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.

Follow


Publications from 2018

PDF

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

Link

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)

Link

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)

Link

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

Link

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

Link

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

Link

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

Link

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

Link

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

Link

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

Link

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

Link

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

PDF

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)

PDF

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

PDF

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

Link

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)

PDF

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

PDF

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

PDF

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

PDF

Heterochromatin drives organization of conventional and inverted nuclei, 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

Link

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

Link

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)

Link

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

Link

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

PDF

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)

Link

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)

PDF

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

Link

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)

Link

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)

PDF

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

PDF

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)

Link

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)

Link

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)

PDF

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)

Link

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)

Link

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

PDF

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)

Link

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)

Link

PRIMA: a gene-centered, RNA-to-protein method for mapping RNA-protein interactions, Alex M. Tamburino, Ebru Kaymak, Shaleen Shrestha, Amy D. Holdorf, Sean P. Ryder, and Albertha J. M. Walhout (Translation (Austin, Tex.), 2017-02-28)

Link

C. elegans and its bacterial diet as a model for systems-level understanding of host-microbiota interactions, Jing Zhang, Amy D. Holdorf, and Albertha J. M. Walhout (Current opinion in biotechnology, 2017-02-08)

Link

Polycomb Repressive Complex 1 Generates Discrete Compacted Domains that Change during Differentiation, Sharmistha Kundu, Fei Ji, Hongjae Sunwoo, Gaurav Jain, Jeannie T. Lee, Ruslan I. Sadreyev, Job Dekker, and Robert E. Kingston (Molecular cell, 2017-02-02)

Link

Metabolic network modeling with model organisms, L. Safak Yilmaz and Albertha J. M. Walhout (Current opinion in chemical biology, 2017-02-01)

PDF

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, and Sheng Zong

PDF

Targeted degradation of CTCF decouples local insulation of chromosome domains from higher-order genomic compartmentalization, Elphege P. Nora, Anton Goloborodko, Anne-Laure Valton, Johan H. Gibcus, Alec Uebersohn, Nezar Abdennur, Job Dekker, Leonid A. Mirny, and Benoit Bruneau

Publications from 2016

PDF

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, 2016-12-15)

Link

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, 2016-12-15)

Link

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

Link

Colony Lift Colorimetric Assay for beta-Galactosidase Activity, Juan Fuxman Bass, John S. Reece-Hoyes, and Albertha J. M. Walhout (Cold Spring Harbor protocols, 2016-12-01)

Link

Gene-Centered Yeast One-Hybrid Assays, Juan Fuxman Bass, John S. Reece-Hoyes, and Albertha J. M. Walhout (Cold Spring Harbor protocols, 2016-12-01)

Link

Generating Bait Strains for Yeast One-Hybrid Assays, Juan Fuxman Bass, John S. Reece-Hoyes, and Albertha J. M. Walhout (Cold Spring Harbor protocols, 2016-12-01)

Link

Performing Yeast One-Hybrid Library Screens, Juan Fuxman Bass, John S. Reece-Hoyes, and Albertha J. M. Walhout (Cold Spring Harbor protocols, 2016-12-01)

Link

Zymolyase-Treatment and Polymerase Chain Reaction Amplification from Genomic and Plasmid Templates from Yeast, Juan Fuxman Bass, John S. Reece-Hoyes, and Albertha J. M. Walhout (Cold Spring Harbor protocols, 2016-12-01)

PDF

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

Link

Mapping the 3D genome: Aiming for consilience, Job Dekker (Nature reviews. Molecular cell biology, 2016-11-21)

Link

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)

PDF

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, 2016-10-25)

PDF

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

PDF

PRIMA: a gene-centered, RNA-to-protein method for mapping RNA-protein interactions, Alex M. Tamburino, Ebru Kaymak, Shaleen Shrestha, Amy D. Holdorf, Sean P. Ryder, and Albertha J. M. Walhout

Link

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, 2016-09-01)

PDF

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)

Link

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, 2016-07-18)

PDF

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

Link

A Caenorhabditis elegans Genome-Scale Metabolic Network Model, L. Safak Yilmaz and Albertha J. M. Walhout (Cell systems, 2016-05-25)

PDF

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, 2016-05-12)

Link

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, 2016-05-05)

Link

The 3D Genome as Moderator of Chromosomal Communication, Job Dekker and Leonid A. Mirny (Cell, 2016-03-10)

PDF

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, 2016-03-08)

Link

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.), 2016-03-03)

PDF

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

PDF

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, 2016-02-02)

Link

TAD disruption as oncogenic driver, Anne-Laure Valton and Job Dekker (Current opinion in genetics and development, 2016-02-01)

Link

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, 2016-01-07)

Publications from 2015

PDF

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

PDF

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

Link

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, 2015-11-23)

Link

Structural and functional diversity of Topologically Associating Domains, Job Dekker and Edith Heard (FEBS letters, 2015-10-07)

Link

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, 2015-10-01)

Link

Long-Range Chromatin Interactions, Job Dekker and Tom Misteli (Cold Spring Harbor perspectives in biology, 2015-10-01)

PDF

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, 2015-09-28)

Link

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, 2015-09-24)

Link

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, 2015-08-26)

Link

Studying Cellular Signal Transduction with OMIC Technologies, Benjamin D. Landry, David C. Clarke, and Michael J. Lee (Journal of molecular biology, 2015-08-03)

Link

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, 2015-08-01)

PDF

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, 2015-07-21)

Link

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, 2015-07-09)

Link

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, 2015-07-02)

Link

Hi-C in Budding Yeast, Jon-Matthew Belton and Job Dekker (Cold Spring Harbor protocols, 2015-07-01)

Link

Measuring Chromatin Structure in Budding Yeast, Jon-Matthew Belton and Job Dekker (Cold Spring Harbor protocols, 2015-07-01)

Link

Chromosome Conformation Capture (3C) in Budding Yeast, Jon-Matthew Belton and Job Dekker (Cold Spring Harbor protocols, 2015-06-01)

Link

Chromosome Conformation Capture Carbon Copy (5C) in Budding Yeast, Jon-Matthew Belton and Job Dekker (Cold Spring Harbor protocols, 2015-06-01)

Link

Randomized ligation control for chromosome conformation capture, Jon-Matthew Belton and Job Dekker (Cold Spring Harbor protocols, 2015-06-01)

Link

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, 2015-04-23)

PDF

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, 2015-04-23)

Link

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, 2015-04-23)

PDF

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, 2015-4)

Link

Let a hundred flowers bloom: the role of context dependence in creating phenotypic diversity following targeted therapy, Michael J. Lee (Molecular cell, 2015-03-05)

Link

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.], 2015-01-05)

Publications from 2014

PDF

DNA-guided establishment of canonical nucleosome patterns in a eukaryotic genome, Leslie Y. Beh, Noam Kaplan, Manuel M. Muller, Tom W. Muir, and Laura F. Landweber

Link

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, 2014-12-18)

PDF

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