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.
Publications from 2019
Constrained mutational sampling of amino acids in HIV-1 protease evolution, Jeffrey I. Boucher, Troy W. Whitfield, Ann Dauphin, Gily S. Nachum, Carl Hollins III, Konstantin B. Zeldovich, Ronald Swanstrom, Celia A. Schiffer, Jeremy Luban, and Daniel N. Bolon
The non-canonical SMC protein SmcHD1 antagonises TAD formation and compartmentalisation on the inactive X chromosome, Michal R. Gdula, Tatyana B. Nesterova, Greta Pintacuda, Jonathan Godwin, Ye Zhan, Hakan Ozadam, Michael McClellan, Daniella Moralli, Felix Krueger, Catherine M. Green, Wolf Reik, Skirmantas Kriaucionis, Edith Heard, Job Dekker, and Neil Brockdorff
DEBrowser: interactive differential expression analysis and visualization tool for count data, Alper Kucukural, Onur Yukselen, Deniz M. Ozata, Melissa J. Moore, and Manuel Garber
Resistance outside the substrate envelope: hepatitis C NS3/4A protease inhibitors, Aysegul Ozen, Kristina L. Prachanronarong, Ashley N. Matthew, Djade I. Soumana, and Celia A. Schiffer
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
Computational investigation into the fluorescence of luciferin analogues, Thom Vreven and Stephen C. Miller
Publications from 2018
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
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
Do Skeletal Dynamics Mediate Sugar Uptake and Transport in Human Erythrocytes, Robert J. Asaro, Qiang Zhu, Pedro Cabrales, and Anthony Carruthers
Evaluation of a method to measure HHV-6B infection in vitro based on cell size, Aniuska Becerra, Tessa Santoro, and Lawrence J. Stern
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
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
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
Ajulemic acid: potential treatment for chronic inflammation, Sumner Burstein
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
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
Effects of Larval Density on Gene Regulation in Caenorhabditis elegans During Routine L1 Synchronization, Io Long Chan, Oliver J. Rando, and Colin C. Conine
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
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
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
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
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
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
Nuclear Export Through Nuclear Envelope Remodeling in Saccharomyces cerevisiae, Baojin Ding, Anne M. Mirza, James A. Ashley, Vivian Budnik, and Mary Munson
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)
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
Role of TRIP6 and Angiomotins in the Regulation of the Hippo Signaling Pathway, Shubham Dutta
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
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
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
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
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
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
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
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
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)
Investigating the Gene Regulatory Network Underlying Caudal Hindbrain Specification in Embryonic Zebrafish, Priyanjali Ghosh
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
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)
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
America's lost dogs, Linda Goodman and Elinor K. Karlsson
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
Optical Temperature Sensing With Infrared Excited Upconversion Nanoparticles, Kory Green, Kai Huang, Hai Pan, Gang Han, and Shuang Fang Lim
Profiling of pluripotency factors in individual stem cells and early embryos, Sarah J. Hainer, Ana Boskovic, Oliver J. Rando, and Thomas G. Fazzio
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
Two-dimensional transition metal carbides and nitrides (MXenes) for biomedical applications, Kai Huang, Zhongjun Li, Jing Lin, Gang Han, and Peng Huang
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
Computer design of microfluidic mixers for protein/RNA folding studies, Venkatesh Inguva, Sagar V. Kathuria, Osman Bilsel, and Blair James Perot
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
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
3C-Based Chromatin Interaction Analyses, Tae Hoon Kim and Job Dekker (Cold Spring Harbor protocols, 2018-09-04)
4C Analysis of 3C, ChIP-Loop, and Control Libraries, Tae Hoon Kim and Job Dekker (Cold Spring Harbor protocols, 2018-09-04)
5C Analysis of 3C, ChIP-Loop, and Control Libraries, Tae Hoon Kim and Job Dekker (Cold Spring Harbor protocols, 2018-09-04)
ChIP, Tae Hoon Kim and Job Dekker (Cold Spring Harbor protocols, 2018-04-02)
ChIP-chip, Tae Hoon Kim and Job Dekker (Cold Spring Harbor protocols, 2018-05-01)
ChIP-Quantitative Polymerase Chain Reaction (ChIP-qPCR), Tae Hoon Kim and Job Dekker (Cold Spring Harbor protocols, 2018-05-01)
ChIP-seq, Tae Hoon Kim and Job Dekker (Cold Spring Harbor protocols, 2018-05-01)
Chromatin Immunoprecipitation (ChIP) Analysis of Protein-DNA Interactions, Tae Hoon Kim and Job Dekker (Cold Spring Harbor protocols, 2018-05-01)
Formaldehyde Cross-Linking, Tae Hoon Kim and Job Dekker (Cold Spring Harbor protocols, 2018-04-02)
Generation of 3C Libraries from Cross-Linked Cells, Tae Hoon Kim and Job Dekker (Cold Spring Harbor protocols, 2018-08-01)
Generation of ChIP-Loop Libraries, Tae Hoon Kim and Job Dekker (Cold Spring Harbor protocols, 2018-08-01)
Generation of Control Ligation Product Libraries for 3C Analyses, Tae Hoon Kim and Job Dekker (Cold Spring Harbor protocols, 2018-08-01)
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)
Preparation of Cross-Linked Chromatin for ChIP, Tae Hoon Kim and Job Dekker (Cold Spring Harbor protocols, 2018-04-02)
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
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
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
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
Understanding Human Erythrocyte Glucose Transporter (GLUT1) Mediated Glucose Transport Phenomena Through Structural Analysis, Kenneth P. Lloyd
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
Kinetic Mechanism of Nicotinamide N-Methyltransferase., Heather S. Loring and Paul R. Thompson
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
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
Angiomotins stimulate LATS kinase autophosphorylation and act as scaffolds that promote Hippo signaling, Sebastian Mana-Capelli and Dannel McCollum
Targeting Drug Resistance In HCV NS3/4A Protease: Mechanisms And Inhibitor Design Strategies, Ashley N. Matthew
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
A parental requirement for dual-specificity phosphatase 6 in zebrafish, Jennifer M. Maurer and Charles G. Sagerstrom
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
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
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
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
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
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)
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
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
Photochemical Control of Protein Arginine Deiminase (PAD) Activity, Santanu Mondal, Sangram S. Parelkar, Mitesh Nagar, and Paul R. Thompson
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
Pet genomics medicine runs wild, Lisa Moses, Steve Niemi, and Elinor K. Karlsson
Donated chemical probes for open science, Susanne Muller, Paul R. Thompson, and Anke Mueller-Fahrnow
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
The N-terminal region of photocleavable peptides that bind HLA-DR1 determines the kinetics of fragment release, Maria P. Negroni and Lawrence J. Stern
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
Development of Activity-Based Proteomic Probes for Protein Citrullination., Venkatesh V. Nemmara and Paul R. Thompson
Citrullination Inactivates Nicotinamide-N-methyltransferase, Venkatesh V. Nemmara, Ronak Tilvawala, Ari J. Salinger, Lacey Miller, Son Hong Nguyen, Eranthie Weerapana, and Paul R. Thompson
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
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
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)
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
A comprehensive genomic history of extinct and living elephants, Eleftheria Palkopoulou, Elinor K. Karlsson, and David Reich