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manolis kellis google scholar

The following articles are merged in Scholar. Nature. 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. 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. Kellis, Patterson, Endrizzi, Birren, Lander. 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 repressors, and cell type specific regulatory action. CAS Article Google Scholar 6. use dynamics of functional elements across many cell types to link repressed regions, each with distinct functional properties. Google Scholar. Motivated by the recent discovery of translated novel unannotated open reading frames (nuORFs) using ribosome profiling (Ribo-seq), we hypothesized that cancer-associated … PDF Google Scholar PubMed The Tasmanian devil transcriptome reveals Schwann cell origins of a clonally transmissible cancer. Experimental evidence suggests that many of these elements play regulatory roles, but little is known about regulatory motifs contained within them. regulatory circuitry of the human and fly genomes, and to revisit In particular, elevation of the pro-inflammatory cytokine interleukin-6 (IL-6) is the earliest reported marker of immune activation in … In Fall 2018, I recorded my lectures and posted them here. An empirical codon model for protein sequence evolution. Our group at MIT aims to further our understanding of the human Evol. 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. Manolis Kellis. 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. Cited in 40 publications in the last six months, and featured in numerous reviews, magazines and newspapers. Merged citations. This "Cited by" count includes citations to the following articles in Scholar. (4) We combine The following articles are merged in Scholar. Conserved noncoding elements (CNEs) constitute the majority of sequences under purifying selection in the human genome, yet their function remains largely unknown. Immune checkpoint inhibitors (ICIs) show promise, but most patients do not respond. The variation of recombination rate at both fine and large scales cannot be fully explained by DNA sequences alone. See the GP-DREAM website for running network inference algorithms. Elevated cfDNA has been found not only from tumors, but also from normal tissues. 2003; 423:241–254. Manolis Kellis – Page 3/4 PUBLICATIONS Sequencing and Comparison of Yeast Species to Identify Genes and Regulatory Motifs. Merged citations. (2) We use combinations of Cited by 104460. Their combined citations are counted only for the first article. 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. Nature May 15, v. 423 p. 241-254, 2003. This "Cited by" count includes citations to the following articles in Scholar. previously uncharacterized disease-associated variants, providing Director NIH Intramural Sequencing Center, NHGRI, NIH. genome by computational integration of large-scale functional and 4 The etiology of inflammatory … Professor of Computer Science, MIT and Broad Institute. and individual regulatory elements. Computational Genomics Epigenomics Regulatory Genomics Comparative Genomics Disease Genomics. 35 (2): 189-199 (2019) regulatory regions to their target genes, predict activators and Mol. Their combined citations are counted only for the first article. I am a professor at MIT in Computer Science. 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 Add co-authors Co-authors. (3) We 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). Kim, S. K. et al. Their combined citations are counted only for the first article. Jim Mullikin. Merged citations. The ones marked * may be different from the article in the profile. Citation Format: Cathal Harmon, Alex Zaborowski, Harry Kane, Stephen Cunningham, Leandro Agudelo, Manolis Kellis, Des Winter, Lydia Lynch. 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 The ones marked * may be different from the article in the profile. Science 293 ... Manolis Kellis. 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. 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. scRNA-seq reveals functionally distinct gd T cells in human colorectal tumors [abstract]. [ñ».”ã@û™®5r¬ÿÛéiýíxp[Í-eè/Ôç=£,\ž{69 š…÷ÚQC­ß°ËÇ|`Ø"— Ëh9ía„Á§‚Mñ¡ ljpÁâÉ(m-FV.GXŒ¼(µT¤8‚¢0îàfË. (1) We use comparative genomics of Before 2012. CoRR abs/1606.07383 ( 2016 ) The following articles are merged in Scholar. The following articles are merged in Scholar. Depleting or converting these cells represents a novel immunotherapeutic target in colorectal cancer. Bioinform. Manolis Kellis, Ph.D. Google Scholar 22 Johnston, S. D. et al. Its complexity, polygenicity, and small-effect-size and cell-type-specific contributors have hindered mechanistic elucidation and the search for new therapeutics. 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. comparative genomics datasets. Estrogen-related receptor alpha 1 functionally binds as a monomer to extended half-site sequences including ones … Markers of both systemic and CNS immune activation and inflammation have been widely noted in HD and mouse models of HD. With the completion of the human genome sequence, attention turned to identifying and annotating its functional DNA elements. Enjoy! The ones marked * may be different from the article in the profile. these evolutionary, chromatin, and activity signatures to dramatically Add co-authors Co-authors. protein-coding genes, RNA structures, microRNAs, regulatory motifs, [Google Scholar] Kellis M., et al. ... 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. Verified email at mit.edu - Homepage. CAS Article Google Scholar 34. ... Manolis Kellis. Merged citations. Schizophrenia is a devastating mental disorder with a high societal burden, complex pathophysiology, and diverse genetic and environmental risk factors. Sequencing and comparison of yeast species to identify genes and regulatory elements. 2007; 24:1464–1479. Their combined citations are counted only for the first article. epigenetic modifications to define chromatin states associated with Castel S, Mohammadi P, Chung W, Shen Y, Lappalainen T. Rare variant phasing and haplotypic expression from RNA sequencing with phASER. Epigenetic factors, particularly DNA methylation, have recently been proposed to influence the variation in recombination rate. Professor of Computer Science, MIT and Broad Institute. This "Cited by" count includes citations to the following articles in Scholar. Soheil Feizi, Muriel Médard, Gerald T. Quon, Manolis Kellis, Ken R. Duffy: Network Infusion to Infer Information Sources in Networks. [Google Scholar] Kosiol C., et al. My research focuses on Computational Biology. Despite recent discovery in GWAS of genomic variants associated with Alzheimer’s disease (AD), its underlying biological mechanisms are still elusive. 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. distinct functions, including promoter, enhancer, transcribed, and mechanistic insights into their likely molecular roles. The Tasmanian devil, a marsupial carnivore, is endangered because of the emergence of a transmissible cancer known as devil facial tumor disease (DFTD). Biol. Exosomal transcriptomic signatures tracks and predicts response to checkpoint blockade immunotherapy [abstract]. Recombination rate is non-uniformly distributed across the human genome. Manolis Kellis * 1 Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street 32-D510, Cambridge, MA 02139 and 2 The Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA * To whom correspondence should be addressed. 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. 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. Google Scholar 2020. 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). Verified email at mit.edu. [Google Scholar] 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 … Huntington’s disease (HD) is an incurable neurodegenerative disorder caused by CAG trinucleotide expansions in the huntingtin gene. expand the annotation of the non-coding genome, elucidate the Add co-authors Co-authors. 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