User profiles for A. J. Hartemink

Alexander J. Hartemink

Professor of Computer Science, Duke University
Verified email at cs.duke.edu
Cited by 12497

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

…, M Gerstein, J Gertz, AJ Hartemink… - Genome …, 2012 - genome.cshlp.org
Chromatin immunoprecipitation (ChIP) followed by high-throughput DNA sequencing (ChIP-seq)
has become a valuable and widely used approach for mapping the genomic location of …

Sparse multinomial logistic regression: Fast algorithms and generalization bounds

…, L Carin, MAT Figueiredo, AJ Hartemink - IEEE transactions on …, 2005 - ieeexplore.ieee.org
Hartemink would like to gratefully acknowledge the support of the Alfred P. Sloan
Foundation and the US National Science Foundation under its CAREER award program. M. …

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

J Yu, VA Smith, PP Wang, AJ Hartemink… - …, 2004 - academic.oup.com
Motivation: Network inference algorithms are powerful computational tools for identifying
putative causal interactions among variables from observational data. Bayesian network …

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

AJ Hartemink, DK Gifford, TS Jaakkola… - Biocomputing …, 2000 - World Scientific
We propose a model-driven approach for analyzing genomic expression data that permits
genetic regulatory networks to be represented in a biologically interpretable computational …

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

…, A Bernard, E Lein, CV Mello, AJ Hartemink… - Science, 2014 - science.org
INTRODUCTION Vocal learning, the ability to imitate sounds, is a trait that has undergone
convergent evolution in several lineages of birds and mammals, including song-learning birds …

Computational and experimental identification of novel human imprinted genes

…, JM Bosko, RL Jirtle, AJ Hartemink - Genome …, 2007 - genome.cshlp.org
Imprinted genes are essential in embryonic development, and imprinting dysregulation
contributes to human disease. We report two new human imprinted genes: KCNK9 is …

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

…, JY Wang, JES Socolar, ES Iversen, AJ Hartemink… - Nature, 2008 - nature.com
A significant fraction of the Saccharomyces cerevisiae genome is transcribed periodically
during the cell division cycle 1 , 2 , indicating that properly timed gene expression is important …

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

AJ Hartemink, DK Gifford, TS Jaakkola… - Biocomputing …, 2001 - World Scientific
We develop principled methods for the automatic induction (discovery) of genetic regulatory
network models from multiple data sources and data modalities. Models of regulatory …

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

…, R Gordān, SK Powell, AJ Hartemink… - Genome …, 2010 - genome.cshlp.org
The origin recognition complex (ORC) is an essential DNA replication initiation factor conserved
in all eukaryotes. In Saccharomyces cerevisiae, ORC binds to specific DNA elements; …

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

…, KA Glass, F Guilak, GE Crawford, AJ Hartemink… - Nature …, 2013 - nature.com
Mammalian genes are regulated by the cooperative and synergistic actions of many transcription
factors. In this study we recapitulate this complex regulation in human cells by targeting …