Manolis Kellis

Manolis Kellis (Greek: Μανώλης Καμβυσέλλης; born

1977) is a professor of Computer Science and Manolis Kellis
Computational Biology at the Massachusetts Institute
of Technology (MIT) 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 is a
Principal Investigator in the Computer Science and
Artificial Intelligence Lab (CSAIL) at MIT.[5]

Kellis is known for his contributions to genomics,

human genetics, epigenomics, gene regulation, genome
evolution, disease mechanism, and single-cell
genomics. He co-led the NIH Roadmap Epigenomics
Project[6] effort to create a comprehensive map of the
human epigenome,[7][8][9] the comparative analysis of
29 mammals to create a comprehensive map of
conserved elements in the human genome,[10][11] the
ENCODE, GENCODE, and modENCODE projects to
characterize the genes, non-coding elements, and Manolis Kellis at the American Society of
circuits of the human genome and model Human Genetics (ASHG) meeting in Orlando
organisms.[12][13][14] A major focus of his work is Florida on October 19, 2017
understanding the effects of genetic variations on
Born Manolis Kamvysellis
human disease,[15] with contributions to
Greek: Μανώλης Καμβυσέλλης
obesity,[16][17][18] diabetes,[19] Alzheimer's
March 13, 1977
disease,[20][21][22] schizophrenia,[23] and cancer.[24]
Athens, Greece
Alma mater Massachusetts Institute of
Technology (PhD)
Education and early career
Known for ENCODE
Kellis was born in Greece, moved with his family to Awards Presidential Early Career Award
France when he was 12, and came to the U.S. in for Scientists and Engineers
1993.[25] He obtained his PhD from MIT, where he (2010)
worked with Eric Lander, founding director of the
NSF CAREER Award (2007)
Broad Institute, and Bonnie Berger, professor at
Sloan Research Fellowship
MIT[26] and received the Sprowls award for the best
(2008)
doctorate thesis in Computer Science,[27] and the first
Paris Kanellakis graduate fellowship.[28] Prior to Scientific career
computational biology, he worked on artificial Fields Computational genomics
Epigenomics
Comparative Genomics[1]
intelligence, sketch and image recognition, robotics, Thesis Computational Comparative
and computational geometry, at MIT and at the Xerox Genomics: Genes, Regulation,
Palo Alto Research Center.[26] Evolution. (https://hdl.handle.net/
1721.1/7999) (2003)
Doctoral Eric Lander[2]
Research and career advisor Bonnie Berger

As of July 2018, Manolis Kellis has authored 187 Website compbio.mit.edu (http://compbio.
journal publications[29] that have been cited 68,380 mit.edu)
times. [1] He has helped direct several large-scale
genomics projects, including the Roadmap Epigenomics project,[30][7] the Encyclopedia of DNA
Elements (ENCODE) project,[31] the Genotype Tissue-Expression (GTEx) project.[15]

Comparative genomics
Kellis started comparing the genomes of yeast species as an MIT graduate student. As part of this work,
which was published in Nature in 2003,[32] he developed computational methods to pinpoint patterns of
similarity and difference between closely related genomes. 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 elements, and their deregulation in human disease.[33] Kellis led several comparative
genomics projects in human,[33] mammals,[34][10] flies,[35][36] and yeast.[37]

Epigenomics
Kellis co-led the NIH government-funded project to catalogue the human epigenome. He said during an
interview with MIT Technology Review[33] “If the genome is the book of life, the epigenome is the
complete set of annotations and bookmarks.”[33] His lab now uses this map to further the understanding
of fundamental processes and disease in humans.

Obesity
Kellis and colleagues used epigenomic data to investigate the mechanistic basis of the strongest genetic
association with obesity, published in the New England Journal of Medicine.[16] 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 a shift from dissipating energy as heat (thermogenesis) to storing energy
as fat.[18] A full understanding of the phenomenon may lead to treatments for people whose 'slow
metabolism' cause them to gain excessive weight.[17]

Alzheimer's disease
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, published in Nature in 2015.[20] 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.[21]

Single-cell Genomics
The Kellis Lab has profiled a large number of human post-mortem brains at single-cell resolution,
studying inter-individual variation associated with genetic differences and disease phenotypes, including
the first single-cell transcriptomic analysis of Alzheimer's disease (https://www.nature.com/articles/s4158
6-019-1195-2) (Nature, 2019), single

Genotype-Tissue Expression (GTEx)

Kellis is a member of the Genotype-Tissue Expression (GTEx) project that seeks to elucidate the basis of
disease predisposition. It is an NIH-sponsored project that seeks to characterize genetic variation in
human tissues with roles in diabetes, heart disease, and cancer.[15]

Kellis is also a Principal Investigator of the enhancing GTEx (eGTEx) consortium, studying epigenomic
changes of regulatory elements and epitranscriptomic changes of RNA transcripts across multiple human
tissues.[38]

Disease Mechanism
To date, his lab has developed specific domain expertise in obesity,[17] diabetes,[19] Alzheimer's
disease,[20] schizophrenia,[23] heart disease,[39] ALS and FTLD,[40] and cancer.[24]

Teaching
In addition to his research, Kellis co-taught for several years MIT's required undergraduate introductory
algorithm courses 6.006: Introduction to Algorithms and 6.046: Design and Analysis of Algorithms[41][42]
with Profs. Ron Rivest, Erik Demaine, Piotr Indyk, Srinivas Devadas and others.

He is also teaching a computational biology course at MIT, titled "Computational Biology: Genomes,
Networks, Evolution."[43] 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.[44] He started 6.881: Computational Personal Genomics: Making sense of complete genomes (http
s://ocw.mit.edu/courses/6-881-computational-personal-genomics-making-sense-of-complete-genomes-spr
ing-2016/), and 6.883/9.S99: Neurogenomics: Computational Molecular Neuroscience (https://twitter.co
m/manoliskellis/status/1486105467839418371) 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.[45]

Awards and honors

Kellis received the US Presidential Early Career Award for Scientists and Engineers (PECASE),[46] the
National Science Foundation CAREER award,[47] a Sloan Research Fellowship,[48] the Gregor Mendel
Medal for Outstanding Achievements in Science by the Mendel Lectures committee, the Athens
Information Technology (AIT) Niki Award for Science and Engineering,[49] the Ruth and Joel Spira
Teaching award,[50] and the George M. Sprowls Award for the best Ph.D. thesis in Computer Science at
MIT.[27] He was named as one of Technology Review's Top 35 Innovators Under 35 for his research in
comparative genomics[51]

Media appearances
Decoding A Genomic Revolution (https://www.youtube.com/watch?v=zlVZ0ORtpPM), 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"[52]
Regulatory Genomics and Epigenomics of Complex Disease (https://www.youtube.com/wat
ch?v=VT7XrH4nJr0), 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 Churchill College, Cambridge[53]
Manolis Kellis Reddit Ask Me Anything (AMA) (https://www.reddit.com/r/science/comments/4
pmivr/science_ama_series_im_manolis_kellis_a_professor/), 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".

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mapping of type 1 diabetes susceptibility loci and evidence for colocalization of causal
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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" (https://www.ncbi.nlm.nih.gov/p
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