J. Ernst

发表

Integrating multiple evidence sources to predict transcription factor binding in the human genome.

Jason B. Ernst, I. Simon, Z. Bar-Joseph, 2010, Genome research.

Discovery and characterization of chromatin states for systematic annotation of the human genome

Manolis Kellis, J. Ernst, 2010, Nature Biotechnology.

ChromHMM: automating chromatin-state discovery and characterization

Manolis Kellis, J. Ernst, 2012, Nature Methods.

Comprehensive analysis of the chromatin landscape in Drosophila

Lovelace J. Luquette, Manolis Kellis, R. Sandstrom, 2010, Nature.

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

Manolis Kellis, A. Mortazavi, B. Wold, 2013, Genome research.

"Systematic"

Timothy J. Durham, T. Mikkelsen, Manolis Kellis, 1966, Comput. J..

Combined static and dynamic analysis for determining the quality of time-series expression profiles

I. Simon, Z. Bar-Joseph, J. Ernst, 2005, Nature Biotechnology.

Reconstructing dynamic regulatory maps

I. Simon, C. T. Harbison, Z. Bar-Joseph, 2007, Molecular systems biology.

Integrative annotation of chromatin elements from ENCODE data

William Stafford Noble, Maxwell W. Libbrecht, Robert S. Harris, 2012, Nucleic acids research.

Systematic analysis of chromatin state dynamics in nine human cell types

Timothy J. Durham, T. Mikkelsen, Manolis Kellis, 2011, Nature.

Integrative analysis of 111 reference human epigenomes

Michael Q. Zhang, Nicholas A. Sinnott-Armstrong, Michael T. McManus, 2015, Nature.

Chromatin-state discovery and genome annotation with ChromHMM

Manolis Kellis, J. Ernst, 2017, Nature Protocols.

Intracellular crowding defines the mode and sequence of substrate uptake by Escherichia coli and constrains its metabolic activity

M. A. de Menezes, A. Barabasi, Z. Oltvai, 2007, Proceedings of the National Academy of Sciences.

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

Raymond K. Auerbach, William Stafford Noble, Stephen C. J. Parker, 2011, PLoS biology.

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

Rochelle L. Tiedemann, Manolis Kellis, S. Dalton, 2012, Cell reports.

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

May E. Montasser, Jonathan M. Bloom, Jonathan M Bloom, 2017, Nature Communications.

Chromosome conformation elucidates regulatory relationships in developing human brain

Daning Lu, Farhad Hormozdiari, Jason L. Stein, 2016, Nature.

Supporting Online Material Materials and Methods Figs. S1 to S50 Tables S1 to S18 References Identification of Functional Elements and Regulatory Circuits by Drosophila Modencode

Gos Micklem, Lincoln D Stein, Daniel Marbach, 2022 .

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

Manolis Kellis, J. Ernst, 2013, Genome research.

Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration.

Manolis Kellis, T. Furey, W. Miller, 2011, Genome research.

Combinatorial Patterning of Chromatin Regulators Uncovered by Genome-wide Location Analysis in Human Cells

Timothy J. Durham, I. Amit, A. Regev, 2011, Cell.

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

Albert J. Vilella, Matthew D. Rasmussen, André L. Martins, 2011, Nature.

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

T. Mikkelsen, Manolis Kellis, J. Ernst, 2016, Nature Biotechnology.

Common Variants at 9p21 and 8q22 Are Associated with Increased Susceptibility to Optic Nerve Degeneration in Glaucoma

Manolis Kellis, B. Yaspan, J. Haines, 2012, PLoS genetics.

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

T. Mikkelsen, Manolis Kellis, J. Ernst, 2013, Genome research.

Cooperative Binding of Transcription Factors Orchestrates Reprogramming

J. Ernst, S. Butz, K. Plath, 2017, Cell.

Large-scale epigenome imputation improves data quality and disease variant enrichment

Manolis Kellis, J. Ernst, 2015, Nature biotechnology.

Alzheimery's disease pathology is associated with early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci

Manolis Kellis, David A Bennett, Towfique Raj, 2014, Nature Neuroscience.

Time-series Expression Miner ( v 1 . 3 . 12 ) User Manual

J. Ernst, 2009 .

Short Time-series Expression Miner ( v 1 . 1 ) User Manual

J. Ernst, 2006 .

Systematic discovery of conservation states for single-nucleotide annotation of the human genome

J. Ernst, Adriana Sperlea, A. Arneson, 2018, Communications Biology.

Long-range chromatin contacts in embryonic stem cells reveal a role for pluripotency factors and polycomb proteins in genome organization.

Matteo Pellegrini, Erik Splinter, Wouter de Laat, 2013, Cell stem cell.

Evidence of reduced recombination rate in human regulatory domains

Manolis Kellis, Pouya Kheradpour, Abhishek Sarkar, 2017, Genome Biology.

Learning a genome-wide score of human–mouse conservation at the functional genomics level

Soo Bin Kwon, J. Ernst, S. B. Kwon, 2020, Nature Communications.

Identification and characterization of constrained non-exonic bases lacking predictive epigenomic and transcription factor binding annotations

Soo Bin Kwon, J. Ernst, K. Lohmueller, 2020, Nature communications.

Identification and characterization of constrained non-exonic bases lacking predictive epigenomic and transcription factor binding annotations

Soo Bin Kwon, J. Ernst, K. Lohmueller, 2019, Nature Communications.

A framework for summarizing chromatin state annotations within and identifying differential annotations across groups of samples

J. Ernst, Petko Fiziev, H. Vu, 2022, bioRxiv.

Systematic discovery of conservation states for single-nucleotide annotation of the human genome.

J. Ernst, A. Arneson, 2019, Communications biology.

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

Ivana V. Yang, Zhaohui S. Qin, Andrew D. Johnson, 2018, Nature Communications.

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

Jonathan M. Bloom, Jonathan M Bloom, M. Daly, 2017, bioRxiv.

Epigenetic clock and methylation studies in vervet monkeys

S. Horvath, N. Freimer, R. Woods, 2020, GeroScience.

Leveraging allelic imbalance to refine fine-mapping for eQTL studies

Stephane E. Castel, E. Eskin, F. Hormozdiari, 2019, PLoS genetics.

Leveraging allele-specific expression to refine fine-mapping for eQTL studies

E. Eskin, F. Hormozdiari, J. Ernst, 2018, bioRxiv.

Modeling Spatio-temporal Dynamics of Chromatin Marks

J. Ernst, Petko Fiziev, P. Fiziev, 2018, bioRxiv.

ChromTime: modeling spatio-temporal dynamics of chromatin marks

J. Ernst, Petko Fiziev, Petko P Fiziev, 2018, Genome Biology.

Chromatin state modeling across individuals reveals global patterns of histone modifications

J. Ernst, Jennifer Zou, 2022, bioRxiv.

Universal DNA Methylation Age Across Mammalian Tissues

Robert W. Williams, S. Horvath, A. Lu, 2021, bioRxiv.

ABSTRACT OF THE THESIS Read Simulator for Single Cell RNA Sequencing

W. Wang, S. Sankararaman, J. Ernst, 2019 .

Integrative analysis of 111 reference human epigenomes Open

David Haussler, Michael Q. Zhang, Gerald T. Quon, 2015, Nat..

Intracellular crowding of macromolecules defines the mode and sequence of substrate uptake by E . coli and constrains its metabolic activity and growth Supporting Information , Part 2 : Experimental protocols and microarray analyses

A. Barabasi, Z. Oltvai, Z. Bar-Joseph, 2007 .

ChromGene: gene-based modeling of epigenomic data

J. Ernst, Artur Jaroszewicz, 2022, bioRxiv.

Distinct and Predictive Histone Lysine Acetylation Patterns at Promoters, Enhancers, and Gene Bodies

Manolis Kellis, B. Ren, J. Ernst, 2014, G3: Genes, Genomes, Genetics.

Single-nucleotide conservation state annotation of the SARS-CoV-2 genome

Soo Bin Kwon, J. Ernst, S. B. Kwon, 2020, Communications Biology.

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

Ryan D. Hernandez, May E. Montasser, Min A. Jhun, 2018, Nature Communications.

IL-3 and Oncogenic Abl Regulate the Myeloblast Transcriptome by Altering mRNA Stability

Jason L. Brown, Z. Bar-Joseph, J. Ernst, 2009, PloS one.

A framework for group-wise summarization and comparison of chromatin state annotations

J. Ernst, Petko Fiziev, H. Vu, 2022, Bioinform..

Kinetics of mRNA nuclear export regulate innate immune response gene expression

Erin M. Wissink, D. Black, Y. Xing, 2022, Nature Communications.

Universal chromatin state annotation of the mouse genome

J. Ernst, H. Vu, 2022, bioRxiv.

Large Scale Comparison of Innate Responses to Viral and Bacterial Pathogens in Mouse and Macaque

Rachel Brower-Sinning, Panayiotis V. Benos, Shaun Mahony, 2011, PloS one.

Transcriptional analysis of cystic fibrosis airways at single-cell resolution reveals altered epithelial cell states and composition

J. Ernst, K. Plath, C. Yao, 2021, Nature Medicine.

STEM: a tool for the analysis of short time series gene expression data

Ziv Bar-Joseph, Jason Ernst, Z. Bar-Joseph, 2006, BMC Bioinformatics.

Computational methods for analyzing and modeling gene regulation dynamics

Jason Ernst, J. Ernst, 2008 .

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

Manolis Kellis, J. Ernst, 2013 .

Investigating enhancer evolution with massively parallel reporter assays

Soo Bin Kwon, J. Ernst, S. B. Kwon, 2018, Genome Biology.

Integration of evidence across human and model organism studies: A meeting report

Robert W. Williams, David O. Walton, Soo Bin Kwon, 2021, Genes, brain, and behavior.

Large-scale epigenome imputation improves data quality and disease variant enrichment

Manolis Kellis, Jason Ernst, Manolis Kellis, 2015, Nature Biotechnology.

A Semi-Supervised Method for Predicting Transcription Factor–Gene Interactions in Escherichia coli

Ziv Bar-Joseph, Zoltán N. Oltvai, Jason Ernst, 2008, PLoS Comput. Biol..

A mammalian methylation array for profiling methylation levels at conserved sequences

Soo Bin Kwon, S. Horvath, A. Lu, 2021, Nature Communications.

ChromTime: modeling spatio-temporal dynamics of chromatin marks

J. Ernst, Petko Fiziev, P. Fiziev, 2018, Genome Biology.

Universal annotation of the human genome through integration of over a thousand epigenomic datasets

J. Ernst, H. Vu, 2022, Genome Biology.

Universal annotation of the human genome through integration of over a thousand epigenomic datasets

Jason Ernst, Ha Vu, J. Ernst, 2020, Genome Biology.

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

Wei Xie, Yan Li, Manolis Kellis, 2013, PLoS Comput. Biol..

Resource Linking DNAMethyltransferases to Epigenetic Marks and Nucleosome Structure Genome-wide in Human Tumor Cells

Rochelle L. Tiedemann, Manolis Kellis, S. Dalton, 2012 .

Clustering short time series gene expression data

Ziv Bar-Joseph, Jason Ernst, Gerard J. Nau, 2005, ISMB.

Dual Roles of RNF2 in Melanoma Progression.

L. Chin, J. Ernst, E. Keung, 2015, Cancer discovery.

DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data

Ziv Bar-Joseph, Marcel H. Schulz, Shan Zhong, 2012, BMC Systems Biology.

Analysis of cardiomyocyte clonal expansion during mouse heart development and injury

Yichen Ding, Rajan P Kulkarni, Sara Ranjbarvaziri, 2018, Nature Communications.

Pan-primate DNA methylation clocks

S. Horvath, A. Lu, M. Pellegrini, 2020, bioRxiv.

Systematic Epigenomic Analysis Reveals Chromatin States Associated with Melanoma Progression.

I. Amit, L. Chin, B. Garcia, 2017, Cell reports.

STAT3 promotes a youthful epigenetic state in articular chondrocytes

S. Horvath, N. Segil, J. Ernst, 2023, Aging cell.

Systematic discovery of conservation states for single-nucleotide annotation of the human genome

J. Ernst, A. Arneson, 2019, Communications Biology.

DNA Methylation Networks Underlying Mammalian Traits

S. Horvath, A. Lu, E. Ostrander, 2021, bioRxiv.

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

Manolis Kellis, A. Mortazavi, B. Wold, 2013 .

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

T. Mikkelsen, Manolis Kellis, J. Ernst, 2013 .

1 Dynamics of the Epigenetic Landscape During Erythroid Differentiation after GATA 1 Restoration Running head : Chromatin state profiles precede gene regulation

Manolis Kellis, T. Furey, W. Miller, 2011 .

differentiation after GATA 1 restoration Dynamics of the epigenetic landscape during erythroid Material

Manolis Kellis, T. Furey, W. Miller, 2011 .

Mapping molecular landmarks of human skeletal ontogeny and pluripotent stem cell-derived articular chondrocytes

J. Ernst, M. Bonaguidi, A. Pyle, 2018, Nature Communications.

IL-3 and Oncogenic Abl Regulate the Myeloblast Transcriptome by Alt= Stability

Jason L. Brown, Z. Bar-Joseph, J. Ernst, 2009 .

Integrative annotation of chromatin elements from ENCODE data

William Stafford Noble, Maxwell W. Libbrecht, Robert S. Harris, 2012, Nucleic Acids Research.

Alzheimer ' s disease : early alterations in brain DNA methylation

S. Gabriel, Manolis Kellis, D. Bennett, 2015 .

Epigenetic clock and methylation studies in the rhesus macaque

S. Horvath, J. Ernst, C. Breeze, 2020, GeroScience.

Single-nucleotide conservation state annotation of the SARS-CoV-2 genome

Soo Bin Kwon, J. Ernst, S. B. Kwon, 2021, Communications biology.

ConsHMM Atlas: conservation state annotations for major genomes and human genetic variation

J. Ernst, A. Arneson, Jennifer Chien, 2020, NAR genomics and bioinformatics.

Correction to ‘ConsHMM Atlas: conservation state annotations for major genomes and human genetic variation’

J. Ernst, A. Arneson, Jennifer Chien, 2020, bioRxiv.

Genome-wide DNA methylation and multi-omics study of human chondrocyte ontogeny and an epigenetic clock analysis of adult chondrocytes

S. Horvath, N. Segil, J. Ernst, 2021, bioRxiv.

Transcriptional, Electrophysiological, and Metabolic Characterizations of hESC-Derived First and Second Heart Fields Demonstrate a Potential Role of TBX5 in Cardiomyocyte Maturation

Douglas J. Chapski, J. Ernst, M. Teitell, 2021, Frontiers in Cell and Developmental Biology.

Pan-primate DNA methylation clocks

S. Horvath, A. Lu, M. Pellegrini, 2021 .

Marginal Contribution Feature Importance - an Axiomatic Approach for Explaining Data

Ran Gilad-Bachrach, Ahuva Weiss-Meilik, Noam Shomron, 2021, ICML.

Impact of the solvent capacity constraint on E. coli metabolism

Ziv Bar-Joseph, Albert-László Barabási, Zoltán N. Oltvai, 2008, BMC Systems Biology.

An Integrative Approach for Fine-Mapping Chromatin Interactions

Jason Ernst, Artur Jaroszewicz, J. Ernst, 2019, bioRxiv.

Circadian variation of the pancreatic islet transcriptome.

J. Ernst, K. Rakshit, A. Matveyenko, 2016, Physiological genomics.

Mapping enhancer and promoter interactions

J. Ernst, 2012, Cell Research.

Systematic analysis of chromatin state dynamics in nine human cell types

Timothy J. Durham, T. Mikkelsen, Manolis Kellis, 2011, Nature.

Genome-wide regulatory model from MPRA data predicts functional regions, eQTLs, and GWAS hits

Pardis C Sabeti, Manolis Kellis, J. Ernst, 2017, bioRxiv.

Integrative epigenomic and functional characterization assay based annotation of regulatory activity across diverse human cell types

J. Ernst, T. U. Dincer, 2023, bioRxiv.

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

Christopher D. Brown, Angela N. Brooks, Patrick E. Meyer, 2010, Science.

DNA methylation networks underlying mammalian traits

Joseph A. Cook, S. Horvath, A. Lu, 2023, Science.

Universal DNA methylation age across mammalian tissues

R. Williams, J. Gaillard, D. Blumstein, 2023, Nature Aging.

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

Christopher D. Brown, Angela N. Brooks, Patrick E. Meyer, 2011 .

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

Angela N. Brooks, Patrick E. Meyer, Michael F. Lin, 2010 .

Systematic discovery of conservation states for single-nucleotide annotation of the human genome

Jason Ernst, Adriana Arneson, J. Ernst, 2018, Communications Biology.

Systematic analysis of chromatin state dynamics in nine human cell types

Jason B. Ernst, Timothy J. Durham, Timothy J. Durham, 2011, Nature.

Impact of the solvent capacity constraint on E. coli metabolism

Z. Oltvai, Z. Bar-Joseph, A. Vazquez, 2008, BMC Systems Biology.

ChromHMM: automating chromatin-state discovery and characterization

Manolis Kellis, J. Ernst, 2012, Nature Methods.

Identification of functional elements and regulatory circuits by Drosophila modENCODE

Angela N. Brooks, Patrick E. Meyer, Michael F. Lin, 2011 .

Impact of the solvent capacity constraint on E. coli metabolism

Z. Oltvai, Z. Bar-Joseph, A. Vazquez, 2008, BMC Systems Biology.

"Systematic"

J. S. Hayden, Timothy J. Durham, T. Mikkelsen, 1966, Comput. J..

Alzheimery's disease pathology is associated with early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci

S. Gabriel, Manolis Kellis, D. Bennett, 2014, Nature neuroscience.

"Systematic"

Timothy J. Durham, T. Mikkelsen, Manolis Kellis, 1966, Comput. J..

DREM 2.0: Improved reconstruction of dynamic regulatory networks from time-series expression data

Marcel H. Schulz, William E. Devanny, Z. Bar-Joseph, 2012, BMC Systems Biology.

Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration.

Manolis Kellis, T. Furey, W. Miller, 2011, Genome research.