B. Wold

发表

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation.

Cole Trapnell, S. Salzberg, B. Williams, 2010, Nature biotechnology.

Sequence census methods for functional genomics

B. Wold, R. Myers, 2008, Nature Methods.

Computation for ChIP-seq and RNA-seq studies

A. Mortazavi, B. Wold, S. Pepke, 2009, Nature Methods.

Genome-Wide Mapping of in Vivo Protein-DNA Interactions

A. Mortazavi, B. Wold, R. Myers, 2007, Science.

Mapping and quantifying mammalian transcriptomes by RNA-Seq

B. Williams, A. Mortazavi, B. Wold, 2008, Nature Methods.

Landscape of transcription in human cells

Nadav S. Bar, Pedro G. Ferreira, Morgan C. Giddings, 2012, Nature.

The Human Cell Atlas

Fabian J Theis, Jay W. Shin, D. Pe’er, 2017, bioRxiv.

Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation

Raymond K. Auerbach, M. Gerstein, A. Mortazavi, 2012, Cell.

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

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

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

Marc D. Perry, James B. Brown, Timothy E. Reddy, 2012, Genome research.

An Integrated Encyclopedia of DNA Elements in the Human Genome

Raymond K. Auerbach, William Stafford Noble, Stephen C. J. Parker, 2012, Nature.

Expanded encyclopaedias of DNA elements in the human and mouse genomes

Michael J. Purcaro, Gene W. Yeo, M. Gerstein, 2020, Nature.

From single-cell to cell-pool transcriptomes: Stochasticity in gene expression and RNA splicing

B. Williams, B. Wold, R. Myers, 2014, Genome research.

The NIH BD2K center for big data in translational genomics

Lior Pachter, David Haussler, David A. Patterson, 2015, J. Am. Medical Informatics Assoc..

Oxygen‐mediated regulation of skeletal muscle satellite cell proliferation and adipogenesis in culture

John C. Doyle, B. Wold, M. Csete, 2001, Journal of cellular physiology.

Transcription factor redundancy and tissue-specific regulation: Evidence from functional and physical network connectivity

B. Williams, B. Wold, P. Sternberg, 2012, Genome research.

Defining functional DNA elements in the human genome

Morgan C. Giddings, E. Birney, M. Gerstein, 2014, 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.

RNA editing in the human ENCODE RNA-seq data

B. Williams, B. Wold, Eddie Park, 2012, Genome research.

An encyclopedia of mouse DNA elements (Mouse ENCODE)

Philip Cayting, Katrina Learned, Daniel Blankenberg, 2012, Genome Biology.

Effects of sequence variation on differential allelic transcription factor occupancy and gene expression

Timothy E. Reddy, B. Williams, A. Mortazavi, 2012, Genome research.

A comparative encyclopedia of DNA elements in the mouse genome

Shane J. Neph, Dmitri D. Pervouchine, Matthew D. Rasmussen, 2014, Nature.

Enhanced Proliferation, Survival, and Dopaminergic Differentiation of CNS Precursors in Lowered Oxygen

Nadine Kabbani, Marie Csete, Barbara Wold, 2000, The Journal of Neuroscience.

Pitfalls of mapping high-throughput sequencing data to repetitive sequences: Piwi's genomic targets still not identified.

Zhiping Weng, Julius Brennecke, Phillip D Zamore, 2015, Developmental cell.

Fully automated high-throughput chromatin immunoprecipitation for ChIP-seq: Identifying ChIP-quality p300 monoclonal antibodies

Barbara J. Wold, Georgi K. Marinov, Jost Vielmetter, 2014, Scientific Reports.

Systematic evaluation of factors influencing ChIP-seq fidelity

P. Bickel, B. Wold, R. Myers, 2012, Nature Methods.

Occupancy maps of 208 chromatin-associated proteins in one human cell type

Andrew A. Hardigan, A. Mortazavi, B. Wold, 2020, Nature.

Occupancy patterns of 208 DNA-associated proteins in a single human cell type

Wold, Andrew A. Hardigan, A. Mortazavi, 2018, bioRxiv.

Dynamic DNA methylation across diverse human cell lines and tissues

Timothy E. Reddy, D. Absher, J. Stamatoyannopoulos, 2013, Genome research.

expression and RNA splicing From single-cell to cell-pool transcriptomes : Stochasticity in gene Material Supplemental

B. Williams, B. Wold, R. Myers, 2014 .

Identification and confirmation of a module of coexpressed genes.

S. Quake, B. Wold, J. Brody, 2002, Genome research.

Role of Rodent Secondary Motor Cortex in Value-based Action Selection Nih Public Access Author Manuscript

Cole Trapnell, S. Salzberg, B. Williams, 2006 .

Single-cell transcriptome analysis reveals dynamic changes in lncRNA expression during reprogramming.

Zakary S. Singer, M. Elowitz, B. Williams, 2015, Cell stem cell.

Applicability of Tandem Affinity Purification MudPIT to Pathway Proteomics in Yeast*S

John R Yates, Johannes Graumann, Barbara J Wold, 2004, Molecular & Cellular Proteomics.

A technology-agnostic long-read analysis pipeline for transcriptome discovery and quantification

Barbara J. Wold, Diane Trout, Stefania Forner, 2019, bioRxiv.

Reconstructing a metazoan genetic pathway with transcriptome-wide epistasis measurements

B. Williams, B. Wold, P. Sternberg, 2017, Proceedings of the National Academy of Sciences.

Genetic Analysis of a Metazoan Pathway using Transcriptomic Phenotypes

B. Williams, B. Wold, P. Sternberg, 2017 .

The Human Cell Atlas

Roland Eils, Alexander van Oudenaarden, Hans Clevers, 2017, bioRxiv.

New computational approaches for analysis of cis-regulatory networks.

Eric H Davidson, Hamid Bolouri, Alistair G Rust, 2002, Developmental biology.

Large-Scale Quality Analysis of Published ChIP-seq Data

B. Wold, A. Kundaje, P. Park, 2013, G3: Genes, Genomes, Genetics.

Genomic DNA as a general cohybridization standard for ratiometric microarrays.

B. Williams, B. Wold, Richele M Gwirtz, 2006, Methods in enzymology.

Poly-L-ornithine-mediated transformation of mammalian cells.

B. Wold, V. C. Bond, 1987, Molecular and cellular biology.

Genomic sequencing and methylation analysis by ligation mediated PCR.

B. Wold, A. Riggs, G. Pfeifer, 1989, Science.

Gene expression changes in a tumor xenograft by a pyrrole-imidazole polyamide

B. Wold, G. Marinov, P. Dervan, 2012, Proceedings of the National Academy of Sciences.

Multigenome DNA sequence conservation identifies Hox cis-regulatory elements.

B. Wold, P. Sternberg, H. Shizuya, 2008, Genome research.

Large-Scale Quality Analysis of Published ChIP-seq Data

B. Wold, A. Kundaje, P. Park, 2013, G3: Genes, Genomes, Genetics.

Dissecting the regulatory activity and sequence content of loci with exceptional numbers of transcription factor associations

Andrew A. Hardigan, B. Wold, R. Myers, 2020, Genome research.

Dissecting the regulatory activity and sequence content of loci with exceptional numbers of transcription factor associations

Andrew A. Hardigan, B. Wold, R. Myers, 2019, bioRxiv.

Phosphorothioate oligonucleotide-directed triple helix formation.

B. Wold, J. Hacia, P. Dervan, 1994, Biochemistry.

A comparitive framework for understanding clustering results

Eric Mjolsness, Barbara J. Wold, B. Bornstein, 2001 .

A highly conserved molecular switch binds MSY-3 to regulate myogenin repression in postnatal muscle.

A. Mortazavi, B. Wold, L. De Angelis, 2008, Genes & development.

Author response: The Human Cell Atlas

Fabian J Theis, Jay W. Shin, D. Pe’er, 2017 .

Genomic DNA as a cohybridization standard for mammalian microarray measurements.

B. Williams, B. Wold, Richele M Gwirtz, 2004, Nucleic acids research.

Dynamics of microRNA expression during mouse prenatal development

Brian S. Roberts, R. Guigó, B. Williams, 2018, Genome Research.

Cloning of mid-G1 serum response genes and identification of a subset regulated by conditional myc expression.

B. Wold, S. Tavtigian, S. Zabludoff, 1994, Molecular biology of the cell.

Stable reduction of thymidine kinase activity in cells expressing high levels of anti-sense RNA

B. Wold, Stuart K. Kim, 1985, Cell.

Dissecting the regulatory activity and key sequence elements of loci with exceptional numbers of transcription factor associations

Andrew A. Hardigan, B. Wold, R. Myers, 2019 .

Isolated sequences from the linked Myf-5 and MRF4 genes drive distinct patterns of muscle-specific expression in transgenic mice.

B. Wold, G. Lyons, A. Patapoutian, 1993, Development.

Tissue-specific Expression of Distinct Spectrin and Transcripts in Erythroid and Nonerythroid Cells Ankyrin

B. Wold, J. Ngai, R. Moon, 2006 .

The Human Cell Atlas White Paper

Roland Eils, Hans Clevers, Mary Carmichael, 2018, 1810.05192.

Evidence for Developmentally Programmed Transdifferentiation in Mouse Esophageal Muscle

B. Wold, A. Patapoutian, R. Wagner, 1995, Science.

c-myc inhibition of MyoD and myogenin-initiated myogenic differentiation

B. Wold, J. Miner, Barbara J. Wold, 1991, Molecular and cellular biology.

Inhibition of Klenow fragment DNA polymerase on double-helical templates by oligonucleotide-directed triple-helix formation.

B. Wold, J. Hacia, P. Dervan, 1994, Biochemistry.

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

Jonathan M. Mudge, Angela N. Brooks, Gloria M. Sheynkman, 2021 .

Poly-L-ornithine-mediated transformation of mammalian cells

B. Wold, V. C. Bond, 1987, Molecular and cellular biology.

Mapping a multiplexed zoo of mRNA expression

Anna C. T. Abelin, Jared R. Leadbetter, Harry M. T. Choi, 2016, Development.

Nucleolar localization of myc transcripts

B. Wold, V. Bond, V. C. Bond, 1993, Molecular and cellular biology.

Expression of transfected vimentin genes in differentiating murine erythroleukemia cells reveals divergent cis-acting regulation of avian and mammalian vimentin sequences.

B. Wold, J. Ngai, E. Lazarides, 1987, Molecular and cellular biology.

Tissue-specific expression of distinct spectrin and ankyrin transcripts in erythroid and nonerythroid cells

B. Wold, J. Ngai, R. Moon, 1985, The Journal of cell biology.

Expression of transfected vimentin genes in differentiating murine erythroleukemia cells reveals divergent cis-acting regulation of avian and mammalian vimentin sequences

B. Wold, J. Ngai, E. Lazarides, 1987, Molecular and cellular biology.

STABLE AND UNSTABLE EXPRESSION OF GENES IN DNA TRANSFORMED CELLS

B. Wold, R. Axel, A. Pellicer, 1980 .

Tissue-specific expression from a compound TATA-dependent and TATA-independent promoter

B. Wold, P. Garrity, 1990, Molecular and cellular biology.

Transformation of mammalian cells with genes from procaryotes and eucaryotes

Tom Maniatis, Raymond Sweet, Richard Axel, 1979, Cell.

Muscle creatine kinase sequence elements regulating skeletal and cardiac muscle expression in transgenic mice

B. Wold, J. Johnson, S. Hauschka, 1989, Molecular and cellular biology.

A human embryonic limb cell atlas resolved in 1 space and time 2

B. Williams, B. Wold, R. Barker, 2022 .

The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models

William Stafford Noble, James C. Wright, Jacob M. Schreiber, 2022, Cell.

Microglia in the Cerebral Cortex in Autism

B. Williams, B. Wold, J. Allman, 2012, Journal of Autism and Developmental Disorders.

Single-cell analysis of regulatory gene expression in quiescent and activated mouse skeletal muscle satellite cells.

B. Wold, D. Cornelison, 1997, Developmental biology.

Structural gene sets active in embryos and adult tissues of the sea urchin

Barbara J. Wold, William H. Klein, Mark M. Davis, 1976, Cell.

Inhibition of DNA binding proteins by oligonucleotide-directed triple helix formation.

B. Wold, L. J. Maher, P. Dervan, 1989, Science.

Kinetic analysis of oligodeoxyribonucleotide-directed triple-helix formation on DNA.

B. Wold, L. J. Maher, P. Dervan, 1990, Biochemistry.

Analysis of promoter-specific repression by triple-helical DNA complexes in a eukaryotic cell-free transcription system.

B. Wold, L. J. Maher, P. Dervan, 1992, Biochemistry.

Mapping and modeling the genomic basis of differential RNA isoform expression at single-cell resolution with LR-Split-seq

A. Mortazavi, B. Wold, Diane Trout, 2021, Genome Biology.

The changing mouse embryo transcriptome at whole tissue and single-cell resolution

Yu Zhang, Barbara J. Wold, Axel Visel, 2020, Nature.

Culture in Reduced Levels of Oxygen Promotes Clonogenic Sympathoadrenal Differentiation by Isolated Neural Crest Stem Cells

David J. Anderson, B. Wold, M. Csete, 2000, The Journal of Neuroscience.

High resolution mapping of Twist to DNA in Drosophila embryos: Efficient functional analysis and evolutionary conservation.

B. Wold, S. Pepke, Kenneth McCue, 2011, Genome research.

Efficient functional analysis and evolutionary conservation embryos : Drosophila High resolution mapping of Twist to DNA in Material Supplemental

B. Wold, S. Pepke, Kenneth McCue, 2011 .

The bHLH regulator pMesogenin1 is required for maturation and segmentation of paraxial mesoderm.

B. Wold, J. Yoon, Jeong Kyo Yoon, 2000, Genes & development.

The bHLH class protein pMesogenin1 can specify paraxial mesoderm phenotypes.

B. Wold, R. Moon, J. Yoon, 2000, Developmental biology.

Skeletal muscle determination and differentiation: story of a core regulatory network and its context.

B. Wold, K. Yun, K. Yun, 1996, Current opinion in cell biology.

p62 overexpression in breast tumors and regulation by prostate-derived Ets factor in breast cancer cells

B. Wold, J. Brody, F. Lin, 2003, Oncogene.

Multi-tissue integrative analysis of personal epigenomes

William Stafford Noble, James C. Wright, Jacob M. Schreiber, 2021 .

Dynamic Transformations of Genome-wide Epigenetic Marking and Transcriptional Control Establish T Cell Identity

B. Williams, A. Mortazavi, B. Wold, 2012, Cell.

Connectivity in the Yeast Cell Cycle Transcription Network: Inferences from Neural Networks

Eric Mjolsness, Barbara J. Wold, Christopher E. Hart, 2006, PLoS Comput. Biol..

Herculin, a fourth member of the MyoD family of myogenic regulatory genes.

B. Wold, J. Miner, 1990, Proceedings of the National Academy of Sciences of the United States of America.

Network: from Single Conserved Sites to Genome-wide Repertoire Comparative Genomics Modeling of the Nrsf/rest Repressor Material Supplemental

Richard M Myers, Ali Mortazavi, Barbara Wold, 2022 .

Ligation-mediated PCR for genomic sequencing and footprinting.

B. Wold, P. Garrity, P. R. Mueller, 2001, Current protocols in molecular biology.

Single-Cell Analysis Reveals Regulatory Gene Expression Dynamics Leading to Lineage Commitment in Early T Cell Development.

Ellen V Rothenberg, Brian A Williams, Barbara J Wold, 2019, Cell systems.

Constitutive and metal-inducible protein:DNA interactions at the mouse metallothionein I promoter examined by in vivo and in vitro footprinting.

B. Wold, P. R. Mueller, S. Salser, 1988, Genes & development.

Comparative analysis of Homo sapiens and Mus musculus cyclin-dependent kinase (CDK) inhibitor genes P16 (MTS1) and P15 (MTS2)

B. Wold, C. Kozak, A. Kamb, 1995, Journal of Molecular Evolution.

Microglia in the Cerebral Cortex in Autism

Brian A Williams, Barbara J Wold, B. Williams, 2012, Journal of Autism and Developmental Disorders.

Multi-tissue integrative analysis of personal epigenomes [preprint] Multi-tissue integrative analysis of personal epigenomes [preprint] you.

Lei, James C. Wright, Jacob M. Schreiber, 2021 .

BRCA1 mRNA is expressed highly during meiosis and spermiogenesis but not during mitosis of male germ cells.

B. Wold, K. Harshman, S. Zabludoff, 1996, Oncogene.

Evidence from functional and physical network connectivity Transcription factor redundancy and tissue-specific regulation : Material Supplemental

B. Williams, B. Wold, P. Sternberg, 2012 .

In vivo footprinting of a muscle specific enhancer by ligation mediated PCR.

B. Wold, P. R. Mueller, P. Mueller, 1990, Science.

network: From single conserved sites to genome-wide repertoire Comparative genomics modeling of the NRSF/REST repressor

A. Mortazavi, B. Wold, R. Myers, 2007 .

GA4GH: International policies and standards for data sharing across genomic research and healthcare

Grant M. Wood, James A. Eddy, Julius O. B. Jacobsen, 2021, Cell genomics.

Altering genotype and phenotype by DNA-mediated gene transfer.

James M. Roberts, B. Wold, R. Axel, 1980, Science.

Evidence for Site-Specific Occupancy of the Mitochondrial Genome by Nuclear Transcription Factors

B. Wold, G. Marinov, David Chan, 2014, PloS one.

TRANSFORMATION OF MAMMALIAN CELLS WITH PROKARYOTIC AND EUKARYOTIC GENES

M. Wigler, B. Wold, T. Maniatis, 1979 .

p27Kip1 is expressed transiently in developing myotomes and enhances myogenesis.

B. Wold, M. Csete, S. Zabludoff, 1998, Cell growth & differentiation : the molecular biology journal of the American Association for Cancer Research.

Transformation of mammalian cells with genes from prokaryotes and eukaryotes. 1979.

M. Wigler, B. Wold, T. Maniatis, 1992, Biotechnology.

Know Your Neighbors: Three Phenotypes in Null Mutants of the Myogenic bHLH Gene MRF4

B. Wold, H. Arnold, P. Rigby, 1996, Cell.

Introduction and expression of a rabbit beta-globin gene in mouse fibroblasts.

M. Wigler, B. Wold, T. Maniatis, 1979, Proceedings of the National Academy of Sciences of the United States of America.

Effects of different DNA polymerases in ligation-mediated PCR: enhanced genomic sequencing and in vivo footprinting.

B. Wold, P. Garrity, 1992, Proceedings of the National Academy of Sciences of the United States of America.

HLH forced dimers: Tethering MyoD to E47 generates a dominant positive myogenic factor insulated from negative regulation by Id

Barbara Wold, B. Wold, Lisa A. Neuhold, 1993, Cell.

Ligation-mediated PCR: Applications to genomic footprinting

Barbara J. Wold, B. Wold, P. R. Mueller, 1991 .

Perspectives on ENCODE

Xintao Wei, Christopher B. Burge, Jason Liu, 2020, Nature.

Scaffolding a Caenorhabditis nematode genome with RNA-seq.

Ali Mortazavi, Lorian Schaeffer, Paul W Sternberg, 2010, Genome research.

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

James B. Brown, Timothy E. Reddy, P. Bickel, 2012 .

Enhanced signals and fast nucleic acid hybridization by microfluidic chaotic mixing.

Stephen Quake, Brian A Williams, Barbara J Wold, 2006, Angewandte Chemie.

Inviability of a DNA2 deletion mutant is due to the DNA damage checkpoint

B. Wold, I. Antoshechkin, Judith L Campbell, 2011, Cell cycle.

Landscape of transcription in human cells

Nadav S. Bar, Pedro G. Ferreira, Morgan C. Giddings, 2012, Nature.

Sea urchin embryo mRNA sequences expressed in the nuclear RNA of adult tissues

B. Wold, R. Britten, E. Davidson, 1978, Cell.

Disruption of the mouse MRF4 gene identifies multiple waves of myogenesis in the myotome.

B. Wold, A. Patapoutian, S. Wang, 1995, Development.

Reproducibility, fidelity, and discriminant validity of mRNA amplification for microarray analysis from primary hematopoietic cells.

B. Wold, B. Shapiro, J. Roden, 2005, The Journal of molecular diagnostics : JMD.

Significance and statistical errors in the analysis of DNA microarray data

Stephen R Quake, James P Brody, Brian A Williams, 2002, Proceedings of the National Academy of Sciences of the United States of America.

nematode genome with RNA-seq Caenorhabditis Scaffolding a Material

B. Williams, A. Mortazavi, B. Wold, 2010 .

Cellerator: extending a computer algebra system to include biochemical arrows for signal transduction simulations

Bruce E. Shapiro, Eric Mjolsness, Andre Levchenko, 2003, Bioinform..

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

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

Genome-Wide Analysis Reveals Coating of the Mitochondrial Genome by TFAM

B. Wold, G. Marinov, Yun E. Wang, 2013, PloS one.

Interleukin-2 transcription is regulated in vivo at the level of coordinated binding of both constitutive and regulated factors

B. Wold, P. Garrity, D. Chen, 1994, Molecular and cellular biology.

Transcriptional regulation by nicotine in dopaminergic neurons.

B. Williams, B. Wold, H. Lester, 2013, Biochemical Pharmacology.

Tissue-specific Expression of Distinct Spectrin and Transcripts in Erythroid and Nonerythroid Cells

B. Wold, E. Lazarides, 2003 .

Mining gene expression data by interpreting principal components

Barbara J. Wold, Diane Trout, Ali Mortazavi, 2006, BMC Bioinformatics.

Isolation and characterization of a Xenopus laevis C protein cDNA: structure and expression of a heterogeneous nuclear ribonucleoprotein core protein.

B. Wold, F. Preugschat, 1988, Proceedings of the National Academy of Sciences of the United States of America.

Differentiation and fiber type-specific activity of a muscle creatine kinase intronic enhancer

A. P. Mackenzie, B. Wold, Katherine I. Fisher-Aylor, 2011, Skeletal Muscle.

Different MRF4 knockout alleles differentially disrupt Myf-5 expression: cis-regulatory interactions at the MRF4/Myf-5 locus.

B. Wold, H. Arnold, E. Olson, 1997, Developmental biology.

A human embryonic limb cell atlas resolved in space and time

B. Williams, B. Wold, R. Barker, 2023, bioRxiv.

MyoD(-/-) satellite cells in single-fiber culture are differentiation defective and MRF4 deficient.

B. Wold, M. Rudnicki, B. Olwin, 2000, Developmental biology.

A ratiometric-based measure of gene co-expression

Barbara J. Wold, Brian A. Williams, Georgi K. Marinov, 2014, BMC Bioinformatics.

Spatiometabolic Stratification of Shewanella oneidensis Biofilms

Barbara J. Wold, Tracy K. Teal, Dianne K. Newman, 2006, Applied and Environmental Microbiology.

Skeletal muscle phenotypes initiated by ectopic MyoD in transgenic mouse heart.

B. Wold, J. Miller, J. Miner, 1992, Development.

The ENCODE Uniform Analysis Pipelines

Daniel S. Kim, Brian T. Lee, Neva C. Durand, 2023, bioRxiv.

The ENCODE4 long-read RNA-seq collection reveals distinct classes of transcript structure diversity

Michael A. Beer, M. Gerstein, Z. Weng, 2023, bioRxiv.

Appearance and persistence of maternal RNA sequences in sea urchin development.

B. Wold, R. Britten, E. Davidson, 1977, Developmental biology.

Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes

M. Gerstein, Z. Weng, Manolis Kellis, 2022, Nature.

Mapping and modeling the genomic basis of differential RNA isoform expression at single-cell resolution with LR-Split-seq

A. Mortazavi, B. Wold, Diane Trout, 2021, Genome Biology.

NIH Public Access Author Manuscript

S. Salzberg, B. Williams, G. Pertea, 2006 .

The ENCODE Uniform Analysis Pipelines

Daniel S. Kim, Brian T. Lee, Neva C. Durand, 2023, Research square.

The Human Cell Atlas

Fabian J Theis, Jay W. Shin, Michael J. T. Stubbington, 2017, bioRxiv.

Methods for “ The effects of genome sequence on differential allelic transcription factor occupancy and gene expression ”

Timothy E. Reddy, B. Williams, A. Mortazavi, 2012 .

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

Jonathan M. Mudge, Angela N. Brooks, Gloria M. Sheynkman, 2023, bioRxiv.

Molecular cloning of cDNA for the nuclear ribonucleoprotein particle C proteins: a conserved gene family.

B. Wold, G. Dreyfuss, M. Swanson, 1986, Proceedings of the National Academy of Sciences of the United States of America.

Systematic assessment of long-read RNA-seq methods for transcript identi cation and quanti cation

Jonathan M. Mudge, Angela N. Brooks, Gloria M. Sheynkman, 2021 .

network : From single conserved sites to genome-wide repertoire Comparative genomics modeling of the NRSF / REST repressor Material Supplemental

A. Mortazavi, B. Wold, R. Myers, 2006 .

Phase I Solicitation

E. Lander, B. Wold, J. Sanes, 2020 .

The ENCODE Uniform Analysis Pipelines

Daniel S. Kim, Brian T. Lee, Neva C. Durand, 2023, Research square.

NIH Public Access Author Manuscript

S. Salzberg, B. Williams, G. Pertea, 2006 .

Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation

Raymond K. Auerbach, M. Gerstein, A. Mortazavi, 2012, Cell.

In vivo footprinting of a muscle specific enhancer by ligation mediated PCR.

B. Wold, P. Mueller, 1990, Science.

The Human Cell Atlas White Paper

Evan Z. Macosko, Jay W. Shin, Allon M. Klein, 2018, 1810.05192.

A comparative encyclopedia of DNA elements in the mouse genome

Mukul S. Bansal, Shane J. Neph, Dmitri D. Pervouchine, 2014, Nature.

Oligonucleotide-directed DNA triple-helix formation: an approach to artificial repressors?

B. Wold, L. J. Maher, P. Dervan, 1991, Antisense research and development.

Defining functional DNA elements in the human genome

Morgan C. Giddings, E. Birney, M. Gerstein, 2014, Proceedings of the National Academy of Sciences.

Connectivity in the Yeast Cell Cycle Transcription Network: Inferences from Neural Networks

Christopher E. Hart, B. Wold, E. Mjolsness, 2006, PLoS Comput. Biol..

Multi-tissue integrative analysis of personal epigenomes

Rachel M. Sherman, C. Nusbaum, R. Guigó, 2021 .

A scalable and integrative system for pathway bioinformatics and systems biology.

Pierre Baldi, Eric Mjolsness, Jianlin Cheng, 2010, Advances in experimental medicine and biology.

Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms

S. Salzberg, B. Williams, G. Pertea, 2010, Nature biotechnology.

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

Morgan C. Giddings, E. Birney, M. Gerstein, 2014, Proceedings of the National Academy of Sciences.

A ratiometric-based measure of gene co-expression

Anna C. T. Abelin, B. Williams, B. Wold, 2014, BMC Bioinformatics.

Genetic Analysis of a Metazoan Pathway using Transcriptomic Phenotypes

B. Williams, B. Wold, P. Sternberg, 2017 .

Ligation‐Mediated PCR for Genomic Sequencing and Footprinting

B. Wold, P. Mueller, 1991, Current protocols in molecular biology.