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Manolis Kellis
Prof. Manolis Kellis at the annual American Society of Human Genetics (ASHG) meeting in Orlando Florida on October 19, 2017.
Manolis Kellis
Born (1977-03-13) March 13, 1977 (age 47)
Athens, Greece
Alma materMassachusetts Institute of Technology
AwardsUS Presidential Early Career Award in Science and Engineering (PECASE), 2010

National Science Foundation CAREER Awards, 2007

Faculty Research Innovation Fellowships, 2015 [1]

Alfred P. Sloan Fellowship [2]

Karl Van Tassel chair, MIT EECS, 2007

Distinguished Alumnus 1964 chair, MIT EECS, 2005

Ruth and Joel Spira Teaching Award in EECS

Athens Information Technology (AIT)  Niki Award for Science and Engineering, 2011

Technology Review TR35 Top Young Innovators, 2006

MIT Sprowls Award for Best PhD Thesis in Computer Science, 2003
Scientific career
InstitutionsBroad Institute of MIT and Harvard
Massachusetts Institute of Technology Harvard Medical School
ThesisComputational Comparative Genomics: Genes, Regulation, Evolution. (2003)
Doctoral advisorEric Lander, Bonnie Berger

Manolis Kellis (Kamvysselis) is a professor of Computer Science at the Massachusetts Institute of Technology (MIT) in the area of Computational Biology and a member of the Broad Institute of MIT and Harvard[3]. He is the head of the Computational Biology Group at MIT[4] and he is a Principal Investigator in the Computer Science and Artificial Intelligence Lab (CSAIL) at MIT[5]. His research interests are in the area of computational biology, genomics, epigenomics, gene regulation, and genome evolution[6].

He is known for his contributions to genomics, including leading an National Institutes of Health effort to create a map of the human epigenome, which constitute the most comprehensive view of the human epigenome to date[7][8]. A major focus of his work is understanding the effects of genetic variations on human disease[9] with contributions to obesity[10][11][12], diabetes[13], Alzheimer's Disease[14][15][16], Schizophrenia[17] and cancer[18].

Education and Career edit

Manolis Kellis was born in Greece, moved with his family to France when he was 12, and came to the U.S. in 1993[19]. He obtained his Ph.D. from MIT, where he received the Sprowls award for the best doctorate thesis in Computer Science[20], and the first Paris Kanellakis graduate fellowship[21]. Prior to computational biology, he worked on artificial intelligence, sketch and image recognition, robotics, and computational geometry, at MIT and at the Xerox Palo Alto Research Center[22].

Manolis Kellis started comparing the genomes of yeast species as an MIT graduate student working with Eric Lander, founding director of the Broad and Bonnie Berger, professor at MIT[22]. As part of this work, which was published in Nature in 2003[23], he developed computational methods to pinpoint patterns of similarity and difference. The goal was to develop methods for understanding genomes with a view to apply them to the human genome. He turned from yeast to flies and ultimately to mammals, comparing multiple species to explore genes, their control and their dysfunction in the human genome[24].  

Research edit

As of July 2018, he has authored 187 journal publications[25] that have been cited 68,380 times[26]. He has helped direct several large-scale genomics projects, including the Roadmap Epigenomics project[27][8], the Encyclopedia of DNA Elements (ENCODE) project[28], the Genotype Tissue-Expression (GTEx) project[9], and comparative genomics projects in humans[24], mammals[29], flies[30] and yeast[31].

He led the NIH government-funded project to catalogue the epigenome. He told during an interview with the MIT Technology Review[24] “If the genome is the book of life, the epigenome is the complete set of annotations and bookmarks”[24]. He now uses the map to further the understanding of fundamental processes and disease in humans.

Following the publication of the Epigenome Roadmap, he and his colleagues used epigenomic data to investigate the process of dissipating energy as heat[10].They showed that this mechanism operates in the fat cells of both humans and mice and detailed how changes within the relevant genomic regions cause shifts in the dissipating energy[12]. A full understanding of the phenomenon might lead to treatments for people whose so-called slow metabolisms cause them to gain excessive weight[11].

In another paper published in 2015, Kellis, Li-Huei Tsai, and others at MIT used epigenomic markings in human and mouse brains to study the mechanisms leading to Alzheimer’s disease[14]. They showed that immune cell activation and inflammation, which have long been associated with the condition, are not simply the result of neurodegeneration, as some researchers have argued. Rather, in mice engineered to develop Alzheimer’s-like symptoms, they found that immune cells start to change even before neural changes are observed[15].

He is leading the MIT team in the new phase of the Genotype-Tissue Expression (GTEx) project to elucidate basis of disease predisposition. It is an NIH-sponsored work to characterize genetic variation in human tissues with roles in diabetes, heart disease, and cancer[9].

To date, his lab has developed specific domain expertise in obesity[11], diabetes[13], Alzheimer's Disease[14], Schizophrenia[17] and cancer[18].

Teaching edit

In addition to his research, he has for several years co-taught MIT's required undergraduate introductory algorithm course 6.006: Introduction to Algorithms and 6.046: Design and Analysis of Algorithms[32]. He is also teaching a computational biology course at MIT, titled "Computational Biology: Genomes, Networks, Evolution"[33]. The course (6.047/6.878) is geared towards advanced undergraduate and early graduate students, seeking to learn the algorithmic and machine learning foundations of computational biology, and also be exposed to current frontiers of research in order to become active practitioners of the field[34]. He started 6.881: Computational Personal Genomics: Making sense of complete genomes[35]. This course is aimed at exploring the computational challenges associated with interpreting how sequence differences between individuals lead to phenotypic differences such as gene expression, disease predisposition, or response to treatment[36].

Awards edit

He received the US Presidential Early Career Award for Scientists and Engineers (PECASE)[37], the National Science Foundation CAREER award[38], the Alfred P. Sloan Foundation Award[39], the Athens Information Technology (AIT) Niki Award for Science and Engineering[40], the Ruth and Joel Spira Teaching award[41], and the George M. Sprowls Award for the best Ph.D. thesis in Computer Science at MIT[20]. He was named as one of Technology Review's Top 35 Innovators Under 35 for his research in comparative genomics[42].

Media appearances edit

  • Decoding A Genomic Revolution, TEDx Cambridge, 2013 "MIT Computational Biologist Manolis Kellis gives us a glimpse of the doctor’s office visit of the future, and uses his own genetic mutations to show us how a revolution in genomics is unlocking treatments that could transform medicine as we know it"[43]
  • Regulatory Genomics and Epigenomics of Complex Disease, Welcome Trust, 2014 "Manolis Kellis, Massachusetts Institute of Technology, USA, gives one of the keynote lectures at Epigenomics of Common Diseases, (28-31 October 2014), organised by the Wellcome Genome Campus Advanced Courses and Scientific Conferences team at the Churchill College, Cambridge, UK"[44]
  • Manolis Kellis Reddit Ask Me Anything (AMA), Reddit Science AMA Series: "I’m Manolis Kellis, a professor of computer science at MIT studying the human genome to learn about what causes obesity, Alzheimer’s, cancer and other conditions. AMA about comp-bio and epigenomics, and how they impact human health".

References edit

  1. ^ "Three EECS faculty selected as Faculty Research Innovation Fellowships". MIT News. Retrieved 2018-07-18.
  2. ^ "Three EECS faculty selected as Faculty Research Innovation Fellowships". MIT News. Retrieved 2018-07-18.
  3. ^ "Manolis Kellis | MIT CSAIL". www.csail.mit.edu. Retrieved 2018-07-19.
  4. ^ "MIT Computational Biology Group". MIT Computational Biology Group Lab Head. Retrieved 2018-07-19.
  5. ^ Kellis, Manolis. "People | MIT CSAIL". www.csail.mit.edu. Retrieved 2018-07-19.
  6. ^ "Researchers generate a reference map of the human epigenome". MIT News. Retrieved 2018-07-18.
  7. ^ "Researchers generate a reference map of the human epigenome". MIT News. Retrieved 2018-07-19.
  8. ^ a b Kundaje, Anshul; Meuleman, Wouter; Ernst, Jason; Bilenky, Misha; Yen, Angela; Heravi-Moussavi, Alireza; Kheradpour, Pouya; Zhang, Zhizhuo; Kellis, Manolis (2015). "Integrative analysis of 111 reference human epigenomes". Nature. 518 (7539): 317–330. doi:10.1038/nature14248. ISSN 0028-0836. PMC 4530010. PMID 25693563.
  9. ^ a b c "Kellis to lead MIT team in new phase of GTEx project to elucidate basis of disease predisposition". MIT News. Retrieved 2018-07-19.
  10. ^ a b "Identifying the gene switch that turns fat cells bad". Science | AAAS. 2015-08-19. Retrieved 2018-07-19.
  11. ^ a b c "A Fat-Burning Gene May Help Weight Loss". Time. Retrieved 2018-07-19.
  12. ^ a b Claussnitzer, Melina; Dankel, Simon N.; Kim, Kyoung-Han; Quon, Gerald; Meuleman, Wouter; Haugen, Christine; Glunk, Viktoria; Sousa, Isabel S.; Kellis, Manolis (2015-09-03). "FTO Obesity Variant Circuitry and Adipocyte Browning in Humans". New England Journal of Medicine. 373 (10): 895–907. doi:10.1056/nejmoa1502214. ISSN 0028-4793. PMC 4959911. PMID 26287746.
  13. ^ a b Onengut-Gumuscu, Suna; Chen, Wei-Min; Burren, Oliver; Cooper, Nick J; Quinlan, Aaron R; Mychaleckyj, Josyf C; Farber, Emily; Bonnie, Jessica K; Kellis, Manolis (2015-03-09). "Fine mapping of type 1 diabetes susceptibility loci and evidence for colocalization of causal variants with lymphoid gene enhancers". Nature Genetics. 47 (4): 381–386. doi:10.1038/ng.3245. ISSN 1061-4036. PMC 4380767. PMID 25751624.
  14. ^ a b c Gjoneska, Elizabeta; Pfenning, Andreas R.; Mathys, Hansruedi; Quon, Gerald; Kundaje, Anshul; Tsai, Li-Huei; Kellis, Manolis (2015). "Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer's disease". Nature. 518 (7539): 365–369. doi:10.1038/nature14252. ISSN 0028-0836. PMC 4530583. PMID 25693568.
  15. ^ a b "Epigenomics of Alzheimer's disease progression". MIT News. Retrieved 2018-07-19.
  16. ^ "Manolis Kellis – Cure Alzheimer's Fund". Cure Alzheimer's Fund. Retrieved 2018-07-19.
  17. ^ a b Manolis, Kellis; Mark, Daly; Kevin, Eggan; Alkes, Price. "NIH Grant, Network-based prediction and validation of causal schizophrenia genes and variants". Grantome.
  18. ^ a b Hornshøj, Henrik; Nielsen, Morten Muhlig; Sinnott-Armstrong, Nicholas A.; Świtnicki, Michał P.; Juul, Malene; Madsen, Tobias; Sallari, Richard; Kellis, Manolis; Ørntoft, Torben (2018-01-11). "Pan-cancer screen for mutations in non-coding elements with conservation and cancer specificity reveals correlations with expression and survival". NPJ Genomic Medicine. 3 (1): 1. doi:10.1038/s41525-017-0040-5. ISSN 2056-7944. PMC 5765157. PMID 29354286.
  19. ^ "Getting to the root of genetics". MIT News. Retrieved 2018-07-19.
  20. ^ a b "All Awards | MIT CSAIL". csail.mit.edu. Retrieved 2018-07-19.
  21. ^ "Kanellakis Fellowships | MIT EECS". www.eecs.mit.edu. Retrieved 2018-07-19.
  22. ^ a b "Manolis Kellis MIT Center for Genome Research Resume" (PDF).
  23. ^ Kellis, Manolis; Patterson, Nick; Endrizzi, Matthew; Birren, Bruce; Lander, Eric S. (2003). "Sequencing and comparison of yeast species to identify genes and regulatory elements". Nature. 423 (6937): 241–254. doi:10.1038/nature01644. ISSN 0028-0836. PMID 12748633. S2CID 1530261.
  24. ^ a b c d Schaffer, Amanda. "Annotating the book of life". MIT Technology Review. Retrieved 2018-07-19.
  25. ^ pubmeddev. "Manolis Kellis - PubMed - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2018-07-19.
  26. ^ "Manolis Kellis - Google Scholar Citations". scholar.google.com. Retrieved 2018-07-19.
  27. ^ "NIH-supported researchers map epigenome of more than 100 tissue and cell types". National Institutes of Health (NIH). 2015-07-03. Retrieved 2018-07-19.
  28. ^ Kellis, Manolis; Wold, Barbara; Snyder, Michael P.; Bernstein, Bradley E.; Kundaje, Anshul; Marinov, Georgi K.; Ward, Lucas D.; Birney, Ewan; Crawford, Gregory E. (2014-04-29). "Defining functional DNA elements in the human genome". Proceedings of the National Academy of Sciences of the United States of America. 111 (17): 6131–6138. doi:10.1073/pnas.1318948111. ISSN 0027-8424. PMC 4035993. PMID 24753594.
  29. ^ Lindblad-Toh, Kerstin; Garber, Manuel; Zuk, Or; Lin, Michael F.; Parker, Brian J.; Washietl, Stefan; Kheradpour, Pouya; Ernst, Jason; Jordan, Gregory (2011). "A high-resolution map of human evolutionary constraint using 29 mammals". Nature. 478 (7370): 476–482. doi:10.1038/nature10530. ISSN 0028-0836. PMC 3207357. PMID 21993624.
  30. ^ Lin, Michael F.; Carlson, Joseph W.; Crosby, Madeline A.; Matthews, Beverley B.; Yu, Charles; Park, Soo; Wan, Kenneth H.; Schroeder, Andrew J.; Gramates, L. Sian (December 2007). "Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes". Genome Research. 17 (12): 1823–1836. doi:10.1101/gr.6679507. ISSN 1088-9051. PMC 2099591. PMID 17989253.
  31. ^ Kellis, Manolis; Birren, Bruce W.; Lander, Eric S. (2004-03-07). "Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae". Nature. 428 (6983): 617–624. doi:10.1038/nature02424. ISSN 0028-0836. PMID 15004568. S2CID 4422074.
  32. ^ "6.006: Introduction to Algorithms - Massachusetts Institute of Technology". courses.csail.mit.edu. Retrieved 2018-07-19.
  33. ^ "6.047/6.878 Class Home". stellar.mit.edu. Retrieved 2018-07-19.
  34. ^ "Computational Biology". MIT OpenCourseWare. Retrieved 2018-07-19.
  35. ^ "6.881 Computational Personal Genomics: Making sense of complete genomes | MIT EECS". www.eecs.mit.edu. Retrieved 2018-07-19.
  36. ^ "Computational Personal Genomics: Making Sense of Complete Genomes". MIT OpenCourseWare. Retrieved 2018-07-19.
  37. ^ "Aaronson, Kellis recipients of PECASE 2010 Award | MIT EECS". www.eecs.mit.edu. Retrieved 2018-07-19.
  38. ^ "NSF Award Search: Award#0644282 - CAREER: Comparative Genomics and Biological Signal Discovery in the Human Genome". www.nsf.gov. Retrieved 2018-07-19.
  39. ^ "Sloan Foundation Fellows". sloan.org. Retrieved 2018-07-19.
  40. ^ "Kellis Wins Niki Award | MIT CSAIL". www.csail.mit.edu. Retrieved 2018-07-19.
  41. ^ "MIT School of Engineering | » Teaching Awards". Mit Engineering. Retrieved 2018-07-19.
  42. ^ MIT Technology Review. "Innovator Under 35: Manolis Kellis, 29". MIT Technology Review. Retrieved 2018-07-19.
  43. ^ "Decoding A Genomic Revolution | TEDxCambridge". TEDxCambridge. Retrieved 2018-07-19.
  44. ^ Wellcome Genome Campus Courses and Conferences (2016-02-25), Regulatory Genomics and Epigenomics of Complex Disease - Manolis Kellis, retrieved 2018-07-19

External links edit

MIT Computational Biology Goup Lab website, Kellis Lab

Manolis Kellis, Publications on Google Scholar

Manolis Kellis, Publications on PubMed

Manolis Kellis, Publications on ResearchGate

Manolis Kellis Twitter



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