Nature. 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. (2) We use combinations of Here we describe a systematic approach to discover and characterize … My research focuses on Computational Biology. This "Cited by" count includes citations to the following articles in Scholar. Schizophrenia is a devastating mental disorder with a high societal burden, complex pathophysiology, and diverse genetic and environmental risk factors. Motivated by the recent discovery of translated novel unannotated open reading frames (nuORFs) using ribosome profiling (Ribo-seq), we hypothesized that cancer-associated … Its complexity, polygenicity, and small-effect-size and cell-type-specific contributors have hindered mechanistic elucidation and the search for new therapeutics. and individual regulatory elements. Cited by 104460. CoRR abs/1606.07383 ( 2016 ) An empirical codon model for protein sequence evolution. Manolis Kellis – Page 3/4 PUBLICATIONS Sequencing and Comparison of Yeast Species to Identify Genes and Regulatory Motifs. Immune checkpoint inhibitors (ICIs) show promise, but most patients do not respond. Elevated cfDNA has been found not only from tumors, but also from normal tissues. See the GP-DREAM website for running network inference algorithms. 2003; 423:241–254. Their combined citations are counted only for the first article. Merged citations. Cited in 40 publications in the last six months, and featured in numerous reviews, magazines and newspapers. The ones marked * may be different from the article in the profile. Kellis, Patterson, Endrizzi, Birren, Lander. Depleting or converting these cells represents a novel immunotherapeutic target in colorectal cancer. Merged citations. use dynamics of functional elements across many cell types to link Their combined citations are counted only for the first article. CAS Article Google Scholar 34. 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. The ones marked * may be different from the article in the profile. 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 Our group at MIT aims to further our understanding of the human 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). Science 293 ... Manolis Kellis. Enjoy! repressors, and cell type specific regulatory action. 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. 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 Professor of Computer Science, MIT and Broad Institute. mechanistic insights into their likely molecular roles. Sequencing and comparison of yeast species to identify genes and regulatory elements. [Google Scholar] CAS Article Google Scholar 6. Bioinform. Google Scholar 2020. 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. distinct functions, including promoter, enhancer, transcribed, and Before 2012. [Google Scholar] Kellis M., et al. With the completion of the human genome sequence, attention turned to identifying and annotating its functional DNA elements. Google Scholar 22 Johnston, S. D. et al. 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. Exosomal transcriptomic signatures tracks and predicts response to checkpoint blockade immunotherapy [abstract]. 2007; 24:1464–1479. ... Manolis Kellis. 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. In particular, elevation of the pro-inflammatory cytokine interleukin-6 (IL-6) is the earliest reported marker of immune activation in … Despite recent discovery in GWAS of genomic variants associated with Alzheimer’s disease (AD), its underlying biological mechanisms are still elusive. In Fall 2018, I recorded my lectures and posted them here. 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