Publications

2017

  • 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 .
  • Honda, S, Loher, P, Morichika, K, Shigematsu, M, Kawamura, T, Kirino, Y et al.. 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 et al.. 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 m(1)G37. Enzymes. 2017;41 :89-115. doi: 10.1016/bs.enz.2017.03.003. PubMed PMID:28601227 .
  • Rigoutsos, I, Lee, SK, Nam, SY, Anfossi, S, Pasculli, B, Pichler, M et al.. 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 et al.. 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 .
  • Andrabi, SBA, Tahara, M, Matsubara, R, Toyama, T, Aonuma, H, Sakakibara, H et al.. 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 .
  • 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 et al.. 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 .
  • Shigematsu, M, Honda, S, Loher, P, Telonis, AG, Rigoutsos, I, Kirino, Y et al.. 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.
  • 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.
  • Magee, R, Telonis, AG, Cherlin, T, Rigoutsos, I, Londin, E. Assessment of isomiR Discrimination Using Commercial qPCR Methods. Non-Coding RNA 2017, 3(2), 18; doi:10.3390/ncrna3020018.

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 et al.. 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 et al.. 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 et al.. 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 et al.. 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 et al.. 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.
  • Ybañez, RH, Leesombun, A, Nishimura, M, Matsubara, R, Kojima, M, Sakakibara, H et al.. 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 et al.. 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 et al.. 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 et al.. 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 et al.. 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.
  • Blanco, FF, Jimbo, M, Wulfkuhle, J, Gallagher, I, Deng, J, Enyenihi, L et al.. 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 .
  • Telonis, AG, Loher, P, Honda, S, Jing, Y, Palazzo, J, Kirino, Y et al.. 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.
  • Jimbo, M, Blanco, FF, Huang, YH, Telonis, AG, Screnci, BA, Cosma, GL et al.. 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.
  • 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 et al.. 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 et al.. 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 et al.. 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 et al.. 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 et al.. Prediction of miRNA targets. Methods Mol. Biol. 2015;1269 :207-29. doi: 10.1007/978-1-4939-2291-8_13. PubMed PMID:25577381 .
  • 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.
  • Correnti, JM, Cook, D, Aksamitiene, E, Swarup, A, Ogunnaike, B, Vadigepalli, R et al.. Adiponectin fine-tuning of liver regeneration dynamics revealed through cellular network modeling. J. Physiol. (Lond.). 2014; :. doi: 10.1113/jphysiol.2014.284109. PubMed PMID:25384784 .
  • 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.
  • 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 et al.. 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.
  • 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.
  • 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 et al.. 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 et al.. 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 et al.. 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.
  • Mercier, I, Gonzales, DM, Quann, K, Pestell, TG, Molchansky, A, Sotgia, F et al.. 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 et al.. 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 et al.. 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.
  • 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.
  • 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 et al.. 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 et al.. 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 et al.. 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 et al.. 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 et al.. 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 et al.. 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 et al.. 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.
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  • 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)
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2012

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2011

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2010

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2009

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2008

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2007

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  • Mavromatis, K, Ivanova, N, Barry, K, Shapiro, H, Goltsman, E, McHardy, AC et al.. 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 et al.. 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 et al.. 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 et al.. 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 .

2006

  • 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 et al.. 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 et al.. 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 .
  • 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 et al.. 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.
  • Kirino, Y, Yasukawa, T, Marjavaara, SK, Jacobs, HT, Holt, IJ, Watanabe, K et al.. 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 et al.. 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 .
  • 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 .
  • 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 .
  • 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.
  • Yasukawa, T, Kirino, Y, Ishii, N, Holt, IJ, Jacobs, HT, Makifuchi, T et al.. 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 et al.. 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 et al.. 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.
  • Limongelli, A, Schaefer, J, Jackson, S, Invernizzi, F, Kirino, Y, Suzuki, T et al.. 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.
  • 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 et al.. 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 et al.. 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 et al.. 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 et al.. 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 et al.. 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 et al.. 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 et al.. 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 .
  • 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 .
  • 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

  • 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 .
  • 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 .
  • 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 et al.. 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 .
  • 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

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

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