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Draft:Isidore Rigoutsos

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  • Comment: Please see WP:EL and rewrite this. This is not me declining the submission, this is me declining to review the submission in its current form. Chetsford (talk) 01:15, 30 October 2024 (UTC)

Isidore Rigoutsos is a Greek-American Computational Biologist and the Richard W. Hevner Professor[1] of Computational medicine at Thomas Jefferson University. Before he joined Thomas Jefferson University in 2010, he worked at the Thomas J. Watson Research Center of IBM Research in Yorktown Heights, NY. While at IBM Research, Rigoutsos was also a Visiting Lecturer in MIT’s Department of Chemical Engineering for 10 years (2000-2010). At MIT, he co-taught the course 10-555: Bioinformatics: Principles, Methods and Applications with Gregory Stephanopoulos for several years.[2][3][4]

Education

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Rigoutsos studied Physics at the University of Athens, Greece. He obtained an MSc. degree from the University of Rochester under the supervision of Chris Brown. He then moved to New York University’s Courant Institute of Mathematical Sciences where he completed a Ph.D. degree, also in computer vision, under the supervision of Bob Hummel. The topic of his PhD thesis was Massively Parallel Model-based Object Recognition.[5]

Career

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Andrea Califano and Isidore Rigoutsos co-founded the Computational Biology Center in IBM Research in 1992. In 1998, Rigoutsos founded the “Bioinformatics and Pattern Discovery” group, which he managed until his departure from the company. In 2010, Rigoutsos joined Thomas Jefferson University where he founded the Computational Medicine Center.[6]

Research Expertise

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Rigoutsos is known for his work on pattern discovery and the molecular biology of small non-coding RNAs (sncRNAs).

- In pattern discovery, he and Aris Floratos designed the Teiresias algorithm. Teiresias[7] was the first deterministic, data-agnostic algorithm for discovering patterns in one-dimensional data streams. The algorithm was also output-sensitive and guaranteed the exhaustive enumeration of patterns. Over the years, Teiresias has been used to create solutions to diverse problems from the fields of computer security, biology, medicine, and others.

- In the field of sncRNAs, the Rigoutsos laboratory made several key contributions:

  • It was among the first to report and validate multiple microRNA targets in the amino acid coding regions of messenger RNAs in 2008.[8]
  • In collaboration with the laboratory of Jeanne Loring it released the first genome-wide methylation maps of differentiating human stem cells in 2010.[9]
  • It demonstrated for several types of sncRNAs that they are produced constitutively in human cells with abundances that depend on a person’s sex and ancestry, and also on tissue and disease type. The laboratory showed this separately for isomiRs,[10][11][12] tRNA-derived fragments (tRFs),[13][14][15] and rRNA-derived fragments (rRFs).[16][17]

Work

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Rigoutsos has authored/co-authored more than 180 peer-reviewed publications in the fields of Computer Science and Biology/Medicine.[18] His articles have received more than 30,000 citations (h-index=75, i10-index=1600) – Source: Google Scholar, October 2024.[19] He is also a named inventor or co-inventor in 29 US Patents.[20]

Honors-Awards

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In 2003, Rigoutsos was elected a Fellow of the American Institute for Medical and Biological Engineering.[21] In 2020, he was elected a fellow of the American Association for the Advancement of Science.[22]

Other

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Isidore Rigoutsos and Marsha Berger developed what is now known as the "Berger-Rigoutsos algorithm".[23] The algorithm solves the problem of dynamic regridding in adaptive mesh refinement methods (numerical analysis) by embedding the grid points where the solution needs to be refined into rectangles that are neither too small nor too big. The Berger-Rigoutsos algorithm has become a standard technique for handling clustering in adaptive mesh refinement. The algorithm is a natural solution to the problem and borrows its key idea from the field of computer vision.

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References

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  1. ^ https://www.facebook.com/photo.php?fbid=1872311359488369&id=133341490052040&set=a.720841204635396
  2. ^ https://web.mit.edu/10.555/Spring2002/
  3. ^ https://web.mit.edu/10.555/Spring2003/
  4. ^ https://web.mit.edu/10.555/Spring2004/
  5. ^ https://cs.nyu.edu/media/publications/rigoutsos_isidore.pdf
  6. ^ https://cm.jefferson.edu/
  7. ^ Rigoutsos I, Floratos A. Combinatorial pattern discovery in biological sequences: The TEIRESIAS algorithm. Bioinformatics. 1998;14(1):55-67. doi: 10.1093/bioinformatics/14.1.55. PubMed PMID: 9520502.
  8. ^ Tay Y, Zhang J, Thomson A, 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.
  9. ^ Laurent L, Wong E, Li G, Huynh T, Tsirigos A, Ong C, Low H, Kin Sung K, Rigoutsos I, Loring J, Wei C. Dynamic changes in the human methylome during differentiation. Genome Res. 2010;20(3):320-31. doi: 10.1101/gr.101907.109. PubMed PMID: 20133333.
  10. ^ Loher P, Londin ER, Rigoutsos I. IsomiR expression profiles in human lymphoblastoid cell lines exhibit population and gender dependencies. Oncotarget. 2014:1-13.
  11. ^ Telonis A, 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.
  12. ^ Telonis A, Magee R, Loher P, Chervoneva I, Londin E, Rigoutsos I. Knowledge about the presence or absence of miRNA isoforms (isomiRs) can successfully discriminate amongst 32 TCGA cancer types. Nucleic Acids Res. 2017;45(6):2973-85. doi: 10.1093/nar/gkx082. PubMed PMID: 28206648.
  13. ^ Telonis A, Loher P, Honda S, Jing Y, Palazzo J, Kirino Y, Rigoutsos I. Dissecting tRNA-derived fragment complexities using personalized transcriptomes reveals novel fragment classes and unexpected dependencies. Oncotarget. 2015;6(28):24797-822. doi: 10.18632/oncotarget.4695. PubMed PMID: 26325506.
  14. ^ Pliatsika V, Loher P, Magee R, Telonis A, Londin E, Shigematsu M, Kirino Y, Rigoutsos I. MINTbase v2.0: a comprehensive database for tRNA-derived fragments that includes nuclear and mitochondrial fragments from all The Cancer Genome Atlas projects. Nucleic Acids Res. 2018;46(D1):D152-D9. doi: 10.1093/nar/gkx1075. PubMed PMID: 29186503.
  15. ^ Telonis A, 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;79(12):3034-49. doi: 10.1158/0008-5472.CAN-19-0789. PubMed PMID: 30996049.
  16. ^ 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;18(1):38. doi: 10.1186/s12915-020-0763-0. PubMed PMID: 32279660.
  17. ^ Pliatsika V, Cherlin T, Loher P, Vlantis P, Nagarkar P, Nersisyan S, Rigoutsos I. MINRbase: a comprehensive database of nuclear- and mitochondrial-ribosomal-RNA-derived fragments (rRFs). Nucleic Acids Res. 2023:gkad833. doi: 10.1093/nar/gkad833. PubMed PMID: 37843123.
  18. ^ https://www.ncbi.nlm.nih.gov/myncbi/isidore.rigoutsos.1/bibliography/public
  19. ^ https://scholar.google.com/citations?user=1H25A1oAAAAJ&hl=en&oi=ao
  20. ^ https://patents.justia.com/inventor/isidore-rigoutsos
  21. ^ https://aimbe.org/college-of-fellows/cof-0836/
  22. ^ https://www.aaas.org/news/aaas-announces-leading-scientists-elected-2020-fellows
  23. ^ Berger M, Rigoutsos I. An algorithm for point clustering and grid generation. IEEE Transactions on Systems, Man, and Cybernetics. 1991;21(5):1278-86.
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