H. Bussemaker

发表

Building a dictionary for genomes: identification of presumptive regulatory sites by statistical analysis.

H. Bussemaker, H. Li, E. Siggia, 2000, Proceedings of the National Academy of Sciences of the United States of America.

Regulatory element detection using correlation with expression

H. Bussemaker, E. Siggia, Hao Li, 2001, Nature Genetics.

Genomic binding by the Drosophila Myc, Max, Mad/Mnt transcription factor network.

B. Edgar, H. Bussemaker, J. Delrow, 2003, Genes & development.

Probing DNA shape and methylation state on a genomic scale with DNase I

R. Sandstrom, J. Stamatoyannopoulos, Tianyin Zhou, 2013, Proceedings of the National Academy of Sciences.

In search of the determinants of enhancer-promoter interaction specificity.

H. Bussemaker, B. van Steensel, Joris van Arensbergen, 2014, Trends in cell biology.

DSSR: an integrated software tool for dissecting the spatial structure of RNA

H. Bussemaker, W. Olson, Xiang-Jun Lu, 2015, Nucleic acids research.

Evaluation of methods for modeling transcription factor sequence specificity

Atina G. Coté, R. Norel, T. Hughes, 2013, Nature Biotechnology.

A Gene Expression Map for the Euchromatic Genome of Drosophila melanogaster

Scott A. Rifkin, K. White, P. Barbano, 2004, Science.

Evolving insights on how cytosine methylation affects protein–DNA binding

Tianyin Zhou, A. C. Dantas Machado, R. Rohs, 2014, Briefings in functional genomics.

22 Evolving insights on how cytosine methylation affects protein-DNA binding

Tianyin Zhou, R. Rohs, H. Bussemaker, 2015, Journal of biomolecular structure & dynamics.

Accurate and sensitive quantification of protein-DNA binding affinity

R. Mann, H. Bussemaker, William Freed-Pastor, 2018, Proceedings of the National Academy of Sciences.

Annual Review of Cell and Developmental Biology Low-Affinity Binding Sites and the Transcription Factor Specificity Paradox in Eukaryotes

Chaitanya Rastogi, R. Mann, H. Bussemaker, 2019 .

Perturbation-based analysis and modeling of combinatorial regulation in the yeast sulfur assimilation pathway

David Botstein, Harmen J. Bussemaker, R. Scott McIsaac, 2012, Molecular biology of the cell.

Genome-wide mapping of autonomous promoter activity in human cells

H. Bussemaker, B. van Steensel, Joris van Arensbergen, 2016, Nature Biotechnology.

Systematic Protein Location Mapping Reveals Five Principal Chromatin Types in Drosophila Cells

Guillaume J. Filion, H. Bussemaker, L. D. Ward, 2010, Cell.

Characterizing a collective and dynamic component of chromatin immunoprecipitation enrichment profiles in yeast

H. Bussemaker, L. D. Ward, Junbai Wang, 2014, bioRxiv.

Characterizing a collective and dynamic component of chromatin immunoprecipitation enrichment profiles in yeast

H. Bussemaker, L. D. Ward, Junbai Wang, 2014, BMC Genomics.

Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster

Ling V. Sun, K. White, H. Bussemaker, 2006, Proceedings of the National Academy of Sciences.

Genomewide analysis of Drosophila GAGA factor target genes reveals context-dependent DNA binding

Harmen J. Bussemaker, H. Bussemaker, J. Delrow, 2003, Proceedings of the National Academy of Sciences of the United States of America.

Profiling condition-specific, genome-wide regulation of mRNA stability in yeast.

Barrett C. Foat, H. Bussemaker, S. S. Houshmandi, 2005, Proceedings of the National Academy of Sciences of the United States of America.

Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution.

Inna Dubchak, Paul Havlak, Madeline A Crosby, 2005, Genome research.

Mean-Field Analysis of a Dynamical Phase Transition in a Cellular Automaton Model for Collective Motion

H. Bussemaker, A. Deutsch, E. Geigant, 1997, physics/9706008.

Towards a mechanistic understanding of DNA methylation readout by transcription factors.

R. Mann, R. Rohs, H. Bussemaker, 2020, Journal of molecular biology.

Systematic prediction of DNA shape changes due to CpG methylation explains epigenetic effects on protein–DNA binding

R. Mann, R. Rohs, H. Bussemaker, 2018, Epigenetics & Chromatin.

Dissection of transient oxidative stress response in Saccharomyces cerevisiae by using DNA microarrays.

M. G. Koerkamp, H. Bussemaker, H. Tabak, 2002, Molecular biology of the cell.

SelexGLM differentiates androgen and glucocorticoid receptor DNA-binding preference over an extended binding site

H. Bussemaker, J. Houtman, Chaitanya Rastogi, 2017, bioRxiv.

Systematic in vitro profiling of off-target affinity, cleavage and efficiency for CRISPR enzymes

H. Bussemaker, M. Behlke, Christopher A. Vakulskas, 2020, Nucleic acids research.

Context-Dependent Gene Regulation by Homeodomain Transcription Factor Complexes Revealed by Shape-Readout Deficient Proteins.

R. Mann, H. Bussemaker, Chaitanya Rastogi, 2020, Molecular cell.

Context-dependent gene regulation by transcription factor complexes

R. Mann, H. Bussemaker, Chaitanya Rastogi, 2019, bioRxiv.

Cofactor Binding Evokes Latent Differences in DNA Binding Specificity between Hox Proteins

R. Mann, B. Honig, Matthew Slattery, 2011, Cell.

SELEX-seq: a method for characterizing the complete repertoire of binding site preferences for transcription factor complexes.

R. Mann, Matthew Slattery, H. Bussemaker, 2014, Methods in molecular biology.

Deconvolving the Recognition of DNA Shape from Sequence

R. Mann, Matthew Slattery, Tianyin Zhou, 2015, Cell.

Building accurate sequence-to-affinity models from high-throughput in vitro protein-DNA binding data using FeatureREDUCE

R. Mann, H. Bussemaker, A. Lazarovici, 2015, eLife.

Quantitative modeling of transcription factor binding specificities using DNA shape

R. Mann, Tianyin Zhou, Lin Yang, 2015, Proceedings of the National Academy of Sciences.

The human transcriptome map reveals extremes in gene density, intron length, GC content, and repeat pattern for domains of highly and weakly expressed genes.

H. Bussemaker, A. V. van Kampen, R. Versteeg, 2003, Genome research.

Detecting transcriptionally active regions using genomic tiling arrays

Xiang-Jun Lu, H. Bussemaker, Xiang-Jun Lu, 2006, Genome Biology.

DAF-16 and PQM-1: Partners in longevity

Ronald G. Tepper, H. Bussemaker, C. Murphy, 2014, Aging.

Generalized Boltzmann equation for lattice gas automata

H. Bussemaker, M. Ernst, J. Dufty, 1994, comp-gas/9404002.

Algebraic spatial correlations in lattice gas automata violating detailed balance

H. Bussemaker, M. Ernst, 1995 .

A unified approach for quantifying and interpreting DNA shape readout by transcription factors

Chaitanya Rastogi, H. Bussemaker, Chaitanya Rastogi, 2018, Molecular systems biology.

Network-based approaches that exploit inferred transcription factor activity to analyze the impact of genetic variation on gene expression.

H. Bussemaker, H. Causton, Eunjee Lee, 2017, Current opinion in systems biology.

Harnessing Natural Sequence Variation to Dissect Posttranscriptional Regulatory Networks in Yeast

H. Bussemaker, H. Causton, Xiang-Jun Lu, 2014, G3: Genes, Genomes, Genetics.

Identifying regulatory mechanisms underlying tumorigenesis using locus expression signature analysis

H. Bussemaker, L. Wessels, Eunjee Lee, 2014, Proceedings of the National Academy of Sciences.

Prediction of protein–ligand binding affinity from sequencing data with interpretable machine learning

R. Mann, H. Bussemaker, Neel H. Shah, 2022, Nature Biotechnology.

UvA-DARE ( Digital Academic Repository ) T-profiler : scoring the activity of predefined groups of genes using gene expression data

Barrett C. Foat, H. Bussemaker, F. Klis, 2005 .

Model-Based Inference of Transcriptional Regulatory Mechanisms from DNA Microarray Data

H. Bussemaker, 2006 .

vitro protein-DNA binding data using FeatureREDUCE

R. Mann, H. Bussemaker, A. Lazarovici, 2015 .

Mean-Field Analysis of a Dynamical Phase Transition in a Cellular Automaton Model for Collective Motion

H. Bussemaker, A. Deutsch, E. Geigant, 1997, physics/9706008.

Identifying genetic regulatory variants that affect transcription factor activity

H. Bussemaker, T. Lappalainen, Xiaoting Li, 2022, bioRxiv.

Systematic invitro proﬁling of off-target afﬁnity, cleavage and efﬁciency for CRISPR enzymes

H. Bussemaker, M. Behlke, Christopher A. Vakulskas, 2020 .

Instabilities and Patterns

H. Bussemaker, M. Ernst, 1993 .

The effect of sequence mismatches on binding affinity and endonuclease activity are decoupled throughout the Cas9 binding site

H. Bussemaker, M. Pufall, H. T. Rube, 2017, bioRxiv.

Systematic Protein Location Mapping Reveals Five Principal Chromatin Types in Drosophila Cells

H. Bussemaker, L. D. Ward, B. Steensel, 2011, Cell.

A fluctuation formula for the nonGalilean factor in lattice gas automata

H. Bussemaker, M. Ernst, R. Brito, 1992 .

Dendritic spikes as a mechanism for cooperative long-term potentiation

Barrett C. Foat, Stuart K. Kim, M. Chalfie, 2022 .

HP1 controls genomic targeting of four novel heterochromatin proteins in Drosophila

H. Bussemaker, B. van Steensel, Elzo de Wit, 2007, The EMBO journal.

Probing molecular specificity with deep sequencing and biophysically interpretable machine learning

R. Mann, H. Bussemaker, Neel H. Shah, 2021, bioRxiv.

Recent progress in understanding transcription factor binding specificity.

H. Bussemaker, 2015, Briefings in functional genomics.

Inferring Condition-Specific Modulation of Transcription Factor Activity in Yeast through Regulon-Based Analysis of Genomewide Expression

Xiang-Jun Lu, Frans M. Klis, Harmen J. Bussemaker, 2008, PloS one.

Identifying the genetic determinants of transcription factor activity

Eunjee Lee, H. Bussemaker, Eunjee Lee, 2010, Molecular systems biology.

Identifying genetic modulators of the connectivity between transcription factors and their transcriptional targets

Eunjee Lee, Helen C Causton, H. Bussemaker, 2016, Proceedings of the National Academy of Sciences.

Transcription factor paralogs orchestrate alternative gene regulatory networks by context-dependent cooperation with multiple cofactors

R. Mann, H. Bussemaker, Chaitanya Rastogi, 2022, Nature Communications.

High-throughput identification of human SNPs affecting regulatory element activity

H. Bussemaker, M. Vermeulen, L. Franke, 2019, Nature Genetics.

Systematic identification of human SNPs affecting regulatory element activity

Joris van Arensbergen, H. Bussemaker, M. Vermeulen, 2018, bioRxiv.

Combinatorial control of diverse metabolic and physiological functions by transcriptional regulators of the yeast sulfur assimilation pathway

David Botstein, Harmen J. Bussemaker, R. Scott McIsaac, 2012, Molecular biology of the cell.

Global Chromatin Domain Organization of the Drosophila Genome

H. Bussemaker, B. van Steensel, Elzo de Wit, 2008, PLoS genetics.

Transcription factor regulation of eQTL activity across individuals and tissues

K. Ardlie, H. Bussemaker, T. Lappalainen, 2021, bioRxiv.

Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE

Alexandre V. Morozov, Harmen J. Bussemaker, Barrett C. Foat, 2006, ISMB.

Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data

Feng Gao, Harmen J. Bussemaker, Barrett C. Foat, 2004, BMC Bioinformatics.

Distinct HP1 and Su(var)3-9 complexes bind to sets of developmentally coexpressed genes depending on chromosomal location.

S. Henikoff, H. Bussemaker, J. Delrow, 2003, Genes & development.

Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences

Lucas D. Ward, Harmen J. Bussemaker, H. Bussemaker, 2008, ISMB.

Revisiting the codon adaptation index from a whole-genome perspective: analyzing the relationship between gene expression and codon occurrence in yeast using a variety of models.

Mark Gerstein, Ronald Jansen, M. Gerstein, 2003, Nucleic acids research.

In vivo Hox binding specificity revealed by systematic changes to a single cis regulatory module

R. Mann, H. Bussemaker, Chaitanya Rastogi, 2019, Nature Communications.

Loss of Subcellular Lipid Transport Due to ARV1 Deficiency Disrupts Organelle Homeostasis and Activates the Unfolded Protein Response*

H. Bussemaker, Eunjee Lee, A. Tinkelenberg, 2011, The Journal of Biological Chemistry.

TransfactomeDB: a resource for exploring the nucleotide sequence specificity and condition-specific regulatory activity of trans-acting factors

Harmen J. Bussemaker, Barrett C. Foat, Ronald G. Tepper, 2007, Nucleic Acids Res..

T-profiler: scoring the activity of predefined groups of genes using gene expression data

Daniel J. Vis, Harmen J. Bussemaker, André Boorsma, 2005, Nucleic Acids Res..

Classification of Saccharomyces cerevisiae promoter regions into distinct chromatin classes reveals the existence of nucleosome-depleted hotspots of transcription factor occupancy

H. Bussemaker, L. D. Ward, Junbai Wang, 2010, 1010.0713.

Quantitative Analysis of the DNA Methylation Sensitivity of Transcription Factor Complexes.

R. Mann, H. Bussemaker, C. Prives, 2017, Cell reports.

TLS/FUS (translocated in liposarcoma/fused in sarcoma) regulates target gene transcription via single-stranded DNA response elements

H. Bussemaker, Todd Riley, J. Manley, 2012, Proceedings of the National Academy of Sciences.

PrePPI: A NOVEL STRUCTURE-BASED METHOD FOR PREDICTING PROTEIN-PROTEIN INTERACTIONS

B. Honig, H. Bussemaker, Chaolin Zhang, 2013 .

Rules of Protein-DNA Recognition : Computational and Experimental Advances

H. Bussemaker, 2016 .

Predictive modeling of genome-wide mRNA expression: from modules to molecules.

Barrett C. Foat, H. Bussemaker, L. D. Ward, 2007, Annual review of biophysics and biomolecular structure.

Nuclear pore component Nup98 is a potential tumor suppressor and regulates posttranscriptional expression of select p53 target genes.

H. Bussemaker, P. Schirmacher, D. Grunwald, 2012, Molecular cell.

The RNA backbone plays a crucial role in mediating the intrinsic stability of the GpU dinucleotide platform and the GpUpA/GpA miniduplex

Xiang-Jun Lu, Wilma K. Olson, Harmen J. Bussemaker, 2010, Nucleic acids research.

Revisiting the Central Dogma One Molecule at a Time

Guillaume J. Filion, H. Bussemaker, L. D. Ward, 2011, Cell.

Thermodynamic stability of folded proteins against mutations

D. Thirumalai, D. Thirumalai, H. Bussemaker, 1997, cond-mat/9709078.

Identification of genes expressed in C. elegans touch receptor neurons

Barrett C. Foat, Stuart K. Kim, M. Chalfie, 2002, Nature.

PQM-1 Complements DAF-16 as a Key Transcriptional Regulator of DAF-2-Mediated Development and Longevity

Ronald G. Tepper, H. Bussemaker, G. Kleemann, 2013, Cell.

ETO family protein Mtg16 regulates the balance of dendritic cell subsets by repressing Id2

L. Staudt, H. Bussemaker, A. Lazarovici, 2014, The Journal of experimental medicine.

Hap4p overexpression in glucose-grown Saccharomyces cerevisiae induces cells to enter a novel metabolic state

André Boorsma, L. Grivell, H. Bussemaker, 2002, Genome Biology.

REDUCE: an online tool for inferring cis-regulatory elements and transcriptional module activities from microarray data

Harmen J. Bussemaker, Crispin Roven, H. Bussemaker, 2003, Nucleic Acids Res..

K-mer Motif Multinomial Mixtures, a scalable framework for multiple motif discovery

Sandhya Prabhakaran, Harmen J. Bussemaker, Brian Loeber Trippe, 2016, bioRxiv.

UvA-DARE ( Digital Academic Repository ) Paired Hormone Response Elements Predict Caveolin-1 as a Glucocorticoid Target Gene

H. Bussemaker, N. Datson, O. Meijer, 2010 .

Regulatory Element Detection Using a Probabilistic Segmentation Model

Hao Li, Harmen J. Bussemaker, Eric D. Siggia, 2000, ISMB.

14 Quantitative modeling of transcription factor binding specificities using DNA shape

R. Mann, Tianyin Zhou, Lin Yang, 2015, Journal of biomolecular structure & dynamics.

ISMB 2010 Organization

Roger L. Chang, S. Batzoglou, L. Cowen, 2010, Bioinformatics.

Regulatory element detection using correlation with expression (abstract only)

Hao Li, Harmen J. Bussemaker, Eric D. Siggia, 2001, RECOMB.

SYSTEMS BIOLOGY: GLOBAL REGULATION OF GENE EXPRESSION

M. Bulyk, H. Bussemaker, B. Bernstein, 2010 .

Systematic prediction of DNA shape changes due to CpG methylation explains epigenetic effects on protein–DNA binding

R. Mann, R. Rohs, H. Bussemaker, 2018, Epigenetics & Chromatin.

Optimisation of TP53 reporters by systematic dissection of synthetic TP53 response elements

H. Bussemaker, B. van Steensel, Chaitanya Rastogi, 2023, bioRxiv.

Toward a Mechanistic Understanding of DNA Methylation Readout by Transcription Factors

R. Mann, R. Rohs, H. Bussemaker, 2020 .

Dissecting complex transcriptional responses using pathway-level scores based on prior information

Lucas D. Ward, Harmen J. Bussemaker, André Boorsma, 2007, BMC Bioinformatics.

Paired Hormone Response Elements Predict Caveolin-1 as a Glucocorticoid Target Gene

H. Bussemaker, N. Datson, J. Polman, 2010, PloS one.

Probing DNA shape and methylation state on a genomic scale with DNase I

R. Sandstrom, J. Stamatoyannopoulos, Tianyin Zhou, 2013, Proceedings of the National Academy of Sciences.

Low-Affinity Binding Sites and the Transcription Factor Specificity Paradox in Eukaryotes.

H. Bussemaker, Chaitanya Rastogi, J. Kribelbauer, 2019, Annual Review of Cell and Developmental Biology.

Predicting the DNA binding specificity of mutated transcription factors using family-level biophysically interpretable machine learning

H. Bussemaker, Christ Leemans, P. Gomez-Alcala, 2024, bioRxiv.

Benchmarking DNA binding affinity models using allele-specific transcription factor binding data

H. Bussemaker, Lucas A. N. Melo, Xiaoting Li, 2023, bioRxiv.

Deconvolving the Recognition of DNA Shape from Sequence

R. Mann, Matthew Slattery, Tianyin Zhou, 2015, Cell.