Harmen J. Bussemaker - Publications, H-index & Citations

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Harmen J. Bussemaker

columbia university department of biological sciences, , new york , ny 10027 ,

47H-index

135Paper Count

1.1WCitation Count

Published Papers 56

Publication Date

Accurate affinity models for SH2 domains from peptide binding assays and free-energy regression

Protein Science

IF5.2

2025-10-14

OAAI

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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Predicting the DNA binding specificity of transcription factor mutants using family-level biophysically interpretable machine learning

Nucleic Acids Research

IF13.1

2025-08-28

OAAI

Shaoxun Liu; Pilar Gomez-Alcala; Christ Leemans; William J Glassford; Lucas A N Melo; Xiang-Jun Lu; Richard S Mann; Harmen J Bussemaker

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

GENOME BIOLOGY

IF9.4

2024-10-31

OAAI

Li, Xiaoting; Melo, Lucas A. N.; Bussemaker, Harmen J.

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Identifying genetic regulatory variants that affect transcription factor activity

CELL GENOMICS

IF9

2023-09-01

OAAI

Li, Xiaoting; Lappalainen, Tuuli; Bussemaker, Harmen J.

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

NUCLEIC ACIDS RESEARCH

IF13.1

2023-08-31

OAAI

Trauernicht, Max; Rastogi, Chaitanya; Manzo, Stefano G.; Bussemaker, Harmen J.; van Steensel, Bas

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

NUCLEIC ACIDS RESEARCH

IF13.1

2023-04-04

OAAI

FitzPatrick, Vincent D.; Leemans, Christ; van Arensbergen, Joris; van Steensel, Bas; Bussemaker, Harmen J.

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Emerging questions in transcriptional regulation

CELL SYSTEMS

IF7.7

2023-04-01

PREAI

Nora, Elphege P.; Aerts, Stein; Wittkopp, Patricia J.; Bussemaker, Harmen J.; Bulyk, Martha; Sinha, Saurabh; Zeitlinger, Julia; Crocker, Justin; Bass, Juan Ignacio Fuxman

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

NATURE COMMUNICATIONS

IF15.7

2022-07-01

OAAI

Feng, Sidian; Rastogig, Chaitanya; Loker, Ryan; Glassford, William J.; Rube, H. Tomas; Bussemaker, Harmen J.; Mann, Richard S.

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

NATURE BIOTECHNOLOGY

IF41.7

2022-05-23

OAAI

Rube, H. Tomas; Rastogi, Chaitanya; Feng, Siqian; Kribelbauer, Judith F.; Li, Allyson; Becerra, Basheer; Melo, Lucas A. N.; Do, Bach Viet; Li, Xiaoting; Adam, Hammaad H.; Shah, Neel H.; Mann, Richard S.; Bussemaker, Harmen J.

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Transcription factor regulation of eQTL activity across individuals and tissues

PLOS GENETICS

IF3.7

2022-01-31

OAAI

Flynn, Elise D.; Tsu, Athena L.; Kasela, Silva; Kim-Hellmuth, Sarah; Aguet, Francois; Ardlie, Kristin; Bussemaker, Harmen; Mohammadi, Pejman; Lappalainen, Tuuli

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

NUCLEIC ACIDS RESEARCH

IF13.1

2020-04-21

OAAI

Zhang, Liyang; Rube, H. Tomas; Vakulskas, Christopher A.; Behlke, Mark A.; Bussemaker, Harmen J.; Pufall, Miles A.

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

MOLECULAR CELL

IF16.6

2020-04-01

OAAI

Kribelbauer, Judith F.; Loker, Ryan E.; Feng, Siqian; Rastogi, Chaitanya; Abe, Namiko; Rube, H. Tomas; Bussemaker, Harmen J.; Mann, Richard S.

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

ANNUAL REVIEW OF CELL AND DEVELOPMENTAL BIOLOGY

IF0

2019-10-06

145

OAAI

Kribelbauer, Judith F.; Rastogi, Chaitanya; Bussemaker, Harmen J.; Mann, Richard S.

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

NATURE COMMUNICATIONS

IF15.7

2019-08-09

OAAI

Sanchez-Higueras, Carlos; Rastogi, Chaitanya; Voutev, Roumen; Bussemaker, Harmen J.; Mann, Richard S.; Hombria, James C-G

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High-throughput identification of human SNPs affecting regulatory element activity

NATURE GENETICS

IF31.8

2019-06-28

142

OAAI

van Arensbergen, Joris; Pagie, Ludo; FitzPatrick, Vincent D.; de Haas, Marcel; Baltissen, Marijke P.; Comoglio, Federico; van der Weide, Robin H.; Teunissen, Hans; Vosa, Urmo; Franke, Lude; de Wit, Elzo; Vermeulen, Michiel; Bussemaker, Harmen J.; van Steensel, Bas

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Accurate and sensitive quantification of protein-DNA binding affinity

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

IF9.1

2018-04-02

OAAI

Rastogi, Chaitanya; Rube, H. Tomas; Kribelbauer, Judith F.; Crocker, Justin; Loker, Ryan E.; Martini, Gabriella D.; Laptenko, Oleg; Freed-Pastor, William A.; Prives, Carol; Stern, David L.; Mann, Richard S.; Bussemaker, Harmen J.

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

MOLECULAR SYSTEMS BIOLOGY

IF7.7

2018-02-22

OAAI

Rube, H. Tomas; Rastogi, Chaitanya; Kribelbauer, Judith F.; Bussemaker, Harmen J.

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

EPIGENETICS & CHROMATIN

IF3.5

2018-02-06

OAAI

Rao, Satyanarayan; Chiu, Tsu-Pei; Kribelbauer, Judith F.; Mann, Richard S.; Bussemaker, Harmen J.; Rohs, Remo

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

GENOME RESEARCH

IF5.5

2017-12-01

OAAI

Zhang, Liyang; Martini, Gabriella D.; Rube, H. Tomas; Kribelbauer, Judith F.; Rastogi, Chaitanya; FitzPatrick, Vincent D.; Houtman, Jon C.; Bussemaker, Harmen J.; Pufall, Miles A.

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Quantitative Analysis of the DNA Methylation Sensitivity of Transcription Factor Complexes

CELL REPORTS

IF6.9

2017-06-01

OAAI

Kribelbauer, Judith F.; Laptenko, Oleg; Chen, Siying; Martini, Gabriella D.; Freed-Pastor, William A.; Prives, Carol; Mann, Richard S.; Bussemaker, Harmen J.

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Research Directions