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 2019

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DEBrowser: interactive differential expression analysis and visualization tool for count data, Alper Kucukural, Onur Yukselen, Deniz M. Ozata, Melissa J. Moore, and Manuel Garber

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Principles for enhancing virus capsid capacity and stability from a thermophilic virus capsid structure, Nicholas P. Stone, Gabriel Demo, Emily Agnello, and Brian A. Kelch

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Computational investigation into the fluorescence of luciferin analogues, Thom Vreven and Stephen C. Miller

Publications from 2018

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NmeCas9 is an intrinsically high-fidelity genome editing platform, Nadia Amrani, Xin D. Gao, Pengpeng Liu, Alireza Edraki, Aamir Mir, Raed Ibraheim, Ankit Gupta, Kanae E. Sasaki, Tong Wu, Thomas G. Fazzio, Lihua Julie Zhu, Scot A. Wolfe, and Erik J. Sontheimer

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NmeCas9 is an intrinsically high-fidelity genome-editing platform, Nadia Amrani, Xin D. Gao, Pengpeng Liu, Alireza Edraki, Aamir Mir, Raed Ibraheim, Ankit Gupta, Kanae E. Sasaki, Tong Wu, Thomas G. Fazzio, Lihua Julie Zhu, Scot A. Wolfe, and Erik J. Sontheimer

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Do Skeletal Dynamics Mediate Sugar Uptake and Transport in Human Erythrocytes, Robert J. Asaro, Qiang Zhu, Pedro Cabrales, and Anthony Carruthers

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Evaluation of a method to measure HHV-6B infection in vitro based on cell size, Aniuska Becerra, Tessa Santoro, and Lawrence J. Stern

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Assembly of human C-terminal binding protein (CtBP) into tetramers, Andrew G. Bellesis, Anne M. Jecrois, Janelle A. Hayes, Celia A. Schiffer, and William E. Royer

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Orthogonal Cas9-Cas9 chimeras provide a versatile platform for genome editing, Mehmet F. Bolukbasi, Pengpeng Liu, Kevin Luk, Samantha F. Kwok, Ankit Gupta, Nadia Amrani, Erik J. Sontheimer, Lihua Julie Zhu, and Scot A. Wolfe

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Analysis of the Human Mucosal Response to Cholera Reveals Sustained Activation of Innate Immune Signaling Pathways, Daniel L. Bourque, Diane P. Genereux, Elinor K. Karlsson, Firdausi Qadri, and Jason B. Harris

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Ajulemic acid: potential treatment for chronic inflammation, Sumner Burstein

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Synonymous Mutations at the Beginning of the Influenza A Virus Hemagglutinin Gene Impact Experimental Fitness, Aneth S. Canale, Sergey V. Venev, Troy W. Whitfield, Daniel R. Caffrey, Wayne A. Marasco, Celia A. Schiffer, Timothy F. Kowalik, Jeffrey D. Jensen, Robert W. Finberg, Konstantin B. Zeldovich, Jennifer P. Wang, and Daniel N. Bolon

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Maelstrom Represses Canonical Polymerase II Transcription within Bi-directional piRNA Clusters in Drosophila melanogaster, Timothy Chang, Eugenio Mattei, Ildar Gainetdinov, Cansu Colpan, Zhiping Weng, and Phillip D. Zamore

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Effects of Larval Density on Gene Regulation in Caenorhabditis elegans During Routine L1 Synchronization, Io Long Chan, Oliver J. Rando, and Colin C. Conine

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

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Illuminating Biology with Membrane Penetrating Sulfonate Delivery Scaffolds and Near-Infrared Azasiline Fluorophores, Adam Choi

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Small RNAs gained during epididymal transit of sperm are essential for embryonic development in mice, Colin C. Conine, Fengyun Sun, Lina Song, Jaime A. Rivera-Perez, and Oliver J. Rando

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Small RNAs Gained during Epididymal Transit of Sperm Are Essential for Embryonic Development in Mice, Colin C. Conine, Fengyun Sun, Lina Song, Jaime A. Rivera-Perez, and Oliver J. Rando

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Immunocontraceptive target repertoire defined by systematic identification of sperm membrane alloantigens in a single species, Nathaly Cormier, John J. McGlone, John D. Leszyk, and Daniel M. Hardy

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The TRIM-NHL protein NHL-2 is a co-factor in the nuclear and somatic RNAi pathways in C. elegans, Gregory M. Davis, Shikui Tu, Jacqueline A. Wilce, Julie M. Claycomb, Zhiping Weng, and Peter R. Boag

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Histone citrullination represses miRNA expression resulting in increased oncogene mRNAs in somatolactotrope cells., Stanley B DeVore, Coleman H. Young, Guangyuan Li, Anitha Sundararajan, Thiruvarangan Ramaraj, Joann Mudge, Faye Schilkey, Aaron Muth, Paul R. Thompson, and Brian D. Cherrington

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

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

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ETV4 transcription factor and MMP13 metalloprotease are interplaying actors of breast tumorigenesis, Mandy Dumortier, Franck Ladam, Isabelle Damour, Sophie Vacher, Ivan Bieche, Nathalie Marchand, Yvan de Launoit, David Tulasne, and Anne Chotteau-Lelievre

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Role of TRIP6 and Angiomotins in the Regulation of the Hippo Signaling Pathway, Shubham Dutta

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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

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Intranuclear and higher-order chromatin organization of the major histone gene cluster in breast cancer, Andrew J. Fritz, Deli Hong, A. Rasim Barutcu, Anthony N. Imbalzano, and Gary S. Stein

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Differential analysis of chromatin accessibility and histone modifications for predicting mouse developmental enhancers, Shaliu Fu, Qin Wang, Jill E. Moore, Michael J. Purcaro, Henry E. Pratt, Kaili Fan, Cuihua Gu, Cizhong Jiang, Ruixin Zhu, Anshul Kundaje, Aiping Lu, and Zhiping Weng

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Elimination of PCR duplicates in RNA-seq and small RNA-seq using unique molecular identifiers, Yu Fu, Pei-Hsuan Wu, Timothy J. Beane, Phillip D. Zamore, and Zhiping Weng

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Elimination of PCR duplicates in RNA-seq and small RNA-seq using unique molecular identifiers, Yu Fu, Pei-Hsuan Wu, Timothy J. Beane, Phillip D. Zamore, and Zhiping Weng

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Elimination of PCR duplicates in RNA-seq and small RNA-seq using unique molecular identifiers, Yu Fu, Pei-Hsuan Wu, Timothy J. Beane, Phillip D. Zamore, and Zhiping Weng

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The genome of the Hi5 germ cell line from Trichoplusia ni, an agricultural pest and novel model for small RNA biology, Yu Fu, Yujing Yang, Han Zhang, Gwen Farley, Junling Wang, Kaycee A. Quarles, Zhiping Weng, and Phillip D. Zamore

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

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

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Investigating the Gene Regulatory Network Underlying Caudal Hindbrain Specification in Embryonic Zebrafish, Priyanjali Ghosh

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Analysis of novel caudal hindbrain genes reveals different regulatory logic for gene expression in rhombomere 4 versus 5/6 in embryonic zebrafish, Priyanjali Ghosh, Jennifer M. Maurer, and Charles G. Sagerstrom

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

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Cell-specific histone modification maps in the human frontal lobe link schizophrenia risk to the neuronal epigenome, Kiran Girdhar, Gabriel E. Hoffman, Yan Jiang, Leanne Brown, Marija Kundakovic, Mads E. Hauberg, Nancy J. Francoeur, Ying-Chih Wang, Hardik Shah, David H. Kavanagh, Elizabeth Zharovsky, Rivka Jacobov, Jennifer R. Wiseman, Royce Park, Jessica S. Johnson, Bibi S. Kassim, Laura Sloofman, Eugenio Mattei, Zhiping Weng, Solveig K. Sieberts, Mette A. Peters, Brent T. Harris, Barbara K. Lipska, Pamela Sklar, Panos Roussos, and Schahram Akbarian

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America's lost dogs, Linda Goodman and Elinor K. Karlsson

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Manganese influx and expression of ZIP8 is essential in primary myoblasts and contributes to activation of SOD2, Shellaina J. V. Gordon, Daniel E. Fenker, Katherine E. Vest, and Teresita Padilla-Benavides

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Optical Temperature Sensing With Infrared Excited Upconversion Nanoparticles, Kory Green, Kai Huang, Hai Pan, Gang Han, and Shuang Fang Lim

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Profiling of pluripotency factors in individual stem cells and early embryos, Sarah J. Hainer, Ana Boskovic, Oliver J. Rando, and Thomas G. Fazzio

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Structural analysis of the active site and DNA binding of human cytidine deaminase APOBEC3B, Shurong Hou, Tania V. Silvas, Florian Leidner, Ellen A. Nalivaika, Hiroshi Matsuo, Nese Kurt Yilmaz, and Celia A. Schiffer

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Two-dimensional transition metal carbides and nitrides (MXenes) for biomedical applications, Kai Huang, Zhongjun Li, Jing Lin, Gang Han, and Peng Huang

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Oligonucleotides targeting TCF4 triplet repeat expansion inhibit RNA foci and mis-splicing in Fuchs' dystrophy, Jiaxin Hu, Ziye Rong, Xin Gong, Zhengyang Zhou, Vivek K. Sharma, Chao Xing, Jonathan K. Watts, David R. Corey, and V. Vinod Mootha

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Computer design of microfluidic mixers for protein/RNA folding studies, Venkatesh Inguva, Sagar V. Kathuria, Osman Bilsel, and Blair James Perot

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A call to arms: Unifying the fight against resistance, Alexis Kaushansky, Lizbeth Hedstrom, Aaron Goldman, Juswinder Singh, Priscilla L. Yang, Pradipsinh K. Rathod, Michael Cynamon, Dominik Wodarz, Daruka Mahadevan, Andrew Tomaras, Manuel A. Navia, and Celia A. Schiffer

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Probing Structural Changes among Analogous Inhibitor-Bound Forms of HIV-1 Protease and a Drug-Resistant Mutant in Solution by Nuclear Magnetic Resonance, Shahid N. Khan, John D. Persons, Janet L. Paulsen, Michel Guerrero, Celia A. Schiffer, Nese Kurt Yilmaz, and Rieko Ishima

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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TALE factors use two distinct functional modes to control an essential zebrafish gene expression program, Franck Ladam, William Stanney, Ian J. Donaldson, Ozge Yildiz, Nicoletta Bobola, and Charles G. Sagerstrom

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BB-Cl-Amidine as a novel therapeutic for canine and feline mammary cancer via activation of the endoplasmic reticulum stress pathway, Melissa M. Ledet, Robyn Anderson, Rebecca Harman, Aaron Muth, Paul R. Thompson, Scott A. Coonrod, and Gerlinde R. Van de Walle

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Hydration Structure and Dynamics of Inhibitor-Bound HIV-1 Protease, Florian Leidner, Nese Kurt Yilmaz, Janet L. Paulsen, Yves A. Muller, and Celia A. Schiffer

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Peptidylarginine deiminases 2 and 4 modulate innate and adaptive immune responses in TLR-7-dependent lupus., Yudong Liu, Yaíma L Lightfoot, Nickie Seto, Santanu Mondal, Padmavathy Nandha Premnath, and Paul R. Thompson

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Understanding Human Erythrocyte Glucose Transporter (GLUT1) Mediated Glucose Transport Phenomena Through Structural Analysis, Kenneth P. Lloyd

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Structural Adaptation of Darunavir Analogs Against Primary Mutations in HIV-1 Protease, Gordon J. Lockbaum, Florian Leidner, Linah N. Rusere, Mina Henes, Klajdi Kosovrasti, Gily S. Nachum, Ellen A. Nalivaika, Akbar Ali, Nese Kurt Yilmaz, and Celia A. Schiffer

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Kinetic Mechanism of Nicotinamide N-Methyltransferase., Heather S. Loring and Paul R. Thompson

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Optogenetic Control of Voltage-Gated Calcium Channels, Guolin Ma, Jindou Liu, Yuepeng Ke, Xin Liu, Minyong Li, Fen Wang, Gang Han, Yun Huang, Youjun Wang, and Yubin Zhou

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Crystal structure of the catalytic domain of HIV-1 restriction factor APOBEC3G in complex with ssDNA, Atanu Maiti, Wazo Myint, Tapan Kanai, Krista Delviks-Frankenberry, Christina Sierra Rodriguez, Vinay K. Pathak, Celia A. Schiffer, and Hiroshi Matsuo

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Angiomotins stimulate LATS kinase autophosphorylation and act as scaffolds that promote Hippo signaling, Sebastian Mana-Capelli and Dannel McCollum

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Targeting Drug Resistance In HCV NS3/4A Protease: Mechanisms And Inhibitor Design Strategies, Ashley N. Matthew

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Molecular Mechanism of Resistance in a Clinically Significant Double-Mutant Variant of HCV NS3/4A Protease, Ashley N. Matthew, Florian Leidner, Alicia Newton, Christos J. Petropoulos, Wei Huang, Akbar Ali, Nese Kurt Yilmaz, and Celia A. Schiffer

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A parental requirement for dual-specificity phosphatase 6 in zebrafish, Jennifer M. Maurer and Charles G. Sagerstrom

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Extending chemical perturbations of the ubiquitin fitness landscape in a classroom setting reveals new constraints on sequence tolerance, David Mavor, Daniel N. Bolon, Martin Kampmann, and James S. Fraser

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RNA binding proteins co-localize with small tau inclusions in tauopathy, Brandon F. Maziuk, Daniel J. Apicco, Anna Lourdes Cruz, Lulu Jiang, Peter E. A. Ash, Edroaldo Lummertz. da Rocha, Cheng Zhang, Wai Haung Yu, John D. Leszyk, Jose F. Abisambra, Hu Li, and Benjamin Wolozin

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Intron-containing RNA from the HIV-1 provirus activates type I interferon and inflammatory cytokines, Sean M. McCauley, Kyusik Kim, Anetta Nowosielska, Ann Dauphin, Leonid Yurkovetskiy, William E. Diehl, and Jeremy Luban

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Intron-containing RNA from the HIV-1 provirus activates type I interferon and inflammatory cytokines, Sean M. McCauley, Kyusik Kim, Anetta Nowosielska, Ann Dauphin, Leonid Yurkovetskiy, William E. Diehl, and Jeremy Luban

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

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

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Heavily and fully modified RNAs guide efficient SpyCas9-mediated genome editing, Aamir Mir, Julia F. Alterman, Matthew R. Hassler, Alexandre J. Debacker, Edward Hudgens, Dimas Echeverria, Michael H. Brodsky, Anastasia Khvorova, Jonathan K. Watts, and Erik J. Sontheimer

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T cell epitope engineering: an avian H7N9 influenza vaccine strategy for pandemic preparedness and response, Leonard Moise, Bethany M. Biron, Christine M. Boyle, Nese Kurt Yilmaz, Hyesun Jang, Celia A. Schiffer, Ted M. Ross, William D. Martin, and Anne S. De Groot

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Photochemical Control of Protein Arginine Deiminase (PAD) Activity, Santanu Mondal, Sangram S. Parelkar, Mitesh Nagar, and Paul R. Thompson

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The Three-Fold Axis of the HIV-1 Capsid Lattice Is the Species-Specific Binding Interface for TRIM5alpha, Damien Morger, Franziska Zosel, Martin Buhlmann, Sara Zuger, Maximilian Mittelviefhaus, Benjamin Schuler, Jeremy Luban, and Markus G. Grutter

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Pet genomics medicine runs wild, Lisa Moses, Steve Niemi, and Elinor K. Karlsson

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Donated chemical probes for open science, Susanne Muller, Paul R. Thompson, and Anke Mueller-Fahrnow

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HLA-DO modulates the diversity of the MHC-II self-peptidome, Padma P. Nanaware, Mollie M. Jurewicz, John D. Leszyk, Scott A. Shaffer, and Lawrence J. Stern

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The N-terminal region of photocleavable peptides that bind HLA-DR1 determines the kinetics of fragment release, Maria P. Negroni and Lawrence J. Stern

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The Development of Benzimidazole-Based Clickable Probes for the Efficient Labeling of Cellular Protein Arginine Deiminases (PADs), Venkatesh V. Nemmara, Venkataraman Subramanian, Aaron Muth, Santanu Mondal, Ari J. Salinger, Aaron J. Maurais, Ronak Tilvawala, Eranthie Weerapana, and Paul R. Thompson

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Development of Activity-Based Proteomic Probes for Protein Citrullination., Venkatesh V. Nemmara and Paul R. Thompson

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Citrullination Inactivates Nicotinamide-N-methyltransferase, Venkatesh V. Nemmara, Ronak Tilvawala, Ari J. Salinger, Lacey Miller, Son Hong Nguyen, Eranthie Weerapana, and Paul R. Thompson

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Red wine and green tea flavonoids are cis-allosteric activators and competitive inhibitors of GLUT1-mediated sugar uptake, Ogooluwa A. Ojelabi, Kenneth P. Lloyd, Julie K. De Zutter, and Anthony Carruthers

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Signaling Pathways Induced by Leptin during Epithelial(-)Mesenchymal Transition in Breast Cancer, Monserrat Olea-Flores, Juan Carlos Juarez-Cruz, Miguel A. Mendoza-Catalan, Teresita Padilla-Benavides, and Napoleon Navarro-Tito

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

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Resistance from Afar: Distal Mutation V36M Allosterically Modulates the Active Site to Accentuate Drug Resistance in HCV NS3/4A Protease, Aysegul Ozen, Kuan-Hung Lin, Keith P. Romano, Davide Tavella, Alicia Newton, Christos J. Petropoulos, Wei Huang, Cihan Aydin, and Celia A. Schiffer

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A comprehensive genomic history of extinct and living elephants, Eleftheria Palkopoulou, Elinor K. Karlsson, and David Reich

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Differential expression of zinc transporters accompanies the differentiation of C2C12 myoblasts, Amanda L. Paskavitz, Julia Quintana, Daniella Cangussu, Cristina Tavera-Montanez, Yao Xiao, Sonia Ortiz-Mirnada, Juan G. Navea, and Teresita Padilla-Benavides

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HIV-1 Protease Uses Bi-Specific S2/S2' Subsites to Optimize Cleavage of Two Classes of Target Sites, Marc Potempa, Sook-Kyung Lee, Nese Kurt Yilmaz, Ellen A. Nalivaika, Amy Rogers, Ean Spielvogel, Charles W. Carter Jr., Celia A. Schiffer, and Ronald Swanstrom

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Mutations in influenza A virus neuraminidase and hemagglutinin confer resistance against a broadly neutralizing hemagglutinin stem antibody, Kristina L. Prachanronarong, Aneth S. Canale, Ping Liu, Mohan Somasundaran, Shurong Hou, Yu-Ping Poh, Thomas Han, Quan Zhu, Nicholas Renzette, Konstantin B. Zeldovich, Timothy F. Kowalik, Nese Kurt Yilmaz, Jeffrey D. Jensen, Daniel N. Bolon, Wayne A. Marasco, Robert W. Finberg, Celia A. Schiffer, and Jennifer P. Wang