Harmen J. Bussemaker
Harmen J. Bussemaker
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Systematic protein location mapping reveals five principal chromatin types in Drosophila cells
GJ Filion, JG van Bemmel, U Braunschweig, W Talhout, J Kind, LD Ward, ...
Cell 143 (2), 212-224, 2010
Regulatory element detection using correlation with expression
HJ Bussemaker, H Li, ED Siggia
Nature genetics 27 (2), 167-174, 2001
Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution
S Richards, Y Liu, BR Bettencourt, P Hradecky, S Letovsky, R Nielsen, ...
Genome research 15 (1), 1-18, 2005
Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins
M Slattery, T Riley, P Liu, N Abe, P Gomez-Alcala, I Dror, T Zhou, R Rohs, ...
Cell 147 (6), 1270-1282, 2011
Genomic binding by the Drosophila Myc, Max, Mad/Mnt transcription factor network
A Orian, B van Steensel, J Delrow, HJ Bussemaker, L Li, T Sawado, ...
Genes & development 17 (9), 1101-1114, 2003
The human transcriptome map reveals extremes in gene density, intron length, GC content, and repeat pattern for domains of highly and weakly expressed genes
R Versteeg, BDC van Schaik, MF van Batenburg, M Roos, R Monajemi, ...
Genome Research 13 (9), 1998-2004, 2003
A gene expression map for the euchromatic genome of Drosophila melanogaster
V Stolc, Z Gauhar, C Mason, G Halasz, MF van Batenburg, SA Rifkin, ...
Science 306 (5696), 655-660, 2004
Evaluation of methods for modeling transcription factor sequence specificity
MT Weirauch, A Cote, R Norel, M Annala, Y Zhao, TR Riley, ...
Nature biotechnology 31 (2), 126-134, 2013
Building a dictionary for genomes: identification of presumptive regulatory sites by statistical analysis
HJ Bussemaker, H Li, ED Siggia
Proceedings of the National Academy of Sciences 97 (18), 10096-10100, 2000
Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data
F Gao, BC Foat, HJ Bussemaker
BMC bioinformatics 5 (1), 31, 2004
Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE
BC Foat, AV Morozov, HJ Bussemaker
Bioinformatics 22 (14), e141-e149, 2006
Identification of genes expressed in C. elegans touch receptor neurons
Y Zhang, C Ma, T Delohery, B Nasipak, BC Foat, A Bounoutas, ...
Nature 418 (6895), 331-335, 2002
PQM-1 complements DAF-16 as a key transcriptional regulator of DAF-2-mediated development and longevity
RG Tepper, J Ashraf, R Kaletsky, G Kleemann, CT Murphy, ...
Cell 154 (3), 676-690, 2013
T-profiler: scoring the activity of predefined groups of genes using gene expression data
A Boorsma, BC Foat, D Vis, F Klis, HJ Bussemaker
Nucleic acids research 33 (suppl 2), W592-W595, 2005
Quantitative modeling of transcription factor binding specificities using DNA shape
T Zhou, N Shen, L Yang, N Abe, J Horton, RS Mann, HJ Bussemaker, ...
Proceedings of the National Academy of Sciences 112 (15), 4654-4659, 2015
Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster
C Moorman, LV Sun, J Wang, E de Wit, W Talhout, LD Ward, F Greil, ...
Proceedings of the National Academy of Sciences 103 (32), 12027-12032, 2006
Distinct HP1 and Su (var) 3-9 complexes bind to sets of developmentally coexpressed genes depending on chromosomal location
F Greil, I van der Kraan, J Delrow, JF Smothers, E de Wit, HJ Bussemaker, ...
Genes & development 17 (22), 2825-2838, 2003
DSSR: an integrated software tool for dissecting the spatial structure of RNA
XJ Lu, HJ Bussemaker, WK Olson
Nucleic acids research 43 (21), e142-e142, 2015
Probing DNA shape and methylation state on a genomic scale with DNase I
A Lazarovici, T Zhou, A Shafer, AC Dantas Machado, TR Riley, ...
Proceedings of the National Academy of Sciences 110 (16), 6376-6381, 2013
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
R Jansen, HJ Bussemaker, M Gerstein
Nucleic acids research 31 (8), 2242-2251, 2003
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