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Employment (1)

Columbia University: New York, NY, US

Employment
Source: Self-asserted source
Harmen Bussemaker

Education and qualifications (1)

Utrecht University: Utrecht, Utrecht, NL

1995 | PhD (Theoretical Physics)
Education
Source: Self-asserted source
Harmen Bussemaker

Works (19)

Accurate sequence-to-affinity models for SH2 domains from multi-round peptide binding assays coupled with free-energy regression

2024-12-23 | Preprint
DOI: 10.1101/2024.12.23.630085
Contributors: Dejan Gagoski; H. Tomas Rube; Chaitanya Rastogi; Lucas A. N. Melo; Xiaoting Li; Rashmi Voleti; Neel H. Shah; Harmen J. Bussemaker
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Crossref

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

Genome Biology
2024-10-31 | Journal article
DOI: 10.1186/s13059-024-03424-2
Contributors: Xiaoting Li; Lucas A. N. Melo; Harmen J. Bussemaker
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Crossref

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

2024-01-29 | Preprint
DOI: 10.1101/2024.01.24.577115
Contributors: Shaoxun Liu; Pilar Gomez-Alcala; Christ Leemans; William J. Glassford; Richard S. Mann; Harmen J. Bussemaker
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Crossref

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

2023-12-15 | Preprint
DOI: 10.1101/2023.12.15.571887
Contributors: Xiaoting Li; Lucas A. N. Melo; Harmen J. Bussemaker
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Crossref

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

Nucleic Acids Research
2023-10-13 | Journal article
DOI: 10.1093/nar/gkad718
Contributors: Max Trauernicht; Chaitanya Rastogi; Stefano G Manzo; Harmen J Bussemaker; Bas van Steensel
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Crossref

Identifying genetic regulatory variants that affect transcription factor activity

Cell Genomics
2023-09 | Journal article
DOI: 10.1016/j.xgen.2023.100382
Contributors: Xiaoting Li; Tuuli Lappalainen; Harmen J. Bussemaker
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Crossref

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

2023-07-27 | Preprint
DOI: 10.1101/2023.07.24.549988
Contributors: Max Trauernicht; Chaitanya Rastogi; Stefano G. Manzo; Harmen J. Bussemaker; Bas van Steensel
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Crossref

Defining the fine structure of promoter activity on a genome-wide scale with CISSECTOR

Nucleic Acids Research
2023-06-23 | Journal article
DOI: 10.1093/nar/gkad232
Contributors: Vincent D FitzPatrick; Christ Leemans; Joris van Arensbergen; Bas van Steensel; Harmen J Bussemaker
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Crossref

Identifying Genetic Regulatory Variants that Affect Transcription Factor Activity

2022-10-21 | Preprint
DOI: 10.1101/2022.10.21.513166
Contributors: Xiaoting Li; Tuuli Lappalainen; Harmen J. Bussemaker
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Crossref

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

Nature Communications
2022-07-01 | Journal article
DOI: 10.1038/s41467-022-31501-2
Contributors: Siqian Feng; Chaitanya Rastogi; Ryan Loker; William J. Glassford; H. Tomas Rube; Harmen J. Bussemaker; Richard S. Mann
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Crossref

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

2022-02-27 | Preprint
DOI: 10.1101/2022.02.26.482133
Contributors: Siqian Feng; Chaitanya Rastogi; Ryan E. Loker; William J. Glassford; H. Tomas Rube; Harmen J. Bussemaker; Richard S. Mann
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Crossref

Transcription factor regulation of eQTL activity across individuals and tissues

PLOS Genetics
2022-01-31 | Journal article
DOI: 10.1371/journal.pgen.1009719
Contributors: Elise D. Flynn; Francesca Luca; Athena L. Tsu; Silva Kasela; Sarah Kim-Hellmuth; Francois Aguet; Kristin G. Ardlie; Harmen J. Bussemaker; Pejman Mohammadi; Tuuli Lappalainen
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Crossref

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

Nucleic acids research
2020-05-01 | Journal article
DOI: 10.1093/nar/gkaa231
PMID: 32315032
PMC: PMC7229833
Contributors: Zhang L; Rube HT; Vakulskas CA; Mark A. Behlke; Bussemaker HJ; Miles Pufall
Source: Self-asserted source
Harmen Bussemaker

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

Molecular cell
2020-02-12 | Journal article
DOI: 10.1016/j.molcel.2020.01.027
PMID: 32053778
PMC: PMC7197192
Contributors: Judith F Kribelbauer-Swietek; Ryan Loker; Siqian Feng; Rastogi C; Abe N; Rube HT; Bussemaker HJ; Mann RS
Source: Self-asserted source
Harmen Bussemaker

Toward a Mechanistic Understanding of DNA Methylation Readout by Transcription Factors.

Journal of molecular biology
2019-11-02 | Journal article
DOI: 10.1016/j.jmb.2019.10.021
PMID: 31689433
PMC: PMC6961349
Contributors: Judith F Kribelbauer-Swietek; Lu XJ; Rohs R; Mann RS; Bussemaker HJ
Source: Self-asserted source
Harmen Bussemaker

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

Nature Communications
2019-08-09 | Journal article
DOI: 10.1038/s41467-019-11416-1
Contributors: Carlos Sánchez-Higueras; Chaitanya Rastogi; Roumen Voutev; Harmen J. Bussemaker; Richard S. Mann; James C.-G. Hombría
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Crossref

Context-dependent gene regulation by transcription factor complexes

2019-07-18 | Other
DOI: 10.1101/706473
Contributors: Judith F. Kribelbauer; Ryan E. Loker; Siqian Feng; Chaitanya Rastogi; Namiko Abe; H. Tomas Rube; Harmen J. Bussemaker; Richard S. Mann
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Crossref

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

Molecular Systems Biology
2018-02 | Journal article
DOI: 10.15252/msb.20177902
Contributors: H Tomas Rube; Chaitanya Rastogi; Judith F Kribelbauer; Harmen J Bussemaker
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Crossref

Genome-wide mapping of autonomous promoter activity in human cells

Nature Biotechnology
2017-02 | Journal article
DOI: 10.1038/nbt.3754
Contributors: Joris van Arensbergen; Vincent D FitzPatrick; Marcel de Haas; Ludo Pagie; Jasper Sluimer; Harmen J Bussemaker; Bas van Steensel
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Crossref
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