Alexander J. Hartemink - Publications

Affiliations: 
Computational Biology and Bioinformatics Duke University, Durham, NC 
Area:
Bioinformatics, Computer Science, Statistics

61 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any innacuracies, 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
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  0.72
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  0.8
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  1
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  1
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  1
2014 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, ... ... Hartemink AJ, et al. Convergent transcriptional specializations in the brains of humans and song-learning birds. Science (New York, N.Y.). 346: 1256846. PMID 25504733 DOI: 10.1126/science.1256846  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2011 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, et al. Verification of systems biology research in the age of collaborative competition. Nature Biotechnology. 29: 811-5. PMID 21904331 DOI: 10.1038/nbt.1968  1
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  1
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  1
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  1
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  1
2010 Robinson JW, Hartemink AJ. Learning non-stationary dynamic bayesian networks Journal of Machine Learning Research. 11: 3647-3680.  1
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  1
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  1
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  1
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  1
2009 Robinson JW, Hartemink AJ. Non-stationary dynamic Bayesian networks Advances in Neural Information Processing Systems 21 - Proceedings of the 2008 Conference. 1369-1376.  1
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  1
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  1
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  1
2008 Bulyk ML, Hartemink AJ, Fraenkel E, Mandel-Gutfreund Y. Protein-nucleic acid interactions: Integrating structure, sequence, and function Pacific Symposium On Biocomputing 2008, Psb 2008. 438-440.  1
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  1
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  1
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  1
2007 Bulyk ML, Hartemink AJ, Fraenkel E, Stormo G. DNA-protein interactions: Integrating structure, sequence, and function Pacific Symposium On Biocomputing 2007, Psb 2007. 470-471.  1
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.  1
2007 Bernard A, Vaughn DS, Hartemink AJ. Reconstructing the topology of protein complexes Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4453: 32-46.  1
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  1
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  1
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  1
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  1
2005 Luedi PP, Hartemink AJ, Jirtle RL. Genome-wide prediction of imprinted murine genes. Genome Research. 15: 875-84. PMID 15930497 DOI: 10.1101/gr.3303505  1
2005 Hartemink AJ. Reverse engineering gene regulatory networks. Nature Biotechnology. 23: 554-5. PMID 15877071 DOI: 10.1038/nbt0505-554  1
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  1
2005 Hartemink AJ, Segal E. Joint learning from multiple types of genomic data. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 445-6. PMID 15759649  1
2005 Yin P, Hartemink AJ. Theoretical and practical advances in genome halving. Bioinformatics (Oxford, England). 21: 869-79. PMID 15513986 DOI: 10.1093/bioinformatics/bti107  1
2005 Krishnapuram B, Williams D, Xue Y, Hartemink A, Carin L, Figueiredo MAT. On semi-supervised classification Advances in Neural Information Processing Systems 1
2004 Krishnapuram B, Hartemink AJ, Carin L, Figueiredo MA. A Bayesian approach to joint feature selection and classifier design. Ieee Transactions On Pattern Analysis and Machine Intelligence. 26: 1105-11. PMID 15742887 DOI: 10.1109/TPAMI.2004.55  1
2004 Krishnapuram B, Carin L, Hartemink AJ. Joint classifier and feature optimization for comprehensive cancer diagnosis using gene expression data. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 11: 227-42. PMID 15285890 DOI: 10.1089/1066527041410463  1
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  1
2003 Smith VA, Jarvis ED, Hartemink AJ. Influence of network topology and data collection on network inference. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 164-75. PMID 12603026  1
2003 Krishnapuram B, Carin L, Hartemink AJ. Joint classifier and feature optimization for cancer diagnosis using gene expression data Proceedings of the Annual International Conference On Computational Molecular Biology, Recomb. 167-175.  1
2003 Liu Q, Krishnapuram B, Pratapa P, Liao X, Hartemink A, Carin L. Identification of differentially expressed proteins using MALDI-TOF mass spectra Conference Record of the Asilomar Conference On Signals, Systems and Computers. 2: 1323-1327.  1
2002 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. A framework for integrating the songbird brain. Journal of Comparative Physiology. a, Neuroethology, Sensory, Neural, and Behavioral Physiology. 188: 961-80. PMID 12471494 DOI: 10.1007/s00359-002-0358-y  1
2002 Smith VA, Jarvis ED, Hartemink AJ. Evaluating functional network inference using simulations of complex biological systems. Bioinformatics (Oxford, England). 18: S216-24. PMID 12169550  1
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  1
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  1
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  1
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  1
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  1
1999 Schechter S, Parnell T, Hartemink A. Anonymous authentication of membership in dynamic groups Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 1648: 184-195.  1
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