The Program in Systems Biology was established as a new interdisciplinary research program at UMass Medical School in 2012. The goal of systems biology as a field is to understand biological processes at a systems level rather than at the level of individual molecules. Systems biology capitalizes on technological advances in the areas of genomics and high-throughput instrumentation, with strong links to computational biology, math, statistics and bioinformatics. Leading the new program as co-directors are Job Dekker, PhD, professor of biochemistry & molecular pharmacology and molecular medicine and a member of the Program in Gene Function and Expression; and Marian Walhout, PhD, professor of molecular medicine. This collection showcases the journal articles, book chapters, and other publications and presentations written by faculty and researchers of the Program in Systems Biology at the University of Massachusetts Medical School.

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Publications from 2016

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CTCF-mediated topological boundaries during development foster appropriate gene regulation, Varun Narendra, Milica Bulajic, Job Dekker, Esteban O. Mazzoni, and Danny Reinberg (Genes and development)

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Genetics and Genomics of Longitudinal Lung Function Patterns in Individuals with Asthma, Michael J. McGeachie, Bryan R. Lajoie, Job Dekker, and CAMP Research Group (American journal of respiratory and critical care medicine)

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Molecular Basis for Differential Patterns of Drug Resistance in Influenza N1 and N2 Neuraminidase, Kristina L. Prachanronarong, Aysegul Ozen, Kelly Thayer, L. Safak Yilmaz, Konstantin B. Zeldovich, Daniel N. Bolon, Timothy F. Kowalik, Jeffrey D. Jensen, Robert W. Finberg, Jennifer P. Wang, Nese Kurt Yilmaz, and Celia A. Schiffer

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Mapping the 3D genome: Aiming for consilience, Job Dekker (Nature reviews. Molecular cell biology)

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RUNX1 contributes to higher-order chromatin organization and gene regulation in breast cancer cells, A. Rasim Barutcu, Deli Hong, Bryan R. Lajoie, Rachel Patton McCord, Andre J. van Wijnen, Jane B. Lian, Janet L. Stein, Job Dekker, Anthony N. Imbalzano, and Gary S. Stein (Biochimica et biophysica acta)

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Crystal structure of the DNA binding domain of the transcription factor T-bet suggests simultaneous recognition of distant genome sites, Ce Feng Liu, Gabriel S. Brandt, Quyen Q. Hoang, Natalia Naumova, Vanja Lazarevic, Eun Sook Hwang, Job Dekker, Laurie H. Glimcher, Dagmar Ringe, and Gregory A. Petsko (Proceedings of the National Academy of Sciences of the United States of America)

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A gene-centered C. elegans protein-DNA interaction network provides a framework for functional predictions, Juan Fuxman Bass, Carles Pons, Lucie Kozlowski, John S. Reece-Hoyes, Shaleen Shrestha, Amy D. Holdorf, Akihiro Mori, Chad L. Myers, and Albertha J. M. Walhout

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Cellular perception and misperception: Internal models for decision-making shaped by evolutionary experience, Amir Mitchell and Wendell Lim (BioEssays : news and reviews in molecular, cellular and developmental biology)

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SMARCA4 regulates gene expression and higher-order chromatin structure in proliferating mammary epithelial cells, A. Rasim Barutcu, Bryan R. Lajoie, Andrew J. Fritz, Rachel P. McCord, Jeffrey A. Nickerson, Andre J. van Wijnen, Jane B. Lian, Janet L. Stein, Job Dekker, Gary S. Stein, and Anthony N. Imbalzano (Genome research)

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Structural organization of the inactive X chromosome in the mouse, Luca Giorgetti, Bryan R. Lajoie, Ava C. Carter, Mikael Attia, Ye Zhan, Jin Xu, Chong Jian Chen, Noam Kaplan, Howard Y. Chang, Edith Heard, and Job Dekker (Nature)

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Metabolic network rewiring of propionate flux compensates vitamin B12 deficiency in C. elegans, Emma Watson, Viridiana Olin-Sandoval, Michael J. Hoy, Chi-Hua Li, Timo Louisse, Victoria Yao, Akihiro Mori, Amy D. Holdorf, Olga G. Troyanskaya, Markus Ralser, and Albertha J. M. Walhout

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A Caenorhabditis elegans Genome-Scale Metabolic Network Model, L. Safak Yilmaz and Albertha J. M. Walhout (Cell systems)

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Patterns of Growth and Decline in Lung Function in Persistent Childhood Asthma, Michael J. McGeachie, Gaurav Jain, Amartya Sanyal, Ye Zhan, Bryan R. Lajoie, Job Dekker, Scott T. Weiss, and CAMP Research Group (The New England journal of medicine)

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Local Genome Topology Can Exhibit an Incompletely Rewired 3D-Folding State during Somatic Cell Reprogramming, Jonathan A. Beagan, Thomas G. Gilgenast, Jesi Kim, Zachary Plona, Heidi K. Norton, Gui Hu, Sarah C. Hsu, Emily J. Shields, Xiaowen Lyu, Effie Apostolou, Konrad Hochedlinger, Victor G. Corces, Job Dekker, and Jennifer E. Phillips-Cremins (Cell stem cell)

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The 3D Genome as Moderator of Chromosomal Communication, Job Dekker and Leonid A. Mirny (Cell)

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Using synthetic biology to make cells tomorrow's test tubes, Hernan G. Garcia, Robert C. Brewster, and Rob Phillips (Integrative biology : quantitative biosciences from nano to macro)

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Activation of proto-oncogenes by disruption of chromosome neighborhoods, Denes Hnisz, Abraham S. Weintraub, Daniel S. Day, Anne-Laure Valton, Rasmus O. Bak, Charles H. Li, Johanna Goldmann, Bryan R. Lajoie, Zi Peng Fan, Alla A. Sigova, Jessica Reddy, Diego Borges-Rivera, Tong Ihn Lee, Rudolf Jaenisch, Matthew H. Porteus, Job Dekker, and Richard A. Young (Science (New York, N.Y.))

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Computational Approaches for the Analysis of Chromosome Conformation Capture Data and Their Application to Study Long-Range Gene Regulation: A Dissertation, Bryan R. Lajoie

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Extremely Long-Range Chromatin Loops Link Topological Domains to Facilitate a Diverse Antibody Repertoire, Lindsey Montefiori, Robert Wuerffel, Damian Roqueiro, Bryan R. Lajoie, Changying Guo, Tatiana Gerasimova, Supriyo De, William Wood, Kevin G. Becker, Job Dekker, Jie Liang, Ranjan Sen, and Amy L. Kenter (Cell reports)

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TAD disruption as oncogenic driver, Anne-Laure Valton and Job Dekker (Current opinion in genetics and development)

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Invariant TAD Boundaries Constrain Cell-Type-Specific Looping Interactions between Promoters and Distal Elements around the CFTR Locus, Emily M. Smith, Bryan R. Lajoie, Gaurav Jain, and Job Dekker (American journal of human genetics)

Publications from 2015

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HiC-Pro: an optimized and flexible pipeline for Hi-C data processing, Nicolas Servant, Nelle Varoquaux, Bryan R. Lajoie, Eric Viara, Chong-Jian Chen, Jean-Philippe Vert, Edith Heard, Job Dekker, and Emmanuel Barillot

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The Conformation of Yeast Chromosome III Is Mating Type Dependent and Controlled by the Recombination Enhancer, Jon-Matthew Belton, Bryan R. Lajoie, Sylvain Audibert, Sylvain Cantaloube, Imen Lassadi, Isabelle Goiffon, Davide Bau, Marc A. Marti-Renom, Kerstin Bystricky, and Job Dekker

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Understanding Metabolic Regulation at a Systems Level: Metabolite Sensing, Mathematical Predictions, and Model Organisms, Emma Watson, L. Safak Yilmaz, and Albertha J. M. Walhout (Annual review of genetics)

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Structural and functional diversity of Topologically Associating Domains, Job Dekker and Edith Heard (FEBS letters)

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Structural and functional diversity of Topologically Associating Domains, Job Dekker and Edith Heard (FEBS letters)

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High-Affinity Sites Form an Interaction Network to Facilitate Spreading of the MSL Complex across the X Chromosome in Drosophila, Fidel Ramirez, Thomas Lingg, Sarah Toscano, Kin Chung. Lam, Plamen Georgiev, Ho-Ryun Chung, Bryan R. Lajoie, Elzo de Wit, Ye Zhan, Wouter de Laat, Job Dekker, Thomas Manke, and Asifa Akhtar (Molecular cell)

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Long-Range Chromatin Interactions, Job Dekker and Tom Misteli (Cold Spring Harbor perspectives in biology)

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Chromatin interaction analysis reveals changes in small chromosome and telomere clustering between epithelial and breast cancer cells, Ahmet Rasim Barutcu, Bryan R. Lajoie, Rachel Patton McCord, Coralee E. Tye, Deli Hong, Terri L. Messier, Gillian Browne, Andre J. van Wijnen, Jane B. Lian, Janet L. Stein, Job Dekker, Anthony N. Imbalzano, and Gary S. Stein (Genome biology)

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Genome-wide Maps of Nuclear Lamina Interactions in Single Human Cells, Jop Kind, Ludo Pagie, Sandra S. de Vries, Leila Nahidiazar, Siddharth S. Dey, Magda Bienko, Ye Zhan, Bryan Lajoie, Carolyn A. de Graaf, Mario Amendola, Geoffrey Fudenberg, Maxim Imakaev, Leonid A. Mirny, Kees Jalink, Job Dekker, Alexander van Oudenaarden, and Bas van Steensel (Cell)

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Transcription Factor Activity Mapping of a Tissue-Specific Gene Regulatory Network, Lesley T. MacNeil, Carles Pons, H. Efsun Arda, Gabrielle E. Giese, Chad L. Myers, and Albertha J. M. Walhout (Cell systems)

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Studying Cellular Signal Transduction with OMIC Technologies, Benjamin D. Landry, David C. Clarke, and Michael J. Lee (Journal of molecular biology)

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Condensin promotes the juxtaposition of DNA flanking its loading site in Bacillus subtilis, Xindan Wang, Tung B. L. Le, Bryan R. Lajoie, Job Dekker, Michael T. Laub, and David Z. Rudner (Genes and development)

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The yeast genome undergoes significant topological reorganization in quiescence, Mark T. Rutledge, Mariano Russo, Jon-Matthew Belton, Job Dekker, and James R. Broach (Nucleic acids research)

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Condensin-driven remodelling of X chromosome topology during dosage compensation, Emily Crane, Qian Bian, Rachel Patton McCord, Bryan R. Lajoie, Bayly S. Wheeler, Edward J. Ralston, Satoru Uzawa, Job Dekker, and Barbara J. Meyer (Nature)

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Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C, Tsung-Han S. Hsieh, Assaf Weiner, Bryan R. Lajoie, Job Dekker, Nir Friedman, and Oliver J. Rando (Cell)

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Hi-C in Budding Yeast, Jon-Matthew Belton and Job Dekker (Cold Spring Harbor protocols)

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Measuring Chromatin Structure in Budding Yeast, Jon-Matthew Belton and Job Dekker (Cold Spring Harbor protocols)

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Chromosome Conformation Capture (3C) in Budding Yeast, Jon-Matthew Belton and Job Dekker (Cold Spring Harbor protocols)

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Chromosome Conformation Capture Carbon Copy (5C) in Budding Yeast, Jon-Matthew Belton and Job Dekker (Cold Spring Harbor protocols)

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Randomized ligation control for chromosome conformation capture, Jon-Matthew Belton and Job Dekker (Cold Spring Harbor protocols)

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Human gene-centered transcription factor networks for enhancers and disease variants, Juan Fuxman Bass, Nidhi Sahni, Shaleen Shrestha, Aurian Garcia-Gonzalez, Akihiro Mori, Numana Bhat, Song Yi, David E. Hill, Marc Vidal, and Albertha J. M. Walhout (Cell)

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Mapping and analysis of Caenorhabditis elegans transcription factor sequence specificities, Kamesh Narasimhan, Samuel A. Lambert, Ally Yang, Jeremy Riddell, Sanie Mnaimneh, Hong Zheng, Mihai Albu, Hamed S. Najafabadi, John S. Reece-Hoyes, Juan Fuxman Bass, Albertha J. M. Walhout, Matthew T. Weirauch, and Timothy R. Hughes (Elife)

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Widespread macromolecular interaction perturbations in human genetic disorders, Nidhi Sahni, Song Yi, Mikko Taipale, Juan Fuxman Bass, Jasmin Coulombe-Huntington, Frederick P. Roth, Yu Xia, Albertha J. M. Walhout, Susan Lindquist, and Marc Vidal (Cell)

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Spatial enhancer clustering and regulation of enhancer-proximal genes by cohesin, Elizabeth Ing-Simmons, Vlad C. Seitan, Andre J. Faure, Paul Flicek, Thomas Carroll, Job Dekker, Amanda G. Fisher, Boris Lenhard, and Matthias Merkenschlager (Genome research)

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Let a hundred flowers bloom: the role of context dependence in creating phenotypic diversity following targeted therapy, Michael J. Lee (Molecular cell)

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RNA Interference in Caenorhabditis elegans, Darryl Conte Jr., Lesley T. MacNeil, Albertha J. M. Walhout, and Craig C. Mello (Current protocols in molecular biology / edited by Frederick M. Ausubel ... [et al.])

Publications from 2014

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Cohesin-dependent globules and heterochromatin shape 3D genome architecture in S. pombe, Takeshi Mizuguchi, Geoffrey Fudenberg, Sameet Mehta, Jon-Matthew Belton, Nitika Taneja, Hernan Diego Folco, Peter FitzGerald, Job Dekker, Leonid Mirny, Jemima Barrowman, and Shiv I. S. Grewal (Nature)

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Two ways to fold the genome during the cell cycle: insights obtained with chromosome conformation capture, Job Dekker

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The Hitchhiker's guide to Hi-C analysis: Practical guidelines, Bryan R. Lajoie, Job Dekker, and Noam Kaplan (Methods (San Diego, Calif.))

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Worms, bacteria, and micronutrients: an elegant model of our diet, L. Safak Yilmaz and Albertha J. M. Walhout (Trends in genetics : TIG)

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Caenorhabditis elegans metabolic gene regulatory networks govern the cellular economy, Emma Watson and Albertha J. M. Walhout (Trends in endocrinology and metabolism: TEM)

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Determination and inference of eukaryotic transcription factor sequence specificity, Matthew T. Weirauch, Ally Yang, Mihai Albu, Atina G. Cote, Alejandro Montenegro-Montero, Philipp Drewe, Hamed S. Najafabadi, Samuel A. Lambert, Ishminder Mann, Kate Cook, Hong Zheng, Alejandra Goity, Harm van Bakel, Jean-Claude Lozano, Mary Galli, Mathew G. Lewsey, Eryong Huang, Tuhin Mukherjee, Xiaoting Chen, John S. Reece-Hoyes, Sridhar Govindarajan, Gad Shaulsky, Albertha J. M. Walhout, Francois-Yves Bouget, Gunnar Ratsch, Luis F. Larrondo, Joseph R. Ecker, and Timothy R. Hughes (Cell)

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Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease, Manolis Kellis, Job Dekker, Zhiping Weng, and Ross C. Hardison (Proceedings of the National Academy of Sciences of the United States of America)

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A nanoparticle-based combination chemotherapy delivery system for enhanced tumor killing by dynamic rewiring of signaling pathways, Stephen W. Morton, Michael J. Lee, Zhou J. Deng, Erik C. Dreaden, Elise Siouve, Kevin E. Shopsowitz, Nisarg J. Shah, Michael B. Yaffe, and Paula T. Hammond (Science signaling)

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Multiple transcription factors directly regulate Hox gene lin-39 expression in ventral hypodermal cells of the C. elegans embryo and larva, including the hypodermal fate regulators LIN-26 and ELT-6, Wan-Ju Liu, John S. Reece-Hoyes, Albertha J. M. Walhout, and David M. Eisenmann (BMC developmental biology)

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Predictive polymer modeling reveals coupled fluctuations in chromosome conformation and transcription, Luca Giorgetti, Rafael Galupa, Elphege P. Nora, Tristan Piolot, France Lam, Job Dekker, Guido Tiana, and Edith Heard (Cell)

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Defining functional DNA elements in the human genome, Manolis Kellis, Barbara Wold, Michael P. Snyder, Bradley E. Bernstein, Anshul Kundaje, Georgi K. Marinov, Lucas D. Ward, Job Dekker, Zhiping Weng, Ross C. Hardison, and ENCODE Project Consortium (Proceedings of the National Academy of Sciences of the United States of America)

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Transcriptional regulation of Caenorhabditis elegans FOXO/DAF-16 modulates lifespan, Ankita Bansal, Eun-Soo Kwon, Darryl Conte Jr., Haibo Liu, Michael J. Gilchrist, Lesley T. MacNeil, and Heidi A. Tissenbaum

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Interspecies Systems Biology Uncovers Metabolites Affecting C. elegans Gene Expression and Life History Traits, Emma Watson, Lesley T. MacNeil, Ashlyn D. Ritter, L. Safak Yilmaz, Adam P. Rosebrock, Amy A. Caudy, and Albertha J. M. Walhout (Cell)

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Genetic adaptation to diet preserves longevity, Albertha J. M. Walhout (Cell Metabolism)

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Transcription factor binding to Caenorhabditis elegans first introns reveals lack of redundancy with gene promoters, Juan I. Fuxman Bass, Alex M. Tamburino, Akihiro Mori, Nathan Beittel, Matthew T. Weirauch, John S. Reece-Hoyes, and Albertha J. M. Walhout (Nucleic acids research)

Publications from 2013

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Cohesin-based chromatin interactions enable regulated gene expression within pre-existing architectural compartments, Vlad Seitan, Andre Faure, Ye Zhan, Rachel Patton McCord, Bryan R. Lajoie, Elizabeth Ing-Simmons, Boris Lenhard, Luca Giorgetti, Edith Heard, Amanda Fisher, Paul Flicek, Job Dekker, and Matthias Merkenschlager (Genome research)

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Using networks to measure similarity between genes: association index selection, Juan I. Fuxman Bass, Alos Diallo, Justin Nelson, Juan M. Soto, Chad L. Myers, and Albertha J. M. Walhout (Nature methods)

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High-throughput genome scaffolding from in vivo DNA interaction frequency, Noam Kaplan and Job Dekker (Nature biotechnology)

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Organization of the mitotic chromosome, Natalia Naumova, Maxim Imakaev, Geoffrey Fudenberg, Ye Zhan, Bryan R. Lajoie, Leonid A. Mirny, and Job Dekker (Science (New York, N.Y.))

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Flexible ordering of antibody class switch and V(D)J joining during B-cell ontogeny, Satyendra Kumar, Robert Wuerffel, Ikbel Achour, Bryan R. Lajoie, Ranjan Sen, Job Dekker, Ann J. Feeney, and Amy L. Kenter (Genes and development)

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Food, pathogen, signal: The multifaceted nature of a bacterial diet, Lesley T. MacNeil and Albertha J. M. Walhout (Worm)

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Biological techniques: Chromosomes captured one by one, Job Dekker and Leonid A. Mirny (Nature)

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Segmental folding of chromosomes: A basis for structural and regulatory chromosomal neighborhoods?, Elphege P. Nora, Job Dekker, and Edith Heard (BioEssays : news and reviews in molecular, cellular and developmental biology)

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Extensive Rewiring and Complex Evolutionary Dynamics in a C. elegans Multiparameter Transcription Factor Network, John S. Reece-Hoyes, Carles Pons, Alos Diallo, Akihiro Mori, Shaleen Shrestha, Sreenath Kadreppa, Justin Nelson, Stephanie Diprima, Amelie Dricot, Bryan R. Lajoie, Philippe Souza Moraes Ribeiro, Matthew T. Weirauch, David E. Hill, Timothy R. Hughes, Chad L. Myers, and Albertha J. M. Walhout (Molecular cell)

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The bromodomain protein Brd4 insulates chromatin from DNA damage signalling, Scott R. Floyd, Michael E. Pacold, Qiuying Huang, Scott M. Clarke, Fred C. Lam, Ian G. Cannell, Bryan D. Bryson, Jonathan Rameseder, Michael J. Lee, Emily J. Blake, Anna Fydrych, Richard Ho, Benjamin A. Greenberger, Grace C. Chen, Amanda Maffa, Amanda M. Del Rosario, David E. Root, Anne E. Carpenter, William C. Hahn, David M. Sabatini, Clark C. Chen, Forest M. White, James E. Bradner, and Michael B. Yaffe (Nature)

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Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment, Jennifer E. Phillips-Cremins, Michael E. G. Sauria, Amartya Sanyal, Tatiana I. Gerasimova, Bryan R. Lajoie, Joshua S. K. Bell, Chin-Tong Ong, Tracy A. Hookway, Changying Guo, Yuhua Sun, Michael J. Bland, William Wagstaff, Stephen Dalton, Todd C. McDevitt, Ranjan Sen, Job Dekker, James Taylor, and Victor G. Corces (Cell)

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Complex expression dynamics and robustness in C. elegans insulin networks, Ashlyn D. Ritter, Yuan Shen, Juan Fuxman Bass, Sankarganesh Jeyaraj, Bart Deplancke, Arnab Mukhopadjay, Jian Xu, Monica Driscoll, Heidi A. Tissenbaum, and Albertha J. M. Walhout (Genome research)

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Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data, Job Dekker, Marc A. Marti-Renom, and Leonid A. Mirny (Nature reviews. Genetics)

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Diet-Induced Developmental Acceleration Independent of TOR and Insulin in C. elegans, Lesley T. MacNeil, Emma Watson, H. Efsun Arda, Lihua Julie Zhu, and Albertha J. M. Walhout (Cell)

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Integration of Metabolic and Gene Regulatory Networks Modulates the C. elegans Dietary Response, Emma Watson, Lesley T. MacNeil, H. Efsun Arda, Lihua Julie Zhu, and Albertha J. M. Walhout (Cell)

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Folding principles of genomes, Job Dekker

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Mating type specific chromosome conformation in Saccharomyces cerevisiae, Jon-Matthew Belton, Davide Bau, Imen Lassardi, Kerstin Bystricky, Marc A. Marti-Renom, and Job Dekker

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Nuclear biology: what's been most surprising, Job Dekker, Joanna Wysocka, Iain Mattaj, Erez Lieberman-Aiden, and Craig Pikaard (Cell)

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The Hierarchy of the 3D Genome, Johan H. Gibcus and Job Dekker (Molecular cell)

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A compendium of Caenorhabditis elegans RNA binding proteins predicts extensive regulation at multiple levels, Alex M. Tamburino, Sean P. Ryder, and Albertha J. M. Walhout (G3 (Bethesda, Md.))

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Correlated alterations in genome organization, histone methylation, and DNA-lamin A/C interactions in Hutchinson-Gilford progeria syndrome, Rachel Patton McCord, Ashley Nazario-Toole, Haoyue Zhang, Peter Chines, Ye Zhan, Michael Erdos, Francis Collins, Job Dekker, and Kan Cao (Genome research)

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Handbook of Systems Biology: Concepts and Insights, Albertha J. M. Walhout, Marc Vidal, and Job Dekker (Program in Systems Biology Publications and Presentations)

Publications from 2012

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3C-based technologies to study the shape of the genome, Wouter de Laat and Job Dekker (Methods (San Diego, Calif.))

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Analysis of long-range chromatin interactions using Chromosome Conformation Capture, Natalia Naumova, Emily M. Smith, Ye Zhan, and Job Dekker (Methods (San Diego, Calif.))

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From cells to chromatin: Capturing snapshots of genome organization with 5C technology, Maria A. Ferraiuolo, Amartya Sanyal, Natalia Naumova, Job Dekker, and Josee Dostie (Methods (San Diego, Calif.))

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HiTC : Exploration of High-Throughput 'C' experiments, Nicolas Servant, Bryan R. Lajoie, Elphege P. Nora, Luca Giorgetti, Chongjian Chen, Edith Heard, Job Dekker, and Emmanuel Barillot (Bioinformatics (Oxford, England))

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An integrated encyclopedia of DNA elements in the human genome, Ian Dunham, Ewan Birney, Bryan R. Lajoie, Amartya Sanyal, Xianjun Dong, Melissa Greven, Xinying Lin, Jie Wang, Troy W. Whitfield, Jiali Zhuang, Job Dekker, Zhiping Weng, Gaurav Jain, and ENCODE Project Consortium (Nature)

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The long-range interaction landscape of gene promoters, Amartya Sanyal, Bryan R. Lajoie, Gaurav Jain, and Job Dekker

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Iterative correction of Hi-C data reveals hallmarks of chromosome organization, Maxim Imakaev, Geoffrey Fudenberg, Rachel Patton McCord, Natalia Naumova, Anton Goloborodko, Bryan R. Lajoie, Job Dekker, and Leonid A. Mirny (Nature methods)

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An encyclopedia of mouse DNA elements (Mouse ENCODE), Mouse ENCODE Consortium, John A. Stamatoyannopoulos, Michael Snyder, Ross Hardison, Bing Ren, Job Dekker, Bryan R. Lajoie, Gaurav Jain, and Amartya Sanyal (Genome biology)

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Yeast one-hybrid assays: A historical and technical perspective, John S. Reece-Hoyes and Albertha J. M. Walhout (Methods (San Diego, Calif.))

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MORC family ATPases required for heterochromatin condensation and gene silencing, Guillaume Moissiard, Shawn J. Cokus, Joshua Cary, Suhua Feng, Allison C. Billi, Hume Stroud, Dylan Husmann, Ye Zhan, Bryan R. Lajoie, Rachel Patton McCord, Christopher J. Hale, Wei Feng, Scott D. Michaels, Alison R. Frand, Matteo Pellegrini, Job Dekker, John K. Kim, and Steven E. Jacobsen (Science (New York, N.Y.))

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CTCF and cohesin help neurons raise their self-awareness, Job Dekker

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Hi-C: A comprehensive technique to capture the conformation of genomes, Jon-Matthew Belton, Rachel Patton McCord, Johan H. Gibcus, Natalia Naumova, Ye Zhan, and Job Dekker

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Understanding the mechanisms of IGF2 gene regulation in hepatocellular carcinoma cells, Amalene Cooper-Morgan, Natalia Naumova, Amartya Sanyal, Bryan R. Lajoie, Job Dekker, and Brian C. Lewis

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Spatial partitioning of the regulatory landscape of the X-inactivation centre, Elphege P. Nora, Bryan R. Lajoie, Edda G. Schulz, Luca Giorgetti, Ikuhiro Okamoto, Nicolas Servant, Tristan Piolot, Nynke L. van Berkum, Johannes Meisig, John Sedat, Joost Gribnau, Emmanuel Barillot, Nils Bluthgen, Job Dekker, and Edith Heard (Nature)

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Sequential application of anticancer drugs enhances cell death by rewiring apoptotic signaling networks, Michael J. Lee, Albert S. Ye, Alexandra K. Gardino, Anne Margriet Heijink, Peter K. Sorger, Gavin MacBeath, and Michael B. Yaffe (Cell)

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Genome architecture and expression, Gary Felsenfeld and Job Dekker (Current opinion in genetics and development)