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Prof. Manolis Kellis (Kamvysselis)
Professor of Computer Science
Institute Member, Broad Institute
Head, MIT Computational Biology Group (CSAIL)
Primary DLC
Department of Electrical Engineering and Computer Science
MIT Room:
32D-524
(617) 253-2419
manoli@mit.edu
https://compbio.mit.edu/
Assistant
Geraldine McGowan
(617) 253-3497
gmcgmit@gmail.com
Areas of Interest and Expertise
Pharmaceutical Discovery
Genome Sequencing
Analysis Pipeline
Gene Regulation
Micro-RNA
Computational Biology, Machine Learning and Algorithms in Genomics
Genome Interpretation, Comparative Genomics, Evolutionary Signatures
Gene Regulation: Regulatory Motifs, Biological Networks, Dimensionality Reduction, Epigenomics
Evolution: Phylogenomics, Population Genomics, Human Variation
Disease: Genome-Wide Association Studies (GWAS), Single-Nucleotide Polymorphisms (SNPs), Personal Genomes, Molecular Underpinnings of Common Disease
Big Data
Research Summary
Professor Kellis' research interests are in the area of computational biology, genomics, epigenomics, gene regulation, and genome evolution. Specifically:
(1) in the area of genome interpretation, we seek to develop comparative genomics methods to identify genes and regulatory elements systematically in the human genome
(2) in the area of gene regulation, we seek to understand the regulatory motifs involved in cell type specification during development, understand their combinatorial relationships, and how these establish expression domains in the developing embryo.
(3) in the area of epigenomics, we seek to understand the chromatin signatures associated with distinct activity states, the changing chromatin states across different cell types and during differentiation, and the sequencing signals responsible for the establishment and maintenance of chromatin marks.
(4) in the area of evolutionary genomics, understanding the dynamics of gene phylogenies across complete genes, the emergence of new gene functions by duplication and mutation, and the algorithmic principles behind phylogenomics.
Recent Work
Projects
August 6, 2014
Department of Electrical Engineering and Computer Science
NIH Genotype-Tissue Expression (GTEx) Project
Principal Investigator
Manolis Kellis (Kamvysselis)
December 9, 2010
Department of Electrical Engineering and Computer Science
Performance and Scalability of Discriminative Metrics for Comparative Gene Identification in 12 Drosophila Genomes
Principal Investigator
Manolis Kellis (Kamvysselis)
December 9, 2010
Department of Electrical Engineering and Computer Science
Imagina: Sketch-Based Image Retrieval using Cognitive Abstraction
Principal Investigator
Manolis Kellis (Kamvysselis)
December 9, 2010
Department of Electrical Engineering and Computer Science
Phylogenetically and Spatially Conserved Word Pairs Associated with Gene-Expression Changes in Yeasts
Principal Investigator
Manolis Kellis (Kamvysselis)
December 9, 2010
Department of Electrical Engineering and Computer Science
Evolution, Biogenesis, Expression, and Target Predictions of a Substantially Expanded Set of Drosophila microRNAs
Principal Investigator
Manolis Kellis (Kamvysselis)
December 9, 2010
Department of Electrical Engineering and Computer Science
Methods in Comparative Genomics: Genome Correspondence, Gene Identification and Regulatory Motif Discovery
Principal Investigator
Manolis Kellis (Kamvysselis)
December 9, 2010
Department of Electrical Engineering and Computer Science
Transcriptional Regulatory Code of a Eukaryotic Genome
Principal Investigator
Manolis Kellis (Kamvysselis)
December 9, 2010
Department of Electrical Engineering and Computer Science
Evolution of Genes and Genomes on the Drosophila Phylogeny
Principal Investigator
Manolis Kellis (Kamvysselis)
December 9, 2010
Department of Electrical Engineering and Computer Science
Proof and Evolutionary Analysis of Ancient Genome Duplication in the Yeast Saccharomyces cerevisiae
Principal Investigator
Manolis Kellis (Kamvysselis)
December 9, 2010
Department of Electrical Engineering and Computer Science
The Consensus Coding Sequence (CCDS) Project: Identifying a Common Protein-Coding Gene set for the Human and Mouse Genomes
Principal Investigator
Manolis Kellis (Kamvysselis)
December 9, 2010
Department of Electrical Engineering and Computer Science
Position Specific Variation in the Rate of Evolution in Transcription Factor Binding Sites
Principal Investigator
Manolis Kellis (Kamvysselis)
December 9, 2010
Department of Electrical Engineering and Computer Science
Discrete Small RNA-Generating Loci as Master Regulators of Transposon Activity in Drosophila
Principal Investigator
Manolis Kellis (Kamvysselis)
December 9, 2010
Department of Electrical Engineering and Computer Science
Computational Comparative Genomics: Genes, Regulation, Evolution
Principal Investigator
Manolis Kellis (Kamvysselis)
December 9, 2010
Department of Electrical Engineering and Computer Science
Histone Modifications at Human Enhancers Reflect Global Cell-Type-Specific Gene Expression
Principal Investigator
Manolis Kellis (Kamvysselis)
December 9, 2010
Department of Electrical Engineering and Computer Science
Genome Analysis of the Platypus Reveals Unique Signatures of Evolution
Principal Investigator
Manolis Kellis (Kamvysselis)
December 9, 2010
Department of Electrical Engineering and Computer Science
Genome Duplication in the Teleost Fish Tetraodon Nigroviridis Reveals the Early Vertebrate Proto-Karyotype
Principal Investigator
Manolis Kellis (Kamvysselis)
December 9, 2010
Department of Electrical Engineering and Computer Science
Optimization of Parameters for Coverage of Low Molecular Weight Proteins
Principal Investigator
Manolis Kellis (Kamvysselis)
December 9, 2010
Department of Electrical Engineering and Computer Science
Motif Discovery in Physiological Datasets: A Methodology for Inferring Predictive Elements
Principal Investigator
Manolis Kellis (Kamvysselis)
December 9, 2010
Department of Electrical Engineering and Computer Science
Conservation of Small RNA Pathways in Platypus
Principal Investigator
Manolis Kellis (Kamvysselis)
December 9, 2010
Department of Electrical Engineering and Computer Science
Information-Theoretic Inference of Regulatory Networks Using Backward Elimination
Principal Investigator
Manolis Kellis (Kamvysselis)
December 9, 2010
Department of Electrical Engineering and Computer Science
Unlocking the Secrets of the Genome
Principal Investigator
Manolis Kellis (Kamvysselis)
December 9, 2010
Department of Electrical Engineering and Computer Science
Evolution of Pathogenicity and Sexual Reproduction in Eight Candida Genomes
Principal Investigator
Manolis Kellis (Kamvysselis)
December 9, 2010
Department of Electrical Engineering and Computer Science
Accurate Gene-Tree Reconstruction by Learning Gene- and Species-Specific Substitution Rates Across Multiple Complete Genomes
Principal Investigator
Manolis Kellis (Kamvysselis)
December 9, 2010
Department of Electrical Engineering and Computer Science
Locating Protein-Coding Sequences Under Purifying Selection for Additional, Overlapping Functions in 29 Mammalian Genomes
Principal Investigator
Manolis Kellis (Kamvysselis)
December 9, 2010
Department of Electrical Engineering and Computer Science
Discovery of Functional Elements in 12 Drosophila Genomes Using Evolutionary Signatures
Principal Investigator
Manolis Kellis (Kamvysselis)
December 9, 2010
Department of Electrical Engineering and Computer Science
Network Motif Discovery Using Motif Enumeration and Symmetry Conditions
Principal Investigator
Manolis Kellis (Kamvysselis)
December 9, 2010
Department of Electrical Engineering and Computer Science
The Tasmanian Devil Transcriptome Reveals Schwann Cell Origins of a Clonally Transmissible Cancer
Principal Investigator
Manolis Kellis (Kamvysselis)
December 9, 2010
Department of Electrical Engineering and Computer Science
Crust: A New Voronoi-Based Surface Reconstruction Algorithm
Principal Investigator
Manolis Kellis (Kamvysselis)
December 9, 2010
Department of Electrical Engineering and Computer Science
A Comprehensive Map of Insulator Elements for the Drosophila Genome
Principal Investigator
Manolis Kellis (Kamvysselis)
December 9, 2010
Department of Electrical Engineering and Computer Science
A Single Hox Locus in Drosophila Produces Functional microRNAs from Opposite DNA Strands
Principal Investigator
Manolis Kellis (Kamvysselis)
December 9, 2010
Department of Electrical Engineering and Computer Science
A Bayesian Approach for Fast and Accurate Gene Tree Reconstruction
Principal Investigator
Manolis Kellis (Kamvysselis)
December 9, 2010
Department of Electrical Engineering and Computer Science
Chromatin Signature Reveals Over a Thousand Highly Conserved Large Non-Coding RNAs in Mammals
Principal Investigator
Manolis Kellis (Kamvysselis)
December 9, 2010
Department of Electrical Engineering and Computer Science
Sequencing and Comparison of Yeast Species to Identify Genes and Regulatory Elements
Principal Investigator
Manolis Kellis (Kamvysselis)
December 9, 2010
Department of Electrical Engineering and Computer Science
The Evolutionary Dynamics of the Saccharomyces cerevisiae Protein Interaction Network After Duplication
Principal Investigator
Manolis Kellis (Kamvysselis)
December 9, 2010
Department of Electrical Engineering and Computer Science
Revisiting the Protein-Coding Gene Catalog of Drosophila melanogaster Using 12 Fly Genomes
Principal Investigator
Manolis Kellis (Kamvysselis)
December 9, 2010
Department of Electrical Engineering and Computer Science
EciMorph: Curve Morphing in Extended Gaussian Space
Principal Investigator
Manolis Kellis (Kamvysselis)
December 9, 2010
Department of Electrical Engineering and Computer Science
Discovery and Characterization of Chromatin States for Systematic Annotation of the Human Genome
Principal Investigator
Manolis Kellis (Kamvysselis)
December 9, 2010
Department of Electrical Engineering and Computer Science
Systematic Discovery of Regulatory Motifs in Human Promoters and 3' UTRs by Comparison of Several Mammals
Principal Investigator
Manolis Kellis (Kamvysselis)
December 9, 2010
Department of Electrical Engineering and Computer Science
A Phylogenomic Approach to the Evolutionary Dynamics of Gene Duplication in Birds
Principal Investigator
Manolis Kellis (Kamvysselis)
December 9, 2010
Department of Electrical Engineering and Computer Science
RNA Polymerase Stalling at Developmental Control Genes in the Drosophila melanogaster Embryo
Principal Investigator
Manolis Kellis (Kamvysselis)
December 9, 2010
Department of Electrical Engineering and Computer Science
Genome Sequence, Comparative Analysis and Haplotype Structure of the Domestic Dog
Principal Investigator
Manolis Kellis (Kamvysselis)
December 9, 2010
Department of Electrical Engineering and Computer Science
Reliable Prediction of Regulator Targets Using 12 Drosophila Genomes
Principal Investigator
Manolis Kellis (Kamvysselis)
December 9, 2010
Department of Electrical Engineering and Computer Science
Distinguishing Protein-Coding and Non-Coding Genes in the Human Genome
Principal Investigator
Manolis Kellis (Kamvysselis)
December 9, 2010
Department of Electrical Engineering and Computer Science
3DMorph: Polygon Model Morphing
Principal Investigator
Manolis Kellis (Kamvysselis)
December 9, 2010
Department of Electrical Engineering and Computer Science
Systematic Discovery of Regulatory Motifs in Conserved Regions of the Human Genome, Including Thousands of CTCF Insulator Sites
Principal Investigator
Manolis Kellis (Kamvysselis)
December 9, 2010
Department of Electrical Engineering and Computer Science
An Endogenous Small Interfering RNA Pathway in Drosophila
Principal Investigator
Manolis Kellis (Kamvysselis)
December 9, 2010
Department of Electrical Engineering and Computer Science
Whole-Genome Comparative Annotation and Motif Discovery in Multiple Yeast Species
Principal Investigator
Manolis Kellis (Kamvysselis)
December 9, 2010
Department of Electrical Engineering and Computer Science
Whole-Genome ChIP-Chip Analysis of Dorsal, Twist, and Snail Suggests Integration of Diverse Patterning Processes in the Drosophila Embryo
Principal Investigator
Manolis Kellis (Kamvysselis)
December 9, 2010
Department of Electrical Engineering and Computer Science
The Genome Sequence of the Filamentous Fungus Neurospora crassa
Principal Investigator
Manolis Kellis (Kamvysselis)
December 9, 2010
Department of Electrical Engineering and Computer Science
SubMAP: Aligning Metabolic Pathways with Subnetwork Mappings
Principal Investigator
Manolis Kellis (Kamvysselis)
June 21, 2007
Department of Electrical Engineering and Computer Science
Systematic Discovery and Characterization of Fly microRNAs Using 12 Drosophila Genomes
Principal Investigator
Manolis Kellis (Kamvysselis)
December 15, 2006
Department of Electrical Engineering and Computer Science
Discovery of DNA Signals
Principal Investigator
Manolis Kellis (Kamvysselis)
December 15, 2006
Department of Electrical Engineering and Computer Science
Computational Biology Group (CBG)
Principal Investigator
Manolis Kellis (Kamvysselis)
Video
10.12.23-AI-Driven-Kellis
October 12, 2023
Conference Video
Duration: 31:42
Show more
Using Biochemical Data Sets, Optimized with Genomic Data, to Train Machine Learning Models for Therapeutic Development
10.12.23-AI-Driven-Panel
October 12, 2023
Conference Video
Duration: 22:39
Show more
Panel Discussion
4.4.23-Health-Kellis
April 4, 2023
Conference Video
Duration: 32:10
Show more
From Genomics to Therapeutics: Single-Cell Dissection and Manipulation of Disease Circuitry
3.25.21-Health-Roundtable
March 25, 2021
Conference Video
Duration: 89:1
Show more
Manolis Kellis
Professor, MIT Computer Science and Artificial Intelligence Lab
Institute Member, Broad Institute of MIT and Harvard
Ernest Fraenkel
Professor, Biological Engineering
Associate Member, Broad InstituteJuan Caicedo
Schmidt Fellow, Broad Institute
Caroline Uhler
Associate Professor, Electrical Engineering and Computer Science and Institute for Data, Systems and Society
Dipen Sangurdekar
Head of Oncology Translational Genomics team, Takeda
3.23.21-Health-Manolis-Kellis
March 23, 2021
Conference Video
Duration: 17:11
Show more
Manolis Kellis
Professor, MIT Computer Science and Artificial Intelligence Lab
Institute Member, Broad Institute of MIT and Harvard
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