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Alexander J. Hartemink - Publications

Affiliations: 
Computational Biology and Bioinformatics Duke University, Durham, NC 
Area:
Bioinformatics, Computer Science, Statistics
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51 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
2022 Luo K, Zhong J, Safi A, Hong LK, Tewari AK, Song L, Reddy TE, Ma L, Crawford GE, Hartemink AJ. Profiling the quantitative occupancy of myriad transcription factors across conditions by modeling chromatin accessibility data. Genome Research. PMID 35609992 DOI: 10.1101/gr.272203.120  0.323
2021 Mitra S, Zhong J, Tran TQ, MacAlpine DM, Hartemink AJ. RoboCOP: jointly computing chromatin occupancy profiles for numerous factors from chromatin accessibility data. Nucleic Acids Research. PMID 34255854 DOI: 10.1093/nar/gkab553  0.38
2021 Tran TQ, MacAlpine HK, Tripuraneni V, Mitra S, MacAlpine DM, Hartemink AJ. Linking the dynamics of chromatin occupancy and transcription with predictive models. Genome Research. PMID 33893157 DOI: 10.1101/gr.267237.120  0.325
2020 Mitra S, Zhong J, MacAlpine DM, Hartemink AJ. RoboCOP: Multivariate State Space Model Integrating Epigenomic Accessibility Data to Elucidate Genome-Wide Chromatin Occupancy. Research in Computational Molecular Biology : ... Annual International Conference, Recomb ... : Proceedings. Recomb (Conference : 2005-). 12074: 136-151. PMID 34386808 DOI: 10.1007/978-3-030-45257-5_9  0.382
2018 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, et al. Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding. Genome Research. PMID 30097539 DOI: 10.1101/Gr.233346.117  0.409
2017 Welch JD, Hartemink AJ, Prins JF. MATCHER: manifold alignment reveals correspondence between single cell transcriptome and epigenome dynamics. Genome Biology. 18: 138. PMID 28738873 DOI: 10.1186/S13059-017-1269-0  0.374
2017 Mayhew MB, Iversen ES, Hartemink AJ. Characterization of dependencies between growth and division in budding yeast. Journal of the Royal Society, Interface. 14. PMID 28228543 DOI: 10.1098/Rsif.2016.0993  0.757
2016 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, et al. Establishment of Expression in the SHORTROOT-SCARECROW Transcriptional Cascade through Opposing Activities of Both Activators and Repressors. Developmental Cell. 39: 585-596. PMID 27923776 DOI: 10.1016/J.Devcel.2016.09.031  0.691
2016 Welch JD, Hartemink AJ, Prins JF. SLICER: inferring branched, nonlinear cellular trajectories from single cell RNA-seq data. Genome Biology. 17: 106. PMID 27215581 DOI: 10.1186/S13059-016-0975-3  0.36
2016 Zhong J, Luo K, Winter PS, Crawford GE, Iversen ES, Hartemink AJ. Mapping nucleosome positions using DNase-seq. Genome Research. PMID 26772197 DOI: 10.1101/Gr.195602.115  0.403
2015 Belsky JA, MacAlpine HK, Lubelsky Y, Hartemink AJ, MacAlpine DM. Genome-wide chromatin footprinting reveals changes in replication origin architecture induced by pre-RC assembly. Genes & Development. 29: 212-24. PMID 25593310 DOI: 10.1101/Gad.247924.114  0.372
2014 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. Core and region-enriched networks of behaviorally regulated genes and the singing genome. Science (New York, N.Y.). 346: 1256780. PMID 25504732 DOI: 10.1126/Science.1256780  0.397
2014 Zhong J, Wasson T, Hartemink AJ. Learning protein-DNA interaction landscapes by integrating experimental data through computational models. Bioinformatics (Oxford, England). 30: 2868-74. PMID 24974204 DOI: 10.1093/Bioinformatics/Btu408  0.767
2013 Mordelet F, Horton J, Hartemink AJ, Engelhardt BE, Gordân R. Stability selection for regression-based models of transcription factor-DNA binding specificity. Bioinformatics (Oxford, England). 29: i117-25. PMID 23812975 DOI: 10.1093/Bioinformatics/Btt221  0.728
2013 Luo K, Hartemink AJ. Using DNase digestion data to accurately identify transcription factor binding sites. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 80-91. PMID 23424114  0.315
2013 Guo X, Bernard A, Orlando DA, Haase SB, Hartemink AJ. Branching process deconvolution algorithm reveals a detailed cell-cycle transcription program. Proceedings of the National Academy of Sciences of the United States of America. 110: E968-77. PMID 23388635 DOI: 10.1073/Pnas.1120991110  0.762
2013 Perez-Pinera P, Ousterout DG, Brunger JM, Farin AM, Glass KA, Guilak F, Crawford GE, Hartemink AJ, Gersbach CA. Synergistic and tunable human gene activation by combinations of synthetic transcription factors. Nature Methods. 10: 239-42. PMID 23377379 DOI: 10.1038/Nmeth.2361  0.349
2013 Mayhew MB, Hartemink AJ. Cell-cycle phenotyping with conditional random fields: A case study in Saccharomyces cerevisiae Proceedings - International Symposium On Biomedical Imaging. 1062-1065. DOI: 10.1109/ISBI.2013.6556661  0.753
2012 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, ... ... Hartemink AJ, et al. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Research. 22: 1813-31. PMID 22955991 DOI: 10.1101/Gr.136184.111  0.365
2012 Guo X, Bulyk ML, Hartemink AJ. Intrinsic disorder within and flanking the DNA-binding domains of human transcription factors. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 104-15. PMID 22174267  0.406
2012 Mayhew MB, Guo X, Haase SB, Hartemink AJ. Close encounters of the collaborative kind Computer. 45: 24-30. DOI: 10.1109/Mc.2012.85  0.738
2012 Mayhew M, Guo X, Haase S, Hartemink A. Systems Biology Feedback (of the Collaborative Kind) Ieee Computer. 1-1. DOI: 10.1109/Mc.2012.118  0.759
2011 Mayhew MB, Robinson JW, Jung B, Haase SB, Hartemink AJ. A generalized model for multi-marker analysis of cell cycle progression in synchrony experiments. Bioinformatics (Oxford, England). 27: i295-303. PMID 21685084 DOI: 10.1093/bioinformatics/btr244  0.774
2011 Miller HB, Robinson TJ, Gordân R, Hartemink AJ, Garcia-Blanco MA. Identification of Tat-SF1 cellular targets by exon array analysis reveals dual roles in transcription and splicing. Rna (New York, N.Y.). 17: 665-74. PMID 21282347 DOI: 10.1261/Rna.2462011  0.696
2010 Gordân R, Narlikar L, Hartemink AJ. Finding regulatory DNA motifs using alignment-free evolutionary conservation information. Nucleic Acids Research. 38: e90. PMID 20047961 DOI: 10.1093/Nar/Gkp1166  0.793
2010 MacAlpine HK, Gordân R, Powell SK, Hartemink AJ, MacAlpine DM. Drosophila ORC localizes to open chromatin and marks sites of cohesin complex loading. Genome Research. 20: 201-11. PMID 19996087 DOI: 10.1101/Gr.097873.109  0.719
2010 Robinson JW, Hartemink AJ. Learning non-stationary dynamic bayesian networks Journal of Machine Learning Research. 11: 3647-3680.  0.491
2009 Orlando DA, Iversen ES, Hartemink AJ, Haase SB. A branching process model for flow cytometry and budding index measurements in cell synchrony experiments. The Annals of Applied Statistics. 3: 1521-1541. PMID 21853014 DOI: 10.1214/09-Aoas264  0.695
2009 Wasson T, Hartemink AJ. An ensemble model of competitive multi-factor binding of the genome. Genome Research. 19: 2101-12. PMID 19720867 DOI: 10.1101/Gr.093450.109  0.768
2009 Gordân R, Hartemink AJ, Bulyk ML. Distinguishing direct versus indirect transcription factor-DNA interactions. Genome Research. 19: 2090-100. PMID 19652015 DOI: 10.1101/Gr.094144.109  0.728
2009 Guo X, Hartemink AJ. Domain-oriented edge-based alignment of protein interaction networks. Bioinformatics (Oxford, England). 25: i240-6. PMID 19477994 DOI: 10.1093/Bioinformatics/Btp202  0.413
2009 Robinson JW, Hartemink AJ. Non-stationary dynamic Bayesian networks Advances in Neural Information Processing Systems 21 - Proceedings of the 2008 Conference. 1369-1376.  0.479
2008 Orlando DA, Lin CY, Bernard A, Wang JY, Socolar JE, Iversen ES, Hartemink AJ, Haase SB. Global control of cell-cycle transcription by coupled CDK and network oscillators. Nature. 453: 944-7. PMID 18463633 DOI: 10.1038/Nature06955  0.764
2008 Gordân R, Hartemink AJ. Using DNA duplex stability information for transcription factor binding site discovery. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 453-64. PMID 18229707  0.71
2008 Gordân R, Narlikar L, Hartemink AJ. A fast, alignment-free, conservation-based method for transcription factor binding site discovery Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4955: 98-111. DOI: 10.1007/978-3-540-78839-3_9  0.755
2007 Luedi PP, Dietrich FS, Weidman JR, Bosko JM, Jirtle RL, Hartemink AJ. Computational and experimental identification of novel human imprinted genes. Genome Research. 17: 1723-30. PMID 18055845 DOI: 10.1101/Gr.6584707  0.319
2007 Narlikar L, Gordân R, Hartemink AJ. A nucleosome-guided map of transcription factor binding sites in yeast. Plos Computational Biology. 3: e215. PMID 17997593 DOI: 10.1371/Journal.Pcbi.0030215  0.809
2007 Orlando DA, Lin CY, Bernard A, Iversen ES, Hartemink AJ, Haase SB. A probabilistic model for cell cycle distributions in synchrony experiments. Cell Cycle (Georgetown, Tex.). 6: 478-88. PMID 17329975 DOI: 10.4161/Cc.6.4.3859  0.748
2007 Narlikar L, Gordân R, Hartemink AJ. Nucleosome occupancy information improves de novo motif discovery Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4453: 107-121.  0.77
2006 Smith VA, Yu J, Smulders TV, Hartemink AJ, Jarvis ED. Computational inference of neural information flow networks. Plos Computational Biology. 2: e161. PMID 17121460 DOI: 10.1371/Journal.Pcbi.0020161  0.315
2006 Narlikar L, Gordân R, Ohler U, Hartemink AJ. Informative priors based on transcription factor structural class improve de novo motif discovery. Bioinformatics (Oxford, England). 22: e384-92. PMID 16873497 DOI: 10.1093/Bioinformatics/Btl251  0.8
2006 Narlikar L, Hartemink AJ. Sequence features of DNA binding sites reveal structural class of associated transcription factor. Bioinformatics (Oxford, England). 22: 157-63. PMID 16267080 DOI: 10.1093/Bioinformatics/Bti731  0.768
2005 Krishnapuram B, Carin L, Figueiredo MA, Hartemink AJ. Sparse multinomial logistic regression: fast algorithms and generalization bounds. Ieee Transactions On Pattern Analysis and Machine Intelligence. 27: 957-68. PMID 15943426 DOI: 10.1109/Tpami.2005.127  0.301
2005 Hartemink AJ. Reverse engineering gene regulatory networks. Nature Biotechnology. 23: 554-5. PMID 15877071 DOI: 10.1038/Nbt0505-554  0.311
2005 Bernard A, Hartemink AJ. Informative structure priors: joint learning of dynamic regulatory networks from multiple types of data. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 459-70. PMID 15759651  0.772
2004 Yu J, Smith VA, Wang PP, Hartemink AJ, Jarvis ED. Advances to Bayesian network inference for generating causal networks from observational biological data. Bioinformatics (Oxford, England). 20: 3594-603. PMID 15284094 DOI: 10.1093/Bioinformatics/Bth448  0.325
2002 Hartemink AJ, Gifford DK, Jaakkola TS, Young RA. Combining location and expression data for principled discovery of genetic regulatory network models. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 437-49. PMID 11928497  0.56
2002 Hartemink AJ, Gifford DK, Jaakkola TS, Young RA. Bayesian methods for elucidating genetic regulatory networks Ieee Intelligent Systems and Their Applications. 17: 37-43. DOI: 10.1109/5254.999218  0.545
2001 Hartemink AJ, Gifford DK, Jaakkola TS, Young RA. Using graphical models and genomic expression data to statistically validate models of genetic regulatory networks. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 422-33. PMID 11262961  0.563
2001 Hartemink AJ, Gifford DK, Jaakkola TS, Young RA. Maximum likelihood estimation of optimal scaling factors for expression array normalization Proceedings of Spie - the International Society For Optical Engineering. 4266: 132-140. DOI: 10.1117/12.427981  0.467
1999 Hartemink AJ, Gifford DK, Khodor J. Automated constraint-based nucleotide sequence selection for DNA computation. Bio Systems. 52: 227-35. PMID 10636048 DOI: 10.1016/S0303-2647(99)00050-7  0.559
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