35 (2): 189-199 (2019) The ones marked * may be different from the article in the profile. use dynamics of functional elements across many cell types to link mechanistic insights into their likely molecular roles. PDF Google Scholar PubMed The Tasmanian devil transcriptome reveals Schwann cell origins of a clonally transmissible cancer. As a complement to genetic and comparative genomics approaches, the Encyclopedia of DNA Elements Project was launched to contribute maps of RNA transcripts, transcriptional regulator binding sites, and chromatin states in many cell types. I am a professor at MIT in Computer Science. Enjoy! The following articles are merged in Scholar. Manolis Kellis – Page 3/4 PUBLICATIONS Sequencing and Comparison of Yeast Species to Identify Genes and Regulatory Motifs. In particular, elevation of the pro-inflammatory cytokine interleukin-6 (IL-6) is the earliest reported marker of immune activation in … Google Scholar 22 Johnston, S. D. et al. comparative genomics datasets. Conserved noncoding elements (CNEs) constitute the majority of sequences under purifying selection in the human genome, yet their function remains largely unknown. Their combined citations are counted only for the first article. Google Scholar. regulatory regions to their target genes, predict activators and Evol. Director NIH Intramural Sequencing Center, NHGRI, NIH. (2) We use combinations of Tumor epitopes – peptides that are presented on surface-bound MHC I proteins - provide targets for cancer immunotherapy and have been identified extensively in the annotated protein-coding regions of the genome. 2007; 24:1464–1479. Add co-authors Co-authors. Verified email at mit.edu - Homepage. these evolutionary, chromatin, and activity signatures to dramatically Its complexity, polygenicity, and small-effect-size and cell-type-specific contributors have hindered mechanistic elucidation and the search for new therapeutics. Huntington’s disease (HD) is an incurable neurodegenerative disorder caused by CAG trinucleotide expansions in the huntingtin gene. CAS Article Google Scholar 34. Immune checkpoint inhibitors (ICIs) show promise, but most patients do not respond. (4) We combine See the GP-DREAM website for running network inference algorithms. Merged citations. Merged citations. Professor, Computer Science, MIT Head, MIT Computational Biology Group Institute Member, Broad Institute of MIT and Harvard Principal Investigator, Computer Science and Artificial Intelligence Lab Stata Center - 32D.524 - 617.253.2419 Awards: - US Presidential Early Career Award ()- Alfred P. Sloan Foundation Award - National Science Foundation CAREER Award Their combined citations are counted only for the first article. scRNA-seq reveals functionally distinct gd T cells in human colorectal tumors [abstract]. Citation Format: Alvin Shi, Jessica A. Cintolo-Gonzalez, Isabel Chien, Dennis T. Frederick, Roman Alpatov, William Michaud, Deborah Plana, David Panka, Ryan Corcoran, Keith Flaherty, Ryan Sullivan, Manolis Kellis, Genevieve Boland. The following articles are merged in Scholar. CAS Article Google Scholar 6. Kellis, Patterson, Endrizzi, Birren, Lander. We identify and validate biomarkers from extracellular vesicles (EVs), allowing non-invasive monitoring of tumor- intrinsic and host immune status, as well as a prediction of ICI response. Soheil Feizi, Muriel Médard, Gerald T. Quon, Manolis Kellis, Ken R. Duffy: Network Infusion to Infer Information Sources in Networks. epigenetic modifications to define chromatin states associated with Epigenetic factors, particularly DNA methylation, have recently been proposed to influence the variation in recombination rate. Their combined citations are counted only for the first article. 2003; 423:241–254. Verified email at mit.edu. Despite recent discovery in GWAS of genomic variants associated with Alzheimer’s disease (AD), its underlying biological mechanisms are still elusive. The Tasmanian devil, a marsupial carnivore, is endangered because of the emergence of a transmissible cancer known as devil facial tumor disease (DFTD). Nature May 15, v. 423 p. 241-254, 2003. Motivated by the recent discovery of translated novel unannotated open reading frames (nuORFs) using ribosome profiling (Ribo-seq), we hypothesized that cancer-associated … repressed regions, each with distinct functional properties. The variation of recombination rate at both fine and large scales cannot be fully explained by DNA sequences alone. Science 293 ... Manolis Kellis. Nature. Sequencing and comparison of yeast species to identify genes and regulatory elements. Add co-authors Co-authors. genome by computational integration of large-scale functional and repressors, and cell type specific regulatory action. Manolis Kellis. Elevated cfDNA has been found not only from tumors, but also from normal tissues. [Google Scholar] Kellis M., et al. protein-coding genes, RNA structures, microRNAs, regulatory motifs, Proceedings: AACR Annual Meeting 2017; April 1-5, 2017; Washington, DC Cell free DNA (cfDNA) has been shown to be an emerging non-invasive biomarker to monitor tumor progression in cancer patients. 4 The etiology of inflammatory … Cited by 104460. Manolis Kellis is an Associate Professor of Computer Science at MIT, a member of the Computer Science and Artificial Intelligence Laboratory and of the Broad Institute of MIT and Harvard, where he directs the MIT Computational Biology distinct functions, including promoter, enhancer, transcribed, and multiple related species to recognize evolutionary signatures of Manolis Kellis, Ph.D. Citation Format: Cathal Harmon, Alex Zaborowski, Harry Kane, Stephen Cunningham, Leandro Agudelo, Manolis Kellis, Des Winter, Lydia Lynch. Google Scholar Databases Google News and PR-distribution services Companies websites And based on the analysis of the descriptive criteria (personal page ... Manolis Kellis MIT Professor USA Boston Top-100 AI Leaders in Drug Discovery and Advanced Healthcare Academia 2/4 9 … and individual regulatory elements. My CompBio course: Genomes, Networks, Evolution, Computer Science and Artificial Intelligence Lab, Manolis Kellis Computational Biology Group, Manolis Kellis at Broad Institute Interview, Manolis Kellis at National Documentation Institute, Manolis Kellis at Epigenomics of Common Diseases 2014, Manolis Kellis at Broad Midsummer Science Night, Adicpocyte Browning underlies FTO Obesity Mechanism, Epigenomics shows Immune Basis of Alzheimer's, Integrative analysis of 111 reference human epigenomes, Genetic + epigenomic discovery of disease loci, Joint Bayesian Inference of Risk Variants, Interpretin variation using cell type specific chromatin state, Chromatin state variation across 19 individuals, Trans-regulatory coding variation affecting TF binding, Interpreting noncoding genetic variation in complex traits and disease, Evidence of regulatory turnover in the human genome, From regions to SNPs, targets, regulators, cell types, Genotype-Expression association across 40 tissues, Integrative analysis of the human ENCODE project, A high-resolution map of evolutionary constraint in the human genome, Functional elements and regulatory circuits in fly, Evolutionary signatures for systematic genome interpretation in fly, Relating biochemical, evolutionary, and genetic approaches, Gene identification and motif discovery in yeast, Combinatorial chromatin patterns for genome annotation, Self organizing maps for epigenomic datasets, Interplay of Chromatin States, TF binding, and Regulatory Motifs, Automating chromatin-state discovery and characterization, Epigenetic signature of monoallelic expression in olfactory neurons, Chromatin landscape of Drosophila genes and regulatory elements, Tissue-specific enhancers in multiple human cell types, Network Deconvolution to distinguish direct dependencies, The wisdom of crowds in network inference, Integrative inference of regulatory networks, Discovering large motifs using symmetry-breaking conditions, Aligning large pathways with subnetwork mapping, Post whole-genome duplication (WGD) network evolution, Three periods of regulatory innovation in vertebrate evolution, Proof and analysis of Whole-Genome Duplication (WGD) in yeast, Evolutionary analysis of 8 candida genomes, Whole-genome duplication in a vertebrate genome, Evolution without sex for an animal species, Dissection of regulatory motifs in 2000 human enhancers, Systematic Discovery of motifs in 427 ENCODE experiments, Regulatory motif instance variation in human and fly, Massively parallel dissection of human enhancers, Using motifs to infer regulatory networks in fly, A cis-regulatory map of the Drosophila genome, lincRNA evolution across 6 mammals and 9 tissues, RNA folding in vivo, in vitro, and in sillico, Computational analysis of non-coding RNAs, RNA folding with soft constraints integrating experimental evidence, Chromatin reveals a new class of long intergenic non-coding RNAs, Discovery of a new class of anti-sense functional microRNAs, Comparative identification of microRNAs in fly, miRNA target identiification and analysis in Drosophila, small RNAs repressing retrotransposons in Drosophila, Evidence of abundant stop codon readthrough in animal genomes, Excess synonymous constraint in 10,000 protein-coding exons in human, Phylogenetic evidence of protein-coding evolutionary signatures, Revisiting fly genome: new genes and exons, unusual gene structures, Comparing evolutionary and single-species metrics, Handling multiple optima in dup/loss/transfer reconciliation, Labeled Coalescent Trees for dup/loss/coal reconciliation, Joint modeling of gene duplication, loss, and incomplete lineage sorting, Bayesian gene-tree phylogenomic reconstruction, Learning common gene-tree properties to overcome sparse information, Domain-level evolution reveals abundant gene fusion and fission events, Statistically informed gene-tree error correction using a species tree, Duplication, Horizontal Transfer and Loss reconciliation modeling, Received Sprowls award for best PhD thesis in CS. Cited in 40 publications in the last six months, and featured in numerous reviews, magazines and newspapers. CoRR abs/1606.07383 ( 2016 ) Jim Mullikin. An empirical codon model for protein sequence evolution. The ones marked * may be different from the article in the profile. Markers of both systemic and CNS immune activation and inflammation have been widely noted in HD and mouse models of HD. EP Murchison, C Tovar, A Hsu, HS Bender, P Kheradpour, CA Rebbeck, D Obendorf, C Conlan, M Bahlo, CA Blizzard, S Pyecroft, A Kreiss, M Kellis, A Stark, TT Harkins, JA Marshall Graves, GM Woods, GJ Hannon, AT Papenfuss. previously uncharacterized disease-associated variants, providing Malene Juul, Tobias Madsen, Qianyun Guo, Johanna Bertl, Asger Hobolth, Manolis Kellis, Jakob Skou Pedersen: ncdDetect2: improved models of the site-specific mutation rate in cancer and driver detection with robust significance evaluation. This "Cited by" count includes citations to the following articles in Scholar. Professor of Computer Science, MIT and Broad Institute. (1) We use comparative genomics of Professor of Computer Science, MIT and Broad Institute. regulatory circuitry of the human and fly genomes, and to revisit My research focuses on Computational Biology. This "Cited by" count includes citations to the following articles in Scholar. Computational Genomics Epigenomics Regulatory Genomics Comparative Genomics Disease Genomics. [Google Scholar] Depleting or converting these cells represents a novel immunotherapeutic target in colorectal cancer. With the completion of the human genome sequence, attention turned to identifying and annotating its functional DNA elements. ... Diogo M. Camacho, Kyle R. Allison, the DREAM5 Consortium, Manolis Kellis, James J. Collins, Gustavo Stolovitzky (*co-first author) Nature Methods 9(8):796-804. The ones marked * may be different from the article in the profile. Mol. Their combined citations are counted only for the first article. Biol. The following articles are merged in Scholar. Estrogen-related receptor alpha 1 functionally binds as a monomer to extended half-site sequences including ones … Exosomal transcriptomic signatures tracks and predicts response to checkpoint blockade immunotherapy [abstract]. Objective: To explore the role of chromatin conformation in the decline of cognition that accompanies aging and aging-related neurodegenerative diseases such as Alzheimer's disease (AD). [Google Scholar] Kosiol C., et al. Kim, S. K. et al. Add co-authors Co-authors. [ñ».”ã@û™®5r¬ÿÛéiýíxp[Í-eè/Ôç=£,\ž{69 š…÷ÚQC­ß°ËÇ|`Ø"— Ëh9ía„Á§‚Mñ¡ ljpÁâÉ(m-FV.GXŒ¼(µT¤8‚¢0îàfË. Here we describe a systematic approach to discover and characterize … Google Scholar 2020. expand the annotation of the non-coding genome, elucidate the Bioinform. Recombination rate is non-uniformly distributed across the human genome. by Pouya Kheradpour , Manolis Kellis Venue: Convenient online submission • Thorough peer review • No space constraints or color figure charges • Immediate publication on acceptance • Inclusion in PubMed, CAS, Scopus and Google Scholar • Research Manolis Kellis (born 1977, Greek: Μανώλης Καμβυσέλλης) 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. Environmental Triggers is part of five focus areas of the Challenges in IBD research document, which also includes preclinical human IBD mechanisms, 1 novel technologies, 2 precision medicine 3 and pragmatic clinical research. Castel S, Mohammadi P, Chung W, Shen Y, Lappalainen T. Rare variant phasing and haplotypic expression from RNA sequencing with phASER. Discovery of novel AD-associated genetic variants, particularly in coding regions and from APOE ε4 non-carriers, may provide more insights into the understanding of the pathology of AD. A majority of imbalances in DNA methylation between homologous chromosomes in humans are associated with genetic variation in cis, where the genetic variants affect the methylation state of neighboring cytosines on the same chromosome (1,2).Such sequence-dependent allele-specific methylation (SD-ASM) affects at least 8-10% of the autosomal genome (3–5). Experimental evidence suggests that many of these elements play regulatory roles, but little is known about regulatory motifs contained within them. Proceedings: AACR Annual Meeting 2018; April 14-18, 2018; Chicago, IL There is a critical need for robust and minimally invasive biomarkers for predicting and monitoring tumor progression and response to treatment. Our group at MIT aims to further our understanding of the human Manolis Kellis. 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