of geometric hashing on the connection machine” Proceedings IEEE Workshop on Directions in Automated CAD-Based Vision Systems, Maui, Hawaii. June 1991
• Aloimonos, J., and I. Rigoutsos “Detection of 3D motion without correspondence; planar surfaces: theory and experiments, curved surfaces: theory” Proceedings AAAI-86 Philadelphia, PA. August 1986
• Aloimonos, J. and I. Rigoutsos “How to determine structure, depth and 3D motion of a textured plane, without correspondence” Proceedings Canadian Artificial Intelligence ‘86 Montreal, Canada. May 1986
• Aloimonos, J. and I. Rigoutsos “Determining the 3D motion of a rigid planar patch without correspondence, under perspective projection” Proceedings IEEE Workshop on Motion Charleston, SC. May 1986

Books

• Yi Jing. Epithelial Mechanisms in Airway Responses Induced by Hyperosmolarity: Application of a novel apparatus in understanding the mechanisms of exercise-induced asthma. VDM Verlag, Saarbrücken, Germany, 2009. ISBN-10: 3639198689
• Rigoutsos, I. and G. Stephanopoulos, Editors, Systems Biology: Genomics Oxford University Press, August 2006
• Rigoutsos, I. and G. Stephanopoulos, Editors, Systems Biology: Networks, Models & Applications, Oxford University Press, August 2006

Book Chapters

• Rigoutsos, I and A. Tsirigos, “MicroRNA Target Prediction”. In MicroRNAs in Development and Cancer, F. Slack (Ed.), Imperial College Press, 2010
• Rigoutsos, I., “Pyknons as putative novel and organism-specific regulatory motifs.” In RNA and the Regulation of Gene Expression, K. Morris (Ed.), Horizon Scientific Press, 2008
• Rigoutsos, I., D. Platt, A. Califano, and B. D. Silverman, “Representation and matching of small flexible molecules in large databases of 3D-molecular information.” In Pattern Discovery in Molecular Biology, J. Wang, B. Shapiro and D. Shasha (Eds.), Oxford University Press, 1999
• Rudin, N., K. Inman, G. Stolovitzky and I. Rigoutsos, “DNA-based identification.” In Biometrics: Personal Identification In Networked Society, A. Jain, R. Bolle and S. Pankanti (Eds.), Kluwer Academic Publishers, 1999
• Silverman, B.D., D. E. Platt, M. Pitman, and I. Rigoutsos, “Comparative molecular moment analysis (CoMMA).” In Perspectives in Drug Discovery and Design, Volumes 12/13/14 3D QSAR in Drug Design: Recent Advances, H. Kubinyi, G. Folkers, and Y.C. Martin (Eds.), Kluwer/Escom, 1998
• Rigoutsos, I., “Visuo-tactual coarseness estimation tasks: experiments and modeling.” In Advances in Machine Vision: Strategies and Applications, Archibald C. and E. Petriu (Eds.), World Scientific Press, Series in Computer Science – vol. 32, Singapore, July 1992