Director of Computational Medicine Center, Professor in the Department of Pathology, Anatomy and Cell Biology, Department of Biochemistry & Molecular Biology, Department of Cancer Biology and member of the Kimmel Cancer Center Isidore Rigoutsos

Director of Computational Medicine Center, Professor in the Department of Pathology, Anatomy and Cell Biology, Department of Biochemistry & Molecular Biology, Department of Cancer Biology and member of the Kimmel Cancer Center

Short Bio

Dr. Rigoutsos is the Director of the Computational Medicine Center at Thomas Jefferson University (TJU). He joined TJU in early 2010 as a Professor with an appointment in the Department of Pathology, Anatomy & Cell Biology. He also has joint appointments in the Department of Cancer Biology, and the Department of Biochemistry & Molecular Biology, and is a member of the Kimmel Cancer Center at TJU. For nearly 18 years prior to joining TJU, Dr. Rigoutsos was with IBM's Thomas J. Watson Research Center where he founded and managed the Bioinformatics and Pattern Discovery group. In parallel to his IBM tenure, Dr. Rigoutsos was for a decade a Visiting Lecturer at MIT's Dept. of Chemical Engineering where he taught graduate-level classes and summer professional courses in Bioinformatics. Dr. Rigoutsos’ involvement in the field of Computational Biology spans the last nearly twenty years. During this time, he has been developing computer algorithms for studying genomic architecture and analyzing very large biological datasets. Since 1996, his efforts have revolved around the theoretical and practical aspects of pattern discovery and the design of pattern-based solutions to a variety of problems from genomics, genetics, molecular biology and medicine. Starting in 2002, Dr. Rigoutsos’ work placed particular emphasis on the study of non-coding RNAs (microRNAs, pyknons, piRNAs, etc.). Of particular interest are the questions surrounding the biogenesis of such non-coding RNAs, the mechanisms of action and the automated discovery of their targets, the discovery of novel organism-specific regulatory sequences, and the elucidation of the roles of non-coding RNAs in the onset and progression of disease. Some of Dr. Rigoutsos earlier work revolved around the solving of partial differential equations in 2 and 3 dimensions, using the adaptive mesh refinement method.  An interesting problem which arises in that context is that of embedding grid points (where the solution needs further refinement) in rectangles in a manner that minimizes the computational effort that is needed to improve the solution at those points. Joint work with Marsha Berger led to the development of a very efficient gridding scheme, now known as the Berger-Rigoutsos algorithm, for solving the problem. This picture, from a shock impacting an inclined slope, shows how the algorithm places rectangles at those locations that require a better-quality solution. A graduate of the Physics Dept. of the National and Kapodistrian University of Athens, Greece, Dr. Rigoutsos received a Master’s in Computer Science from the University of Rochester, and a Master’s and Doctoral degrees in Computer Science from New York University’s Courant Institute of Mathematical Sciences.

Publications

Papers

 

2017

  • 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.
  • 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; :. 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 .
  • 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

  • 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.
  • 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.
  • 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):883-97. doi: 10.1016/j.ajhg.2016.03.007. PubMed PMID:27132591 PubMed Central PMC4863560.
  • 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.
  • 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 .

2015

  • 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.
  • 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.
  • 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.
  • 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.
  • 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.

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.
  • 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.
  • 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.
  • 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.

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.
  • 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.
  • Bray, PF, McKenzie, SE, Edelstein, LC, Nagalla, S, Delgrosso, K, Ertel, A et al.. 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.
  • Benetatos, L, Hatzimichael, E, Londin, E, Vartholomatos, G, Loher, P, Rigoutsos, I et al.. 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 .
  • 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

2012

  • Rossi, S, Di Narzo, AF, Mestdagh, P, Jacobs, B, Bosman, FT, Gustavsson, B et al.. microRNAs in colon cancer: a roadmap for discovery. FEBS Lett. 2012;586 (19):3000-7. . PubMed PMID:23166923 .
  • 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 .
  • Xia, Z, Clark, P, Huynh, T, Loher, P, Zhao, Y, Chen, HW et al.. 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.
  • Pineda, DM, Rittenhouse, DW, Valley, CC, Cozzitorto, JA, Burkhart, RA, Leiby, B et al.. 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.

2011

  • Tay, Y, Kats, L, Salmena, L, Weiss, D, Tan, SM, Ala, U et al.. 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 et al.. 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.
  • 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.
  • Gao, JS, Zhang, Y, Tang, X, Tucker, LD, Tarwater, PM, Quesenberry, PJ et al.. 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.
  • Rossi, S, Tsirigos, A, Amoroso, A, Mascellani, N, Rigoutsos, I, Calin, GA et al.. 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 .

2010

  • Rigoutsos, I, Furnari, F. Gene-expression forum: Decoy for microRNAs. Nature. 2010;465 (7301):1016-7. doi: 10.1038/4651016a. PubMed PMID:20577197 .
  • 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 et al.. 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 et al.. 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.
  • 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 et al.. 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.
  • Zhang, Y, Gao, JS, Tang, X, Tucker, LD, Quesenberry, P, Rigoutsos, I et al.. 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.
  • Navarro, F, Gutman, D, Meire, E, Cáceres, M, Rigoutsos, I, Bentwich, Z et al.. 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 .
  • Kirino, Y, Kim, N, de Planell-Saguer, M, Khandros, E, Chiorean, S, Klein, PS et al.. 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 .

2008

  • 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 .
  • Kalyuzhnaya, MG, Lapidus, A, Ivanova, N, Copeland, AC, McHardy, AC, Szeto, E et al.. 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 .
  • Holland, LZ, Albalat, R, Azumi, K, Benito-Gutiérrez, E, Blow, MJ, Bronner-Fraser, M et al.. 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.
  • 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.
  • 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 et al.. 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.

2007

  • Warnecke, F, Luginbühl, P, Ivanova, N, Ghassemian, M, Richardson, TH, Stege, JT et al.. 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 .
  • 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 et al.. 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 .
  • 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 .
  • 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 .
  • 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.
  • 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

  • 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.
  • 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.

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 .
  • 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.
  • 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 .
  • 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.
  • 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 .
  • 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

  • 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 .
  • 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

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