Harmen J. Bussemaker, Ph.D. - Publications

2001- Biological Sciences Columbia University, New York, NY 

63 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Zhang L, Rube HT, Vakulskas CA, Behlke MA, Bussemaker HJ, Pufall MA. Systematic in vitro profiling of off-target affinity, cleavage and efficiency for CRISPR enzymes. Nucleic Acids Research. PMID 32315032 DOI: 10.1093/Nar/Gkaa231  0.4
2020 Kribelbauer JF, Loker RE, Feng S, Rastogi C, Abe N, Rube HT, Bussemaker HJ, Mann RS. Context-Dependent Gene Regulation by Homeodomain Transcription Factor Complexes Revealed by Shape-Readout Deficient Proteins. Molecular Cell. PMID 32053778 DOI: 10.1016/J.Molcel.2020.01.027  0.76
2019 Kribelbauer JF, Lu XJ, Rohs R, Mann RS, Bussemaker HJ. Towards a mechanistic understanding of DNA methylation readout by transcription factors. Journal of Molecular Biology. PMID 31689433 DOI: 10.1016/J.Jmb.2019.10.021  0.8
2019 Sánchez-Higueras C, Rastogi C, Voutev R, Bussemaker HJ, Mann RS, Hombría JC. In vivo Hox binding specificity revealed by systematic changes to a single cis regulatory module. Nature Communications. 10: 3597. PMID 31399572 DOI: 10.1038/S41467-019-11416-1  0.76
2019 Kribelbauer JF, Rastogi C, Bussemaker HJ, Mann RS. Low-Affinity Binding Sites and the Transcription Factor Specificity Paradox in Eukaryotes. Annual Review of Cell and Developmental Biology. PMID 31283382 DOI: 10.1146/Annurev-Cellbio-100617-062719  0.76
2018 Rastogi C, Rube HT, Kribelbauer JF, Crocker J, Loker RE, Martini GD, Laptenko O, Freed-Pastor WA, Prives C, Stern DL, Mann RS, Bussemaker HJ. Accurate and sensitive quantification of protein-DNA binding affinity. Proceedings of the National Academy of Sciences of the United States of America. PMID 29610332 DOI: 10.1073/Pnas.1714376115  0.76
2018 Rube HT, Rastogi C, Kribelbauer JF, Bussemaker HJ. A unified approach for quantifying and interpreting DNA shape readout by transcription factors. Molecular Systems Biology. 14: e7902. PMID 29472273 DOI: 10.15252/Msb.20177902  0.4
2018 Rao S, Chiu TP, Kribelbauer JF, Mann RS, Bussemaker HJ, Rohs R. Systematic prediction of DNA shape changes due to CpG methylation explains epigenetic effects on protein-DNA binding. Epigenetics & Chromatin. 11: 6. PMID 29409522 DOI: 10.1186/S13072-018-0174-4  0.76
2017 Zhang L, Martini GD, Rube HT, Kribelbauer JF, Rastogi C, FitzPatrick VD, Houtman JC, Bussemaker HJ, Pufall MA. SelexGLM differentiates androgen and glucocorticoid receptor DNA-binding preference over an extended binding site. Genome Research. PMID 29196557 DOI: 10.1101/Gr.222844.117  0.4
2017 Bussemaker HJ, Causton HC, Fazlollahi M, Lee E, Muroff I. Network-based approaches that exploit inferred transcription factor activity to analyze the impact of genetic variation on gene expression. Current Opinion in Systems Biology. 2: 98-102. PMID 28691107 DOI: 10.1016/J.Coisb.2017.04.002  1
2017 Kribelbauer JF, Laptenko O, Chen S, Martini GD, Freed-Pastor WA, Prives C, Mann RS, Bussemaker HJ. Quantitative Analysis of the DNA Methylation Sensitivity of Transcription Factor Complexes. Cell Reports. 19: 2383-2395. PMID 28614722 DOI: 10.1016/J.Celrep.2017.05.069  0.76
2016 Fazlollahi M, Muroff I, Lee E, Causton HC, Bussemaker HJ. Identifying genetic modulators of the connectivity between transcription factors and their transcriptional targets. Proceedings of the National Academy of Sciences of the United States of America. 113: E1835-43. PMID 26966232 DOI: 10.1073/Pnas.1517140113  1
2015 Riley TR, Lazarovici A, Mann RS, Bussemaker HJ. Building accurate sequence-to-affinity models from high-throughput in vitro protein-DNA binding data using FeatureREDUCE. Elife. 4. PMID 26701911 DOI: 10.7554/Elife.06397  0.76
2015 Lu XJ, Bussemaker HJ, Olson WK. DSSR: an integrated software tool for dissecting the spatial structure of RNA. Nucleic Acids Research. PMID 26184874 DOI: 10.1093/Nar/Gkv716  0.8
2015 Rao S, Carolina Dantas Machado A, Zhou T, Rastogi C, Bussemaker HJ, Rohs R. 22 Evolving insights on how cytosine methylation affects protein-DNA binding. Journal of Biomolecular Structure & Dynamics. 33: 12. PMID 26103232 DOI: 10.1080/07391102.2015.1032562  0.56
2015 Zhou T, Shen N, Yang L, Abe N, Horton J, Mann RS, Bussemaker HJ, Gordân R, Rohs R. 14 Quantitative modeling of transcription factor binding specificities using DNA shape. Journal of Biomolecular Structure & Dynamics. 33: 8-9. PMID 26103224 DOI: 10.1080/07391102.2015.1032554  0.76
2015 Abe N, Dror I, Yang L, Slattery M, Zhou T, Bussemaker HJ, Rohs R, Mann RS. Deconvolving the recognition of DNA shape from sequence. Cell. 161: 307-18. PMID 25843630 DOI: 10.1016/J.Cell.2015.02.008  1
2015 Zhou T, Shen N, Yang L, Abe N, Horton J, Mann RS, Bussemaker HJ, Gordân R, Rohs R. Quantitative modeling of transcription factor binding specificities using DNA shape. Proceedings of the National Academy of Sciences of the United States of America. 112: 4654-9. PMID 25775564 DOI: 10.1080/07391102.2015.1032554  1
2015 Dantas Machado AC, Zhou T, Rao S, Goel P, Rastogi C, Lazarovici A, Bussemaker HJ, Rohs R. Evolving insights on how cytosine methylation affects protein-DNA binding. Briefings in Functional Genomics. 14: 61-73. PMID 25319759 DOI: 10.1093/Bfgp/Elu040  1
2015 Riley TR, Lazarovici A, Mann RS, Bussemaker HJ. Author response: Building accurate sequence-to-affinity models from high-throughput in vitro protein-DNA binding data using FeatureREDUCE Elife. DOI: 10.7554/Elife.06397.030  0.76
2014 Riley TR, Slattery M, Abe N, Rastogi C, Liu D, Mann RS, Bussemaker HJ. SELEX-seq: a method for characterizing the complete repertoire of binding site preferences for transcription factor complexes. Methods in Molecular Biology (Clifton, N.J.). 1196: 255-78. PMID 25151169 DOI: 10.1007/978-1-4939-1242-1_16  1
2014 Ghosh HS, Ceribelli M, Matos I, Lazarovici A, Bussemaker HJ, Lasorella A, Hiebert SW, Liu K, Staudt LM, Reizis B. ETO family protein Mtg16 regulates the balance of dendritic cell subsets by repressing Id2. The Journal of Experimental Medicine. 211: 1623-35. PMID 24980046 DOI: 10.1084/Jem.20132121  1
2014 Ward LD, Wang J, Bussemaker HJ. Characterizing a collective and dynamic component of chromatin immunoprecipitation enrichment profiles in yeast. Bmc Genomics. 15: 494. PMID 24947676 DOI: 10.1186/1471-2164-15-494  1
2014 Fazlollahi M, Lee E, Muroff I, Lu XJ, Gomez-Alcala P, Causton HC, Bussemaker HJ. Harnessing natural sequence variation to dissect posttranscriptional regulatory networks in yeast. G3 (Bethesda, Md.). 4: 1539-53. PMID 24938291 DOI: 10.1534/G3.114.012039  1
2014 Lee E, de Ridder J, Kool J, Wessels LF, Bussemaker HJ. Identifying regulatory mechanisms underlying tumorigenesis using locus expression signature analysis. Proceedings of the National Academy of Sciences of the United States of America. 111: 5747-52. PMID 24706889 DOI: 10.1073/Pnas.1309293111  1
2014 Tepper RG, Murphy CT, Bussemaker HJ. DAF-16 and PQM-1: partners in longevity. Aging. 6: 5-6. PMID 24398388  1
2013 Tepper RG, Ashraf J, Kaletsky R, Kleemann G, Murphy CT, Bussemaker HJ. PQM-1 complements DAF-16 as a key transcriptional regulator of DAF-2-mediated development and longevity. Cell. 154: 676-90. PMID 23911329 DOI: 10.1016/J.Cell.2013.07.006  1
2013 Lazarovici A, Zhou T, Shafer A, Dantas Machado AC, Riley TR, Sandstrom R, Sabo PJ, Lu Y, Rohs R, Stamatoyannopoulos JA, Bussemaker HJ. Probing DNA shape and methylation state on a genomic scale with DNase I. Proceedings of the National Academy of Sciences of the United States of America. 110: 6376-81. PMID 23576721 DOI: 10.1073/Pnas.1216822110  0.76
2013 Weirauch MT, Cote A, Norel R, Annala M, Zhao Y, Riley TR, Saez-Rodriguez J, Cokelaer T, Vedenko A, Talukder S, Bussemaker HJ, Morris QD, Bulyk ML, Stolovitzky G, et al. Evaluation of methods for modeling transcription factor sequence specificity. Nature Biotechnology. 31: 126-34. PMID 23354101 DOI: 10.1038/Nbt.2486  1
2012 Singer S, Zhao R, Barsotti AM, Ouwehand A, Fazollahi M, Coutavas E, Breuhahn K, Neumann O, Longerich T, Pusterla T, Powers MA, Giles KM, Leedman PJ, Hess J, Grunwald D, ... Bussemaker HJ, et al. Nuclear pore component Nup98 is a potential tumor suppressor and regulates posttranscriptional expression of select p53 target genes. Molecular Cell. 48: 799-810. PMID 23102701 DOI: 10.1016/J.Molcel.2012.09.020  1
2012 McIsaac RS, Petti AA, Bussemaker HJ, Botstein D. Perturbation-based analysis and modeling of combinatorial regulation in the yeast sulfur assimilation pathway. Molecular Biology of the Cell. 23: 2993-3007. PMID 22696683 DOI: 10.1091/Mbc.E12-03-0232  1
2012 Petti AA, McIsaac RS, Ho-Shing O, Bussemaker HJ, Botstein D. Combinatorial control of diverse metabolic and physiological functions by transcriptional regulators of the yeast sulfur assimilation pathway. Molecular Biology of the Cell. 23: 3008-24. PMID 22696679 DOI: 10.1091/Mbc.E12-03-0233  1
2012 Tan AY, Riley TR, Coady T, Bussemaker HJ, Manley JL. TLS/FUS (translocated in liposarcoma/fused in sarcoma) regulates target gene transcription via single-stranded DNA response elements. Proceedings of the National Academy of Sciences of the United States of America. 109: 6030-5. PMID 22460799 DOI: 10.1073/Pnas.1203028109  1
2011 Slattery M, Riley T, Liu P, Abe N, Gomez-Alcala P, Dror I, Zhou T, Rohs R, Honig B, Bussemaker HJ, Mann RS. Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins. Cell. 147: 1270-82. PMID 22153072 DOI: 10.1016/J.Cell.2011.10.053  1
2011 Shechtman CF, Henneberry AL, Seimon TA, Tinkelenberg AH, Wilcox LJ, Lee E, Fazlollahi M, Munkacsi AB, Bussemaker HJ, Tabas I, Sturley SL. Loss of subcellular lipid transport due to ARV1 deficiency disrupts organelle homeostasis and activates the unfolded protein response. The Journal of Biological Chemistry. 286: 11951-9. PMID 21266578 DOI: 10.1074/Jbc.M110.215038  1
2010 Filion GJ, van Bemmel JG, Braunschweig U, Talhout W, Kind J, Ward LD, Brugman W, de Castro IJ, Kerkhoven RM, Bussemaker HJ, van Steensel B. Systematic protein location mapping reveals five principal chromatin types in Drosophila cells. Cell. 143: 212-24. PMID 20888037 DOI: 10.1016/J.Cell.2010.09.009  1
2010 Lee E, Bussemaker HJ. Identifying the genetic determinants of transcription factor activity. Molecular Systems Biology. 6: 412. PMID 20865005 DOI: 10.1038/Msb.2010.64  1
2010 Lu XJ, Olson WK, Bussemaker HJ. The RNA backbone plays a crucial role in mediating the intrinsic stability of the GpU dinucleotide platform and the GpUpA/GpA miniduplex. Nucleic Acids Research. 38: 4868-76. PMID 20223772 DOI: 10.1093/Nar/Gkq155  1
2010 van Batenburg MF, Li H, Polman JA, Lachize S, Datson NA, Bussemaker HJ, Meijer OC. Paired hormone response elements predict caveolin-1 as a glucocorticoid target gene. Plos One. 5: e8839. PMID 20098621 DOI: 10.1371/Journal.Pone.0008839  0.52
2008 Boorsma A, Lu XJ, Zakrzewska A, Klis FM, Bussemaker HJ. Inferring condition-specific modulation of transcription factor activity in yeast through regulon-based analysis of genomewide expression. Plos One. 3: e3112. PMID 18769540 DOI: 10.1371/Journal.Pone.0003112  0.8
2008 Ward LD, Bussemaker HJ. Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences. Bioinformatics (Oxford, England). 24: i165-71. PMID 18586710 DOI: 10.1093/bioinformatics/btn154  1
2008 de Wit E, Braunschweig U, Greil F, Bussemaker HJ, van Steensel B. Global chromatin domain organization of the Drosophila genome. Plos Genetics. 4: e1000045. PMID 18369463 DOI: 10.1371/Journal.Pgen.1000045  1
2008 Foat BC, Tepper RG, Bussemaker HJ. TransfactomeDB: a resource for exploring the nucleotide sequence specificity and condition-specific regulatory activity of trans-acting factors. Nucleic Acids Research. 36: D125-31. PMID 17947326 DOI: 10.1093/Nar/Gkm828  1
2007 Bussemaker HJ, Ward LD, Boorsma A. Dissecting complex transcriptional responses using pathway-level scores based on prior information. Bmc Bioinformatics. 8: S6. PMID 17903287 DOI: 10.1186/1471-2105-8-S6-S6  1
2007 Bussemaker HJ, Foat BC, Ward LD. Predictive modeling of genome-wide mRNA expression: from modules to molecules. Annual Review of Biophysics and Biomolecular Structure. 36: 329-47. PMID 17311525 DOI: 10.1146/Annurev.Biophys.36.040306.132725  1
2007 Greil F, de Wit E, Bussemaker HJ, van Steensel B. HP1 controls genomic targeting of four novel heterochromatin proteins in Drosophila. The Embo Journal. 26: 741-51. PMID 17255947 DOI: 10.1038/Sj.Emboj.7601527  1
2006 Moorman C, Sun LV, Wang J, de Wit E, Talhout W, Ward LD, Greil F, Lu XJ, White KP, Bussemaker HJ, van Steensel B. Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster. Proceedings of the National Academy of Sciences of the United States of America. 103: 12027-32. PMID 16880385 DOI: 10.1073/Pnas.0605003103  1
2006 Foat BC, Morozov AV, Bussemaker HJ. Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE. Bioinformatics (Oxford, England). 22: e141-9. PMID 16873464 DOI: 10.1093/Bioinformatics/Btl223  1
2006 Halasz G, van Batenburg MF, Perusse J, Hua S, Lu XJ, White KP, Bussemaker HJ. Detecting transcriptionally active regions using genomic tiling arrays. Genome Biology. 7: R59. PMID 16859498 DOI: 10.1186/Gb-2006-7-7-R59  1
2005 Foat BC, Houshmandi SS, Olivas WM, Bussemaker HJ. Profiling condition-specific, genome-wide regulation of mRNA stability in yeast. Proceedings of the National Academy of Sciences of the United States of America. 102: 17675-80. PMID 16317069 DOI: 10.1073/Pnas.0503803102  1
2005 Boorsma A, Foat BC, Vis D, Klis F, Bussemaker HJ. T-profiler: scoring the activity of predefined groups of genes using gene expression data. Nucleic Acids Research. 33: W592-5. PMID 15980543 DOI: 10.1093/Nar/Gki484  1
2005 Richards S, Liu Y, Bettencourt BR, Hradecky P, Letovsky S, Nielsen R, Thornton K, Hubisz MJ, Chen R, Meisel RP, Couronne O, Hua S, Smith MA, Zhang P, Liu J, ... Bussemaker HJ, et al. Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution. Genome Research. 15: 1-18. PMID 15632085 DOI: 10.1101/Gr.3059305  1
2004 Stolc V, Gauhar Z, Mason C, Halasz G, van Batenburg MF, Rifkin SA, Hua S, Herreman T, Tongprasit W, Barbano PE, Bussemaker HJ, White KP. A gene expression map for the euchromatic genome of Drosophila melanogaster. Science (New York, N.Y.). 306: 655-60. PMID 15499012 DOI: 10.1126/Science.1101312  0.52
2004 Gao F, Foat BC, Bussemaker HJ. Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data. Bmc Bioinformatics. 5: 31. PMID 15113405 DOI: 10.1186/1471-2105-5-31  1
2003 Greil F, van der Kraan I, Delrow J, Smothers JF, de Wit E, Bussemaker HJ, van Driel R, Henikoff S, van Steensel B. Distinct HP1 and Su(var)3-9 complexes bind to sets of developmentally coexpressed genes depending on chromosomal location. Genes & Development. 17: 2825-38. PMID 14630943 DOI: 10.1101/Gad.281503  1
2003 Versteeg R, van Schaik BDC, van Batenburg MF, Roos M, Monajemi R, Caron H, Bussemaker HJ, van Kampen AHC. The human transcriptome map reveals extremes in gene dentistry, intron length, GC content, and repeat pattern for domains of highly and weakly expressed genes Genome Research. 13: 1998-2004. PMID 12915492 DOI: 10.1101/Gr.1649303  1
2003 Orian A, van Steensel B, Delrow J, Bussemaker HJ, Li L, Sawado T, Williams E, Loo LW, Cowley SM, Yost C, Pierce S, Edgar BA, Parkhurst SM, Eisenman RN. Genomic binding by the Drosophila Myc, Max, Mad/Mnt transcription factor network. Genes & Development. 17: 1101-14. PMID 12695332 DOI: 10.1101/Gad.1066903  1
2003 Jansen R, Bussemaker HJ, Gerstein M. 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. Nucleic Acids Research. 31: 2242-51. PMID 12682375 DOI: 10.1093/Nar/Gkg306  1
2003 Lascaris R, Bussemaker HJ, Boorsma A, Piper M, van der Spek H, Grivell L, Blom J. Hap4p overexpression in glucose-grown Saccharomyces cerevisiae induces cells to enter a novel metabolic state. Genome Biology. 4: R3. PMID 12537548 DOI: 10.1186/Gb-2002-4-1-R3  0.64
2002 Zhang Y, Ma C, Delohery T, Nasipak B, Foat BC, Bounoutas A, Bussemaker HJ, Kim SK, Chalfie M. Identification of genes expressed in C. elegans touch receptor neurons. Nature. 418: 331-5. PMID 12124626 DOI: 10.1038/Nature00891  1
2001 Bussemaker HJ, Li H, Siggia ED. Regulatory element detection using correlation with expression. Nature Genetics. 27: 167-71. PMID 11175784 DOI: 10.1038/84792  0.6
1995 Bussemaker HJ, Ernst MH, Dufty JW. Generalized Boltzmann equation for lattice gas automata Journal of Statistical Physics. 78: 1521-1554. DOI: 10.1007/Bf02180141  0.56
1992 Brito R, Bussemaker HJ, Ernst MH. A fluctuation formula for the nonGalilean factor in lattice gas automata Journal of Physics a: General Physics. 25. DOI: 10.1088/0305-4470/25/15/009  0.56
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