2026 Alexander J. Hartemink: Computer Science Researcher – H-Index, Publications & Awards

Discipline name	D-Index	World Ranking	Current World Ranking	National Ranking	Current National Ranking	Publications	Citations
Computer Science	40	9084	8823	3862	3704	85	11005

Overview

Alexander J. Hartemink is affiliated with Duke University in the United States. Their research spans multiple topics within the broader field of Biochemistry, Genetics, and Molecular Biology, with a significant focus on Molecular Biology, Genetics, Biophysics, and Cancer Research.

Their main research topics include:

Genomics and Chromatin Dynamics
Gene expression and cancer classification
Epigenetics and DNA Methylation
RNA Research and Splicing
DNA Repair Mechanisms
Single-cell and spatial transcriptomics
Bacterial Genetics and Biotechnology

Hartemink has contributed to a range of recent papers published in venues such as Genome Research, Nature Genetics, and UNC Libraries. Notable recent publications include:

"ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia" (2020, UNC Libraries)
"Single-cell multi-ome regression models identify functional and disease-associated enhancers and enable chromatin potential analysis" (2024, Nature Genetics)
"Local nucleosome dynamics and eviction following a double-strand break are reversible by NHEJ-mediated repair in the absence of DNA replication" (2021, Genome Research)
"Linking the dynamics of chromatin occupancy and transcription with predictive models" (2021, Genome Research)
"Spatiotemporal kinetics of CAF-1-dependent chromatin maturation ensures transcription fidelity during S-phase" (2023, Genome Research)

Their frequent coauthors reflect collaboration mainly in the genomics and molecular biology domains. These include:

David M. MacAlpine
Sneha Mitra
Heather K. MacAlpine
Jianling Zhong
Trung Q. Tran

Alexander J. Hartemink's work has been regularly published in several key venues, with the highest number of publications appearing in bioRxiv (Cold Spring Harbor Laboratory) and Genome Research. Other publication venues include Nature Genetics, UNC Libraries, and Nucleic Acids Research.

Best Publications

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

Stephen G. Landt;Georgi K. Marinov;Anshul Kundaje;Pouya Kheradpour

2471
Citations
Sparse multinomial logistic regression: fast algorithms and generalization bounds

B. Krishnapuram;L. Carin;M.A.T. Figueiredo;A.J. Hartemink

1112
Citations
Advances to Bayesian network inference for generating causal networks from observational biological data

Jing Yu;V. Anne Smith;Paul P. Wang;Alexander J. Hartemink

900
Citations
Using graphical models and genomic expression data to statistically validate models of genetic regulatory networks.

Alexander J. Hartemink;David K. Gifford;Tommi S. Jaakkola;Richard A. Young

596
Citations
Convergent transcriptional specializations in the brains of humans and song-learning birds

Andreas R. Pfenning;Erina Hara;Osceola Whitney;Miriam V. Rivas

540
Citations
Computational and experimental identification of novel human imprinted genes

Philippe P. Luedi;Fred S. Dietrich;Jennifer R. Weidman;Jason M. Bosko

490
Citations
Combining location and expression data for principled discovery of genetic regulatory network models.

Alexander J. Hartemink;David K. Gifford;Tommi S. Jaakkola;Richard A. Young

434
Citations
Informative structure priors: joint learning of dynamic regulatory networks from multiple types of data.

Allister Bernard;Alexander J. Hartemink

251
Citations
A Bayesian approach to joint feature selection and classifier design

B. Krishnapuram;A.J. Harternink;L. Carin;M.A.T. Figueiredo

231
Citations
Learning Non-Stationary Dynamic Bayesian Networks

Joshua W. Robinson;Alexander J. Hartemink

207
Citations
Reverse engineering gene regulatory networks

Alexander J Hartemink

204
Citations
Evaluating functional network inference using simulations of complex biological systems.

V. Anne Smith;Erich D. Jarvis;Alexander J. Hartemink

200
Citations
SLICER: inferring branched, nonlinear cellular trajectories from single cell RNA-seq data.

Joshua D. Welch;Alexander J. Hartemink;Jan F. Prins

194
Citations
Computational Inference of Neural Information Flow Networks

V Anne Smith;Jing Yu;Tom Smulders;Alexander J. Hartemink

192
Citations
Distinguishing direct versus indirect transcription Factor-DNA interactions

Raluca Gordân;Alexander J. Hartemink;Martha L. Bulyk

176
Citations
On Semi-Supervised Classification

Balaji Krishnapuram;David Williams;Ya Xue;Lawrence Carin

165
Citations
Maximum likelihood estimation of optimal scaling factors for expression array normalization

Alexander J. Hartemink;David K. Gifford;Tommi S. Jaakkola;Richard A. Young

161
Citations
MATCHER: manifold alignment reveals correspondence between single cell transcriptome and epigenome dynamics.

Joshua D. Welch;Alexander J. Hartemink;Jan F. Prins

160
Citations
Automated constraint-based nucleotide sequence selection for DNA computation.

Alexander J. Hartemink;David K. Gifford;Julia Khodor

143
Citations
An ensemble model of competitive multi-factor binding of the genome

Todd Wasson;Alexander J. Hartemink

138
Citations

Frequent Co-Authors

Erich D. Jarvis Rockefeller University

Lawrence Carin Duke University

David K. Gifford MIT

Jan F. Prins University of North Carolina at Chapel Hill

Martha L. Bulyk Harvard University

Tommi S. Jaakkola MIT

Richard A. Young MIT

Gregory E. Crawford Duke University

Manolis Kellis MIT

Saurabh Sinha University of Illinois at Urbana-Champaign

External Links

Personal website of Alexander J. Hartemink

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