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Towards a mechanistic understanding of DNA methylation readout by transcription factors.

Kribelbauer JF, Lu XJ, Rohs R, Mann RS, Bussemaker HJ.

J Mol Biol. 2019 Nov 2. pii: S0022-2836(19)30617-5. doi: 10.1016/j.jmb.2019.10.021. [Epub ahead of print] Review.


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

Sánchez-Higueras C, Rastogi C, Voutev R, Bussemaker HJ, Mann RS, Hombría JC.

Nat Commun. 2019 Aug 9;10(1):3597. doi: 10.1038/s41467-019-11416-1.


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

Kribelbauer JF, Rastogi C, Bussemaker HJ, Mann RS.

Annu Rev Cell Dev Biol. 2019 Oct 6;35:357-379. doi: 10.1146/annurev-cellbio-100617-062719. Epub 2019 Jul 5.


High-throughput identification of human SNPs affecting regulatory element activity.

van Arensbergen J, Pagie L, FitzPatrick VD, de Haas M, Baltissen MP, Comoglio F, van der Weide RH, Teunissen H, Võsa U, Franke L, de Wit E, Vermeulen M, Bussemaker HJ, van Steensel B.

Nat Genet. 2019 Jul;51(7):1160-1169. doi: 10.1038/s41588-019-0455-2. Epub 2019 Jun 28.


Accurate and sensitive quantification of protein-DNA binding affinity.

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.

Proc Natl Acad Sci U S A. 2018 Apr 17;115(16):E3692-E3701. doi: 10.1073/pnas.1714376115. Epub 2018 Apr 2.


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

Rube HT, Rastogi C, Kribelbauer JF, Bussemaker HJ.

Mol Syst Biol. 2018 Feb 22;14(2):e7902. doi: 10.15252/msb.20177902.


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

Rao S, Chiu TP, Kribelbauer JF, Mann RS, Bussemaker HJ, Rohs R.

Epigenetics Chromatin. 2018 Feb 6;11(1):6. doi: 10.1186/s13072-018-0174-4.


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

Zhang L, Martini GD, Rube HT, Kribelbauer JF, Rastogi C, FitzPatrick VD, Houtman JC, Bussemaker HJ, Pufall MA.

Genome Res. 2018 Jan;28(1):111-121. doi: 10.1101/gr.222844.117. Epub 2017 Dec 1.


Network-based approaches that exploit inferred transcription factor activity to analyze the impact of genetic variation on gene expression.

Bussemaker HJ, Causton HC, Fazlollahi M, Lee E, Muroff I.

Curr Opin Syst Biol. 2017 Apr;2:98-102. doi: 10.1016/j.coisb.2017.04.002. Epub 2017 Apr 17.


Quantitative Analysis of the DNA Methylation Sensitivity of Transcription Factor Complexes.

Kribelbauer JF, Laptenko O, Chen S, Martini GD, Freed-Pastor WA, Prives C, Mann RS, Bussemaker HJ.

Cell Rep. 2017 Jun 13;19(11):2383-2395. doi: 10.1016/j.celrep.2017.05.069.


Genome-wide mapping of autonomous promoter activity in human cells.

van Arensbergen J, FitzPatrick VD, de Haas M, Pagie L, Sluimer J, Bussemaker HJ, van Steensel B.

Nat Biotechnol. 2017 Feb;35(2):145-153. doi: 10.1038/nbt.3754. Epub 2016 Dec 26.


Identifying genetic modulators of the connectivity between transcription factors and their transcriptional targets.

Fazlollahi M, Muroff I, Lee E, Causton HC, Bussemaker HJ.

Proc Natl Acad Sci U S A. 2016 Mar 29;113(13):E1835-43. doi: 10.1073/pnas.1517140113. Epub 2016 Mar 10.


Building accurate sequence-to-affinity models from high-throughput in vitro protein-DNA binding data using FeatureREDUCE.

Riley TR, Lazarovici A, Mann RS, Bussemaker HJ.

Elife. 2015 Dec 23;4. pii: e06397. doi: 10.7554/eLife.06397.


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

Lu XJ, Bussemaker HJ, Olson WK.

Nucleic Acids Res. 2015 Dec 2;43(21):e142. doi: 10.1093/nar/gkv716. Epub 2015 Jul 15.


Deconvolving the recognition of DNA shape from sequence.

Abe N, Dror I, Yang L, Slattery M, Zhou T, Bussemaker HJ, Rohs R, Mann RS.

Cell. 2015 Apr 9;161(2):307-18. doi: 10.1016/j.cell.2015.02.008. Epub 2015 Apr 2.


Quantitative modeling of transcription factor binding specificities using DNA shape.

Zhou T, Shen N, Yang L, Abe N, Horton J, Mann RS, Bussemaker HJ, Gordân R, Rohs R.

Proc Natl Acad Sci U S A. 2015 Apr 14;112(15):4654-9. doi: 10.1073/pnas.1422023112. Epub 2015 Mar 9.


Recent progress in understanding transcription factor binding specificity.

Bussemaker HJ.

Brief Funct Genomics. 2015 Jan;14(1):1-2. doi: 10.1093/bfgp/elu050. No abstract available.


Evolving insights on how cytosine methylation affects protein-DNA binding.

Dantas Machado AC, Zhou T, Rao S, Goel P, Rastogi C, Lazarovici A, Bussemaker HJ, Rohs R.

Brief Funct Genomics. 2015 Jan;14(1):61-73. doi: 10.1093/bfgp/elu040. Epub 2014 Oct 14. Review.


In search of the determinants of enhancer-promoter interaction specificity.

van Arensbergen J, van Steensel B, Bussemaker HJ.

Trends Cell Biol. 2014 Nov;24(11):695-702. doi: 10.1016/j.tcb.2014.07.004. Epub 2014 Aug 24. Review.


SELEX-seq: a method for characterizing the complete repertoire of binding site preferences for transcription factor complexes.

Riley TR, Slattery M, Abe N, Rastogi C, Liu D, Mann RS, Bussemaker HJ.

Methods Mol Biol. 2014;1196:255-78. doi: 10.1007/978-1-4939-1242-1_16.


ETO family protein Mtg16 regulates the balance of dendritic cell subsets by repressing Id2.

Ghosh HS, Ceribelli M, Matos I, Lazarovici A, Bussemaker HJ, Lasorella A, Hiebert SW, Liu K, Staudt LM, Reizis B.

J Exp Med. 2014 Jul 28;211(8):1623-35. doi: 10.1084/jem.20132121. Epub 2014 Jun 30.


Characterizing a collective and dynamic component of chromatin immunoprecipitation enrichment profiles in yeast.

Ward LD, Wang J, Bussemaker HJ.

BMC Genomics. 2014 Jun 19;15:494. doi: 10.1186/1471-2164-15-494.


Harnessing natural sequence variation to dissect posttranscriptional regulatory networks in yeast.

Fazlollahi M, Lee E, Muroff I, Lu XJ, Gomez-Alcala P, Causton HC, Bussemaker HJ.

G3 (Bethesda). 2014 Jun 17;4(8):1539-53. doi: 10.1534/g3.114.012039. Erratum in: G3 (Bethesda). 2014 Nov;4(11):2295.


Identifying regulatory mechanisms underlying tumorigenesis using locus expression signature analysis.

Lee E, de Ridder J, Kool J, Wessels LF, Bussemaker HJ.

Proc Natl Acad Sci U S A. 2014 Apr 15;111(15):5747-52. doi: 10.1073/pnas.1309293111. Epub 2014 Apr 2.


DAF-16 and PQM-1: partners in longevity.

Tepper RG, Murphy CT, Bussemaker HJ.

Aging (Albany NY). 2014 Jan;6(1):5-6. No abstract available.


PQM-1 complements DAF-16 as a key transcriptional regulator of DAF-2-mediated development and longevity.

Tepper RG, Ashraf J, Kaletsky R, Kleemann G, Murphy CT, Bussemaker HJ.

Cell. 2013 Aug 1;154(3):676-690. doi: 10.1016/j.cell.2013.07.006.


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

Lazarovici A, Zhou T, Shafer A, Dantas Machado AC, Riley TR, Sandstrom R, Sabo PJ, Lu Y, Rohs R, Stamatoyannopoulos JA, Bussemaker HJ.

Proc Natl Acad Sci U S A. 2013 Apr 16;110(16):6376-81. doi: 10.1073/pnas.1216822110. Epub 2013 Apr 1.


Evaluation of methods for modeling transcription factor sequence specificity.

Weirauch MT, Cote A, Norel R, Annala M, Zhao Y, Riley TR, Saez-Rodriguez J, Cokelaer T, Vedenko A, Talukder S; DREAM5 Consortium, Bussemaker HJ, Morris QD, Bulyk ML, Stolovitzky G, Hughes TR.

Nat Biotechnol. 2013 Feb;31(2):126-34. doi: 10.1038/nbt.2486. Epub 2013 Jan 27.


Nuclear pore component Nup98 is a potential tumor suppressor and regulates posttranscriptional expression of select p53 target genes.

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, Singer RH, Schirmacher P, Prives C.

Mol Cell. 2012 Dec 14;48(5):799-810. doi: 10.1016/j.molcel.2012.09.020. Epub 2012 Oct 24.


Perturbation-based analysis and modeling of combinatorial regulation in the yeast sulfur assimilation pathway.

McIsaac RS, Petti AA, Bussemaker HJ, Botstein D.

Mol Biol Cell. 2012 Aug;23(15):2993-3007. doi: 10.1091/mbc.E12-03-0232. Epub 2012 Jun 13.


Combinatorial control of diverse metabolic and physiological functions by transcriptional regulators of the yeast sulfur assimilation pathway.

Petti AA, McIsaac RS, Ho-Shing O, Bussemaker HJ, Botstein D.

Mol Biol Cell. 2012 Aug;23(15):3008-24. doi: 10.1091/mbc.E12-03-0233. Epub 2012 Jun 13. Erratum in: Mol Biol Cell. 2014 Apr;25(8):1409.


TLS/FUS (translocated in liposarcoma/fused in sarcoma) regulates target gene transcription via single-stranded DNA response elements.

Tan AY, Riley TR, Coady T, Bussemaker HJ, Manley JL.

Proc Natl Acad Sci U S A. 2012 Apr 17;109(16):6030-5. doi: 10.1073/pnas.1203028109. Epub 2012 Mar 29.


Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins.

Slattery M, Riley T, Liu P, Abe N, Gomez-Alcala P, Dror I, Zhou T, Rohs R, Honig B, Bussemaker HJ, Mann RS.

Cell. 2011 Dec 9;147(6):1270-82. doi: 10.1016/j.cell.2011.10.053.


Loss of subcellular lipid transport due to ARV1 deficiency disrupts organelle homeostasis and activates the unfolded protein response.

Shechtman CF, Henneberry AL, Seimon TA, Tinkelenberg AH, Wilcox LJ, Lee E, Fazlollahi M, Munkacsi AB, Bussemaker HJ, Tabas I, Sturley SL.

J Biol Chem. 2011 Apr 8;286(14):11951-9. doi: 10.1074/jbc.M110.215038. Epub 2011 Jan 25.


Systematic protein location mapping reveals five principal chromatin types in Drosophila cells.

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.

Cell. 2010 Oct 15;143(2):212-24. doi: 10.1016/j.cell.2010.09.009. Epub 2010 Sep 30. Erratum in: Cell. 2011 Apr 1;145(1):160.


Identifying the genetic determinants of transcription factor activity.

Lee E, Bussemaker HJ.

Mol Syst Biol. 2010 Sep 21;6:412. doi: 10.1038/msb.2010.64.


The RNA backbone plays a crucial role in mediating the intrinsic stability of the GpU dinucleotide platform and the GpUpA/GpA miniduplex.

Lu XJ, Olson WK, Bussemaker HJ.

Nucleic Acids Res. 2010 Aug;38(14):4868-76. doi: 10.1093/nar/gkq155. Epub 2010 Mar 11.


Paired hormone response elements predict caveolin-1 as a glucocorticoid target gene.

van Batenburg MF, Li H, Polman JA, Lachize S, Datson NA, Bussemaker HJ, Meijer OC.

PLoS One. 2010 Jan 21;5(1):e8839. doi: 10.1371/journal.pone.0008839.


Inferring condition-specific modulation of transcription factor activity in yeast through regulon-based analysis of genomewide expression.

Boorsma A, Lu XJ, Zakrzewska A, Klis FM, Bussemaker HJ.

PLoS One. 2008 Sep 3;3(9):e3112. doi: 10.1371/journal.pone.0003112.


Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences.

Ward LD, Bussemaker HJ.

Bioinformatics. 2008 Jul 1;24(13):i165-71. doi: 10.1093/bioinformatics/btn154.


Global chromatin domain organization of the Drosophila genome.

de Wit E, Braunschweig U, Greil F, Bussemaker HJ, van Steensel B.

PLoS Genet. 2008 Mar 28;4(3):e1000045. doi: 10.1371/journal.pgen.1000045.


TransfactomeDB: a resource for exploring the nucleotide sequence specificity and condition-specific regulatory activity of trans-acting factors.

Foat BC, Tepper RG, Bussemaker HJ.

Nucleic Acids Res. 2008 Jan;36(Database issue):D125-31. Epub 2007 Oct 18.


Dissecting complex transcriptional responses using pathway-level scores based on prior information.

Bussemaker HJ, Ward LD, Boorsma A.

BMC Bioinformatics. 2007 Sep 27;8 Suppl 6:S6. Review.


Predictive modeling of genome-wide mRNA expression: from modules to molecules.

Bussemaker HJ, Foat BC, Ward LD.

Annu Rev Biophys Biomol Struct. 2007;36:329-47. Review.


HP1 controls genomic targeting of four novel heterochromatin proteins in Drosophila.

Greil F, de Wit E, Bussemaker HJ, van Steensel B.

EMBO J. 2007 Feb 7;26(3):741-51. Epub 2007 Jan 25.


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

Moorman C, Sun LV, Wang J, de Wit E, Talhout W, Ward LD, Greil F, Lu XJ, White KP, Bussemaker HJ, van Steensel B.

Proc Natl Acad Sci U S A. 2006 Aug 8;103(32):12027-32. Epub 2006 Jul 31.


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

Foat BC, Morozov AV, Bussemaker HJ.

Bioinformatics. 2006 Jul 15;22(14):e141-9.


Detecting transcriptionally active regions using genomic tiling arrays.

Halasz G, van Batenburg MF, Perusse J, Hua S, Lu XJ, White KP, Bussemaker HJ.

Genome Biol. 2006;7(7):R59.


Modeling gene expression control using Omes Law.

Bussemaker HJ.

Mol Syst Biol. 2006;2:2006.0013. Epub 2006 Apr 18. No abstract available.


Profiling condition-specific, genome-wide regulation of mRNA stability in yeast.

Foat BC, Houshmandi SS, Olivas WM, Bussemaker HJ.

Proc Natl Acad Sci U S A. 2005 Dec 6;102(49):17675-80. Epub 2005 Nov 29.

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