Alexander J. Hartemink
Alexander J. Hartemink
Professor of Computer Science, Duke University
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ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
SG Landt, GK Marinov, A Kundaje, P Kheradpour, F Pauli, S Batzoglou, ...
Genome Research 22 (9), 1813-1831, 2012
Sparse multinomial logistic regression: Fast algorithms and generalization bounds
B Krishnapuram, L Carin, MAT Figueiredo, AJ Hartemink
Pattern Analysis and Machine Intelligence, IEEE Transactions on 27 (6), 957-968, 2005
Advances to Bayesian network inference for generating causal networks from observational biological data
J Yu, VA Smith, PP Wang, AJ Hartemink, ED Jarvis
Bioinformatics 20 (18), 3594-3603, 2004
Using graphical models and genomic expression data to statistically validate models of genetic regulatory networks
AJ Hartemink, DK Gifford, TS Jaakkola, RA Young
Pacific Symposium on Biocomputing 2001 6, 422-433, 2001
Convergent transcriptional specializations in the brains of humans and song-learning birds
AR Pfenning, E Hara, O Whitney, MV Rivas, R Wang, PL Roulhac, ...
Science 346 (6215), 1256846, 2014
Computational and experimental identification of novel human imprinted genes
PP Luedi, FS Dietrich, JR Weidman, JM Bosko, RL Jirtle, AJ Hartemink
Genome Research 17 (12), 1723-1730, 2007
Combining location and expression data for principled discovery of genetic regulatory network models
AJ Hartemink, DK Gifford, TS Jaakkola, RA Young
Pacific Symposium on Biocomputing 2002 7, 437-449, 2002
Global control of cell-cycle transcription by coupled CDK and network oscillators
DA Orlando, CY Lin, A Bernard, JY Wang, JES Socolar, ES Iversen, ...
Nature 453 (7197), 944-947, 2008
Genome-wide prediction of imprinted murine genes
PP Luedi, AJ Hartemink, RL Jirtle
Genome Research 15 (6), 875-884, 2005
Synergistic and tunable human gene activation by combinations of synthetic transcription factors
P Perez-Pinera, DG Ousterout, JM Brunger, AM Farin, KA Glass, F Guilak, ...
Nature Methods 10 (3), 239-242, 2013
Drosophila ORC localizes to open chromatin and marks sites of cohesin complex loading
HK MacAlpine, R Gordân, SK Powell, AJ Hartemink, DM MacAlpine
Genome Research 20 (2), 201-211, 2010
Informative structure priors: Joint learning of dynamic regulatory networks from multiple types of data
A Bernard, AJ Hartemink
Pacific Symposium on Biocomputing 2005 10, 459-470, 2005
A Bayesian approach to joint feature selection and classifier design
B Krishnapuram, AJ Hartemink, L Carin, MAT Figueiredo
Pattern Analysis and Machine Intelligence, IEEE Transactions on 26 (9), 1105 …, 2004
Learning non-stationary dynamic Bayesian networks
JW Robinson, AJ Hartemink
Journal of Machine Learning Research 11 (12), 3647-3680, 2010
Reverse engineering gene regulatory networks
AJ Hartemink
Nature Biotechnology 23 (5), 554-555, 2005
Evaluating functional network inference using simulations of complex biological systems
VA Smith, ED Jarvis, AJ Hartemink
Bioinformatics 18 (S1), S216-S224, 2002
Computational inference of neural information flow networks
VA Smith, J Yu, TV Smulders, AJ Hartemink, ED Jarvis
PLoS Computational Biology 2 (11), 1436-1449, 2006
SLICER: Inferring branched, nonlinear cellular trajectories from single cell RNA-seq data
JD Welch, AJ Hartemink, JF Prins
Genome Biology 17 (106), 1-15, 2016
Distinguishing direct versus indirect transcription factor–DNA interactions
R Gordân, AJ Hartemink, ML Bulyk
Genome Research 19 (11), 2090-2100, 2009
On semi-supervised classification
B Krishnapuram, D Williams, Y Xue, AJ Hartemink, L Carin, ...
Advances in Neural Information Processing Systems 17, 721-728, 2005
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