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. This collection showcases the journal articles and other publications written by faculty and researchers of the Program in Systems Biology at the University of Massachusetts Medical School.

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Publications from 2020

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Metabolic interactions in microbial communities, Elizabeth A. Shank

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Large domains of heterochromatin direct the formation of short mitotic chromosome loops, Maximilian H. Fitz-James, Pin Tong, Alison L. Pidoux, Hakan Ozadam, Liyan Yang, Sharon A. White, Job Dekker, and Robin C. Allshire

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Natural variation in a glucuronosyltransferase modulates propionate sensitivity in a C. elegans propionic acidemia model, Huimin Na, Stefan Zdraljevic, Robyn E. Tanny, Albertha J. M. Walhout, and Erik C. Andersen

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Unmasking Oncogene Addiction to the Epidermal Growth Factor Receptor in Triple Negative Breast Cancer: a Lesson in Intrinsic Resistance, Peter G. Cruz-Gordillo

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Inherent regulatory asymmetry emanating from network architecture in a prevalent autoregulatory motif, Zulfikar Ali, Vinuselvi Parisutham, Sandeep Choubey, and Robert C. Brewster

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Expanded encyclopaedias of DNA elements in the human and mouse genomes, ENCODE Project Consortium, Jill E. Moore, Michael J. Purcaro, Henry E. Pratt, Xiao-Ou Zhang, Shaimae I. Elhajjajy, Jack Huey, Job Dekker, J. Michael Cherry, Richard M. Myers, Bing Ren, Brenton R. Graveley, Mark B. Gerstein, Len A. Pennacchio, Michael P. Snyder, Bradley E. Bernstein, Barbara Wold, Ross C. Hardison, Thomas R. Gingeras, John A. Stamatoyannopoulos, and Zhiping Weng

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Building the Interphase Nucleus: A study on the kinetics of 3D chromosome formation, temporal relation to active transcription, and the role of nuclear RNAs, Kristin N. Abramo

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Chromosome-scale assembly of the coral endosymbiont Symbiodinium microadriaticum genome provides insight into the unique biology of dinoflagellate chromosomes [preprint], Ankita Nand, Ye Zhan, Octavio R. Salazar, Manuel Aranda, Christian R. Voolstra, and Job Dekker

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Drug antagonism and single-agent dominance result from differences in death kinetics, Ryan Richards, Hannah R. Schwartz, Megan E. Honeywell, Mariah S. Stewart, Peter Cruz-Gordillo, Anna J. Joyce, Benjamin D. Landry, and Michael J. Lee

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Mechanisms and Functions of Chromosome Compartmentalization, Erica M. Hildebrand and Job Dekker

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Probing Mechanisms of Transcription Elongation Through Cell-to-Cell Variability of RNA Polymerase, Zulfikar Ali, Sandeep Choubey, Dipjyoti Das, and Robert C. Brewster (Biophysical journal, 2020-04-07)

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Flexibility and constraint in preimplantation gene regulation in mouse [preprint], Colin C. Conine, Marina Krykbaeva, Lina Song, Robert C. Brewster, Nir Friedman, and Oliver J. Rando

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Ultrastructural Details of Mammalian Chromosome Architecture, Nils Krietenstein, Sameer Abraham, Sergey V. Venev, Nezar Abdennur, Johan H. Gibcus, Tsung-Han S. Hsieh, Krishna M. Parsi, Liyan Yang, Rene Maehr, Leonid A. Mirny, Job Dekker, and Oliver J. Rando (Molecular cell, 2020-03-14)

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Detecting chromatin interactions along and between sister chromatids with SisterC [preprint], Marlies E. Oomen, Adam K. Hedger, Jonathan K. Watts, and Job Dekker

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The Cancer Microbiome: Distinguishing Direct and Indirect Effects Requires a Systemic View, Joao B. Xavier and Amir Mitchell

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SPEN integrates transcriptional and epigenetic control of X-inactivation, Francois Dossin, Ines Pinheiro, Jan J. Zylicz, Julia Roensch, Samuel Collombet, Agnes Le Saux, Tomasz Chelmicki, Mikael Attia, Varun Kapoor, Ye Zhan, Florent Dingli, Damarys Loew, Thomas Mercher, Job Dekker, and Edith Heard (Nature, 2020-02-05)

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Transcriptional Silencers in Drosophila Serve a Dual Role as Transcriptional Enhancers in Alternate Cellular Contexts, Stephen S. Gisselbrecht, Alexandre Palagi, Jesse V. Kurland, Julia M. Rogers, Hakan Ozadam, Ye Zhan, Job Dekker, and Martha L. Bulyk (Molecular cell, 2020-01-16)

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Beclin 1 Promotes Endosome Recruitment of Hepatocyte Growth Factor Tyrosine Kinase Substrate to Suppress Tumor Proliferation, Asia N. Matthew-Onabanjo, Jenny Janusis, Jose Mercado-Matos, Anne E. Carlisle, Dohoon Kim, Fayola Levine, Peter Cruz-Gordillo, Ryan Richards, Michael J. Lee, and Leslie M. Shaw (Cancer research, 2020-01-15)

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LncRNA RP11-19E11 is an E2F1 target required for proliferation and survival of basal breast cancer, A. Giro-Perafita, L. Luo, A. Khodadadi-Jamayran, M. Thompson, Betul Akgol-Oksuz, A. Tsirigos, B. D. Dynlacht, I. Sanchez, and F. J. Esteva

Publications from 2019

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WormCat: An Online Tool for Annotation and Visualization of Caenorhabditis elegans Genome-Scale Data, Amy D. Holdorf, Daniel P. Higgins, Anne C. Hart, Peter R. Boag, Gregory J. Pazour, Albertha J. M. Walhout, and Amy K. Walker (Genetics, 2019-12-06)

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Regulatory asymmetry in the negative single-input module network motif: Role of network size, growth rate and binding affinity [preprint], Zulfikar Ali, Vinuselvi Parisutham, Sandeep Choubey, and Robert C. Brewster

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WormCat: an online tool for annotation and visualization of Caenorhabditis elegans genome-scale data [preprint], Amy D. Holdorf, Daniel P. Higgins, Anne C. Hart, Peter R. Boag, Gregory J. Pazour, Albertha J. M. Walhout, and Amy K. Walker

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A Cohesin Subunit Variant Identified from a Peripheral Sclerocornea Pedigree, Bi Ning Zhang, Tommy Chung Yan Chan, Pancy Oi Sin Tam, Yu Liu, Chi Pui Pang, Vishal Jhanji, Li Jia Chen, and Wai Kit Chu

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A chromosome folding intermediate at the condensin-to-cohesin transition during telophase, Kristin Abramo, Anne-Laure Valton, Sergey V. Venev, Hakan Ozadam, A. Nicole Fox, and Job Dekker (Nature cell biology, 2019-11-01)

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MDT-28/PLIN-1 mediates lipid droplet-microtubule interaction via DLC-1 in Caenorhabditis elegans, Kang Xie, Peng Zhang, Huimin Na, Yangli Liu, Hong Zhang, and Pingsheng Liu

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Highly structured homolog pairing reflects functional organization of the Drosophila genome, Jumana AlHaj Abed, Jelena Erceg, Anton Goloborodko, Son C. Nguyen, Ruth B. McCole, Wren Saylor, Geoffrey Fudenberg, Bryan R. Lajoie, Job Dekker, Leonid A. Mirny, and C-Ting Wu (Nature communications, 2019-10-03)

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The genome-wide multi-layered architecture of chromosome pairing in early Drosophila embryos, Jelena Erceg, Jumana AlHaj Abed, Anton Goloborodko, Bryan R. Lajoie, Geoffrey Fudenberg, Nezar Abdennur, Maxim Imakaev, Ruth B. McCole, Son C. Nguyen, Wren Saylor, Eric F. Joyce, T. Niroshini Senaratne, Mohammed A. Hannan, Guy Nir, Job Dekker, Leonid A. Mirny, and C-Ting Wu (Nature communications, 2019-10-03)

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A Delicate Balance between Bacterial Iron and Reactive Oxygen Species Supports Optimal C. elegans Development, Jingyan Zhang, Xuhang Li, Maria Olmedo, Amy D. Holdorf, Ye Shang, Marta Artal-Sanz, L. Safak Yilmaz, and Albertha J. M. Walhout (Cell host and microbe, 2019-09-11)

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Cohesin Members Stag1 and Stag2 Display Distinct Roles in Chromatin Accessibility and Topological Control of HSC Self-Renewal and Differentiation, Aaron D. Viny, Yu Liu, Job Dekker, and Ross L. Levine (Cell stem cell, 2019-08-30)

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Modeling of Cisplatin-Induced Signaling Dynamics in Triple-Negative Breast Cancer Cells Reveals Mediators of Sensitivity, Anne Margriet Heijink, Marieke Everts, Megan E. Honeywell, Ryan Richards, Yannick P. Kok, Elisabeth G. E. de Vries, Michael J. Lee, and Marcel A T M van Vugt

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Chromatin Interaction Dynamics Revealed by Liquid Chromatin Hi-C, Houda Belaghzal

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Rapid Irreversible Transcriptional Reprogramming in Human Stem Cells Accompanied by Discordance between Replication Timing and Chromatin Compartment, Vishnu Dileep, Rachel Patton McCord, Job Dekker, and David M. Gilbert

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Harnessing robotic automation and web-based technologies to modernize scientific outreach, Orna Dahan, Bat-Shahar Dorfman, Serkan Sayin, Brittany Rosener, Tiffany Hua, Anat Yarden, and Amir Mitchell

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A chromosome folding intermediate at the condensin-to-cohesin transition during telophase [preprint], Kristin Abramo, Anne-Laure Valton, Sergey V. Venev, Hakan Ozadam, A. Nicole Fox, and Job Dekker

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Heterochromatin drives compartmentalization of inverted and conventional nuclei, Martin Falk, Yana Feodorova, Natalia Naumova, Maxim Imakaev, Bryan R. Lajoie, Heinrich Leonhardt, Boris Joffe, Job Dekker, Geoffrey Fudenberg, Irina Solovei, and Leonid A. Mirny (Nature, 2019-06-05)

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Caenorhabditis elegans as a Model for Host-Microbe-Drug Interactions, Aurian P. Garcia Gonzalez

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Measuring the reproducibility and quality of Hi-C data, Galip Gurkan Yardimci, Hakan Ozadam, Bryan R. Lajoie, Ye Zhan, Job Dekker, and William S. Noble

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Genome-wide prediction of synthetic rescue mediators of resistance to targeted and immunotherapy, Avinash Das Sahu, Olga Ponomarova, and Eytan Ruppin

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Extensive Heterogeneity and Intrinsic Variation in Spatial Genome Organization, Elizabeth H. Finn, Gianluca Pegoraro, Hugo B. Brandao, Anne-Laure Valton, Marlies E. Oomen, Job Dekker, Leonid Mirny, and Tom Misteli (Cell, 2019-03-07)

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CTCF sites display cell cycle-dependent dynamics in factor binding and nucleosome positioning, Marlies E. Oomen, Anders S. Hansen, Yu Liu, Xavier Darzacq, and Job Dekker (Genome research, 2019-02-01)

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A Persistence Detector for Metabolic Network Rewiring in an Animal, Jote T. Bulcha, Gabrielle E. Giese, Zulfikar Ali, Yong-Uk Lee, Melissa D. Walker, Amy D. Holdorf, L. Safak Yilmaz, Robert C. Brewster, and Albertha J. M. Walhout

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The non-canonical SMC protein SmcHD1 antagonises TAD formation and compartmentalisation on the inactive X chromosome, Michal R. Gdula, Tatyana B. Nesterova, Greta Pintacuda, Jonathan Godwin, Ye Zhan, Hakan Ozadam, Michael McClellan, Daniella Moralli, Felix Krueger, Catherine M. Green, Wolf Reik, Skirmantas Kriaucionis, Edith Heard, Job Dekker, and Neil Brockdorff

Publications from 2018

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The Caenorhabditis elegans Oxidative Stress Response Requires the NHR-49 Transcription Factor, Queenie Hu, Dayana R. D'Amora, Lesley T. MacNeil, Albertha J. M. Walhout, and Terrance J. Kubiseski

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Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains, A. Marieke Oudelaar, James O. J. Davies, Lars L. P. Hanssen, Jelena M. Telenius, Ron Schwessinger, Yu Liu, Jill M. Brown, Damien J. Downes, Andrea M. Chiariello, Simona Bianco, Mario Nicodemi, Veronica J. Buckle, Job Dekker, Douglas R. Higgs, and Jim R. Hughes (Nature genetics, 2018-12)

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Higher-Order Organization Principles of Pre-translational mRNPs, Mihir Metkar, Hakan Ozadam, Bryan R. Lajoie, Maxim Imakaev, Leonid A. Mirny, Job Dekker, and Melissa J. Moore (Molecular cell, 2018-11-15)

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Tumor-stroma interactions differentially alter drug sensitivity based on the origin of stromal cells, Benjamin D. Landry

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Covalent Docking Identifies a Potent and Selective MKK7 Inhibitor, Amit Shraga, Payam Khoshkenar, Amir Mitchell, and Nir London (Cell chemical biology, 2018-10-24)

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Functional conservation of a developmental switch in mammals since the Jurassic age, Jayati Mookerjee-Basu, Xiang Hua, Lu Ge, Emmanuelle Nicolas, Qin Li, Philip Czyzewicz, Dai Zhongping, Suraj Peri, Juan Fuxman Bass, Albertha J. M. Walhout, and Dietmar J. Kappes (Molecular biology and evolution, 2018-10-08)

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Integrative detection and analysis of structural variation in cancer genomes, Jesse R. Dixon, Ye Zhan, Hakan Ozadam, Bryan R. Lajoie, Ferhat Ay, William Stafford Noble, Job Dekker, David M. Gilbert, and Feng Yue (Nature genetics, 2018-10)

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3C-Based Chromatin Interaction Analyses, Tae Hoon Kim and Job Dekker (Cold Spring Harbor protocols, 2018-09-04)

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4C Analysis of 3C, ChIP-Loop, and Control Libraries, Tae Hoon Kim and Job Dekker (Cold Spring Harbor protocols, 2018-09-04)

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5C Analysis of 3C, ChIP-Loop, and Control Libraries, Tae Hoon Kim and Job Dekker (Cold Spring Harbor protocols, 2018-09-04)

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Polymerase Chain Reaction (PCR) Detection of 3C Ligation Products Present in 3C, ChIP-Loop, and Control Libraries: Library Titration and Interaction Frequency Analysis, Tae Hoon Kim and Job Dekker (Cold Spring Harbor protocols, 2018-09-04)

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Tumor-stroma interactions differentially alter drug sensitivity based on the origin of stromal cells, Benjamin D. Landry, Thomas Leete, Ryan Richards, Peter Cruz-Gordillo, Hannah R. Schwartz, Megan E. Honeywell, Gary Ren, Alyssa D. Schwartz, Shelly R. Peyton, and Michael J. Lee (Molecular systems biology, 2018-08-06)

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A Persistence Detector for Metabolic Network Rewiring in an Animal [preprint], Jote T. Bulcha, Gabrielle E. Giese, Zulfikar Ali, Yong-Uk Lee, Melissa D. Walker, Amy D. Holdorf, L. Safak Yilmaz, Robert C. Brewster, and Albertha J. M. Walhout

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Generation of 3C Libraries from Cross-Linked Cells, Tae Hoon Kim and Job Dekker (Cold Spring Harbor protocols, 2018-08-01)

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Generation of ChIP-Loop Libraries, Tae Hoon Kim and Job Dekker (Cold Spring Harbor protocols, 2018-08-01)

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Generation of Control Ligation Product Libraries for 3C Analyses, Tae Hoon Kim and Job Dekker (Cold Spring Harbor protocols, 2018-08-01)

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Gateway-Compatible Yeast One-Hybrid and Two-Hybrid Assays, John S. Reece-Hoyes and Albertha J. M. Walhout (Cold Spring Harbor protocols, 2018-07-02)

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Generating Yeast One-Hybrid DNA-Bait Strains, John S. Reece-Hoyes and Albertha J. M. Walhout (Cold Spring Harbor protocols, 2018-07-02)

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Generating Yeast Two-Hybrid Bait Strains, John S. Reece-Hoyes and Albertha J. M. Walhout (Cold Spring Harbor protocols, 2018-07-02)

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High-Efficiency Yeast Transformation, John S. Reece-Hoyes and Albertha J. M. Walhout (Cold Spring Harbor protocols, 2018-07-02)

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Identifying Interactors from an Activation Domain Prey Library, John S. Reece-Hoyes and Albertha J. M. Walhout (Cold Spring Harbor protocols, 2018-07-02)

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CBFbeta-SMMHC Inhibition Triggers Apoptosis by Disrupting MYC Chromatin Dynamics in Acute Myeloid Leukemia, John A. Pulikkan, Mahesh Hegde, Hafiz Mohd Ahmad, Houda Belaghzal, Anuradha Illendula, Jun Yu, Kelsey O'Hagan, Jianhong Ou, Carsten Muller-Tidow, Scot A. Wolfe, Lihua J. Zhu, Job Dekker, John Hackett Bushweller, and Lucio H. Castilla (Cell, 2018-06-28)

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C-BERST: defining subnuclear proteomic landscapes at genomic elements with dCas9-APEX2, Xin D. Gao, Li-Chun Tu, Aamir Mir, Tomas Rodriguez, Yue-He Ding, John D. Leszyk, Job Dekker, Scott A. Shaffer, Lihua Julie Zhu, Scot A. Wolfe, and Erik J. Sontheimer (Nature methods, 2018-05-07)

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Transcriptome-wide Interrogation of the Functional Intronome by Spliceosome Profiling, Weijun Chen, Jill E. Moore, Hakan Ozadam, Hennady P. Shulha, Nicholas Rhind, Zhiping Weng, and Melissa J. Moore

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ChIP-chip, Tae Hoon Kim and Job Dekker (Cold Spring Harbor protocols, 2018-05-01)

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ChIP-Quantitative Polymerase Chain Reaction (ChIP-qPCR), Tae Hoon Kim and Job Dekker (Cold Spring Harbor protocols, 2018-05-01)

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ChIP-seq, Tae Hoon Kim and Job Dekker (Cold Spring Harbor protocols, 2018-05-01)

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Chromatin Immunoprecipitation (ChIP) Analysis of Protein-DNA Interactions, Tae Hoon Kim and Job Dekker (Cold Spring Harbor protocols, 2018-05-01)

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If two deletions don't stop growth, try three, Albertha J. M. Walhout (Science (New York, N.Y.), 2018-04-20)

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ChIP, Tae Hoon Kim and Job Dekker (Cold Spring Harbor protocols, 2018-04-02)

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Formaldehyde Cross-Linking, Tae Hoon Kim and Job Dekker (Cold Spring Harbor protocols, 2018-04-02)

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Preparation of Cross-Linked Chromatin for ChIP, Tae Hoon Kim and Job Dekker (Cold Spring Harbor protocols, 2018-04-02)

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C. elegans MRP-5 Exports Vitamin B12 from Mother to Offspring to Support Embryonic Development, Huimin Na, Olga Ponomarova, Gabrielle E. Giese, and Albertha J. M. Walhout (Cell reports, 2018-03-20)

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Higher-Order Organization Principles of Pre-translational mRNPs [preprint], Mihir Metkar, Hakan Ozadam, Bryan R. Lajoie, Maxim Imakaev, Leonid A. Mirny, Job Dekker, and Melissa J. Moore

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DZNep inhibits H3K27me3 deposition and delays retinal degeneration in the rd1 mice, Shijie Zheng, Lirong Xiao, Yu Liu, Yujiao Wang, Lin Cheng, Junjun Zhang, Naihong Yan, and Danian Chen

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A pathway for mitotic chromosome formation, Johan H. Gibcus, Kumiko Samejima, Anton Goloborodko, Itaru Samejima, Natalia Naumova, Johannes Nuebler, Masato T. Kanemaki, Linfeng Xie, James R. Paulson, William C. Earnshaw, Leonid A. Mirny, and Job Dekker (Science (New York, N.Y.), 2018-02-09)

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Prognostic role of elevated mir-24-3p in breast cancer and its association with the metastatic process, Alireza Khodadadi-Jamayran, Betul Akgol-Oksuz, Yelena Afanasyeva, Adriana Heguy, Marae Thompson, Karina Ray, Ariadna Giro-Perafita, Irma Sanchez, Xifeng Wu, Debu Tripathy, Anne Zeleniuch-Jacquotte, Aristotelis Tsirigos, and Francisco J. Esteva

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C-BERST: Defining subnuclear proteomic landscapes at genomic elements with dCas9-APEX2 [preprint], Xin D. Gao, Li-Chun Tu, Aamir Mir, Tomas Rodriguez, Yue-He Ding, John D. Leszyk, Job Dekker, Scott A. Shaffer, Lihua Julie Zhu, Scot A. Wolfe, and Erik J. Sontheimer

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C. elegans Multidrug Resistance Protein 5 (MRP-5) Transports Vitamin B12 from the Intestine to the Gonad to Support Embryonic Development [preprint], Huimin Na, Olga Ponomarova, Gabrielle E. Giese, and Albertha J. M. Walhout

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Heterochromatin drives organization of conventional and inverted nuclei [preprint], Martin Falk; Yana Feodorova; Natasha Naumova; Massachusetts Institute of Technology; Illumina Incorporated; Heinrich Leonhardt; Ludwig Maximilians Universitat, Munchen; Job Dekker; University of California, San Francisco; Ludwig Maximilians Universitat, Munchen; and Massachusetts Institute of Technology

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Gateway Recombinational Cloning, John S. Reece-Hoyes and Albertha J. M. Walhout (Cold Spring Harbor protocols, 2018-01-02)

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Generating an Open Reading Frame (ORF) Entry Clone and Destination Clone, John S. Reece-Hoyes and Albertha J. M. Walhout (Cold Spring Harbor protocols, 2018-01-02)

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Propagating Gateway Vectors, John S. Reece-Hoyes and Albertha J. M. Walhout (Cold Spring Harbor protocols, 2018-01-02)

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Using Multisite LR Cloning to Generate a Destination Clone, John S. Reece-Hoyes and Albertha J. M. Walhout (Cold Spring Harbor protocols, 2018-01-02)

Publications from 2017

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The HoxD cluster is a dynamic and resilient TAD boundary controlling the segregation of antagonistic regulatory landscapes, Eddie Rodriguez-Carballo, Lucille Lopez-Delisle, Ye Zhan, Pierre J. Fabre, Leonardo Beccari, Imane El-Idrissi, Thi Hanh Nguyen Huynh, Hakan Ozadam, Job Dekker, and Denis Duboule (Genes and development, 2017-11-15)

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The 4D nucleome project, Job Dekker, Andrew S. Belmont, Mitchell Guttman, Victor O. Leshyk, John T. Lis, Stavros Lomvardas, Leonid A. Mirny, Clodagh C. O'Shea, Peter J. Park, Bing Ren, Joan C. Ritland Politz, Jay Shendure, Sheng Zhong, and 4D Nucleome Network (Nature, 2017-09-13)

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5C analysis of the Epidermal Differentiation Complex locus reveals distinct chromatin interaction networks between gene-rich and gene-poor TADs in skin epithelial cells, Krzysztof Poterlowicz, Joanne L. Yarker, Igor Malashchuk, Brian R. Lajoie, Andrei N. Mardaryev, Michal R. Gdula, Andrey A. Sharov, Terumi Kohwi-Shigematsu, Vladimir A. Botchkarev, and Michael Y. Fessing

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Many transcription factors contribute to C. elegans growth and fat storage, Akihiro Mori, Amy D. Holdorf, and Albertha J. M. Walhout (Genes to cells : devoted to molecular and cellular mechanisms, 2017-09-01)

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SMC complexes differentially compact mitotic chromosomes according to genomic context, Stephanie Andrea Schalbetter, Anton Goloborodko, Geoffrey Fudenberg, Jon-Matthew Belton, Catrina Miles, Miao Yu, Job Dekker, Leonid Mirny, and Jonathan Baxter (Nature cell biology, 2017-09-01)

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Heterogeneity and Intrinsic Variation in Spatial Genome Organization [preprint], Elizabeth Finn, Gianluca Pegoraro, Hugo B. Brandao, Anne-Laure Valton, Marlies E. Oomen, Job Dekker, Leonid Mirny, and Tom Misteli

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Self-consistent theory of transcriptional control in complex regulatory architectures, Jasper Landman, Robert C. Brewster, Franz M. Weinert, Rob Phillips, and Willem K. Kegel (PloS one, 2017-07-07)

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Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation, Houda Belaghzal, Job Dekker, and Johan H. Gibcus (Methods (San Diego, Calif.), 2017-07-01)

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The Oxidative Stress Response in Caenorhabditis elegans Requires the GATA Transcription Factor ELT-3 and SKN-1/Nrf2, Queenie Hu, Dayana R. D'Amora, Lesley T. MacNeil, Albertha J. M. Walhout, and Terrance J. Kubiseski (Genetics, 2017-06-09)

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Shelterin components mediate genome reorganization in response to replication stress, Takeshi Mizuguchi, Nitika Taneja, Emiko Matsuda, Jon-Matthew Belton, Peter FitzGerald, Job Dekker, and Shiv I. Grewal S (Proceedings of the National Academy of Sciences of the United States of America, 2017-05-23)

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Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization, Elphege P. Nora, Anton Goloborodko, Anne-Laure Valton, Johan H. Gibcus, Alec Uebersohn, Nezar Abdennur, Job Dekker, Leonid A. Mirny, and Benoit G. Bruneau (Cell, 2017-05-18)

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Bacterial Metabolism Affects the C. elegans Response to Cancer Chemotherapeutics, Aurian Garcia-Gonzalez, Ashlyn D. Ritter, Shaleen Shrestha, Erik C. Andersen, L. Safak Yilmaz, and Albertha J. M. Walhout

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Effect of transcription factor resource sharing on gene expression noise, Dipjyoti Das, Supravat Dey, Robert C. Brewster, and Sandeep Choubey (PLoS computational biology, 2017-04-17)

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Epigenetic characteristics of the mitotic chromosome in 1D and 3D, Marlies E. Oomen and Job Dekker (Critical reviews in biochemistry and molecular biology, 2017-04-01)