Publications from 2013
MicroRNA Control of Vascular Endothelial Growth Factor Signaling Output During Vascular Development, Lan T. H. Dang, Nathan D. Lawson, and Jason E. Fish
U2AF65 adapts to diverse pre-mRNA splice sites through conformational selection of specific and promiscuous RNA recognition motifs, Jermaine L. Jenkins, Anant A. Agrawal, Ankit Gupta, Michael R. Green, and Clara L. Kielkopf
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
Efficient targeted mutagenesis in the monarch butterfly using zinc finger nucleases, Christine Merlin, Lauren E. Beaver, Orley R. Taylor, Scot A. Wolfe, and Steven M. Reppert
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
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
GABP transcription factor is required for development of chronic myelogenous leukemia via its control of PRKD2, Zhongfa Yang, Haojian Zhang, Leyuan Ma, Cong Peng, Yaoyu Chen, Junling Wang, Michael R. Green, Shaoguang Li, and Alan G. Rosmarin
Using defined finger-finger interfaces as units of assembly for constructing zinc-finger nucleases, Cong Zhu, Ankit Gupta, Victoria L. Hall, Amy L. Rayla, Ryan G. Christensen, Benjamin Dake, Abirami Lakshmanan, Charlotte Kuperwasser, Gary D. Stormo, and Scot A. Wolfe
Publications from 2012
Cytoplasmic polyadenylation element binding protein deficiency stimulates PTEN and Stat3 mRNA translation and induces hepatic insulin resistance, Ilya M. Alexandrov, Maria Ivshina, Dae Young Jung, Randall H. Friedline, Hwi Jin Ko, Mei Xu, Bryan O'Sullivan-Murphy, Rita Bortell, Yen-Tsung Huang, Fumihiko Urano, Jason K. Kim, and Joel D. Richter
Releasing the break on X chromosome inactivation: Rnf12/RLIM targets REX1 for degradation, Ingolf Bach
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
Coordination of cell growth and division by the ubiquitin-proteasome system, Jennifer A. Benanti
Recognition models to predict DNA-binding specificities of homeodomain proteins, Ryan G. Christensen, Metewo Selase Enuameh, Marcus Blaine Noyes, Michael H. Brodsky, Scot A. Wolfe, and Gary D. Stormo
Exploring the DNA-recognition potential of homeodomains, Stephanie W. Chu, Marcus Blaine Noyes, Ryan G. Christensen, Brian G. Pierce, Lihua Julie Zhu, Zhiping Weng, Gary D. Stormo, and Scot A. Wolfe
Recent trends in post-discharge mortality among patients with an initial acute myocardial infarction, Andrew H. Coles, Kimberly A. Fisher, Chad E. Darling, David D. McManus, Oscar Maitas, Jorge L. Yarzebski, Joel M. Gore, Darleen M. Lessard, and Robert J. Goldberg
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
International trends in pancreatic cancer incidence and mortality rates, Wilfredo E. DeJesus-Monge and Bruce A. Barton
CTCF and cohesin help neurons raise their self-awareness, Job Dekker
Novel paths to antifungal therapeutics, Ahmed Fazly, Charu Jain, Reeta Prusty Rao, and Paul D. Kaufman
NURDs are required for diversity, Thomas G. Fazzio and Oliver J. Rando
A regulatory cascade of three transcription factors in a single specific neuron, DVC, in Caenorhabditis elegans, Huiyun Feng, John S. Reece-Hoyes, Albertha J. M. Walhout, and Ian A. Hope
From cells to chromatin: Capturing snapshots of genome organization with 5C technology, Maria A. Ferraiuolo, Amartya Sanyal, Natalia Naumova, Job Dekker, and Josee Dostie
Wolfram syndrome 1 and adenylyl cyclase 8 interact at the plasma membrane to regulate insulin production and secretion, Sonya G. Fonseca, Fumihiko Urano, Gordon C. Weir, Jesper Gromada, and Mark Burcin
The context of gene expression regulation, Johan H. Gibcus and Job Dekker
An optimized two-finger archive for ZFN-mediated gene targeting, Ankit Gupta, Amy L. Rayla, Abirami Lakshmanan, Scot A. Wolfe, Ryan G. Christensen, and Gary D. Stormo
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
Paternal RLIM/Rnf12 Is a Survival Factor for Milk-Producing Alveolar Cells, Baowei Jiao, Hong Ma, Maxim N. Shokhirev, Alexander Drung, Qin Yang, JongDae Shin, Shaolei Lu, Meg Byron, Sundeep Kalantry, Arthur M. Mercurio, Jeanne B. Lawrence, Alexander Hoffmann, and Ingolf Bach
F-box protein specificity for g1 cyclins is dictated by subcellular localization, Benjamin D. Landry, John P. Doyle, David P. Toczyski, and Jennifer A. Benanti
Analysis of Gal4-directed transcription activation using Tra1 mutants selectively defective for interaction with Gal4, Ling Lin, Lynn Chamberlain, Lihua Julie Zhu, and Michael R. Green
Characterization of Enhancer Function from Genome-Wide Analyses, Glenn A. Maston, Stephen G. Landt, Michael Snyder, and Michael R. Green
Non-canonical TAF complexes regulate active promoters in human embryonic stem cells, Glenn A. Maston, Lihua Julie Zhu, Lynn Chamberlain, Ling Lin, Minggang Fang, and Michael R. Green
Analysis of long-range chromatin interactions using Chromosome Conformation Capture, Natalia Naumova, Emily M. Smith, Ye Zhan, and Job Dekker
miR-221 is required for endothelial tip cell behaviors during vascular development, Stefania Nicoli, Carl-Philipp Knyphausen, Lihua Julie Zhu, Abirami Lakshmanan, and Nathan D. Lawson
ER stress as a trigger for beta-cell dysfunction and autoimmunity in type 1 diabetes, Bryan M. O'Sullivan-Murphy and Fumihiko Urano
The histone demethylase jhdm1a regulates hepatic gluconeogenesis, Dongning Pan, Chunxiao Mao, Tie Zou, Annie Y. Yao, Marcus P. Cooper, Victor L. Boyartchuk, and Yong-Xu Wang
Integration of beta-Catenin, Sirtuin, and FOXO Signaling Protects from Mutant Huntingtin Toxicity, J. Alex Parker, Rafael P. Vazquez-Manrique, Cendrine Tourette, Francesca Farina, Nicolas Offner, Arnab Mukhopadhyay, Anne-Marie Orfila, Aurelie Darbois, Sophie Menet, Heidi A. Tissenbaum, and Christian Neri
Thrombopoietin/MPL participates in initiating and maintaining RUNX1-ETO acute myeloid leukemia via PI3K/AKT signaling, Jon Anto Pulikkan, Dmitri Madera, Liting Xue, Paul Bradley, Sean F. Landrette, Ya-Huei Kuo, Saman Abbas, Lihua Julie Zhu, Peter J. Valk, and Lucio H. Castilla
The activity of Gli transcription factors is essential for Kras-induced pancreatic tumorigenesis, Mihir Rajurkar, Wilfredo E. De Jesus-Monge, David R. Driscoll, Victoria A. Appleman, He Huang, Jennifer L. Cotton, David S. Klimstra, Lihua Julie Zhu, Karl Simin, Lan Xu, Andrew P. McMahon, Brian C. Lewis, and Junhao Mao
Gene-centered yeast one-hybrid assays, John S. Reece-Hoyes and Albertha J. M. Walhout
The classical pink-eyed dilution mutation affects angiogenic responsiveness, Michael S. Rogers, Victor L. Boyartchuk, Richard M. Rohan, Amy E. Birsner, William F. Dietrich, and Robert J. D'Amato
The long-range interaction landscape of gene promoters, Amartya Sanyal, Bryan R. Lajoie, Gaurav Jain, and Job Dekker
Genetics, Life Span, Health Span, and the Aging Process in Caenorhabditis elegans, Heidi A. Tissenbaum
Regulation of CHMP4/ESCRT-III function in human immunodeficiency virus type 1 budding by CC2D1A, Yoshiko Usami, Sergei Popov, Eric R. Weiss, Christie Vriesema-Magnuson, Arianna Calistri, and Heinrich G. Gottlinger
Transcription factor ATF5 is required for terminal differentiation and survival of olfactory sensory neurons, Shu-Zong Wang, Jianhong Ou, Lihua Julie Zhu, and Michael R. Green
A Synthetic Interaction Screen Identifies Factors Selectively Required for Proliferation and TERT Transcription in p53-Deficient Human Cancer Cells, Li Xie, Claude Gazin, Sung Mi Park, Lihua Julie Zhu, Marie-Anne Debily, Ellen L. W. Kittler, Maria L. Zapp, David S. Lapointe, Stephane Gobeil, Ching-Man A. Virbasius, and Michael R. Green
The Blk pathway functions as a tumor suppressor in chronic myeloid leukemia stem cells, Haojian Zhang, Cong Peng, Yiguo Hu, Huawei Li, Zhi Sheng, Yaoyu Chen, Con Sullivan, Jan Cerny, Lloyd Hutchinson, Anne Higgins, Patricia M. Miron, Xueqing Zhang, Michael A. Brehm, Dongguang Li, Michael R. Green, and Shaoguang Li
Chondrolectin mediates growth cone interactions of motor axons with an intermediate target, Zhen Zhong, Jochen Ohnmacht, Michell M. Reimer, Ingolf Bach, Thomas C. Becker, and Catherina G. Becker
Publications from 2011
Genomics in 2011: challenges and opportunities, David J. Adams, Bonnie Berger, Olivier Harismendy, Curtis Huttenhower, X. Shirley Liu, Chad L. Myers, Alicia Oshlack, John L. Rinn, and Albertha J. M. Walhout
Identification of cis regulatory features in the embryonic zebrafish genome through large-scale profiling of H3K4me1 and H3K4me3 binding sites, Aaron W. Aday, Lihua Julie Zhu, Abirami Lakshmanan, Jie Wang, and Nathan D. Lawson
The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules, Davide Bau, Amartya Sanyal, Bryan R. Lajoie, Emidio Capriotti, Meg Byron, Jeanne B. Lawrence, Job Dekker, and Marc A. Marti-Renom
A stele-enriched gene regulatory network in the Arabidopsis root, Siobhan M. Brady, Lifang Zhang, Molly Megraw, Natalia Julia Martinez, Eric Jiang, Charles S. Yi, Weilin Liu, Anna Zeng, Mallorie Taylor-Teeples, Dahae Kim, Sebastian Ahnert, Uwe Ohler, Doreen Ware, Albertha J. M. Walhout, and Philip N. Benfey
A modified bacterial one-hybrid system yields improved quantitative models of transcription factor specificity, Ryan G. Christensen, Ankit Gupta, Zheng Zuo, Lawrence A. Schriefer, Scot A. Wolfe, and Gary D. Stormo
The cilia protein IFT88 is required for spindle orientation in mitosis, Benedicte Delaval, Alison Bright, Nathan D. Lawson, and Stephen J. Doxsey
Centrin depletion causes cyst formation and other ciliopathy-related phenotypes in zebrafish, Benedicte Delaval, Laurence D. Covassin, Nathan D. Lawson, and Stephen J. Doxsey
Using a structural and logics systems approach to infer bHLH-DNA binding specificity determinants, Federico De Masi, Christian A. Grove, Anastasia Vedenko, Andreu Alibés, Stephen S. Gisselbrecht, Luis Serrano, Martha L. Bulyk, and Albertha J. M. Walhout
Endoplasmic reticulum stress and pancreatic beta-cell death, Sonya G. Fonseca, Jesper Gromada, and Fumihiko Urano
Enhanced Y1H assays for Arabidopsis, Allison Gaudinier, Lifang Zhang, John S. Reece-Hoyes, Mallorie Taylor-Teeples, Li Pu, Zhijie Liu, Ghislain Breton, Jose L. Pruneda-Paz, Dahae Kim, Steve A. Kay, Albertha J. M. Walhout, Doreen Ware, and Siobhan M. Brady
Zinc finger protein-dependent and -independent contributions to the in vivo off-target activity of zinc finger nucleases, Ankit Gupta, Xiangdong Meng, Lihua Julie Zhu, Nathan D. Lawson, and Scot A. Wolfe
The COPI vesicle complex binds and moves with survival motor neuron within axons, Cyril P. Jayakumar, Matthew C. Evans, Venugopal Thayanithy, Naoko Taniguchi-Ishigaki, Ingolf Bach, Adrianne L. Kolpak, Gary J. Bassell, Rossoll Wilfried, Christian L. Lorson, Zheng-Zheng Bao, and Elliot J. Androphy
New partners for HP1 in transcriptional gene silencing, Paul D. Kaufman
Genome surveyor 2.0: cis-regulatory analysis in Drosophila, Majid Kazemian, Michael H. Brodsky, and Saurabh Sinha
The transcription factor PlagL2 activates Mpl transcription and signaling in hematopoietic progenitor and leukemia cells, Sean F. Landrette, Dmitri Madera, Feng He, and Lucio H. Castilla
Forward and reverse genetic approaches for the analysis of vertebrate development in the zebrafish, Nathan D. Lawson and Scot A. Wolfe
Overlapping regulation of CenH3 localization and histone H3 turnover by CAF-1 and HIR proteins in Saccharomyces cerevisiae, Jessica Lopes da Rosa Spiegler, John Holik, Erin M. Green, Oliver J. Rando, and Paul D. Kaufman
Gene regulatory networks and the role of robustness and stochasticity in the control of gene expression, Lesley T. MacNeil and Albertha J. M. Walhout
Translocation mapping exposes the risky lifestyle of B cells, Rachel Patton McCord and Job Dekker
A User's Guide to the Encyclopedia of DNA Elements (ENCODE), Richard M. Meyers, ENCODE Project Consortium, Job Dekker, Bryan R. Lajoie, Amartya Sanyal, Zhiping Weng, Troy W. Whitfield, and Jie Wang
PDP-1 Links the TGF-β and IIS Pathways to Regulate Longevity, Development, and Metabolism, Sri Devi Narasimhan, Kelvin Yen, Ankita Bansal, Eun-Soo Kwon, Srivatsan Padmanabhan, and Heidi A. Tissenbaum
Measuring ER stress and the unfolded protein response using mammalian tissue culture system, Christine M. Oslowski and Fumihiko Urano
Yeast one-hybrid assays for gene-centered human gene regulatory network mapping, John S. Reece-Hoyes, A. Rasim Barutcu, Rachel Patton McCord, Jun Seop Jeong, Lizhi Jiang, Andrew Macwilliams, Xinping Yang, Kourosh Salehi-Ashtiani, David E. Hill, Seth Blackshaw, Heng Zhu, Job Dekker, and Albertha J. M. Walhout
Enhanced yeast one-hybrid assays for high-throughput gene-centered regulatory network mapping, John S. Reece-Hoyes, Alos Diallo, Bryan R. Lajoie, Amanda Kent, Shaleen Shrestha, Sreenath Kadreppa, Colin Pesyna, Job Dekker, Chad L. Myers, and Albertha J. M. Walhout
Chromatin globules: a common motif of higher order chromosome structure, Amartya Sanyal, Davide Bau, Marc A. Marti-Renom, and Job Dekker
BCR-ABL suppresses autophagy through ATF5-mediated regulation of mTOR transcription, Zhi Sheng, Leyuan Ma, Jiaoyuan Sun, Lihua Julie Zhu, and Michael R. Green
Transcription factor Lhx2 is necessary and sufficient to suppress astrogliogenesis and promote neurogenesis in the developing hippocampus, Lakshmi Subramanian, Anindita Sarkar, Ashwin S. Shetty, Bhavana Muralidharan, Hari Padmanabhan, Michael Piper, Edwin S. Monuki, Ingolf Bach, Richard M. Gronostajski, Linda J. Richards, and Shubha Tole
Chromosome-Biased Binding and Gene Regulation by the Caenorhabditis elegans DRM Complex, Tomoko M. Tabuchi, Bart Deplancke, Naoki Osato, Lihua Julie Zhu, Inmaculada M. Barrasa, Melissa M. Harrison, Robert H. Horvitz, Albertha J. M. Walhout, and Kirsten A. Hagstrom
The IRE1alpha-XBP1 pathway is essential for osteoblast differentiation through promoting transcription of Osterix, Takahide Tohmonda, Yoshiteru Miyauchi, Rajarshi Ghosh, Masaki Yoda, Shinichi Uchikawa, Jiro Takito, Hideo Morioka, Masaya Nakamura, Takao Iwawaki, Kazuhiro Chiba, Yoshiaki Toyama, Fumihiko Urano, and Keisuke Horiuchi
The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation, Mark A. Umbarger, Esteban Toro, Matthew A. Wright, Gregory J. Porreca, Davide Bau, Sun-Hae Hong, Michael J. Fero, Lihua Julie Zhu, Marc A. Marti-Renom, Harley H. McAdams, Lucy Shapiro, Job Dekker, and George M. Church
Gene-centered regulatory network mapping, Albertha J. M. Walhout
What does biologically meaningful mean? A perspective on gene regulatory network validation, Albertha J. M. Walhout
A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression, Kevin C. Wang, Yul W. Yang, Bo Liu, Amartya Sanyal, Ryan Corces-Zimmerman, Yong Chen, Bryan R. Lajoie, Angeline Protacio, Ryan A. Flynn, Rajnish A. Gupta, Joanna Wysocka, Ming Lei, Job Dekker, Jill A. Helms, and Howard Y. Chang
RNF34 is a cold-regulated E3 ubiquitin ligase for PGC-1alpha and modulates brown fat cell metabolism, Ping Wei, Dongning Pan, Chunxiao Mao, and Yong-Xu Wang
The role of cellular factors in promoting HIV budding, Eric R. Weiss and Heinrich G. Gottlinger
DAF-16/Forkhead box O transcription factor: many paths to a single Fork(head) in the road, Kelvin Yen, Sri Devi Narasimhan, and Heidi A. Tissenbaum
Mbd3/NURD complex regulates expression of 5-hydroxymethylcytosine marked genes in embryonic stem cells, Ozlem Yildirim, Ruowang Li, Jui-Hung Hung, Poshen B. Chen, Xianjun Dong, Ly-Sha Ee, Zhiping Weng, Oliver J. Rando, and Thomas G. Fazzio
Sphingosine kinases and their metabolites modulate endolysosomal trafficking in photoreceptors, Ikuko Yonamine, Takeshi Bamba, Niraj K. Nirala, Nahid Jesmin, Teresa Kosakowska-Cholody, Kunio Nagashima, Eiichiro Fukasaki, Jairaj K. Acharya, and Usha Acharya
CDase is a pan-ceramidase in Drosophila, Changqing Yuan, Raghavendra Pralhada Rao, Nahid Jesmin, Takeshi Bamba, Kunio Nagashima, Alberto Pascual, Thomas Preat, Eiichiro Fukusaki, Usha Acharya, and Jairaj K. Acharya
SSDP cofactors regulate neural patterning and differentiation of specific axonal projections, Zhen Zhong, Hong Ma, Naoko Taniguchi-Ishigaki, Lalitha Nagarajan, Catherina G. Becker, Ingolf Bach, and Thomas Becker
Evaluation and application of modularly assembled zinc-finger nucleases in zebrafish, Cong Zhu, Tom Smith, Joseph C. McNulty, Amy L. Rayla, Abirami Lakshmanan, Arndt F. Siekmann, Matthew Buffardi, Xiangdong Meng, Jimann Shin, Arun Padmanabhan, Daniel Cifuentes, Antonio J. Giraldez, A. Thomas Look, Jonathan A. Epstein, Nathan D. Lawson, and Scot A. Wolfe
FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system, Lihua Julie Zhu, Ryan G. Christensen, Majid Kazemian, Christopher J. Hull, Metewo Selase Enuameh, Matthew D. Basciotta, Jessie A. Brasefield, Cong Zhu, Yuna Asriyan, David S. Lapointe, Saurabh Sinha, Scot A. Wolfe, and Michael H. Brodsky
Listeria monocytogenes infection induces prosurvival metabolic signaling in macrophages, Tie Zou, Oleg Garifulin, Robert Berland, and Victor L. Boyartchuk
Publications from 2010
Functional modularity of nuclear hormone receptors in a Caenorhabditis elegans metabolic gene regulatory network., H. Efsun Arda, Stefan Taubert, Lesley T. MacNeil, Colin C. Conine, Ben Tsuda, Marc Van Gilst, Reynaldo Sequerra, Lynn Doucette-Stamm, Keith R. Yamamoto, and Albertha J. M. Walhout
Gene-centered regulatory networks, H. Efsun Arda and Albertha J. M. Walhout
Chemical genetic strategy identifies histone deacetylase 1 (HDAC1) and HDAC2 as therapeutic targets in sickle cell disease, James E. Bradner, Raymond Mak, Shyam K. Tanguturi, Ralph Mazitschek, Stephen J. Haggarty, Kenneth Ross, Cindy Y. Chang, Jocelyn Bosco, Nathan West, Elizabeth Morse, Katherine Lin, John Paul Shen, Nicholas P. Kwiatkowski, Nele Gheldof, Job Dekker, Daniel J. DeAngelo, Steven A. Carr, Stuart L. Schreiber, Todd R. Golub, and Benjamin L. Ebert
Visual presentation as a welcome alternative to textual presentation of gene annotation information, Jairav Desai, Jared M. Flatow, Jie Song, Lihua Julie Zhu, Pan Du, Chiang-Ching Huang, Hui Lu, Simon M. Lin, and Warren A. Kibbe
A mammalian siderophore synthesized by an enzyme with a bacterial homolog involved in enterobactin production, Laxminarayana R. Devireddy, Daniel O. Hart, David H. Goetz, and Michael R. Green
Wolfram syndrome 1 gene negatively regulates ER stress signaling in rodent and human cells, Sonya G. Fonseca, Shinsuke Ishigaki, Christine M. Oslowski, Simin Lu, Kathryn L. Lipson, Rajarshi Ghosh, Emiko Hayashi, Hisamitsu Ishihara, Yoshitomo Oka, M. Alan Permutt, and Fumihiko Urano
Stress hypERactivation in the beta-cell, Sonya G. Fonseca, Fumihiko Urano, Mark Burcin, and Jesper Gromada
Cell-type-specific long-range looping interactions identify distant regulatory elements of the CFTR gene, Nele Gheldof, Emily M. Smith, Tomoko M. Tabuchi, Christoph M. Koch, Ian Dunham, John A. Stamatoyannopoulos, and Job Dekker
Transcriptional regulation of VEGF-A by the unfolded protein response pathway, Rajarshi Ghosh, Kathryn L. Lipson, Karen E. Sargent, Arthur M. Mercurio, Joan S. Hunt, David Ron, and Fumihiko Urano
p53 represses class switch recombination to IgG2a through its antioxidant function, Jeroen E. J. Guikema, Carol E. Schrader, Michael H. Brodsky, Erin K. Linehan, Adam Richards, Nahla El Falaky, Daniel H. LI, Hayla Karen Sluss, Eva Szomolanyi-Tsuda, and Janet Stavnezer