This collection showcases the books, journal articles, book reviews, and other publications and presentations written by faculty and researchers of the Department of Biochemistry and Molecular Pharmacology.

Follow


Publications from 2017

PDF

Nuclear Export Through Nuclear Envelope Remodeling in Saccharomyces cerevisiae [preprint], Baojin Ding, Anne M. Mirza, James A. Ashley, Vivian Budnik, and Mary Munson

PDF

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

Link

DTNB-Based Quantification of In Vitro Enzymatic N-Terminal Acetyltransferase Activity., Havard Foyn, Paul R. Thompson, and Thomas Arnesen

PDF

Exploring the Role of Large Clusters of Branched Aliphatic Residues on the Folding Free Energy Landscape of (βα)8 TIM Barrel Proteins, Kevin T. Halloran

PDF

Temporal regulation of chromatin during myoblast differentiation, Akihito Harada, Yasuyuki Ohkawa, and Anthony N. Imbalzano

Link

PGBD5 promotes site-specific oncogenic mutations in human tumors, Anton G. Henssen, Jiali Zhuang, Zhiping Weng, and Alex Kentsis

PDF

The large terminase DNA packaging motor grips DNA with its ATPase domain for cleavage by the flexible nuclease domain, Brendan J. Hilbert, Janelle A. Hayes, Nicholas P. Stone, Rui-Gang Xu, and Brian A. Kelch

PDF

Role of peptidylarginine deiminase 2 (PAD2) in mammary carcinoma cell migration, Sachi Horibata, Katherine E. Rogers, David Sadegh, Lynne J. Anguish, John L. McElwee, Pragya Shah, Paul R. Thompson, and Scott A. Coonrod

PDF

Three-dimensional Folding of Eukaryotic Genomes, Tsung-Han S. Hsieh

Link

Discovering cis-Regulatory Motifs, Jui-Hung Hung and Zhiping Weng

Link

Identifying Regions Enriched in a ChIP-seq Data Set (Peak Finding), Jui-Hung Hung and Zhiping Weng

Link

Mapping Short Sequence Reads to a Reference Genome, Jui-Hung Hung and Zhiping Weng

Link

Motif Finding, Jui-Hung Hung and Zhiping Weng

PDF

Global increase in replication fork speed during a p57KIP2-regulated erythroid cell fate switch, Yung Hwang, Melinda Futran, Daniel Hidalgo, Ramona Pop, Divya Ramalingam Iyer, Ralph Scully, Nicholas R. Rhind, and Merav Socolovsky

PDF

A synthetic biology approach to probing nucleosome symmetry [preprint], Yuichi Ichikawa, Yuanyuan Chen, Vineeta Bajaj, Caitlin M. Connolly, Hsin-Jung Chou, Upasna Sharma, Hsiuyi V. Chen, Daniel N. Bolon, Oliver J. Rando, and Paul D. Kaufman

PDF

A synthetic biology approach to probing nucleosome symmetry, Yuichi Ichikawa, Caitlin M. Connolly, Hsin-Jung Chou, Yuanyuan Chen, Upasna Sharma, Hsuiyi V. Chen, Vineeta Bajaj, Daniel Na. Bolon, Oliver J. Rando, and Paul D. Kaufman

PDF

Single-Molecule Studies of Replication Kinetics in Response to DNA Damage, Divya Ramalingam Iyer

PDF

Replication fork slowing and stalling are distinct, checkpoint-independent consequences of replicating damaged DNA, Divya Ramalingam Iyer and Nicholas R. Rhind

PDF

The Intra-S Checkpoint Responses to DNA Damage, Divya Ramalingam Iyer and Nicholas R. Rhind

Link

LINE-1 activation after fertilization regulates global chromatin accessibility in the early mouse embryo, Joanna W. Jachowicz, Xin Y. Bing, Julien Pontabry, Ana Boskovic, Oliver J. Rando, and Maria-Elena Torres-Padilla

PDF

Size-Dependent Expression of the Mitotic Activator Cdc25 as a Mechanism of Size Control in Fission Yeast [preprint], Daniel L. Keifenheim, Xi-Ming Sun, Edridge D'Souza, Makoto J. Ohira, Mira Magner, Lawrence Livermore National Laboratory, Samuel Marguerat, and Nicholas R. Rhind

PDF

Diverse stimuli engage different neutrophil extracellular trap pathways, Elaine F. Kenny, Alf Herzig, Renate Krüger, Aaron Muth, Santanu Mondal, Paul R. Thompson, Volker Brinkmann, Horst Von Bernuth, and Arturo Zychlinsky

Link

The chemical evolution of oligonucleotide therapies of clinical utility, Anastasia Khvorova and Jonathan K. Watts

PDF

Genome-Wide Identification of Early-Firing Human Replication Origins by Optical Replication Mapping [preprint], Kyle Klein, Weitao Wang, Tyler M. Borrman, Saki Chan, Denghong Zhang, Zhiping Weng, Alex Hastie, Chunlong Chen, David M. Gilbert, and Nicholas R. Rhind

PDF

Small methyltransferase RlmH assembles a composite active site to methylate a ribosomal pseudouridine, Cha San Koh, Rohini Madireddy, Timothy J. Beane, Phillip D. Zamore, and Andrei A. Korostelev

PDF

Chloramidine/Bisindolylmaleimide-I-Mediated Inhibition of Exosome and Microvesicle Release and Enhanced Efficacy of Cancer Chemotherapy, Uchini S. Kosgodage, Rita P. Trindade, Paul R. Thompson, Jameel M. Inal, and Sigrun Lange

PDF

Crystal structure of APOBEC3A bound to single-stranded DNA reveals structural basis for cytidine deamination and specificity, Takahide Kouno, Tania V. Silvas, Brendan J. Hilbert, Shivender Shandilya, Markus-Frederik Bohn, Brian A. Kelch, William E. Royer, Mohan Somasundaran, Nese Kurt Yilmaz, Hiroshi Matsuo, and Celia A. Schiffer

Link

The TREM2-APOE Pathway Drives the Transcriptional Phenotype of Dysfunctional Microglia in Neurodegenerative Diseases, Susanne Krasemann, Yang Xu, Zhiping Weng, Hao Chen, Vladimir Litvak, and Oleg Butovsky

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)

PDF

The Dkk3 gene encodes a vital intracellular regulator of cell proliferation, Jack L. Leonard, Deborah Marie Leonard, Scot A. Wolfe, Jilin Liu, Jaime A. Rivera-Perez, Michelle Yang, Ryan T. Leonard, Jacob P. S. Johnson, Prashant Kumar, Kate L. Liebmann, Amanda A. Tutto, Zhongming Mou, and Karl J. Simin

PDF

Dengue Virus Hijacks a Noncanonical Oxidoreductase Function of a Cellular Oligosaccharyltransferase Complex, David L. Lin, Natalia A. Cherepanova, Leonia Bozzacco, Margaret R. MacDonald, Reid Gilmore, and Andrew W. Tai

PDF

Dengue virus hijacks a noncanonical oxidoreductase function of a cellular oligosaccharyltransferase complex [preprint], David L. Lin, Natalia A. Cherepanova, Leonia Bozzacco, Margaret R. MacDonald, Reid Gilmore, and Andrew W. Tai

PDF

Dengue Virus NS2B/NS3 Protease Inhibitors Exploiting the Prime Side, Kuan-Hung Lin, Akbar Ali, Linah Rusere, Djade I. Soumana, Nese Kurt Yilmaz, and Celia A. Schiffer

PDF

Single Molecule Approaches to Mapping DNA Replication Origins, Victor Liu

PDF

Reconciling contradictory findings: Glucose transporter 1 (GLUT1) functions as an oligomer of allosteric, alternating access transporters, Kenneth P. Lloyd, Ogooluwa A. Ojelabi, Julie K. De Zutter, and Anthony Carruthers

PDF

A tissue-specific, Gata6-driven transcriptional program instructs remodeling of the mature arterial tree, Marta Losa, Victor Latorre, Munazah Andrabi, Franck Ladam, Charles G. Sagerstrom, Ana Novoa, Peyman Zarrineh, Laure Bridoux, Neil A. Hanley, Moises Mallo, and Nicoletta Bobola

Link

Ensemble cryo-EM elucidates the mechanism of translation fidelity, Anna B. Loveland, Gabriel Demo, Nikolaus Grigorieff, and Andrei A. Korostelev

PDF

The Fission Yeast S-Phase Cyclin Cig2 Can Drive Mitosis [preprint], Mira Magner, Daniel L. Keifenheim, and Nicholas R. Rhind

PDF

CRISPR-Based DNA Imaging in Living Cells Reveals Cell Cycle-Dependent Chromosome Dynamics [preprint], Hanhui Ma, Li-Chun Tu, University of Central Florida, Yu-Chieh Chung, David Grünwald, Shaojie Zhang, and Thoru Pederson

Link

CRISPR-Cas9-mediated saturated mutagenesis screen predicts clinical drug resistance with improved accuracy, Leyuan Ma, Jeffrey I. Boucher, Janet L. Paulsen, Sebastian Matuszewski, Christopher A. Eide, Jianhong Ou, Garrett Eickelberg, Richard D. Press, Lihua (Julie) Zhu, Brian J. Druker, Susan Branford, Scot A. Wolfe, Jeffrey D. Jensen, Celia A. Schiffer, Michael R. Green, and Daniel N. Bolon

Link

Mavyret: A Pan-Genotypic Combination Therapy for the Treatment of Hepatitis C Infection - Published as part of the Biochemistry series "Biochemistry to Bedside", Ashley N. Matthew, Nese Kurt Yilmaz, and Celia A. Schiffer

Link

Hepatitis C Virus NS3/4A Protease Inhibitors Incorporating Flexible P2 Quinoxalines Target Drug Resistant Viral Variants, Ashley N. Matthew, Jacqueto Zephyr, Caitlin J. Hill, Muhammad Jahangir, Alicia Newton, Christos J. Petropoulos, Wei Huang, Nese Kurt Yilmaz, Celia A. Schiffer, and Akbar Ali

PDF

Regulation of the FGF/ERK Signaling Pathway: Roles in Zebrafish Gametogenesis and Embryogenesis, Jennifer M. Maurer

PDF

Extending Chemical Perturbations Of The Ubiquitin Fitness Landscape In A Classroom Setting [preprint], David Mavor, Daniel N. Bolon, Martin Kampmann, and James S. Fraser

Link

Nitric oxide prevents a pathogen-permissive granulocytic inflammation during tuberculosis, Bibhuti B. Mishra, Rustin R. Lovewell, Andrew J. Olive, Clare M. Smith, Jia Yao Phuah, Jarukit E. Long, Michelle L. Dubuke, Samantha G. Palace, Jon D. Goguen, Richard E. Baker, Subhalaxmi Nambi, Rabinarayan Mishra, Matthew G. Booty, Christina E. Baer, Scott A. Shaffer, Beth A. McCormick, and Christopher M. Sassetti

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)

PDF

IRaPPA: information retrieval based integration of biophysical models for protein assembly selection, Iain H. Moal, Didier Barradas-Bautista, Brian Jimenez-Garcia, Mieczyslaw Torchala, Arjan van der Velde, Thom Vreven, Zhiping Weng, Paul A. Bates, and Juan Fernandez-Recio

PDF

Genetic disruption of oncogenic Kras sensitizes lung cancer cells to Fas receptor-mediated apoptosis, Haiwei Mou, Jill Moore, Sunil K. Malonia, Yingxiang Li, Deniz M. Ozata, Soren Hough, Chun-Qing Song, Jordan L. Smith, Andrew H. Fischer, Zhiping Weng, Michael R. Green, and Wen Xue

PDF

CRISPR/Cas9-mediated genome editing induces exon skipping by alternative splicing or exon deletion, Haiwei Mou, Jordan L. Smith, Lingtao Peng, Jill Moore, Xiao-Ou Zhang, Chun-Qing Song, Ankur Sheel, Deniz M. Ozata, Yingxiang Li, Charles P. Emerson Jr., Erik J. Sontheimer, Melissa J. Moore, Zhiping Weng, and Wen Xue

Link

Development of a Selective Inhibitor of Protein Arginine Deiminase 2., Aaron Muth, Venkataraman Subramanian, Edward Beaumont, Mitesh Nagar, Philip Kerry, Paul McEwan, Hema Srinath, Kathleen W. Clancy, Sangram Parelkar, and Paul R. Thompson

PDF

Surveillance for sulfadoxine-pyrimethamine resistant malaria parasites in the Lake and Southern Zones, Tanzania, using pooling and next-generation sequencing, Jeremiah M. Ngondi, Nicholas J. Hathaway, Jeffrey A. Bailey, and Julie Gutman

PDF

Mammalian SWI/SNF Enzymes and the Epigenetics of Tumor Cell Metabolic Reprogramming, Jeffrey A. Nickerson, Qiong Wu, and Anthony N. Imbalzano

PDF

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

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)

PDF

An Estradiol-Inducible Promoter Enables Fast, Graduated Control of Gene Expression in Fission Yeast [preprint], Makoto J. Ohira, David G. Hendrickson, R. Scott McIsaac, and Nicholas R. Rhind

PDF

Small Molecule Modulation of GLUT1-Mediated Glucose Transport, Ogooluwa A. Ojelabi

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)

PDF

The Combined Effect of Oseltamivir and Favipiravir on Influenza A Virus Evolution, Louise Ormond, Ping Liu, Sebastian Matuszewski, Nicholas Renzette, Claudia Bank, Konstantin B. Zeldovich, Daniel N. Bolon, Timothy F. Kowalik, Robert W. Finberg, Jeffrey D. Jensen, and Jennifer P. Wang

PDF

RNA sequencing and proteomics approaches reveal novel deficits in the cortex of Mecp2-deficient mice, a model for Rett syndrome, Natasha L. Pacheco, Michael R. Heaven, Leanne M. Holt, David K. Crossman, Kristin J. Boggio, Scott A. Shaffer, Daniel L. Flint, and Michelle L. Olsen

PDF

Casein kinase 2-mediated phosphorylation of Brahma-related gene 1 controls myoblast proliferation and contributes to SWI/SNF complex composition, Teresita Padilla-Benavides, Brian T. Nasipak, Amanda L. Paskavitz, Dominic T. Haokip, Jake M. Schnabl, Jeffrey A. Nickerson, and Anthony N. Imbalzano

Link

Getting mRNA-Containing Ribonucleoprotein Granules Out of a Nuclear Back Door, Anup Parchure, Mary Munson, and Vivian Budnik

Link

Adaptive Evolution Leads to Cross-Species Incompatibility in the piRNA Transposon Silencing Machinery, Swapnil S. Parhad, Shikui Tu, Zhiping Weng, and William E. Theurkauf

PDF

Interdependence of Inhibitor Recognition in HIV-1 Protease, Janet L. Paulsen, Florian Leidner, Debra A. Ragland, Nese Kurt Yilmaz, and Celia A. Schiffer

PDF

Locked Nucleic Acid Gapmers and Conjugates Potently Silence ADAM33, an Asthma-Associated Metalloprotease with Nuclear-Localized mRNA, Hannah M. Pendergraff, Pranathi Meda Krishnamurthy, Alexandre J. Debacker, Michael P. Moazami, Vivek K. Sharma, Liisa Niitsoo, Yong Yu, Yen Nee Tan, Hans Michael Haitchi, and Jonathan K. Watts

PDF

Structure-Based Design of Hepatitis C Virus Vaccines That Elicit Neutralizing Antibody Responses to a Conserved Epitope, Brian G. Pierce, Elisabeth N. Boucher, Kurt H. Piepenbrink, Ejemel Monir, Chelsea A. Rapp, William D. Thomas Jr., Eric J. Sundberg, Zhiping Weng, and Yan Wang

PDF

Hereditary Renal Amyloidosis Associated With a Novel Apolipoprotein A-II Variant, Tatiana Prokaeva, Harun Akar, Brian Spencer, Andrea Havasi, Haili Cui, Carl J. O'Hara, Olga Gursky, John D. Leszyk, Martin Steffen, Sabrina Browning, Allison Rosenberg, and Lawreen H. Connors

Link

PAD1 promotes epithelial-mesenchymal transition and metastasis in triple-negative breast cancer cells by regulating MEK1-ERK1/2-MMP2 signaling., Hao Qin, Xiaoqiu Liu, Fujun Li, Lixia Miao, Tingting Li, Boqun Xu, Xiaofei An, Aaron Muth, Paul R. Thompson, Scott A. Coonrod, and Xuesen Zhang

Link

Elucidating the Interdependence of Drug Resistance from Combinations of Mutations, Debra A. Ragland, Troy W. Whitfield, Sook-Kyung Lee, Ronald Swanstrom, Konstantin B. Zeldovich, Nese Kurt Yilmaz, and Celia A. Schiffer

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

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)

Link

A novel homozygous VPS45 p.P468L mutation leading to severe congenital neutropenia with myelofibrosis, Rikin K. Shah, Mary Munson, Klaas J. Wierenga, Hanumantha R. Pokala, Peter E. Newburger, and David Crawford

Link

Metabolic Inputs into the Epigenome, Upasna Sharma and Oliver J. Rando

PDF

Small RNAs are trafficked from the epididymis to developing mammalian sperm [preprint], Upasna Sharma, Fengyun Sun, Brian Reichholf, Veronika Herzog, Stefan Ameres, and Oliver J. Rando

PDF

Atomistic structural ensemble refinement reveals non-native structure stabilizes a sub-millisecond folding intermediate of CheY, Jade Shi, R Paul. Nobrega, Christian Schwantes, Sagar V. Kathuria, Osman Bilsel, C. Robert Matthews, T J. Lane, and Vijay S. Pande

Link

Emerging Concepts in TCR Specificity: Rationalizing and (Maybe) Predicting Outcomes, Nishant K. Singh, Timothy P. Riley, Sarah Catherine B. Baker, Tyler M. Borrman, Zhiping Weng, and Brian M. Baker

Link

Genome-Wide CRISPR Screen Identifies Regulators of Mitogen-Activated Protein Kinase as Suppressors of Liver Tumors in Mice, Chun-Qing Song, Yingxiang Li, Haiwei Mou, Jill Moore, Angela I. Park, Soren Hough, Zachary Kennedy, Andrew H. Fischer, Darryl Conte Jr., Zhiping Weng, and Wen Xue

PDF

A hyperthermophilic phage decoration protein suggests common evolutionary origin with Herpesvirus Triplex proteins and an anti-CRISPR protein [preprint], Nicholas P. Stone, Brendan J. Hilbert, Daniel Hidalgo, Kevin T. Halloran, and Brian A. Kelch

Link

Citrullination of NF-kappaB p65 promotes its nuclear localization and TLR-induced expression of IL-1beta and TNFalpha, Bo Sun, Nishant Dwivedi, Tyler J. Bechtel, Janet L. Paulsen, Aaron Muth, Mandar Bawadekar, Gang Li, Paul R. Thompson, Miriam A. Shelef, Celia A. Schiffer, Eranthie Weerapana, and I-Cheng Ho

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)

PDF

Intergenerational Effects of Nicotine in an Animal Model of Paternal Nicotine Exposure, Markus Parzival Vallaster

PDF

Paternal nicotine exposure alters hepatic xenobiotic metabolism in offspring, Markus P. Vallaster, Shweta Kukreja, Xin Y. Bing, Jennifer Ngolab, Rubing Zhao-Shea, Paul D. Gardner, Andrew R. Tapper, and Oliver J. Rando

Link

Diatrack particle tracking software: Review of applications and performance evaluation, Pascal Vallotton, Antoine M. van Oijen, Cynthia B. Whitchurch, Vladimir Gelfand, Leslie Yeo, Georgios Tsiavaliaris, Stephanie Heinrich, Elisa Dultz, Karsten Weis, and David Grünwald

Link

Performance of ZDOCK and IRAD in CAPRI rounds 28-34, Thom Vreven, Brian G. Pierce, Tyler M. Borrman, and Zhiping Weng

PDF

Rlim-Dependent and -Independent Pathways for X Chromosome Inactivation in Female ESCs, Feng Wang, Kurtis N. McCannell, Ana Boskovic, Xiaochun Zhu, JongDae Shin, Jun Yu, Judith Gallant, Meg Byron, Jeanne B. Lawrence, Lihua Julie Zhu, Stephen N. Jones, Oliver J. Rando, Thomas G. Fazzio, and Ingolf Bach

PDF

Unexpected CRISPR off-target mutation pattern in vivo are not typically germline-like [preprint], Zhiting Wei, Funan He, Guohui Chuai, Hanhui Ma, Zhixi Su, and Qi Liu

PDF

The BRG1 ATPase of human SWI/SNF chromatin remodeling enzymes as a driver of cancer, Qiong Wu, Jane B. Lian, Janet L. Stein, Gary S. Stein, Jeffrey A. Nickerson, and Anthony N. Imbalzano

Link

Structure-guided chemical modification of guide RNA enables potent non-viral in vivo genome editing, Hao Yin, Chun-Qing Song, Esther Mintzer, Mehmet F. Bolukbasi, Lihua Julie Zhu, Haiwei Mou, Suet-Yan Kwan, Scot A. Wolfe, Wen Xue, and Daniel G. Anderson

Link

Citrullination regulates the expression of insulin-like growth factor-binding protein 1 (IGFBP1) in ovine uterine luminal epithelial cells., Coleman H. Young, Heather M. Rothfuss, Philip F. Gard, Aaron Muth, Paul R. Thompson, Ryan L. Ashley, and Brian D. Cherrington

PDF

Bivalent Epigenetic Control of Oncofetal Gene Expression in Cancer, Sayyed K. Zaidi, Seth E. Frietze, Jonathan A. Gordon, Jessica L. Heath, Terri Messier, Deli Hong, Joseph R. Boyd, Mingu Kang, Anthony N. Imbalzano, Jane B. Lian, Janet L. Stein, and Gary S. Stein

PDF

Predicting human splicing branchpoints by combining sequence-derived features and multi-label learning methods, Wen Zhang, Xiaopeng Zhu, Yu Fu, Junko Tsuji, and Zhiping Weng

PDF

GUIDEseq: a bioconductor package to analyze GUIDE-Seq datasets for CRISPR-Cas nucleases, Lihua Julie Zhu, Michael Lawrence, Ankit Gupta, Herve Pages, Alper Kucukural, Manuel Garber, and Scot A. Wolfe

Publications from 2016

PDF

Ensemble cryo-EM uncovers inchworm-like translocation of a viral IRES through the ribosome, Priyanka D. Abeyrathne, Cha San Koh, Timothy Grant, Nikolaus Grigorieff, and Andrei A. Korostelev

PDF

Type I Interferon Induction by Neisseria gonorrhoeae: Dual Requirement of Cyclic GMP-AMP Synthase and Toll-like Receptor 4, Warrison A. Andrade, Sarika Agarwal, Shunyan Mo, Scott A. Shaffer, Joseph P. Dillard, Tobias Schmidt, Veit Hornung, Katherine A. Fitzgerald, Evelyn A. Kurt-Jones, and Douglas T. Golenbock

Link

A Long Noncoding RNA lincRNA-EPS Acts as a Transcriptional Brake to Restrain Inflammation, Maninjay K. Atianand, Emiliano P. Ricci, Ankit Bhatta, Stefan A. Schattgen, Jason D. McGowan, Juliana Blin, Joerg E. Braun, Pallavi Gandhi, Melissa J. Moore, Daniel R. Caffrey, and Katherine A. Fitzgerald

PDF

On the (un-)predictability of a large intragenic fitness landscape [preprint], Claudia Bank, Sebastian Matuszewski, Ryan T. Hietpas, and Jeffrey D. Jensen

PDF

An experimental evaluation of drug-induced mutational meltdown as an antiviral treatment strategy [preprint], Claudia Bank, Nicholas Renzette, Ping Liu, Sebastian Matuszewski, Hyunjin Shim, Matthieu Foll, Daniel N. Bolon, Konstantin B. Zeldovich, Timothy F. Kowalik, Robert W. Finberg, Jennifer P. Wang, and Jeffrey D. Jensen

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

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)

PDF

Tumor necrosis factor alpha, citrullination, and peptidylarginine deiminase 4 in lung and joint inflammation, Mandar Bawadekar, Annette Gendron-Fitzpatrick, Ryan Rebernick, Daeun Shim, Thomas F. Warner, Anthony P. Nicholas, Lennart K. Lundblad A, Paul R. Thompson, and Miriam A. Shelef

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)