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Items: 49

1.

Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding.

McDowell IC, Barrera A, D'Ippolito AM, Vockley CM, Hong LK, Leichter SM, Bartelt LC, Majoros WH, Song L, Safi A, Koçak DD, Gersbach CA, Hartemink AJ, Crawford GE, Engelhardt BE, Reddy TE.

Genome Res. 2018 Sep;28(9):1272-1284. doi: 10.1101/gr.233346.117. Epub 2018 Aug 10.

2.

MATCHER: manifold alignment reveals correspondence between single cell transcriptome and epigenome dynamics.

Welch JD, Hartemink AJ, Prins JF.

Genome Biol. 2017 Jul 24;18(1):138. doi: 10.1186/s13059-017-1269-0.

3.

Characterization of dependencies between growth and division in budding yeast.

Mayhew MB, Iversen ES, Hartemink AJ.

J R Soc Interface. 2017 Feb;14(127). pii: 20160993. doi: 10.1098/rsif.2016.0993.

4.

Establishment of Expression in the SHORTROOT-SCARECROW Transcriptional Cascade through Opposing Activities of Both Activators and Repressors.

Sparks EE, Drapek C, Gaudinier A, Li S, Ansariola M, Shen N, Hennacy JH, Zhang J, Turco G, Petricka JJ, Foret J, Hartemink AJ, Gordân R, Megraw M, Brady SM, Benfey PN.

Dev Cell. 2016 Dec 5;39(5):585-596. doi: 10.1016/j.devcel.2016.09.031. Epub 2016 Oct 27.

5.

SLICER: inferring branched, nonlinear cellular trajectories from single cell RNA-seq data.

Welch JD, Hartemink AJ, Prins JF.

Genome Biol. 2016 May 23;17(1):106. doi: 10.1186/s13059-016-0975-3.

6.

Mapping nucleosome positions using DNase-seq.

Zhong J, Luo K, Winter PS, Crawford GE, Iversen ES, Hartemink AJ.

Genome Res. 2016 Mar;26(3):351-64. doi: 10.1101/gr.195602.115. Epub 2016 Jan 15.

7.

Genome-wide chromatin footprinting reveals changes in replication origin architecture induced by pre-RC assembly.

Belsky JA, MacAlpine HK, Lubelsky Y, Hartemink AJ, MacAlpine DM.

Genes Dev. 2015 Jan 15;29(2):212-24. doi: 10.1101/gad.247924.114.

8.

Convergent transcriptional specializations in the brains of humans and song-learning birds.

Pfenning AR, Hara E, Whitney O, Rivas MV, Wang R, Roulhac PL, Howard JT, Wirthlin M, Lovell PV, Ganapathy G, Mouncastle J, Moseley MA, Thompson JW, Soderblom EJ, Iriki A, Kato M, Gilbert MT, Zhang G, Bakken T, Bongaarts A, Bernard A, Lein E, Mello CV, Hartemink AJ, Jarvis ED.

Science. 2014 Dec 12;346(6215):1256846. doi: 10.1126/science.1256846.

9.

Core and region-enriched networks of behaviorally regulated genes and the singing genome.

Whitney O, Pfenning AR, Howard JT, Blatti CA, Liu F, Ward JM, Wang R, Audet JN, Kellis M, Mukherjee S, Sinha S, Hartemink AJ, West AE, Jarvis ED.

Science. 2014 Dec 12;346(6215):1256780. doi: 10.1126/science.1256780.

10.

Learning protein-DNA interaction landscapes by integrating experimental data through computational models.

Zhong J, Wasson T, Hartemink AJ.

Bioinformatics. 2014 Oct 15;30(20):2868-74. doi: 10.1093/bioinformatics/btu408. Epub 2014 Jun 27.

11.

Stability selection for regression-based models of transcription factor-DNA binding specificity.

Mordelet F, Horton J, Hartemink AJ, Engelhardt BE, Gordân R.

Bioinformatics. 2013 Jul 1;29(13):i117-25. doi: 10.1093/bioinformatics/btt221.

12.
13.

Branching process deconvolution algorithm reveals a detailed cell-cycle transcription program.

Guo X, Bernard A, Orlando DA, Haase SB, Hartemink AJ.

Proc Natl Acad Sci U S A. 2013 Mar 5;110(10):E968-77. doi: 10.1073/pnas.1120991110. Epub 2013 Feb 6.

14.

Synergistic and tunable human gene activation by combinations of synthetic transcription factors.

Perez-Pinera P, Ousterout DG, Brunger JM, Farin AM, Glass KA, Guilak F, Crawford GE, Hartemink AJ, Gersbach CA.

Nat Methods. 2013 Mar;10(3):239-42. doi: 10.1038/nmeth.2361. Epub 2013 Feb 3.

15.

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.

Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P, Chen Y, DeSalvo G, Epstein C, Fisher-Aylor KI, Euskirchen G, Gerstein M, Gertz J, Hartemink AJ, Hoffman MM, Iyer VR, Jung YL, Karmakar S, Kellis M, Kharchenko PV, Li Q, Liu T, Liu XS, Ma L, Milosavljevic A, Myers RM, Park PJ, Pazin MJ, Perry MD, Raha D, Reddy TE, Rozowsky J, Shoresh N, Sidow A, Slattery M, Stamatoyannopoulos JA, Tolstorukov MY, White KP, Xi S, Farnham PJ, Lieb JD, Wold BJ, Snyder M.

Genome Res. 2012 Sep;22(9):1813-31. doi: 10.1101/gr.136184.111.

16.
17.

Verification of systems biology research in the age of collaborative competition.

Meyer P, Alexopoulos LG, Bonk T, Califano A, Cho CR, de la Fuente A, de Graaf D, Hartemink AJ, Hoeng J, Ivanov NV, Koeppl H, Linding R, Marbach D, Norel R, Peitsch MC, Rice JJ, Royyuru A, Schacherer F, Sprengel J, Stolle K, Vitkup D, Stolovitzky G.

Nat Biotechnol. 2011 Sep 8;29(9):811-5. doi: 10.1038/nbt.1968. No abstract available.

PMID:
21904331
18.

A generalized model for multi-marker analysis of cell cycle progression in synchrony experiments.

Mayhew MB, Robinson JW, Jung B, Haase SB, Hartemink AJ.

Bioinformatics. 2011 Jul 1;27(13):i295-303. doi: 10.1093/bioinformatics/btr244.

19.

Identification of Tat-SF1 cellular targets by exon array analysis reveals dual roles in transcription and splicing.

Miller HB, Robinson TJ, Gordân R, Hartemink AJ, Garcia-Blanco MA.

RNA. 2011 Apr;17(4):665-74. doi: 10.1261/rna.2462011. Epub 2011 Jan 31.

20.

Finding regulatory DNA motifs using alignment-free evolutionary conservation information.

Gordân R, Narlikar L, Hartemink AJ.

Nucleic Acids Res. 2010 Apr;38(6):e90. doi: 10.1093/nar/gkp1166. Epub 2010 Jan 4.

21.

Drosophila ORC localizes to open chromatin and marks sites of cohesin complex loading.

MacAlpine HK, Gordân R, Powell SK, Hartemink AJ, MacAlpine DM.

Genome Res. 2010 Feb;20(2):201-11. doi: 10.1101/gr.097873.109. Epub 2009 Dec 7.

22.

An ensemble model of competitive multi-factor binding of the genome.

Wasson T, Hartemink AJ.

Genome Res. 2009 Nov;19(11):2101-12. doi: 10.1101/gr.093450.109. Epub 2009 Aug 31.

23.

Distinguishing direct versus indirect transcription factor-DNA interactions.

Gordân R, Hartemink AJ, Bulyk ML.

Genome Res. 2009 Nov;19(11):2090-100. doi: 10.1101/gr.094144.109. Epub 2009 Aug 3.

24.

Domain-oriented edge-based alignment of protein interaction networks.

Guo X, Hartemink AJ.

Bioinformatics. 2009 Jun 15;25(12):i240-6. doi: 10.1093/bioinformatics/btp202.

25.

A branching process model for flow cytometry and budding index measurements in cell synchrony experiments.

Orlando DA, Iversen ES Jr, Hartemink AJ, Haase SB.

Ann Appl Stat. 2009 Winter;3(4):1521-1541.

26.

Global control of cell-cycle transcription by coupled CDK and network oscillators.

Orlando DA, Lin CY, Bernard A, Wang JY, Socolar JE, Iversen ES, Hartemink AJ, Haase SB.

Nature. 2008 Jun 12;453(7197):944-7. doi: 10.1038/nature06955. Epub 2008 May 7.

27.
28.

Computational and experimental identification of novel human imprinted genes.

Luedi PP, Dietrich FS, Weidman JR, Bosko JM, Jirtle RL, Hartemink AJ.

Genome Res. 2007 Dec;17(12):1723-30. Epub 2007 Nov 30.

29.

A nucleosome-guided map of transcription factor binding sites in yeast.

Narlikar L, Gordân R, Hartemink AJ.

PLoS Comput Biol. 2007 Nov;3(11):e215. Epub 2007 Sep 24.

30.

A probabilistic model for cell cycle distributions in synchrony experiments.

Orlando DA, Lin CY, Bernard A, Iversen ES, Hartemink AJ, Haase SB.

Cell Cycle. 2007 Feb 15;6(4):478-88. Epub 2007 Feb 12.

PMID:
17329975
31.

Computational inference of neural information flow networks.

Smith VA, Yu J, Smulders TV, Hartemink AJ, Jarvis ED.

PLoS Comput Biol. 2006 Nov 24;2(11):e161. Epub 2006 Oct 12.

32.

Finding diagnostic biomarkers in proteomic spectra.

Pratapa PN, Patz EF Jr, Hartemink AJ.

Pac Symp Biocomput. 2006:279-90.

33.

Informative priors based on transcription factor structural class improve de novo motif discovery.

Narlikar L, Gordân R, Ohler U, Hartemink AJ.

Bioinformatics. 2006 Jul 15;22(14):e384-92.

PMID:
16873497
34.

Sequence features of DNA binding sites reveal structural class of associated transcription factor.

Narlikar L, Hartemink AJ.

Bioinformatics. 2006 Jan 15;22(2):157-63. Epub 2005 Nov 2.

PMID:
16267080
35.

Sparse multinomial logistic regression: fast algorithms and generalization bounds.

Krishnapuram B, Carin L, Figueiredo MA, Hartemink AJ.

IEEE Trans Pattern Anal Mach Intell. 2005 Jun;27(6):957-68.

PMID:
15943426
36.

Genome-wide prediction of imprinted murine genes.

Luedi PP, Hartemink AJ, Jirtle RL.

Genome Res. 2005 Jun;15(6):875-84.

37.

Reverse engineering gene regulatory networks.

Hartemink AJ.

Nat Biotechnol. 2005 May;23(5):554-5. No abstract available.

PMID:
15877071
38.
39.

Joint learning from multiple types of genomic data.

Hartemink AJ, Segal E.

Pac Symp Biocomput. 2005:445-6. No abstract available.

PMID:
15759649
40.

A Bayesian approach to joint feature selection and classifier design.

Krishnapuram B, Hartemink AJ, Carin L, Figueiredo MA.

IEEE Trans Pattern Anal Mach Intell. 2004 Sep;26(9):1105-11.

PMID:
15742887
41.

Theoretical and practical advances in genome halving.

Yin P, Hartemink AJ.

Bioinformatics. 2005 Apr 1;21(7):869-79. Epub 2004 Oct 28.

PMID:
15513986
42.

Joint classifier and feature optimization for comprehensive cancer diagnosis using gene expression data.

Krishnapuram B, Carin L, Hartemink AJ.

J Comput Biol. 2004;11(2-3):227-42.

PMID:
15285890
43.

Advances to Bayesian network inference for generating causal networks from observational biological data.

Yu J, Smith VA, Wang PP, Hartemink AJ, Jarvis ED.

Bioinformatics. 2004 Dec 12;20(18):3594-603. Epub 2004 Jul 29.

PMID:
15284094
44.

Influence of network topology and data collection on network inference.

Smith VA, Jarvis ED, Hartemink AJ.

Pac Symp Biocomput. 2003:164-75.

45.

A framework for integrating the songbird brain.

Jarvis ED, Smith VA, Wada K, Rivas MV, McElroy M, Smulders TV, Carninci P, Hayashizaki Y, Dietrich F, Wu X, McConnell P, Yu J, Wang PP, Hartemink AJ, Lin S.

J Comp Physiol A Neuroethol Sens Neural Behav Physiol. 2002 Dec;188(11-12):961-80. Epub 2002 Nov 15. Review.

46.

Evaluating functional network inference using simulations of complex biological systems.

Smith VA, Jarvis ED, Hartemink AJ.

Bioinformatics. 2002;18 Suppl 1:S216-24.

PMID:
12169550
47.

Combining location and expression data for principled discovery of genetic regulatory network models.

Hartemink AJ, Gifford DK, Jaakkola TS, Young RA.

Pac Symp Biocomput. 2002:437-49.

48.

Using graphical models and genomic expression data to statistically validate models of genetic regulatory networks.

Hartemink AJ, Gifford DK, Jaakkola TS, Young RA.

Pac Symp Biocomput. 2001:422-33.

49.

Automated constraint-based nucleotide sequence selection for DNA computation.

Hartemink AJ, Gifford DK, Khodor J.

Biosystems. 1999 Oct;52(1-3):227-35.

PMID:
10636048

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