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Harmen J. Bussemaker

Harmen J. Bussemaker

D-Index & Metrics

Genetics

D-Index
52
Citations
12740
World Ranking
3779
National Ranking
1629

Research.com Recognitions

  • 2010 - Fellow of John Simon Guggenheim Memorial Foundation

Overview

Harmen J. Bussemaker is affiliated with Columbia University in the United States. Their research primarily spans areas within biochemistry, genetics, and molecular biology.

The scientist's work has a strong focus on several interconnected fields including:

  • Molecular Biology
  • Genetics
  • Oncology
  • Surgery
  • Cell Biology

Bussemaker's main research topics address:

  • Genomics and Chromatin Dynamics
  • RNA Research and Splicing
  • RNA and protein synthesis mechanisms
  • Bioinformatics and Genomic Networks
  • Genetic Mapping and Diversity in Plants and Animals
  • Developmental Biology and Gene Regulation
  • Cancer-related Molecular Pathways

The scientist has published extensively in venues including:

  • bioRxiv (Cold Spring Harbor Laboratory)
  • Nucleic Acids Research
  • Zenodo (CERN European Organization for Nuclear Research)
  • Nature Biotechnology
  • PLoS Genetics

Some of the recent papers authored or coauthored by Bussemaker are:

  • Prediction of protein-ligand binding affinity from sequencing data with interpretable machine learning, 2022, Nature Biotechnology
  • Transcription factor regulation of eQTL activity across individuals and tissues, 2022, PLoS Genetics
  • Systematic in vitro profiling of off-target affinity, cleavage and efficiency for CRISPR enzymes, 2020, Nucleic Acids Research
  • Transcription factor paralogs orchestrate alternative gene regulatory networks by context-dependent cooperation with multiple cofactors, 2022, Nature Communications
  • Context-Dependent Gene Regulation by Homeodomain Transcription Factor Complexes Revealed by Shape-Readout Deficient Proteins, 2020, Molecular Cell

Frequent collaborators include:

  • Chaitanya Rastogi
  • H. Tomas Rube
  • Xiaoting Li
  • Lucas A. N. Melo
  • Richard S. Mann

In 2010, Bussemaker was named a Fellow of the John Simon Guggenheim Memorial Foundation.

Best Publications

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

    Guillaume J. Filion;Joke G. van Bemmel;Ulrich Braunschweig;Wendy Talhout

  • Regulatory element detection using correlation with expression

    Harmen J. Bussemaker;Hao Li;Eric D. Siggia

  • Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution

    Stephen Richards;Yue Liu;Brian R. Bettencourt;Pavel Hradecky

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

    Matthew G Slattery;Todd Riley;Peng Liu;Peng Liu;Namiko Abe

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

    Amir Orian;Bas van Steensel;Jeffrey Delrow;Harmen J. Bussemaker

  • The Human Transcriptome Map Reveals Extremes in Gene Density, Intron Length, GC Content, and Repeat Pattern for Domains of Highly and Weakly Expressed Genes

    Rogier Versteeg;Barbera D.C. van Schaik;Marinus F. van Batenburg;Marco Roos

  • Evaluation of methods for modeling transcription factor sequence specificity

    Matthew T Weirauch;Atina Cote;Raquel Norel;Matti Annala

  • A Gene Expression Map for the Euchromatic Genome of Drosophila melanogaster

    Viktor Stolc;Viktor Stolc;Zareen Gauhar;Christopher Mason;Gabor Halasz

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

    Harmen J. Bussemaker;Hao Li;Eric D. Siggia

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

    Barrett C. Foat;Alexandre V. Morozov;Harmen J. Bussemaker

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

    Feng Gao;Barrett C Foat;Harmen J Bussemaker

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

    Ronald G. Tepper;Jasmine Ashraf;Rachel Kaletsky;Gunnar Kleemann

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

    Xiang-Jun Lu;Harmen J. Bussemaker;Wilma K. Olson

  • Identification of genes expressed in C. elegans touch receptor neurons

    Yun Zhang;Charles Ma;Thomas Delohery;Thomas Delohery;Brian Nasipak

  • Quantitative modeling of transcription factor binding specificities using DNA shape

    Tianyin Zhou;Ning Shen;Lin Yang;Namiko Abe

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

    André Boorsma;Barrett C Foat;Daniel J. Vis;Frans M. Klis

  • Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster.

    Celine Moorman;Ling V. Sun;Junbai Wang;Elzo de Wit

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

    Allan Lazarovici;Tianyin Zhou;Anthony Shafer;Ana Carolina Dantas Machado

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

    Frauke Greil;Ineke van der Kraan;Jeffrey Delrow;James F. Smothers

  • Deconvolving the recognition of DNA shape from sequence.

    Namiko Abe;Iris Dror;Iris Dror;Lin Yang;Matthew G Slattery

Frequent Co-Authors

Richard S. Mann
Richard S. Mann Columbia University
Bas van Steensel
Bas van Steensel Antoni van Leeuwenhoek Hospital
Remo Rohs
Remo Rohs University of Southern California
Elzo de Wit
Elzo de Wit Antoni van Leeuwenhoek Hospital
Jeffrey J. Delrow
Jeffrey J. Delrow Fred Hutchinson Cancer Research Center
Kevin P. White
Kevin P. White National University of Singapore
Carol Prives
Carol Prives Columbia University
Coleen T. Murphy
Coleen T. Murphy Princeton University
John A. Stamatoyannopoulos
John A. Stamatoyannopoulos University of Washington
Lude Franke
Lude Franke University Medical Center Groningen

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