| 2020 | RECOMB | RoboCOP: Multivariate State Space Model Integrating Epigenomic Accessibility Data to Elucidate Genome-Wide Chromatin Occupancy. | Sneha Mitra, Jianling Zhong, David M. MacAlpine, Alexander J. Hartemink |
| 2017 | RECOMB | E Pluribus Unum: United States of Single Cells. | Joshua D. Welch, Alexander J. Hartemink, Jan F. Prins |
| 2016 | AAAI | Learning a Hybrid Architecture for Sequence Regression and Annotation. | Yizhe Zhang, Ricardo Henao, Lawrence Carin, Jianling Zhong, Alexander J. Hartemink |
| 2016 | RECOMB | SLICER: Inferring Branched, Nonlinear Cellular Trajectories from Single Cell RNA-seq Data. | Joshua D. Welch, Ziqing Liu, Li Wang, Junjie Lu, Paul Lerou, Jeremy E. Purvis, Li Qian, Alexander J. Hartemink, Jan F. Prins |
| 2014 | RECOMB | Learning Protein-DNA Interaction Landscapes by Integrating Experimental Data through Computational Models. | Jianling Zhong, Todd Wasson, Alexander J. Hartemink |
| 2013 | PSB | Session Introduction. | Alexander J. Hartemink, Manolis Kellis, William Stafford Noble, Zhiping Weng |
| 2013 | PSB | Using DNase Digestion Data to Accurately Identify Transcription Factor Binding Sites. | Kaixuan Luo, Alexander J. Hartemink |
| 2012 | PSB | Intrinsic Disorder Within and Flanking the DNA-Binding Domains of Human Transcription Factors. | Xin Guo, Martha L. Bulyk, Alexander J. Hartemink |
| 2010 | RECOMB | Distinguishing Direct versus Indirect Transcription Factor-DNA Interactions. | Raluca Gordn, Alexander J. Hartemink, Martha L. Bulyk |
| 2008 | PSB | Session Introduction. | Martha L. Bulyk, Ernest Fraenkel, Alexander J. Hartemink, Yael Mandel-Gutfreund |
| 2008 | PSB | Using DNA Duplex Stability Information for Transcription Factor Binding Site Discovery. | Raluca Gordn, Alexander J. Hartemink |
| 2008 | RECOMB | A Fast, Alignment-Free, Conservation-Based Method for Transcription Factor Binding Site Discovery. | Raluca Gordn, Leelavati Narlikar, Alexander J. Hartemink |
| 2007 | PSB | Session Introduction. | Martha L. Bulyk, Alexander J. Hartemink, Ernest Fraenkel, Gary D. Stormo |
| 2007 | RECOMB | Reconstructing the Topology of Protein Complexes. | Allister Bernard, David S. Vaughn, Alexander J. Hartemink |
| 2007 | RECOMB | Nucleosome Occupancy Information Improves | Leelavati Narlikar, Raluca Gordn, Alexander J. Hartemink |
| 2006 | ISMB | Informative priors based on transcription factor structural class improve | Leelavati Narlikar, Raluca Gordn, Uwe Ohler, Alexander J. Hartemink |
| 2006 | PSB | Finding Diagnostic Biomarkers in Proteomic Spectra. | Pallavi N. Pratapa, Edward F. Patz Jr., Alexander J. Hartemink |
| 2005 | PSB | Informative Structure Priors: Joint Learning of Dynamic Regulatory Networks from Multiple Types of Data. | Allister Bernard, Alexander J. Hartemink |
| 2005 | PSB | Session Introduction: Joint Learning from Multiple Types of Genomic Data. | Alexander J. Hartemink, Eran Segal |
| 2004 | PSB | Session Introduction. | Alexander J. Hartemink, Eran Segal |
| 2003 | PSB | Genome, Pathway, and Interaction Bioinformatics - Session Introduction. | Peter D. Karp, Eric P. Neumann, Alexander J. Hartemink, Pedro Romero |
| 2003 | PSB | Influence of Network Topology and Data Collection on Network Inference. | V. Anne Smith, Erich D. Jarvis, Alexander J. Hartemink |
| 2003 | RECOMB | Joint classifier and feature optimization for cancer diagnosis using gene expression data. | Balaji Krishnapuram, Lawrence Carin, Alexander J. Hartemink |
| 2002 | ISMB | Evaluating functional network inference using simulations of complex biological systems. | V. Anne Smith, Erich D. Jarvis, Alexander J. Hartemink |
| 2002 | PSB | 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 |
| 2001 | PSB | 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 |
| 1999 | FC | Anonymous Authentication of Membership in Dynamic Groups. | Stuart E. Schechter, Todd Parnell, Alexander J. Hartemink |