Isidore Rigoutsos

TitleProfessor
InstitutionThomas Jefferson University
DepartmentComputational Med Center
Address1020 Locust St.
Philadelphia PA 19107
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. 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. PMID: 33765992.
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    2. 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. PMID: 33471076.
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    3. 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 12 11; 10(1):21782. PMID: 33311640.
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    4. Magee R, Rigoutsos I. On the expanding roles of tRNA fragments in modulating cell behavior. Nucleic Acids Res. 2020 09 25; 48(17):9433-9448. PMID: 32890397.
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    5. 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. 2020 Apr 13; 18(1):38. PMID: 32279660.
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    6. 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. 2020 Jan 27. PMID: 31988194.
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    7. 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. PMID: 31512554.
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    8. 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. PMID: 31504201.
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    9. 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. PMID: 31323485.
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    10. 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 Jul 08. PMID: 31283110.
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    11. Magee R, Londin E, Rigoutsos I. TRNA-derived fragments as sex-dependent circulating candidate biomarkers for Parkinson's disease. Parkinsonism Relat Disord. 2019 May 25. PMID: 31402278.
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    12. 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. PMID: 30996049.
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    13. 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 04; 177(2):446-462.e16. PMID: 30951671.
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    14. Magee RG, Telonis AG, Loher P, Londin E, Rigoutsos I. Profiles of miRNA Isoforms and tRNA Fragments in Prostate Cancer. Sci Rep. 2018 Mar 28; 8(1):5314. PMID: 29593348.
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    15. 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 Jan 04; 46(D1):D152-D159. PMID: 29186503.
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    16. 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. PMID: 29030853.
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    17. Telonis AG, Rigoutsos I. Race disparities in the contribution of miRNA isoforms and tRNA-derived fragments to triple-negative breast cancer. Cancer Res. 2017 Dec 11. PMID: 29229607.
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    18. 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 Jun 23; 7(1):4110. PMID: 28646211.
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    19. 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 Jun 22. PMID: 28645172.
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    20. 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 May 24; 18(1):98. PMID: 28535802.
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    21. 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 May 19; 45(9):e70. PMID: 28108659.
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    22. Viswanathan V, Damle S, Zhang T, Opdenaker L, Modarai S, Accerbi M, Schmidt S, Green P, Galileo D, Palazzo J, Fields J, Haghighat S, Rigoutsos I, Gonye G, Boman BM. An miRNA Expression Signature for the Human Colonic Stem Cell Niche Distinguishes Malignant from Normal Epithelia. Cancer Res. 2017 May 09. PMID: 28487386.
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    23. 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 Apr 07; 45(6):2973-2985. PMID: 28206648.
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    24. Magee R, Telonis AG, Cherlin T, Rigoutsos I, Londin E. Assessment of isomiR Discrimination Using Commercial qPCR Methods. Noncoding RNA. 2017 Jun; 3(2). PMID: 28730153.
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    25. 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 Feb 21; 7:41184. PMID: 28220888.
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    26. Magee R, Loher P, Londin E, Rigoutsos I. Threshold-seq: a tool for determining the threshold in short RNA-seq datasets. Bioinformatics. 2017 Feb 14. PMID: 28203700.
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    27. 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 Nov 08; 7(45):72395-72414. PMID: 27590350.
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    28. 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 Nov 01; 311(5):G964-G973. PMID: 27634012.
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    29. 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. PMID: 27630665.
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    30. 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 May 5; 98(5):883-97. PMID: 27132591.
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    31. Pliatsika V, Loher P, Telonis AG, Rigoutsos I. MINTbase: a framework for the interactive exploration of mitochondrial and nuclear tRNA fragments. Bioinformatics. 2016 Aug 15; 32(16):2481-9. PMID: 27153631.
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    32. Telonis AG, Loher P, Kirino Y, Rigoutsos I. Consequential considerations when mapping tRNA fragments. BMC Bioinformatics. 2016; 17(1):123. PMID: 26961774.
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    33. 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 Sep 22; 6(28):24797-822. PMID: 26325506.
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    34. 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 Oct 30; 43(19):9158-75. PMID: 26400174.
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    35. 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. PMID: 26257769.
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    36. 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 Jul 21; 112(29):E3816-25. PMID: 26124144.
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    37. 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 Jun 2; 112(22):E2851. PMID: 25979943.
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    38. Telonis AG, Kirino Y, Rigoutsos I. Mitochondrial tRNA-lookalikes in nuclear chromosomes: Could they be functional? RNA Biol. 2015 Apr 3; 12(4):375-80. PMID: 25849196.
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    39. 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 Mar 10; 112(10):E1106-15. PMID: 25713380.
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    40. Pliatsika V, Rigoutsos I. "Off-Spotter": very fast and exhaustive enumeration of genomic lookalikes for designing CRISPR/Cas guide RNAs. Biol Direct. 2015; 10(1):4. PMID: 25630343.
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    41. Zhou H, Rigoutsos I. The emerging roles of GPRC5A in diseases. Oncoscience. 2014; 1(12):765-76. PMID: 25621293.
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    42. Telonis AG, Loher P, Kirino Y, Rigoutsos I. Nuclear and mitochondrial tRNA-lookalikes in the human genome. Front Genet. 2014; 5:344. PMID: 25339973.
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    43. Loher P, Londin ER, Rigoutsos I. IsomiR Expression Profiles in Human Lymphoblastoid Cell Lines Exhibit Population and Gender Dependencies. Oncotarget. 2014 Sep 30; 5(18):8790-802. PMID: 25229428.
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    44. 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. PMID: 25103560.
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    45. Zhou H, Rigoutsos I. MiR-103a-3p targets the 5' UTR of GPRC5A in pancreatic cells. RNA. 2014 Sep; 20(9):1431-9. PMID: 24984703.
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    46. 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 Feb 15; 74(4):1128-40. PMID: 24536047.
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    47. 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(1):3. PMID: 24524654.
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    48. 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 Aug 1; 10(8):1312-23. PMID: 23807417.
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    49. 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. PMID: 23323973.
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    50. Loher P, Rigoutsos I. Interactive exploration of RNA22 microRNA target predictions. Bioinformatics. 2012 Dec 1; 28(24):3322-3. PMID: 23074262.
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    51. 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 Sep 21; 586(19):3000-7. PMID: 23166923.
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    52. Xia Z, Clark P, Huynh T, Loher P, Zhao Y, Chen HW, 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. PMID: 22888400.
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    53. 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 Aug; 13(10):946-55. PMID: 22785201.
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    54. 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 Mar; 70(5):795-814. PMID: 22825660.
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    55. 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 Oct 14; 147(2):344-57. PMID: 22000013.
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    56. 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 Dec; 31(24):5037-45. PMID: 21986497.
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    57. 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. PMID: 21915294.
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    58. 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 Feb 18; 585(4):693-9. PMID: 21276449.
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    59. 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 Feb; 97(2):71-6. PMID: 20974243.
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    60. Rigoutsos I, Furnari F. Gene-expression forum: Decoy for microRNAs. Nature. 2010 Jun 24; 465(7301):1016-7. PMID: 20577197.
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    61. Rigoutsos I. Short RNAs: how big is this iceberg? Curr Biol. 2010 Feb 9; 20(3):R110-3. PMID: 20144771.
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    62. 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 Mar; 20(3):320-31. PMID: 20133333.
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    63. 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 May; 38(9):2775-87. PMID: 20097657.
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    64. 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 Dec; 5(12):e1000610. PMID: 20019790.
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    65. 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 Dec; 5(4):328-33. PMID: 20058197.
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    66. 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 Nov 19; 583(22):3725-30. PMID: 19818772.
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    67. 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 Sep 3; 114(10):2181-92. PMID: 19584398.
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    68. 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 May; 11(5):652-8. PMID: 19377467.
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    69. Rigoutsos I. New tricks for animal microRNAS: targeting of amino acid coding regions at conserved and nonconserved sites. Cancer Res. 2009 Apr 15; 69(8):3245-8. PMID: 19351814.
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    70. 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 Oct 23; 455(7216):1124-8. PMID: 18806776.
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    71. 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 Sep; 26(9):1029-34. PMID: 18711340.
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    72. 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 Jul; 18(7):1100-11. PMID: 18562680.
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    73. 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 Jun; 36(10):3484-93. PMID: 18450818.
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    74. Styczynski MP, Jensen KL, Rigoutsos I, Stephanopoulos G. BLOSUM62 miscalculations improve search performance. Nat Biotechnol. 2008 Mar; 26(3):274-5. PMID: 18327232.
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    75. 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 Jan 30; 28(5):1213-23. PMID: 18234899.
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    76. 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 Nov 22; 450(7169):560-5. PMID: 18033299.
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    77. McHardy AC, Rigoutsos I. What's in the mix: phylogenetic classification of metagenome sequence samples. Curr Opin Microbiol. 2007 Oct; 10(5):499-503. PMID: 17933580.
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    78. 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 Jan; 26(1):17-29. PMID: 17916804.
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    79. 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 Jun; 4(6):495-500. PMID: 17468765.
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    80. Höhl M, Rigoutsos I, Ragan MA. Pattern-based phylogenetic distance estimation and tree reconstruction. Evol Bioinform Online. 2006; 2:359-75. PMID: 19455227.
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    81. McHardy AC, Martín HG, Tsirigos A, Hugenholtz P, Rigoutsos I. Accurate phylogenetic classification of variable-length DNA fragments. Nat Methods. 2007 Jan; 4(1):63-72. PMID: 17179938.
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    82. Loose C, Jensen K, Rigoutsos I, Stephanopoulos G. A linguistic model for the rational design of antimicrobial peptides. Nature. 2006 Oct 19; 443(7113):867-9. PMID: 17051220.
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    83. 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 Oct; 24(10):1263-9. PMID: 16998472.
      Citations:    
    84. 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 Sep 22; 126(6):1203-17. PMID: 16990141.
      Citations:    
    85. 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 Apr 25; 103(17):6605-10. PMID: 16636294.
      Citations:    
    86. 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 Dec; 36(12):1351-77. PMID: 16375883.
      Citations:    
    87. 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 Dec 1; 61(4):926-37. PMID: 16224785.
      Citations:    
    88. Jensen KL, Styczynski MP, Rigoutsos I, Stephanopoulos GN. A generic motif discovery algorithm for sequential data. Bioinformatics. 2006 Jan 1; 22(1):21-8. PMID: 16257985.
      Citations:    
    89. 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. PMID: 16006619.
      Citations:    
    90. Wouters MA, Rigoutsos I, Chu CK, Feng LL, Sparrow DB, Dunwoodie SL. Evolution of distinct EGF domains with specific functions. Protein Sci. 2005 Apr; 14(4):1091-103. PMID: 15772310.
      Citations:    
    91. Tsirigos A, Rigoutsos I. A new computational method for the detection of horizontal gene transfer events. Nucleic Acids Res. 2005; 33(3):922-33. PMID: 15716310.
      Citations:    
    92. Huynh T, Rigoutsos I. The web server of IBM's Bioinformatics and Pattern Discovery group: 2004 update. Nucleic Acids Res. 2004 Jul 1; 32(Web Server issue):W10-5. PMID: 15215340.
      Citations:    
    93. Paredes CJ, Rigoutsos I, Papoutsakis ET. Transcriptional organization of the Clostridium acetobutylicum genome. Nucleic Acids Res. 2004; 32(6):1973-81. PMID: 15060177.
      Citations:    
    94. 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 Jan 15; 16(2):247-55. PMID: 14612591.
      Citations:    
    95. 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. PMID: 15706492.
      Citations:    
    96. Platt DE, Guerra C, Zanotti G, Rigoutsos I. Global secondary structure packing angle bias in proteins. Proteins. 2003 Nov 1; 53(2):252-61. PMID: 14517976.
      Citations:    
    97. Murphy E, Rigoutsos I, Shibuya T, Shenk TE. Reevaluation of human cytomegalovirus coding potential. Proc Natl Acad Sci U S A. 2003 Nov 11; 100(23):13585-90. PMID: 14593199.
      Citations:    
    98. 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 Nov; 55(8):570-81. PMID: 14530883.
      Citations:    
    99. 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 Aug 1; 31(15):4625-31. PMID: 12888523.
      Citations:    
    100. 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 Jul 1; 31(13):3645-50. PMID: 12824385.
      Citations:    
    101. 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 Apr 12; 19(6):717-26. PMID: 12691983.
      Citations:    
    102. 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 Apr; 77(7):4326-44. PMID: 12634390.
      Citations:    
    103. 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 Dec 13; 298(5601):2157-67. PMID: 12481130.
      Citations:    
    104. Rigoutsos I, Huynh T, Floratos A, Parida L, Platt D. Dictionary-driven protein annotation. Nucleic Acids Res. 2002 Sep 1; 30(17):3901-16. PMID: 12202776.
      Citations:    
    105. Shibuya T, Rigoutsos I. Dictionary-driven prokaryotic gene finding. Nucleic Acids Res. 2002 Jun 15; 30(12):2710-25. PMID: 12060689.
      Citations:    
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