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List of works by Manolis Kellis

52 Genetic Loci Influencing Myocardial Mass

scientific article

A Bayesian approach for fast and accurate gene tree reconstruction

scientific article

A cis-regulatory map of the Drosophila genome.

scientific article

A comparative encyclopedia of DNA elements in the mouse genome

scientific article

A comprehensive map of insulator elements for the Drosophila genome

scientific article

A gene expression atlas of embryonic neurogenesis in reveals complex spatiotemporal regulation of lncRNAs

article

A high-resolution map of human evolutionary constraint using 29 mammals

scientific article

A high-throughput screening and computation platform for identifying synthetic promoters with enhanced cell-state specificity (SPECS)

scientific article published on 28 June 2019

A multiresolution framework to characterize single-cell state landscapes

scientific article published on 26 October 2020

A single Hox locus in Drosophila produces functional microRNAs from opposite DNA strands

scientific article (publication date: 2008)

A wealth of discovery built on the Human Genome Project — by the numbers

scientific article published on 10 February 2021

Accurate gene-tree reconstruction by learning gene- and species-specific substitution rates across multiple complete genomes

scientific article

Activity-Induced DNA Breaks Govern the Expression of Neuronal Early-Response Genes

scientific article

Allele-specific epigenome maps reveal sequence-dependent stochastic switching at regulatory loci

scientific article published in Science

Alternatives to amyloid for Alzheimer's disease therapies-a symposium report

scientific article published on 29 May 2020

Alzheimer's disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci

scientific article

Alzheimer's loci: epigenetic associations and interaction with genetic factors

scientific article published on 24 April 2015

An AR-ERG transcriptional signature defined by long-range chromatin interactomes in prostate cancer cells

scientific article published on 03 January 2019

An endogenous small interfering RNA pathway in Drosophila

scientific article

An epigenetic signature for monoallelic olfactory receptor expression

scientific article

Analyses of mRNA structure dynamics identify embryonic gene regulatory programs

scientific article published on 30 July 2018

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes

scientific article published on 05 February 2020

Analysis of Genetically Regulated Gene Expression Identifies a Prefrontal PTSD Gene, SNRNP35, Specific to Military Cohorts

scientific article published on 01 June 2020

Analysis of Genetically Regulated Gene Expression identifies a trauma type specific PTSD gene, SNRNP35

article

Analysis of variation at transcription factor binding sites in Drosophila and humans

scientific article published in 2012

Arboretum: reconstruction and analysis of the evolutionary history of condition-specific transcriptional modules

scientific article

Association studies of up to 1.2 million individuals yield new insights into the genetic etiology of tobacco and alcohol use

scientific article published on 14 January 2019

Author Correction: Single-cell transcriptomic analysis of Alzheimer's disease

scientific article published on 01 July 2019

BRCA1 recruitment to transcriptional pause sites is required for R-loop-driven DNA damage repair

scientific article

CHD8 regulates neurodevelopmental pathways associated with autism spectrum disorder in neural progenitors

scientific article

Cell Type-Specific Transcriptomics Reveals that Mutant Huntingtin Leads to Mitochondrial RNA Release and Neuronal Innate Immune Activation

scientific article published on 15 July 2020

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

scientific article

Challenges in IBD Research: Environmental Triggers

scientific article published on 01 May 2019

ChromHMM: automating chromatin-state discovery and characterization ⬇️

scientific article published on February 28, 2012

Chromatin Accessibility Impacts Transcriptional Reprogramming in Oocytes

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

scientific article (publication date: 12 March 2009)

Chromatin-state discovery and genome annotation with ChromHMM.

scientific article published on 9 November 2017

Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells

scientific article published in December 2011

Common genetic variants modulate pathogen-sensing responses in human dendritic cells

scientific article

Common variants at 9p21 and 8q22 are associated with increased susceptibility to optic nerve degeneration in glaucoma

scientific article

Comparative analysis of metazoan chromatin organization

scientific article

Comparative analysis of regulatory information and circuits across distant species

scientific article

Comparative functional genomics of the fission yeasts

scientific article

Comparative validation of the D. melanogaster modENCODE transcriptome annotation.

scientific article

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster

scientific article

Computational analysis of noncoding RNAs

scientific article

Conflicting and ambiguous names of overlapping ORFs in the SARS-CoV-2 genome: A homology-based resolution

scientific article

Conservation of small RNA pathways in platypus

scientific article

Conserved Epigenetic Regulatory Logic Infers Genes Governing Cell Identity

scientific article published on 01 December 2020

Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer's disease

scientific article

Constitutive nuclear lamina-genome interactions are highly conserved and associated with A/T-rich sequence

scientific article

Context influences on TALE-DNA binding revealed by quantitative profiling

scientific article published on 11 June 2015

Core and region-enriched networks of behaviorally regulated genes and the singing genome

scientific article

Correction: Evolutionary principles of modular gene regulation in yeasts

scientific article published on 2 July 2013

Corrigendum: Loss of LDAH associated with prostate cancer and hearing loss

scientific article published on 01 May 2019

Corrigendum: Network deconvolution as a general method to distinguish direct dependencies in networks

scientific article published on 01 April 2015

Deep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestries

article published in 2017

Deep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestries.

scientific article

Deep learning for regulatory genomics

scientific article published in August 2015

Deep-coverage whole genome sequences and blood lipids among 16,324 individuals

scientific article published in Nature Communications

Deep-coverage whole genome sequences and blood lipids among 16,324 individuals

Defining functional DNA elements in the human genome

scientific article

Discovery and characterization of coding and non-coding driver mutations in more than 2,500 whole cancer genomes

Discovery and validation of sub-threshold genome-wide association study loci using epigenomic signatures

scientific article (publication date: 10 May 2016)

Discovery of Genetic Variation on Chromosome 5q22 Associated with Mortality in Heart Failure

scientific article

Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures

scientific article

Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci

scientific article published on 19 September 2019

Discovery of human sORF-encoded polypeptides (SEPs) in cell lines and tissue

scientific article published on 14 February 2014

Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila

scientific article

Disruption of a large intergenic noncoding RNA in subjects with neurodevelopmental disabilities

scientific article

Distinct and predictive histone lysine acetylation patterns at promoters, enhancers, and gene bodies

scientific article

Distinct metabolic programs established in the thymus control effector functions of γδ T cell subsets in tumor microenvironments

scientific article published on 18 January 2021

Distinguishing protein-coding and noncoding genes in the human genome

scientific article

Diverse patterns of genomic targeting by transcriptional regulators in Drosophila melanogaster

scientific article

Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration

scientific article

Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss

scientific article

Elucidation of Codon Usage Signatures across the Domains of Life

scientific article published on 01 October 2019

Energy-based RNA consensus secondary structure prediction in multiple sequence alignments

scientific article published on January 2014

Error and error mitigation in low-coverage genome assemblies

scientific article

Evidence for a novel overlapping coding sequence in POLG initiated at a CUG start codon

scientific article published on 06 March 2020

Evidence for secondary-variant genetic burden and non-random distribution across biological modules in a recessive ciliopathy

Evidence for secondary-variant genetic burden and non-random distribution across biological modules in a recessive ciliopathy

scientific article published on 12 October 2020

Evidence of abundant purifying selection in humans for recently acquired regulatory functions

scientific article published on 5 September 2012

Evidence of abundant stop codon readthrough in Drosophila and other metazoa

scientific article published on 12 October 2011

Evidence of efficient stop codon readthrough in four mammalian genes

scientific article

Evidence of reduced recombination rate in human regulatory domains

scientific article

Evolution at the Subgene Level: Domain Rearrangements in the Drosophila Phylogeny ⬇️

scientific article published on September 7, 2011

Evolution of delayed resistance to immunotherapy in a melanoma responder

scientific article published on 03 May 2021

Evolution of genes and genomes on the Drosophila phylogeny

scientific article

Evolution of pathogenicity and sexual reproduction in eight Candida genomes

scientific article

Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs

scientific article

Evolutionary Dynamics of Abundant Stop Codon Readthrough

scientific article published on 07 September 2016

Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals

scientific article published on 15 January 2014

Evolutionary principles of modular gene regulation in yeasts ⬇️

scientific article published on June 18, 2013

Expanded encyclopaedias of DNA elements in the human and mouse genomes

scientific article published on 29 July 2020

Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters

scientific article

Extensive variation in chromatin states across humans

scientific article

FRESCo: finding regions of excess synonymous constraint in diverse viruses

scientific article

FTO Obesity Variant Circuitry and Adipocyte Browning in Humans

scientific article

FTO Obesity Variant and Adipocyte Browning in Humans

scientific article published on 01 January 2016

Few SINEs of life: Alu elements have little evidence for biological relevance despite elevated translation

scientific article published on 19 December 2019

Fine mapping of type 1 diabetes susceptibility loci and evidence for colocalization of causal variants with lymphoid gene enhancers

scientific article

GENCODE 2021 ⬇️

scientific article published on 03 December 2020

GENCODE reference annotation for the human and mouse genomes

scientific article published on 01 January 2019

GENCODE: the reference human genome annotation for The ENCODE Project

scientific article

Genetic association study of QT interval highlights role for calcium signaling pathways in myocardial repolarization

scientific article

Genome analysis of the platypus reveals unique signatures of evolution

scientific article

Genome analysis of the platypus reveals unique signatures of evolution

scientific article published in Nature

Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype

scientific article

Genome sequence, comparative analysis and haplotype structure of the domestic dog

scientific article

Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions

scientific article published on 3 October 2016

Genome-wide In Vivo CNS Screening Identifies Genes that Modify CNS Neuronal Survival and mHTT Toxicity

scientific article published on 24 January 2020

Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo

scientific article published on 15 December 2013

Genomic RNA Elements Drive Phase Separation of the SARS-CoV-2 Nucleocapsid

scientific article published on 27 November 2020

Genomic analyses identify hundreds of variants associated with age at menarche and support a role for puberty timing in cancer risk

scientific article published on 24 April 2017

Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga

scientific article

Genus-wide characterization of bumblebee genomes provides insights into their evolution and variation in ecological and behavioral traits

scientific article published on 18 September 2020

HaploReg v4: systematic mining of putative causal variants, cell types, regulators and target genes for human complex traits and disease

scientific article

HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants

scientific article (publication date: 2012)

Heterologous Stop Codon Readthrough of Metazoan Readthrough Candidates in Yeast ⬇️

scientific article published on March 27, 2013

High depth, whole-genome sequencing of cholera isolates from Haiti and the Dominican Republic.

scientific article

High-resolution genome-wide functional dissection of transcriptional regulatory regions and nucleotides in human

scientific article published in Nature Communications

High-throughput 5' UTR engineering for enhanced protein production in non-viral gene therapies

scientific article published on 06 July 2021

Histone modifications at human enhancers reflect global cell-type-specific gene expression

scientific article (publication date: 7 May 2009)

Human Primordial Germ Cells Are Specified from Lineage-Primed Progenitors

scientific article published on 01 December 2019

Improved Identification and Analysis of Small Open Reading Frame Encoded Polypeptides

scientific article published on 24 March 2016

Improved gene tree error correction in the presence of horizontal gene transfer

scientific article

Improved haplotype inference by exploiting long-range linking and allelic imbalance in RNA-seq datasets

scientific article published on 16 September 2020

Inferring multimodal latent topics from electronic health records

scientific article published on 21 May 2020

Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps

scientific article published on 29 October 2013

Integrative annotation of chromatin elements from ENCODE data

scientific article

Integrative construction of regulatory region networks in 127 human reference epigenomes by matrix factorization

scientific article published on 01 August 2019

Interleukin-6 deficiency exacerbates Huntington's disease model phenotypes

scientific article published on 24 May 2020

Intermediate DNA methylation is a conserved signature of genome regulation

scientific article

Interplay between chromatin state, regulator binding, and regulatory motifs in six human cell types

scientific article (publication date: July 2013)

Interpreting noncoding genetic variation in complex traits and human disease

scientific article published on 8 November 2012

Joint Bayesian inference of risk variants and tissue-specific epigenomic enrichments across multiple complex human diseases

scientific article published on 12 July 2016

Joint profiling of DNA methylation and chromatin architecture in single cells

scientific article published on 05 August 2019

Large-scale discovery and validation of functional elements in the human genome

scientific article

Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues

scientific article published on 18 February 2015

Linking DNA methyltransferases to epigenetic marks and nucleosome structure genome-wide in human tumor cells

scientific article published on 21 November 2012

Local genetic effects on gene expression across 44 human tissues

article

Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes

scientific article

Long noncoding RNAs regulate adipogenesis

scientific article

Loose ends: almost one in five human genes still have unresolved coding status

scientific article published on 01 August 2018

Loose ends: almost one in five human genes still have unresolved coding status

scientific article published on 01 December 2018

Loss of LDAH associated with prostate cancer and hearing loss

scientific article published on 01 December 2018

Mapping the epigenomic and transcriptomic interplay during memory formation and recall in the hippocampal engram ensemble

scientific article published on 05 October 2020

Methods in comparative genomics: genome correspondence, gene identification and regulatory motif discovery

scientific article published in January 2004

MicroRNA and gene expression changes in unruptured human cerebral aneurysms

scientific article published on 26 February 2016

Mosquito genomics. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes

scientific article published on 27 November 2014

Most parsimonious reconciliation in the presence of gene duplication, loss, and deep coalescence using labeled coalescent trees

scientific article published on 05 December 2013

Motif Discovery in Physiological Datasets: A Methodology for Inferring Predictive Elements

scientific article published on January 2010

Multi-scale chromatin state annotation using a hierarchical hidden Markov model

scientific article published on 7 April 2017

Multiple knockout mouse models reveal lincRNAs are required for life and brain development

scientific article (publication date: 31 December 2013)

N6-methyladenosine RNA modification regulates embryonic neural stem cell self-renewal through histone modifications.

scientific article published on 15 January 2018

Network Motif Discovery Using Subgraph Enumeration and Symmetry-Breaking

Network deconvolution as a general method to distinguish direct dependencies in networks ⬇️

scientific article published on July 14, 2013

New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes

scientific article

Optimization of parameters for coverage of low molecular weight proteins

scientific article published on 28 August 2010

PRC2 Is Required to Maintain Expression of the Maternal Gtl2-Rian-Mirg Locus by Preventing De Novo DNA Methylation in Mouse Embryonic Stem Cells

scientific article published on 19 August 2015

Pan-cancer screen for mutations in non-coding elements with conservation and cancer specificity reveals correlations with expression and survival

scientific article published on 11 January 2018

Pan-cancer screen for mutations in non-coding elements with conservation and cancer specificity reveals correlations with expression and survival

Pareto-optimal phylogenetic tree reconciliation

scientific article

Performance and scalability of discriminative metrics for comparative gene identification in 12 Drosophila genomes

scientific article

PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions ⬇️

scientific article published on July 1, 2011

Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeasts

scientific article

Plasma-derived extracellular vesicle analysis and deconvolution enable prediction and tracking of melanoma checkpoint blockade outcome

scientific article published on 13 November 2020

Position specific variation in the rate of evolution in transcription factor binding sites

scientific article

Predicting gene expression in massively parallel reporter assays: A comparative study

scientific article published on 21 February 2017

Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks

scientific article

Preface

scholarly article by Manolis Kellis published in February 2011

Preface: RECOMB Systems Biology, Regulatory Genomics, and DREAM 2011 special issue

scientific article published on 01 February 2012

Preface: RECOMB systems biology, regulatory genomics, and DREAM 2012 special issue

scientific article

Preface: RECOMB/ISCB systems biology, regulatory genomics, and DREAM 2014 Special Issue

scientific article published on 01 April 2015

Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae

scientific article (publication date: 8 April 2004)

Publisher Correction: Deep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestries

scientific article published in Nature Communications

Publisher Correction: Deep coverage whole genome sequences and plasma lipoprotein(a) in individuals of European and African ancestries

scientific article published on 01 April 2020

Publisher Correction: N6-methyladenosine RNA modification regulates embryonic neural stem cell self-renewal through histone modifications

scholarly article published in Nature Neuroscience

RANGER-DTL 2.0: rigorous reconstruction of gene-family evolution by duplication, transfer and loss

scientific article published on 01 September 2018

RECOMB/ISCB systems biology, regulatory genomics, and DREAM 2013 special issue

scientific article published on 01 May 2014

RFECS: A Random-Forest Based Algorithm for Enhancer Identification from Chromatin State ⬇️

scientific article published on March 14, 2013

RNA folding with soft constraints: reconciliation of probing data and thermodynamic secondary structure prediction

scientific article

RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo

scientific article

Rate of brain aging and APOE ε4 are synergistic risk factors for Alzheimer's disease

scientific article published on 27 May 2019

Reconciliation revisited: handling multiple optima when reconciling with duplication, transfer, and loss

scientific article published on 14 September 2013

Reconstruction of Cell-type-Specific Interactomes at Single-Cell Resolution

scientific article published on 27 November 2019

Reconstruction of the human blood-brain barrier in vitro reveals a pathogenic mechanism of APOE4 in pericytes

scientific article published on 08 June 2020

Reliable prediction of regulator targets using 12 Drosophila genomes

scientific article

Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease

scientific article published on August 2014

Response to comment on "Evidence of abundant purifying selection in humans for recently acquired regulatory functions".

scientific article

Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes

scientific article

SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes

scientific article published on 01 October 2020

Sarbecovirus comparative genomics elucidates gene content of SARS-CoV-2 and functional impact of COVID-19 pandemic mutations

scientific article published on 03 June 2020

Sequences to systems

scientific article published on 25 May 2010

Sequencing and comparison of yeast species to identify genes and regulatory elements ⬇️

scientific article published on May 15, 2003

Sharing and Specificity of Co-expression Networks across 35 Human Tissues

scientific article

Single-cell dissection of the human brain vasculature

scientific article

Single-cell transcriptomic analysis of Alzheimer's disease

scientific article published on 01 May 2019

Single-cell transcriptomic atlas of the human retina identifies cell types associated with age-related macular degeneration

scientific article published on 25 October 2019

Soft X-Ray Tomography Reveals Gradual Chromatin Compaction and Reorganization during Neurogenesis In Vivo

scientific article

Spatial expression of transcription factors in Drosophila embryonic organ development

scientific article

Stop codon readthrough generates a C-terminally extended variant of the human vitamin D receptor with reduced calcitriol response

scientific article published on 31 January 2018

SubMAP: aligning metabolic pathways with subnetwork mappings

scientific article

Survey of variation in human transcription factors reveals prevalent DNA binding changes

scientific article

SwiSpot: modeling riboswitches by spotting out switching sequences

scientific article

Systematic chromatin state comparison of epigenomes associated with diverse properties including sex and tissue type

scientific article

Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes

scientific article

Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments

scientific article published on 13 December 2013

Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites

scientific article

Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals

scientific article

Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay

scientific article

Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay

scientific article published on 19 March 2013

Target site specificity and in vivo complexity of the mammalian arginylome

scientific article published in Scientific Reports

The GENCODE human gene set

scientific article

The NF-κB genomic landscape in lymphoblastoid B cells

scientific article

The NIH Roadmap Epigenomics Mapping Consortium

scientific article (publication date: October 2010)

The Tasmanian devil transcriptome reveals Schwann cell origins of a clonally transmissible cancer

scientific article

The Tissue-Specific lncRNA Fendrr Is an Essential Regulator of Heart and Body Wall Development in the Mouse ⬇️

scientific article published on January 28, 2013

The changing face of genomics

scientific article

The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes

scientific article

The evolutionary dynamics of the Saccharomyces cerevisiae protein interaction network after duplication

scholarly article

Thousands of novel unannotated proteins expand the MHC I immunopeptidome in cancer

scientific article

Three periods of regulatory innovation during vertebrate evolution ⬇️

scientific article

Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases

scientific article published on 07 March 2016

Transcriptional regulatory code of a eukaryotic genome

scientific article

Translation Initiation Site Profiling Reveals Widespread Synthesis of Non-AUG-Initiated Protein Isoforms in Yeast

scientific article published on 20 July 2020

TreeFix: statistically informed gene tree error correction using species trees

scientific article

Unified modeling of gene duplication, loss, and coalescence using a locus tree

scientific article published on 23 January 2012

Unlocking the secrets of the genome

scientific article

Using an atlas of gene regulation across 44 human tissues to inform complex disease- and trait-associated variation

article

Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo

scientific article published on February 2007

Wisdom of crowds for robust gene network inference ⬇️

scientific article published on July 15, 2012

ncdDetect2: improved models of the site-specific mutation rate in cancer and driver detection with robust significance evaluation

scientific article published on 01 January 2019

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