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.

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Publications from 2016

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Inhibition of APOBEC3G activity impedes double-stranded DNA repair, Ponnandy Prabhu, Shivender Shandilya, Elena Britan-Rosich, Adi Nagler, Celia A. Schiffer, and Moshe Kotler

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MMB-GUI: a fast morphing method demonstrates a possible ribosomal tRNA translocation trajectory, Alex Tek, Andrei A. Korostelev, and Samuel Coulbourn Flores

Publications from 2015

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The PsychENCODE project, Schahram Akbarian, Zhiping Weng, Eugenio Mattei, Michael Purcaro, Junko Tsuji, Geetha Senthil, Thomas Lehner, Pamela Sklar, Nenad Sestan, and PsychENCODE Consortium

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Epigenetic dysregulation of hairy and enhancer of split 4 (HES4) is associated with striatal degeneration in postmortem Huntington brains, Guang Bai, Iris Cheung, Hennady P. Shulha, Joana E. Coelho, Ping Li, Xianjun Dong, Mira Jakovcevski, Yumei Wang, Anastasia Grigorenko, Yan Jiang, Andrew Hoss, Krupal Patel, Ming Zheng, Evgeny Rogaev, Richard H. Myers, Zhiping Weng, Schahram Akbarian, and Jiang-Fan Chen

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A systematic survey of an intragenic epistatic landscape, Claudia Bank, Ryan T. Hietpas, Jeffrey D. Jensen, and Daniel N. Bolon

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

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

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

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Hi-C in Budding Yeast, Jon-Matthew Belton and Job Dekker

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Measuring Chromatin Structure in Budding Yeast, Jon-Matthew Belton and Job Dekker

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Randomized ligation control for chromosome conformation capture, Jon-Matthew Belton and Job Dekker

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

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Novel Observations From Next-Generation RNA Sequencing of Highly Purified Human Adult and Fetal Islet Cell Subsets, David M. Blodgett, Anetta Nowosielska, Shaked Afik, Susanne Pechhold, Anthony J. Cura, Norman J. Kennedy, Soyoung Kim, Alper Kucukural, Roger J. Davis, Sally C. Kent, Dale L. Greiner, Manuel Garber, David M. Harlan, and Philip J. diLorio Jr.

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REdiii: a pipeline for automated structure solution, Markus-Frederik Bohn and Celia A. Schiffer

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The ssDNA Mutator APOBEC3A Is Regulated by Cooperative Dimerization, Markus-Frederik Bohn, Shivender Shandilya, Tania V. Silvas, Ellen A. Nalivaika, Takahide Kouno, Brian Kelch, Sean P. Ryder, Nese Kurt Yilmaz, Mohan Somasundaran, and Celia A. Schiffer

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DNA-binding-domain fusions enhance the targeting range and precision of Cas9, Mehmet Fatih Bolukbasi, Ankit Gupta, Sarah Oikemus, Alan G. Derr, Manuel Garber, Michael H. Brodsky, Lihua (Julie) Zhu, and Scot A. Wolfe

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DNA-binding-domain fusions enhance the targeting range and precision of Cas9, Mehmet Fatih Bolukbasi, Ankit Gupta, Sarah Oikemus, Alan G. Derr, Manuel Garber, Michael H. Brodsky, Lihua Julie Zhu, and Scot A. Wolfe

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Structural basis for mutation-induced destabilization of profilin 1 in ALS, Sivakumar Boopathy, Tania V. Silvas, Maeve Tischbein, Silvia Jansen, Shivender Shandilya, Jill A. Zitzewitz, John E. Landers, Bruce L. Goode, Celia A. Schiffer, and Daryl A. Bosco

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R loops regulate promoter-proximal chromatin architecture and cellular differentiation, Poshen B. Chen, Hsiuyi V. Chen, Diwash Acharya, Oliver J. Rando, and Thomas G. Fazzio

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Tailor: a computational framework for detecting non-templated tailing of small silencing RNAs, Min-Te Chou, Bo W. Han, Chiung-Po Hsiao, Phillip D. Zamore, Zhiping Weng, and Jui-Hung Hung

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

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Structural and functional diversity of Topologically Associating Domains, Job Dekker and Edith Heard

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Long-Range Chromatin Interactions, Job Dekker and Tom Misteli

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The Lipid Droplet Protein Hypoxia-inducible Gene 2 Promotes Hepatic Triglyceride Deposition by Inhibiting Lipolysis, Marina T. DiStefano, Laura V. Danai, Rachel J. Roth Flach, Anil K. Chawla, David J. Pedersen, Adilson L. Guilherme, and Michael P. Czech

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Epigenomics and the structure of the living genome, Nir Friedman and Oliver J. Rando

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Chemical Biology of Protein Arginine Modifications in Epigenetic Regulation, Jakob Fuhrmann, Kathleen W. Clancy, and Paul R. Thompson

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Synthesis and Use of a Phosphonate Amidine to Generate an Anti-Phosphoarginine-Specific Antibody, Jakob Fuhrmann, Venkataraman Subramanian, and Paul R. Thompson

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Glycolytic enzymes localize to ribonucleoprotein granules in Drosophila germ cells, bind Tudor and protect from transposable elements, Ming Gao, Travis Thomson, T Michael Creed, Shikui Tu, Sudan N. Loganathan, Christina A. Jackson, Patrick McCluskey, Yanyan Lin, Scott E. Collier, Zhiping Weng, Paul Lasko, Melanie D. Ohi, and Alexey L. Arkov

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Suppression of pervasive noncoding transcription in embryonic stem cells by esBAF, Sarah J. Hainer, Weifeng Gu, Benjamin R. Carone, Benjamin D. Landry, Oliver J. Rando, Craig C. Mello, and Thomas G. Fazzio

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Using Experimental and Computational Strategies to Understand the Biogenesis of microRNAs and piRNAs: A Dissertation, Bo W. Han

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Noncoding RNA. piRNA-guided transposon cleavage initiates Zucchini-dependent, phased piRNA production, Bo W. Han, Wei Wang, Chengjian Li, Zhiping Weng, and Phillip D. Zamore

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piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing, Bo W. Han, Wei Wang, Phillip D. Zamore, and Zhiping Weng

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Near-infrared photoactivatable control of Ca signaling and optogenetic immunomodulation, Lian He, Yuanwei Zhang, Guolin Ma, Peng Tan, Zhan Jun Li, Shengbing Zhang, Xiang Wu, Ji Jing, Shaohai Fang, Lijuan Zhou, Youjun Wang, Yun Huang, Patrick Hogan, Gang Han, and Yubin Zhou

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An optimized kit-free method for making strand-specific deep sequencing libraries from RNA fragments, Erin E. Heyer, Hakan Ozadam, Emiliano P. Ricci, Can Cenik, and Melissa J. Moore

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Structure-Guided Design of a High Affinity Inhibitor to Human CtBP, Brendan J. Hilbert, Benjamin L. Morris, Keith C. Ellis, Janet L. Paulsen, Celia A. Schiffer, Steven R. Grossman, and William E. Royer

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Utilization of the Soft Agar Colony Formation Assay to Identify Inhibitors of Tumorigenicity in Breast Cancer Cells, Sachi Horibata, Tommy V. Vo, Venkataraman Subramanian, Paul R. Thompson, and Scott A. Coonrod

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miR-10b-5p expression in Huntington's disease brain relates to age of onset and the extent of striatal involvement, Andrew G. Hoss, Adam Labadorf, Jeanne C. Latourelle, Vinay K. Kartha, Tiffany C. Hadzi, James F. Gusella, Marcy E. MacDonald, Jiang-Fan Chen, Schahram Akbarian, Zhiping Weng, Jean Paul Vonsattel, and Richard H. Myers

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

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

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A Balance between Inhibitor Binding and Substrate Processing Confers Influenza Drug Resistance, Li Jiang, Ping Liu, Claudia Bank, Nicholas Renzette, Kristina L. Prachanronarong, L. Safak Yilmaz, Daniel R. Caffrey, Konstantin B. Zeldovich, Celia A. Schiffer, Timothy F. Kowalik, Jeffrey D. Jensen, Robert W. Finberg, Jennifer P. Wang, and Daniel N. Bolon

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Investigating the Effects of Mutant FUS on Stress Response in Amyotrophic Lateral Sclerosis: A Thesis, Laura J. Kaushansky

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Functional annotation of native enhancers with a Cas9-histone demethylase fusion, Nicola A. Kearns, Hannah Pham, Barbara Tabak, Ryan M. J. Genga, Noah J. Silverstein, Manuel Garber, and Rene Maehr

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

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Structure of the Vif-binding domain of the antiviral enzyme APOBEC3G, Takahide Kouno, Elizabeth M. Luengas, Megumi Shigematsu, Shivender Shandilya, JingYing Zhang, Luan Chen, Mayuko Hara, Celia A. Schiffer, Reuben S. Harris, and Hiroshi Matsuo

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Chemical Proteomic Platform To Identify Citrullinated Proteins, Daniel M. Lewallen, Kevin L. Bicker, Venkataraman Subramanian, Kathleen W. Clancy, Daniel J. Slade, Julianne Martell, Christina J. Dreyton, Jeremy Sokolove, Eranthie Weerapana, and Paul R. Thompson

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Inhibition of PAD4 activity is sufficient to disrupt mouse and human NET formation., Huw D. Lewis and Paul R. Thompson

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Using Amplicon Deep Sequencing to Detect Genetic Signatures of Plasmodium vivax Relapse, Jessica T. Lin, Nicholas J. Hathaway, David L. Saunders, Chanthap Lon, Sujata Balasubramanian, Oksana Kharabora, Panita Gosi, Sabaithip Sriwichai, Laurel Kartchner, Char Meng Chuor, Prom Satharath, Charlotte Lanteri, Jeffrey A. Bailey, and Jonathan J. Juliano

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Multicolor CRISPR labeling of chromosomal loci in human cells, Hanhui Ma, Ardalan Naseri, Pablo Reyes-Gutierrez, Scot A. Wolfe, Shaojie Zhang, and Thoru Pederson

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Pitfalls of mapping high-throughput sequencing data to repetitive sequences: Piwi's genomic targets still not identified, Georgi K. Marinov, Jie Wang, Dominik Handler, Barbara J. Wold, Zhiping Weng, Gregory J. Hannon, Alexei A. Aravin, Phillip D. Zamore, Julius Brennecke, and Katalin Fejes Toth

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Pushing The Boundaries of Bioluminescence Using Synthetic Luciferins: A Dissertation, David M. Mofford

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Opposing calcium-dependent signalling pathways control skeletal muscle differentiation by regulating a chromatin remodelling enzyme, Brian T. Nasipak, Teresita Padilla-Benavides, Karin M. Green, John D. Leszyk, Wenjie Mao, Silvana Konda, Said Sif, Scott A. Shaffer, Yasuyuki Ohkawa, and Anthony N. Imbalzano

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Simultaneously Targeting the NS3 Protease and Helicase Activities for More Effective Hepatitis C Virus Therapy, Jean Ndjomou, M Josie. Corby, Noreena L. Sweeney, Alicia M. Hanson, Cihan Aydin, Akbar Ali, Celia A. Schiffer, Kelin Li, Kevin J. Frankowski, Frank J. Schoenen, and David N. Frick

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Guanabenz (Wytensin) selectively enhances uptake and efficacy of hydrophobically modified siRNAs, Maire F. Osborn, Julia F. Alterman, Mehran Nikan, Hong Cao, Marie C. Didiot, Matthew R. Hassler, Andrew H. Coles, and Anastasia Khvorova

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Drug-resistant HIV-1 protease regains functional dynamics through cleavage site coevolution, Nevra Ozer, Aysegul Ozen, Celia A. Schiffer, and Turkan Haliloglu

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Advancements in the Synthesis and Application of Near-Infrared Imaging Reagents: A Dissertation, Steven M. Pauff

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Toward a sustainable biomedical research enterprise: Finding consensus and implementing recommendations, Christopher L. Pickett, Benjamin W. Corb, C. Robert Matthews, Wesley I. Sundquist, and Jeremy M. Berg

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A Direct Interaction with RNA Dramatically Enhances the Catalytic Activity of the HIV-1 Protease In Vitro, Marc Potempa, Ellen A. Nalivaika, Debra A. Ragland, Sook-Kyung Lee, Celia A. Schiffer, and Ronald Swanstrom

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

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Evaluation of novel imidazotetrazine analogues designed to overcome temozolomide resistance and glioblastoma regrowth, Yulian P. Ramirez, Ann C. Mladek, Roger M. Phillips, Mikko Gynther, Jarkko Rautio, Alonzo H. Ross, Richard T. Wheelhouse, and Jann N. Sakaria

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Chromatin Dynamics and the RNA Exosome Function in Concert to Regulate Transcriptional Homeostasis, Mayuri Rege, Vidya Subramanian, Chenchen Zhu, Tsung-Han S. Hsieh, Assaf Weiner, Nir Friedman, Sandra Clauder-Munster, Lars M. Steinmetz, Oliver J. Rando, Laurie A. Boyer, and Craig L. Peterson

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Caenorhabditis elegans microRNAs of the let-7 family act in innate immune response circuits and confer robust developmental timing against pathogen stress, Zhiji Ren and Victor R. Ambros

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Identifying, Targeting, and Exploiting a Common Misfolded, Toxic Conformation of SOD1 in ALS: A Dissertation, Melissa S. Rotunno

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Assessing long-distance RNA sequence connectivity via RNA-templated DNA-DNA ligation, Christian K. Roy, Sara Olson, Brenton R. Graveley, Phillip D. Zamore, and Melissa J. Moore

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

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Caffeine inhibits glucose transport by binding at the GLUT1 nucleotide-binding site, Jay M. Sage, Anthony J. Cura, Kenneth P. Lloyd, and Anthony Carruthers

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Single-Molecule Imaging Reveals that Argonaute Reshapes the Binding Properties of Its Nucleic Acid Guides, William E. Salomon, Samson M. Jolly, Melissa J. Moore, Phillip D. Zamore, and Victor Serebrov

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

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Simultaneous generation of many RNA-seq libraries in a single reaction, Alexander A. Shishkin, Georgia Giannoukos, Alper Kucukural, Dawn Ciulla, Michele Busby, Christine Surka, Jenny Chen, Roby P. Bhattacharyya, Robert F. Rudy, Milesh M. Patel, Nathaniel Novod, Deborah T. Hung, Andreas Gnirke, Manuel Garber, Mitchell Guttman, and Jonathan Livny

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Protein arginine deiminase 2 binds calcium in an ordered fashion: implications for inhibitor design, Daniel J. Slade, Pengfei Fang, Christina J. Dreyton, Ying Zhang, Jakob Fuhrmann, Don Rempel, Benjamin D. Bax, Scott A. Coonrod, Huw D. Lewis, Min Guo, Michael L. Gross, and Paul R. Thompson

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A 4D view on mRNA, Carlas Smith, Li-Chun Tu, and David Grünwald

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Circulating Levels of sFlt1 Splice Variants as Predictive Markers for the Development of Preeclampsia, Colby A. Souders, Sharon E. Maynard, Jing Yan, Yan Wang, Naomi Boatright, Jessica Sedan, David Balyozian, Peter S. Cheslock, Deborah C. Molrine, and Tiffany A. Moore Simas

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Structural and Thermodynamic Effects of Macrocyclization in HCV NS3/4A Inhibitor MK-5172, Djade I. Soumana, Nese Kurt Yilmaz, Kristina L. Prachanronarong, Cihan Aydin, Akbar Ali, and Celia A. Schiffer

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Design, synthesis, and biological evaluation of tetrazole analogs of Cl-amidine as protein arginine deiminase inhibitors., Venkataraman Subramanian, Jason S. Knight, Sangram Parelkar, Lynne Anguish, Scott A. Coonrod, Mariana J. Kaplan, and Paul R. Thompson

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The Shape of Silence: The Solution-State Conformation of Sir Heterochromatin: A Dissertation, Sarah G. Swygert

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Differential Toxicity of Nuclear RNA Foci versus Dipeptide Repeat Proteins in a Drosophila Model of C9ORF72 FTD/ALS, Helene Tran, Sandra Almeida, Jill Moore, Tania F. Gendron, UmaDevi Chalasani, Yubing Lu, Xing Du, Jeffrey A. Nickerson, Leonard Petrucelli, Zhiping Weng, and Fen-Biao Gao

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Evaluation of preprocessing, mapping and postprocessing algorithms for analyzing whole genome bisulfite sequencing data, Junko Tsuji and Zhiping Weng

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Comparative functional characterization of the CSR-1 22G-RNA pathway in Caenorhabditis nematodes, Shikui Tu, Monica Z. Wu, Jie Wang, Asher D. Cutter, Zhiping Weng, and Julie M. Claycomb

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Variation in the Microbiota of Ixodes Ticks with Regard to Geography, Species, and Sex, Will Van Treuren, Loganathan Ponnusamy, R Jory Brinkerhoff, Antonio Gonzalez, Christian M. Parobek, Jonathan J. Juliano, Theodore G. Andreadis, Richard C. Falco, Lorenza Beati Ziegler, Nicholas J. Hathaway, Corinna Keeler, Michael Emch, Jeffrey A. Bailey, R. Michael Roe, Charles S. Apperson, Rob Knight, and Steven R. Meshnick

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Massively parallel sampling of lattice proteins reveals foundations of thermal adaptation, Sergey V. Venev and Konstantin B. Zeldovich

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Activated mTORC1 promotes long-term cone survival in retinitis pigmentosa mice, Aditya Venkatesh, Shan Ma, Yun Z. Le, Michael N. Hall, Markus A. Ruegg, and Claudio Punzo

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Jagged 1 Rescues the Duchenne Muscular Dystrophy Phenotype, Natassia M. Vieira, Ingegerd Elvers, Matthew S. Alexander, Yuri B. Moreira, Alal Eran, Juliana P. Gomes, Jamie L. Marshall, Elinor K. Karlsson, Sergio Verjovski-Almeida, Kerstin Lindblad-Toh, Louis M. Kunkel, and Mayana Zatz

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Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2, Thom Vreven, Iain H. Moal, Anna Vangone, Brian G. Pierce, Panagiotis L. Kastritis, Mieczyslaw Torchala, Raphael Chaleil, Brian Jimenez-Garcia, Paul A. Bates, Juan Fernandez-Recio, Alexandre M. J. J. Bonvin, and Zhiping Weng

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Adenovirus-Mediated Somatic Genome Editing of Pten by CRISPR/Cas9 in Mouse Liver in Spite of Cas9-Specific Immune Responses, Dan Wang, Haiwei Mou, Shaoyong Li, Yingxiang Li, Soren Hough, Karen Tran, Jia Li, Hao Yin, Daniel G. Anderson, Erik J. Sontheimer, Zhiping Weng, Guangping Gao, and Wen Xue

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Slicing and Binding by Ago3 or Aub Trigger Piwi-Bound piRNA Production by Distinct Mechanisms, Wei Wang, Bo W. Han, Cindy Tipping, Daniel Tianfang Ge, Zhao Zhang, Zhiping Weng, and Phillip D. Zamore

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

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High-resolution chromatin dynamics during a yeast stress response, Assaf Weiner, Tsung-Han S. Hsieh, Alon Appleboim, Hsiuyi V. Chen, Ayelet Rahat, Ido Amit, Oliver J. Rando, and Nir Friedman

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Systemic AAV9 gene transfer in adult GM1 gangliosidosis mice reduces lysosomal storage in CNS and extends lifespan, Cara M. Weismann, Jennifer Ferreira, Allison M. Keeler, Qin Su, Linghua Qiu, Scott A. Shaffer, Zuoshang Xu, Guangping Gao, and Miguel Sena-Esteves

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Molecular targeting of protein arginine deiminases to suppress colitis and prevent colon cancer, Erin E. Witalison, Xiangli Cui, Corey P. Causey, Paul R. Thompson, and Lorne J. Hofseth

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Inhibiting protein arginine deiminases has antioxidant consequences., Erin E. Witalison, Xiangli Cui, Anne B. Hofseth, Venkataraman Subramanian, Corey P. Causey, Paul R. Thompson, and Lorne J. Hofseth

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Protein Arginine Deiminases and Associated Citrullination: Physiological Functions and Diseases Associated with Dysregulation., Erin E. Witalison, Paul R. Thompson, and Lorne J. Hofseth

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Subnuclear domain proteins in cancer cells support the functions of RUNX2 in the DNA damage response, Seungchan Yang, Alexandre Jose Christino Quaresma, Jeffrey A. Nickerson, Karin M. Green, Scott A. Shaffer, Anthony N. Imbalzano, Lori A. Martin-Buley, Jane B. Lian, Janet L. Stein, Andre J. Van Wijnen, and Gary S. Stein

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Positive Selection Drives Preferred Segment Combinations during Influenza Virus Reassortment, Konstantin B. Zeldovich, Ping Liu, Nicholas Renzette, Matthieu Foll, Serena T. Pham, Sergey V. Venev, Glen R. Gallagher, Daniel N. Bolon, Evelyn A. Kurt-Jones, Jeffrey D. Jensen, Daniel R. Caffrey, Celia A. Schiffer, Timothy F. Kowalik, Jennifer P. Wang, and Robert W. Finberg

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Cross-talk between PRMT1-mediated methylation and ubiquitylation on RBM15 controls RNA splicing, Li Zhang, Ngoc-Tung Tran, Hairui Su, Rui Wang, Yuheng Lu, Haiping Tang, Sayura Aoyagi, Ailan Guo, Alireza Khodadadi-Jamayran, Dewang Zhou, Kun Qian, Todd Hricik, Jocelyn Cote, Xiaosi Han, Wenping Zhou, Suparna Laha, Omar Abdel-Wahab, Ross L. Levine, Glen Raffel, Yanyan Liu, Dongquan Chen, Haitao Li, Tim Townes, Hengbin Wang, Haiteng Deng, Yujun George Zheng, Christina Leslie, Minkui Luo, and Xinyang Zhao

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Modulation of HIV protease flexibility by the T80N mutation, Hao Zhou, Shangyang Li, John Badger, Ellen A. Nalivaika, Yufeng Cai, Jennifer E. Foulkes-Murzycki, Celia A. Schiffer, and Lee Makowski

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Local sequence assembly reveals a high-resolution profile of somatic structural variations in 97 cancer genomes, Jiali Zhuang and Zhiping Weng

Publications from 2014

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High-throughput sequencing analysis of post-liver transplantation HCV E2 glycoprotein evolution in the presence and absence of neutralizing monoclonal antibody, Gregory J. Babcock, Sowmya Iyer, Heidi L. Smith, Yan Wang, Kirk Rowley, Donna M. Ambrosino, Phillip D. Zamore, Brian G. Pierce, Deborah C. Molrine, and Zhiping Weng

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A bayesian MCMC approach to assess the complete distribution of fitness effects of new mutations: uncovering the potential for adaptive walks in challenging environments, Claudia Bank, Ryan T. Hietpas, Alex Wong, Daniel N. Bolon, and Jeffrey D. Jensen

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Viewing protein fitness landscapes through a next-gen lens, Jeffrey I. Boucher, Pamela Cote, Julia Flynn, Li Jiang, Aneth Laban, Parul Mishra, Benjamin P. Roscoe, and Daniel N. Bolon

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Drug Resistance Mutations Alter Dynamics of Inhibitor-Bound HIV-1 Protease, Yufeng Cai, Wazo Myint, Janet L. Paulsen, Celia A. Schiffer, Rieko Ishima, and Nese Kurt Yilmaz

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High-resolution mapping of chromatin packaging in mouse embryonic stem cells and sperm, Benjamin R. Carone, Jui-Hung Hung, Sarah J. Hainer, Min-Te Chou, Dawn M. Carone, Zhiping Weng, Thomas G. Fazzio, and Oliver J. Rando