Publications of Alexander J. Hartemink    :chronological  alphabetical  combined  bibtex listing:

Journal articles or Book chapters PUBLISHED

1. Mitra, S; Malik, R; Wong, W; Rahman, A; Hartemink, AJ; Pritykin, Y; Dey, KK; Leslie, CS, Single-cell multi-ome regression models identify functional and disease-associated enhancers and enable chromatin potential analysis., Nature genetics (March, 2024) [doi]  [abs]
2. Chen, B; MacAlpine, HK; Hartemink, AJ; MacAlpine, DM, Spatiotemporal kinetics of CAF-1-dependent chromatin maturation ensures transcription fidelity during S-phase., Genome Res, vol. 33 no. 12 (December, 2023), pp. 2108-2118, Cold Spring Harbor Laboratory [doi]  [abs]
3. 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 Res, vol. 32 no. 6 (June, 2022), pp. 1183-1198 [doi]  [abs]
4. Li, Y; Hartemink, AJ; MacAlpine, DM, Cell-Cycle-Dependent Chromatin Dynamics at Replication Origins., Genes (Basel), vol. 12 no. 12 (December, 2021) [doi]  [abs]
5. Li, Y; Hartemink, AJ; MacAlpine, DM, Cell cycle-dependent chromatin dynamics at replication origins (November, 2021) [doi]  [abs]
6. 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 Res, vol. 49 no. 14 (August, 2021), pp. 7925-7938 [doi]  [abs]
7. Tran, TQ; MacAlpine, HK; Tripuraneni, V; Mitra, S; MacAlpine, DM; Hartemink, AJ, Linking the dynamics of chromatin occupancy and transcription with predictive models., Genome Res, vol. 31 no. 6 (June, 2021), pp. 1035-1046 [doi]  [abs]
8. Tripuraneni, V; Memisoglu, G; MacAlpine, HK; Tran, TQ; Zhu, W; Hartemink, AJ; Haber, JE; MacAlpine, DM, Local nucleosome dynamics and eviction following a double-strand break are reversible by NHEJ-mediated repair in the absence of DNA replication., Genome Res, vol. 31 no. 5 (May, 2021), pp. 775-788 [doi]  [abs]
9. Tran, TQ; MacAlpine, HK; Tripuraneni, V; Mitra, S; MacAlpine, DM; Hartemink, AJ, Linking the dynamics of chromatin occupancy and transcription with predictive models (June, 2020) [doi]  [abs]
10. Luo, K; Zhong, J; Safi, A; Hong, LK; Tewari, AK; Song, L; Reddy, TE; Ma, L; Crawford, GE; Hartemink, AJ, Quantitative occupancy of myriad transcription factors from one DNase experiment enables efficient comparisons across conditions (June, 2020) [doi]  [abs]
11. Mitra, S; Zhong, J; MacAlpine, DM; Hartemink, AJ, RoboCOP: Jointly computing chromatin occupancy profiles for numerous factors from chromatin accessibility data (June, 2020) [doi]  [abs]
12. Mitra, S; Zhong, J; MacAlpine, DM; Hartemink, AJ, RoboCOP: Multivariate State Space Model Integrating Epigenomic Accessibility Data to Elucidate Genome-Wide Chromatin Occupancy., edited by Schwartz, R, Res Comput Mol Biol, vol. 12074 (May, 2020), pp. 136-151, SPRINGER, ISBN 978-3-030-45256-8 [doi]  [abs]
13. Tripuraneni, V; Memisoglu, G; Zhu, W; Tran, T; Hartemink, AJ; Haber, JE; MacAlpine, DM, Local nucleosome dynamics and eviction following a double-strand break are reversible by NHEJ-mediated repair in the absence of DNA replication (December, 2019) [doi]  [abs]
14. 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, Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding., Genome Res, vol. 28 no. 9 (September, 2018), pp. 1272-1284 [doi]  [abs]
15. Welch, JD; Hartemink, AJ; Prins, JF, MATCHER: manifold alignment reveals correspondence between single cell transcriptome and epigenome dynamics., Genome Biol, vol. 18 no. 1 (July, 2017), pp. 138 [doi]  [abs]
16. Welch, JD; Hartemink, AJ; Prins, JF, Manifold alignment reveals correspondence between single cell transcriptome and epigenome dynamics (April, 2017) [doi]  [abs]
17. Mayhew, MB; Iversen, ES; Hartemink, AJ, Characterization of dependencies between growth and division in budding yeast., J R Soc Interface, vol. 14 no. 127 (February, 2017), pp. 20160993 [doi]  [abs]
18. Welch, JD; Hartemink, A; Prins, JF, E pluribus unum: United states of single cells, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 10229 LNCS (January, 2017), pp. 400-401, ISBN 9783319569697
19. 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, Establishment of Expression in the SHORTROOT-SCARECROW Transcriptional Cascade through Opposing Activities of Both Activators and Repressors., Dev Cell, vol. 39 no. 5 (December, 2016), pp. 585-596 [doi]  [abs]
20. Welch, JD; Hartemink, AJ; Prins, JF, SLICER: inferring branched, nonlinear cellular trajectories from single cell RNA-seq data., Genome Biol, vol. 17 no. 1 (May, 2016), pp. 106 [doi]  [abs]
21. Zhong, J; Luo, K; Winter, PS; Crawford, GE; Iversen, ES; Hartemink, AJ, Mapping nucleosome positions using DNase-seq., Genome Res, vol. 26 no. 3 (March, 2016), pp. 351-364 [doi]  [abs]
22. Zhang, Y; Henao, R; Carin, L; Zhong, J; Hartemink, AJ, Learning a Hybrid Architecture for Sequence Regression and Annotation., edited by Schuurmans, D; Wellman, MP, AAAI (2016), pp. 1415-1421, AAAI Press, ISBN 978-1-57735-760-5  [abs]
23. 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 Dev, vol. 29 no. 2 (January, 2015), pp. 212-224, ISSN 0890-9369 [doi]  [abs]
24. Whitney, O; Pfenning, AR; Howard, JT; Blatti, CA; Liu, F; Ward, JM; Wang, R; Audet, J-N; 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, vol. 346 no. 6215 (December, 2014), pp. 1256780, ISSN 0036-8075 [repository], [doi]  [abs]
25. 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, MTP; Zhang, G; Bakken, T; Bongaarts, A; Bernard, A; Lein, E; Mello, CV; Hartemink, AJ; Jarvis, ED, Convergent transcriptional specializations in the brains of humans and song-learning birds., Science, vol. 346 no. 6215 (December, 2014), pp. 1256846, ISSN 0036-8075 [repository], [doi]  [abs]
26. Zhong, J; Wasson, T; Hartemink, AJ, Learning protein-DNA interaction landscapes by integrating experimental data through computational models., Bioinformatics, vol. 30 no. 20 (October, 2014), pp. 2868-2874, ISSN 1367-4803 [doi]  [abs]
27. Zhong, J; Wasson, T; Hartemink, AJ, Learning Protein-DNA Interaction Landscapes by Integrating Experimental Data through Computational Models., edited by Sharan, R, RECOMB, vol. 8394 (2014), pp. 433-447, Springer, ISBN 978-3-319-05268-7 [doi]  [abs]
28. Meyer, P; Siwo, G; Zeevi, D; Sharon, E; Norel, R; DREAM6 Promoter Prediction Consortium, ; Segal, E; Stolovitzky, G, Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach., Genome Res, vol. 23 no. 11 (November, 2013), pp. 1928-1937 [doi]  [abs]
29. Mordelet, F; Horton, J; Hartemink, AJ; Engelhardt, BE; Gordân, R, Stability selection for regression-based models of transcription factor-DNA binding specificity., Bioinformatics, vol. 29 no. 13 (July, 2013), pp. i117-i125 [23812975], [doi]  [abs]
30. Perez-Pinera, P; Ousterout, DG; Brunger, JM; Farin, AM; Glass, KA; Guilak, F; Crawford, GE; Hartemink, AJ; Gersbach, CA, Synergistic and Tunable Gene Activation by Combinations of Synthetic Transcription Factors, MOLECULAR THERAPY, vol. 21 (June, 2013), pp. S93-S93, NATURE PUBLISHING GROUP, ISSN 1525-0016 [Gateway.cgi]
31. 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, vol. 110 no. 10 (March, 2013), pp. E968-E977 [23388635], [doi]  [abs]
32. 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., Nat Methods, vol. 10 no. 3 (March, 2013), pp. 239-242 [23377379], [doi]  [abs]
33. Mayhew, MB; Hartemink, AJ, Cell-cycle phenotyping with conditional random fields: A case study in Saccharomyces cerevisiae, Proceedings - International Symposium on Biomedical Imaging (January, 2013), pp. 1062-1065, IEEE, ISSN 1945-7928, ISBN 9781467364546 [doi]  [abs]
34. Luo, K; Hartemink, AJ, Using DNase digestion data to accurately identify transcription factor binding sites., Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing (January, 2013), pp. 80-91, ISSN 2335-6936 [23424114]  [abs]
35. Hartemink, AJ; Kellis, M; Noble, WS; Weng, Z, (Session Introduction) Epigenomics, in Proceedings of the Pacific Symposium on Biocomputing, PSB 2013, Kohala Coast, Hawaii, USA, January 3-7, 2013, edited by Altman, RB; Dunker, AK; Hunter, L; Murray, T; Klein, TE (2013), pp. 65-68, World Scientific Publishing, ISSN 2335-6936, ISBN 978-1-62748-016-1 [23424112]  [abs]
36. 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, ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia., Genome Res, vol. 22 no. 9 (September, 2012), pp. 1813-1831 [22955991], [doi]  [abs]
37. Mayhew, MB; Guo, X; Haase, SB; Hartemink, AJ, Close Encounters of the Collaborative Kind, Computer, vol. 45 no. 3 (March, 2012), pp. 24-30, Institute of Electrical and Electronics Engineers (IEEE), ISSN 0018-9162 [doi]  [abs]
38. 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 (January, 2012), pp. 104-115, ISSN 2335-6936 [22174267]  [abs]
39. 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, Verification of systems biology research in the age of collaborative competition., Nature biotechnology, vol. 29 no. 9 (September, 2011), pp. 811-815 [21904331], [doi]
40. 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), vol. 27 no. 13 (July, 2011), pp. i295-i303 [21685084], [doi]  [abs]
41. 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, vol. 17 no. 4 (April, 2011), pp. 665-674 [21282347], [doi]  [abs]
42. Robinson, JW; Hartemink, AJ, Learning non-stationary dynamic bayesian networks, Journal of Machine Learning Research, vol. 11 (December, 2010), pp. 3647-3680, ISSN 1532-4435  [abs]
43. Gordân, R; Narlikar, L; Hartemink, AJ, Finding regulatory DNA motifs using alignment-free evolutionary conservation information., Nucleic Acids Res, vol. 38 no. 6 (April, 2010), pp. e90 [20047961], [doi]  [abs]
44. MacAlpine, HK; Gordân, R; Powell, SK; Hartemink, AJ; MacAlpine, DM, Drosophila ORC localizes to open chromatin and marks sites of cohesin complex loading., Genome Res, vol. 20 no. 2 (February, 2010), pp. 201-211 [19996087], [doi]  [abs]
45. Gordân, R; Narlikar, L; Hartemink, AJ, Finding regulatory DNA motifs using alignment-free evolutionary conservation information, Nucleic Acids Research, vol. 38 no. 6 (January, 2010), pp. e90.1-e90.12, ISSN 0305-1048 [doi]  [abs]
46. Gordan, R; Hartemink, AJ; Bulyk, ML, Distinguishing Direct versus Indirect Transcription Factor-DNA Interactions, edited by Berger, B, RESEARCH IN COMPUTATIONAL MOLECULAR BIOLOGY, PROCEEDINGS, vol. 6044 (January, 2010), pp. 574-574, SPRINGER-VERLAG BERLIN, ISBN 978-3-642-12682-6 [978-3-642-12683-3], [doi]
47. Wasson, T; Hartemink, AJ, An ensemble model of competitive multi-factor binding of the genome., Genome research, vol. 19 no. 11 (November, 2009), pp. 2101-2112 [19720867], [doi]  [abs]
48. Gordân, R; Hartemink, AJ; Bulyk, ML, Distinguishing direct versus indirect transcription factor-DNA interactions., Genome Res, vol. 19 no. 11 (November, 2009), pp. 2090-2100 [19652015], [doi]  [abs]
49. Guo, X; Hartemink, AJ, Domain-oriented edge-based alignment of protein interaction networks., Bioinformatics (Oxford, England), vol. 25 no. 12 (June, 2009), pp. i240-i246 [19477994], [doi]  [abs]
50. Robinson, JW; Hartemink, AJ, Non-stationary dynamic Bayesian networks, Advances in Neural Information Processing Systems 21 - Proceedings of the 2008 Conference (January, 2009), pp. 1369-1376  [abs]
51. 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, vol. 3 no. 4 (January, 2009), pp. 1521-1541, ISSN 1932-6157 [21853014], [doi]  [abs]
52. Orlando, DA; Lin, CY; Bernard, A; Wang, JY; Socolar, JES; Iversen, ES; Hartemink, AJ; Haase, SB, Global control of cell-cycle transcription by coupled CDK and network oscillators., Nature, vol. 453 no. 7197 (June, 2008), pp. 944-947 [18463633], [doi]  [abs]
53. Bulyk, ML; Fraenkel, E; Hartemink, AJ; Mandel-Gutfreund, Y, (Session Introduction) Protein-nucleic acid interactions: Integrating structure, sequence, and function, in Proceedings of the Pacific Symposium on Biocomputing, PSB 2008, Kohala Coast, Hawaii, USA, 4-8 January 2008, edited by Altman, RB; Dunker, AK; Hunter, L; Murray, T; Klein, TE (2008), pp. 438-440, World Scientific, ISBN 978-981-277-608-2 [html]
54. Gordân, R; Hartemink, AJ, Using DNA duplex stability information for transcription factor binding site discovery., Pac Symp Biocomput (2008), pp. 453-464, ISSN 2335-6936 [18229707]  [abs]
55. Gordân, R; Narlikar, L; Hartemink, AJ, A Fast, Alignment-Free, Conservation-Based Method for Transcription Factor Binding Site Discovery., edited by Vingron, M; Wong, L, RECOMB, vol. 4955 (2008), pp. 98-111, Springer, ISSN 0302-9743, ISBN 978-3-540-78838-6 [doi]  [abs]
56. Luedi, PP; Dietrich, FS; Weidman, JR; Bosko, JM; Jirtle, RL; Hartemink, AJ, Computational and experimental identification of novel human imprinted genes., Genome Res, vol. 17 no. 12 (December, 2007), pp. 1723-1730, ISSN 1088-9051 [18055845], [doi]  [abs]
57. Narlikar, L; Gordân, R; Hartemink, AJ, A nucleosome-guided map of transcription factor binding sites in yeast., PLoS Comput Biol, vol. 3 no. 11 (November, 2007), pp. e215 [17997593], [doi]  [abs]
58. 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.), vol. 6 no. 4 (February, 2007), pp. 478-488 [17329975], [doi]  [abs]
59. Bulyk, ML; Hartemink, AJ; Fraenkel, E; Stormo, GD, (Session Introduction) DNA-protein interactions: Integrating structure, sequence, and function, in Proceedings of the Pacific Symposium on Biocomputing, PSB 2007, Maui, Hawaii, USA, 3-7 January 2007, edited by Altman, RB; Dunker, AK; Hunter, L; Murray, T; Klein, TE (2007), pp. 470-471, World Scientific, ISBN 981-270-417-5 [html]
60. Bernard, A; Vaughn, DS; Hartemink, AJ, Reconstructing the Topology of Protein Complexes., edited by Speed, TP; Huang, H, RECOMB, vol. 4453 (2007), pp. 32-46, Springer, ISSN 0302-9743, ISBN 3-540-71680-7 [doi]  [abs]
61. Narlikar, L; Gordân, R; Hartemink, AJ, Nucleosome Occupancy Information Improves de novo Motif Discovery., edited by Speed, TP; Huang, H, RECOMB, vol. 4453 (2007), pp. 107-121, Springer, ISSN 0302-9743, ISBN 3-540-71680-7 [doi]  [abs]
62. Smith, VA; Yu, J; Smulders, TV; Hartemink, AJ; Jarvis, ED, Computational inference of neural information flow networks., PLoS Comput Biol, vol. 2 no. 11 (November, 2006), pp. e161 [17121460], [doi]  [abs]
63. Narlikar, L; Gordân, R; Ohler, U; Hartemink, AJ, Informative priors based on transcription factor structural class improve de novo motif discovery., Bioinformatics, vol. 22 no. 14 (July, 2006), pp. e384-e392 [16873497], [doi]  [abs]
64. Narlikar, L; Hartemink, AJ, Sequence features of DNA binding sites reveal structural class of associated transcription factor., Bioinformatics (Oxford, England), vol. 22 no. 2 (January, 2006), pp. 157-163, ISSN 1367-4803 [16267080], [doi]  [abs]
65. Pratapa, PN; Patz, EF; Hartemink, AJ, Finding diagnostic biomarkers in proteomic spectra., Pac Symp Biocomput (2006), pp. 279-290, ISSN 2335-6936 [17094246]  [abs]
66. Hartemink, AJ, Bayesian Networks and Informative Priors: Transcriptional Regulatory Network Models, in BAYESIAN INFERENCE FOR GENE EXPRESSION AND PROTEOMICS (2006), pp. 401-424
67. Luedi, PP; Hartemink, AJ; Jirtle, RL, Genome-wide prediction of imprinted murine genes., Genome research, vol. 15 no. 6 (June, 2005), pp. 875-884, ISSN 1088-9051 [15930497], [doi]  [abs]
68. Krishnapuram, B; Carin, L; Figueiredo, MAT; Hartemink, AJ, Sparse multinomial logistic regression: fast algorithms and generalization bounds., IEEE transactions on pattern analysis and machine intelligence, vol. 27 no. 6 (June, 2005), pp. 957-968, ISSN 0162-8828 [15943426], [doi]  [abs]
69. Hartemink, AJ, Reverse engineering gene regulatory networks., Nature biotechnology, vol. 23 no. 5 (May, 2005), pp. 554-555, ISSN 1087-0156 [15877071], [doi]
70. Yin, P; Hartemink, AJ, Theoretical and practical advances in genome halving., Bioinformatics (Oxford, England), vol. 21 no. 7 (April, 2005), pp. 869-879, ISSN 1367-4803 [15513986], [doi]  [abs]
71. Krishnapuram, B; Williams, D; Xue, Y; Hartemink, A; Carin, L; Figueiredo, MAT, On semi-supervised classification, Advances in Neural Information Processing Systems (January, 2005), pp. 721-728, ISBN 9780262195348 [advances-in-neural-information-processing-systems-17-2004]  [abs]
72. 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 (January, 2005), pp. 459-470, ISSN 2335-6936 [15759651]  [abs]
73. Hartemink, AJ; Segal, E, (Session Introduction) Joint Learning from Multiple Types of Genomic Data, in Proceedings of the 10th Pacific Symposium on Biocomputing, PSB 2005, Hawaii, USA, 4-8 January 2005, edited by Altman, RB; Jung, TA; Klein, TE; Dunker, AK; Hunter, L (2005), pp. 445-446, World Scientific, ISSN 2335-6936, ISBN 981-256-046-7 [15759649]
74. Yu, J; Smith, VA; Wang, PP; Hartemink, AJ; Jarvis, ED, Advances to Bayesian network inference for generating causal networks from observational biological data., Bioinformatics, vol. 20 no. 18 (December, 2004), pp. 3594-3603, ISSN 1367-4803 [15284094], [doi]  [abs]
75. Krishnapuram, B; Hartemink, AJ; Carin, L; Figueiredo, MAT, A Bayesian approach to joint feature selection and classifier design., IEEE transactions on pattern analysis and machine intelligence, vol. 26 no. 9 (September, 2004), pp. 1105-1111, ISSN 0162-8828 [15742887], [doi]  [abs]
76. 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, vol. 11 no. 2-3 (January, 2004), pp. 227-242, ISSN 1066-5277 [15285890], [doi]  [abs]
77. Hartemink, AJ; Segal, E, (Session Introduction) Joint Learning from Multiple Types of Genomic Data, in Proceedings of the 9th Pacific Symposium on Biocomputing, PSB 2004, Hawaii, USA, 6-10 January 2004, edited by Altman, RB; Dunker, AK; Hunter, L; Jung, TA; Klein, TE (2004), pp. 262-263, World Scientific, ISBN 981-238-598-3 [html]
78. Liu, Q; Krishnapuram, B; Pratapa, P; Liao, X; Hartemink, A; Carin, L, Identification of differentially expressed proteins using MALDI-TOF mass spectra, in Asilomar 2003, Conference Record of the Asilomar Conference on Signals, Systems and Computers, vol. 2 (December, 2003), pp. 1323-1327, ISSN 1058-6393  [abs]
79. Krishnapuram, B; Carin, L; Hartemink, AJ, Joint classifier and feature optimization for cancer diagnosis using gene expression data, in Research in Computational Molecular Biology, Proceedings of the Annual International Conference on Computational Molecular Biology, RECOMB (January, 2003), pp. 167-175 [doi]  [abs]
80. Karp, PD; Neumann, EP; Hartemink, AJ; Romero, P, (Session Introduction) Genome, Pathway, and Interaction Bioinformatics, in Proceedings of the 8th Pacific Symposium on Biocomputing, PSB 2003, Lihue, Hawaii, USA, January 3-7, 2003, edited by Altman, RB; Dunker, AK; Hunter, L; Klein, TE (2003), pp. 101-103 [available here]
81. Smith, VA; Jarvis, ED; Hartemink, AJ, Influence of network topology and data collection on network inference., Pac Symp Biocomput (2003), pp. 164-175, ISSN 2335-6936 [12603026]  [abs]
82. 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., J Comp Physiol A Neuroethol Sens Neural Behav Physiol, vol. 188 no. 11-12 (December, 2002), pp. 961-980, ISSN 0340-7594 [12471494], [doi]  [abs]
83. 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 (January, 2002), pp. 437-449, ISSN 2335-6936 [11928497]  [abs]
84. Hartemink, AJ; Gifford, DK; Jaakkola, TS; Young, RA, Bayesian Methods for Elucidating Genetic Regulatory Networks, IEEE Intelligent Systems, vol. 17 no. 2 (January, 2002), pp. 37-43, Institute of Electrical and Electronics Engineers (IEEE), ISSN 1094-7167 (special issue on Intelligent Systems in Biology.) [doi]  [abs]
85. Hartemink, A., Gifford, D., Jaakkola, T., & Young, R., Combining Location and Expression Data for Principled Discovery of Genetic Regulatory Networks, Pacific Symposium on Biocomputing (2002)
86. Smith, VA; Jarvis, ED; Hartemink, AJ, Evaluating functional network inference using simulations of complex biological systems., Bioinformatics, vol. 18 Suppl 1 (2002), pp. S216-S224, ISSN 1367-4803 [12169550], [doi]  [abs]
87. 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 (January, 2001), pp. 422-433, ISSN 2335-6936 [11262961], [doi]  [abs]
88. 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, vol. 4266 (January, 2001), pp. 132-140, SPIE [doi]  [abs]
89. Hartemink, AJ; Gifford, DK; Khodor, J, Automated constraint-based nucleotide sequence selection for DNA computation., Bio Systems, vol. 52 no. 1-3 (October, 1999), pp. 227-235, Elsevier Press, ISSN 0303-2647 [10636048], [doi]  [abs]
90. Schechter, S; Parnell, T; Hartemink, A, Anonymous authentication of membership in dynamic groups, in Financial Cryptography '99, Lecture Notes in Computer Science, 1648, pp. 184-195, edited by Franklin, MK, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 1648 (January, 1999), pp. 184-195, SPRINGER, ISBN 9783540663621 [html], [doi]  [abs]
91. Hartemink, A. & Gifford, D., Thermodynamic Simulation of Deoxyoligonucleotide Hybridization for DNA Computation, in DNA Based Computers III, DIMACS Series in Discrete Mathematics and Theoretical Computer Science, 48, pp. 25-38, edited by Rubin, H. & Wood, D. (1999), American Mathematical Society
92. Hartemink, AJ; Mikkelsen, TS; Gifford, DK, Simulating biological reactions: A modular approach., in DNA Based Computers V., DIMACS Series in Discrete Mathematics and Theoretical Computer Science, edited by Winfree, E; Gifford, DK, DNA Based Computers, vol. 54 (1999), pp. 111-122, DIMACS/AMS
93. Hartemink, AJ; Gifford, DK, Thermodynamic simulation of deoxyoligonucleotide hybridization for DNA computation., edited by Rubin, H; Wood, DH, DNA Based Computers, vol. 48 (1997), pp. 25-38, DIMACS/AMS

Journal or Book articles OFFICIALLY ACCEPTED

1. Krishnapuram, Balaji and Carin, Larry and Hartemink, Alexander, Gene Expression Analysis: Joint Feature Selection and Classifier Design, in Kernel Methods in Computational Biology, edited by Scholkopf, Bernhard and Tsuda, Koji and Vert, Jean-Philippe (2003), MIT Press
2. Krishnapuram, Balaji and Carin, Larry and Hartemink, Alexander, Joint Classifier and Feature Optimization for Comprehensive Cancer Diagnosis Using Gene Expression Data, Journal of Computational Biology (2003)

Journal or Book articles being REFEREED

1. Krishnapuram, Balaji and Carin, Larry and Figueiredo, Mario and Hartemink, Alexander, An EM Algorithm for Joint Feature Selection and Classifier Design (2003)

Conference articles PUBLISHED

1. Smith, V. Anne and Jarvis, Erich and Hartemink, Alexander, Influence of Topology and Data Collection on Functional Network Inference, in Pacific Symposium on Biocomputing, edited by Altman, Russ and Dunker, A. Keith and Hunter, Larry and Jung, Tiffany and Klein, Teri (January, 2003), pp. 164-175, World Scientific

Workshop abstract or talk (no official publication)

1. Krishnapuram, Balaji and Carin, Larry and Hartemink, Alexander, Joint Classifier and Kernel Design (April, 2003)

Conference articles IN SUBMISSION

1. Krishnapuram, Balaji and Figueiredo, Mario and Carin, Larry and Hartemink, Alexander, Learning sparse Bayesian classifiers: Multi-class formulation, fast algorithms, and generalization bounds (November, 2003)