The Program in Biochemistry & Molecular Pharmacology is an academic program of the Graduate School of Biomedical Sciences (GSBS) at the University of Massachusetts Medical School. The program offers graduate study and research focused in the areas of molecular, cellular and regulatory biochemistry; molecular biophysics; chemical biology; and structural biology. This collection showcases publications and presentations authored by students in this program.

Attention GSBS Biochemistry & Molecular Pharmacology students: To submit your publications, go to GSBS Student Publications and click on Submit Research in the left sidebar. You’ll need to log in or create a free account. If you have the article's PubMed ID, submission is very easy. Enter the PubMed ID and information from PubMed will be used to populate the submission form. Questions? Contact Lisa Palmer.

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Publications from 2015

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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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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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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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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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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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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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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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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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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

Publications from 2014

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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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Allosteric inhibition of a stem cell RNA-binding protein by an intermediary metabolite, Carina C. Clingman, Laura M. Deveau, Samantha A. Hay, Ryan M. J. Genga, Shivender Shandilya, Francesca Massi, and Sean P. Ryder

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An improved predictive recognition model for Cys(2)-His(2) zinc finger proteins, Ankit Gupta, Ryan G. Christensen, Heather A. Bell, Mathew Goodwin, Ronak Y. Patel, Manishi Pandey, Metewo Selase Enuameh, Amy L. Rayla, Cong Zhu, Stacey Thibodeau-Beganny, Michael H. Brodsky, J. Keith Joung, Scot A. Wolfe, and Gary D. Stormo

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Crystal structures of human CtBP in complex with substrate MTOB reveal active site features useful for inhibitor design, Brendan J. Hilbert, Steven R. Grossman, Celia A. Schiffer, and William E. Royer

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Mechanisms underlying nucleosome positioning in vivo, Amanda Hughes and Oliver J. Rando

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A co-CRISPR strategy for efficient genome editing in Caenorhabditis elegans, Heesun Kim, Takao Ishidate, Krishna S. Ghanta, Meetu Seth, Darryl Conte Jr., Masaki Shirayama, and Craig C. Mello

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Construction and application of site-specific artificial nucleases for targeted gene editing, Fatma O. Kok, Ankit Gupta, Nathan D. Lawson, and Scot A. Wolfe

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Insight into the allosteric mechanism of Scapharca dimeric hemoglobin, Jennifer M. Laine, Miguel Amat, Brittany R. Morgan, William E. Royer, and Francesca Massi

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The long noncoding RNA THRIL regulates TNFalpha expression through its interaction with hnRNPL, Zhonghan Li, Ti-Chun Chao, Kung-Yen Chang, Nianwei Lin, Veena S. Patil, Chisato Shimizu, Steven R. Head, Jane C. Burns, and Tariq M. Rana

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The middle X residue influences cotranslational N-glycosylation consensus site skipping, Heidi Malaby and William R. Kobertz

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Angiomotins link F-actin architecture to Hippo pathway signaling, Sebastian Mana-Capelli, Murugan Paramasivam, Shubham Dutta, and Dannel McCollum

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Direct interactions promote eviction of the Sir3 heterochromatin protein by the SWI/SNF chromatin remodeling enzyme, Benjamin J. Manning and Craig L. Peterson

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Clot injection technique affects thrombolytic efficacy in a rat embolic stroke model: implications for translaboratory collaborations, Marilena Marinescu, James P. Bouley, Juyu Chueh, Marc Fisher, and Nils Henninger

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Calmodulation meta-analysis: Predicting calmodulin binding via canonical motif clustering, Karen Mruk, Brian M. Farley, Alan W. Ritacco, and William R. Kobertz

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Modulation of frustration in folding by sequence permutation, Robert P. Nobrega, Karunesh Arora, Sagar V. Kathuria, Rita Graceffa, Raul A. Barrea, Liang Guo, Srinivas Chakravarthy, Osman Bilsel, Thomas C. Irving, Charles L. Brooks 3rd, and C. Robert Matthews

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Structural basis and distal effects of Gag substrate coevolution in drug resistance to HIV-1 protease, Aysegul Ozen, Kuan-Hung Lin, Nese Kurt Yilmaz, and Celia A. Schiffer

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Regulation of cyclin-substrate docking by a G1 arrest signaling pathway and the Cdk inhibitor Far1, Patricia A. Pope, Samyabrata Bhaduri, and Peter M. Pryciak

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Systematic exploration of ubiquitin sequence, E1 activation efficiency, and experimental fitness in yeast, Benjamin P. Roscoe and Daniel N. A. Bolon

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Kinome-wide functional analysis highlights the role of cytoskeletal remodeling in somatic cell reprogramming, Kumi Sakurai, Indrani Talukdar, Veena S. Patil, Jason Dang, Zhonghan Li, Kung-Yen Chang, Chih-Chung Lu, Violaine Delorme-Walker, Celine Dermardirossian, Karen Anderson, Dorit Hanein, Chao-Shun Yang, Dongmei Wu, Yang Liu, and Tariq M. Rana

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Functions of FUS/TLS from DNA repair to stress response: implications for ALS, Reddy Ranjith Kumar Sama, Catherine L. Ward, and Daryl A. Bosco

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Resistance to vemurafenib resulting from a novel mutation in the BRAFV600E kinase domain, Timothy R. Wagenaar, Leyuan Ma, Benjamin P. Roscoe, Sung Mi Park, Daniel N. Bolon, and Michael R. Green

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Targeted germ line disruptions reveal general and species-specific roles for paralog group 1 hox genes in zebrafish, Steven E. Weicksel, Ankit Gupta, Denise A. Zannino, Scot A. Wolfe, and Charles G. Sagerstrom

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Genome-wide functional analysis reveals factors needed at the transition steps of induced reprogramming, Chao-Shun Yang, Kung-Yen Chang, and Tariq M. Rana

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A conserved three-nucleotide core motif defines Musashi RNA binding specificity, Nancy R. Zearfoss, Laura M. Deveau, Carina C. Clingman, Eric Schmidt, Emily S. Johnson, Francesca Massi, and Sean P. Ryder

Publications from 2013

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Evaluating the Role of Macrocycles in the Susceptibility of Hepatitis C Virus NS3/4A Protease Inhibitors to Drug Resistance, Akbar Ali, Cihan Aydin, Reinhold Gildemeister, Keith P. Romano, Hong Cao, Aysegul Ozen, Djade Soumana, Alicia Newton, Christos J. Petropoulos, Wei Huang, and Celia A. Schiffer

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Sub-millisecond time-resolved SAXS using a continuous-flow mixer and X-ray micro-beam, Rita Graceffa, Robert P. Nobrega, Raul Barrea, Sagar V. Kathuria, Srinivas Chakravarthy, Osman Bilsel, and Thomas Irving

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Latent effects of Hsp90 mutants revealed at reduced expression levels, Li Jiang, Parul Mishra, Ryan T. Hietpas, Konstantin B. Zeldovich, and Daniel N. A. Bolon

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Advances in turbulent mixing techniques to study microsecond protein folding reactions, Sagar V. Kathuria, Alexander Chan, Rita Graceffa, Robert P. Nobrega, C. Robert Matthews, Thomas C. Irving, Blair Perot, and Osman Bilsel

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UPF1 is Crucial for the Infectivity of Human Immunodeficiency Virus type 1 Progeny Virions, Anna Kristina Serquina, Suman R. Das, Elena Popova, Ogooluwa A. Ojelabi, Christian K. Roy, and Heinrich G. Gottlinger

Publications from 2012

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POS-1 and GLD-1 repress glp-1 translation through a conserved binding-site cluster, Brian M. Farley and Sean P. Ryder

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An optimized two-finger archive for ZFN-mediated gene targeting, Ankit Gupta, Amy L. Rayla, Abirami Lakshmanan, Scot A. Wolfe, Ryan G. Christensen, and Gary D. Stormo

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Fitness analyses of all possible point mutations for regions of genes in yeast, Ryan T. Hietpas, Benjamin P. Roscoe, Li Jiang, and Daniel N. A. Bolon

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Extreme Entropy-Enthalpy Compensation in a Drug-Resistant Variant of HIV-1 Protease, Nancy M. King, Moses Prabu-Jeyabalan, Rajintha M. Bandaranayake, Madhavi N. L. Nalam, Ellen A. Nalivaika, Aysegul Ozen, Turkan Haliloglu, Nese Kurt Yilmaz, and Celia A. Schiffer

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Context surrounding processing sites is crucial in determining cleavage rate of a subset of processing sites in HIV-1 Gag and Gag-Pro-Pol polyprotein precursors by viral protease, Sook-Kyung Lee, Marc Potempa, Madhavi Kolli, Aysegul Ozen, Celia A. Schiffer, and Ronald I. Swanstrom

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Structural insights into neuronal K+ channel-calmodulin complexes, Karen Mruk, Shivender Shandilya, Robert O. Blaustein, Celia A. Schiffer, and William R. Kobertz

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Immune responses in cystic fibrosis: are they intrinsically defective?, Dmitry Ratner and Christian Mueller

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The Molecular Basis of Drug Resistance against Hepatitis C Virus NS3/4A Protease Inhibitors, Keith P. Romano, Akbar Ali, Cihan Aydin, Djade Soumana, Aysegul Ozen, Laura M. Deveau, Casey Silver, Hong Cao, Alicia Newton, Christos J. Petropoulos, Wei Huang, and Celia A. Schiffer

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Sequence Determinants of GLUT1-mediated Accelerated-exchange Transport: Analysis by Homology-Scanning Mutagenesis, Sabrina S. Vollers and Anthony Carruthers

Publications from 2011

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Phosphate and R2D2 Restrict the Substrate Specificity of Dicer-2, an ATP-Driven Ribonuclease, Elif Sarinay Cenik, Ryuya Fukunaga, Gang Lu, Robert Dutcher, Yeming Wang, Traci M. Tanaka Hall, and Phillip D. Zamore

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Argonaute proteins, Elif Sarinay Cenik and Phillip D. Zamore

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A modified bacterial one-hybrid system yields improved quantitative models of transcription factor specificity, Ryan G. Christensen, Ankit Gupta, Zheng Zuo, Lawrence A. Schriefer, Scot A. Wolfe, and Gary D. Stormo

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Zinc finger protein-dependent and -independent contributions to the in vivo off-target activity of zinc finger nucleases, Ankit Gupta, Xiangdong Meng, Lihua Julie Zhu, Nathan D. Lawson, and Scot A. Wolfe

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Experimental illumination of a fitness landscape, Ryan T. Hietpas, Jeffrey D. Jensen, and Daniel N. A. Bolon

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FBF represses the Cip/Kip cell-cycle inhibitor CKI-2 to promote self-renewal of germline stem cells in C. elegans, Irene Kalchhauser, Brian M. Farley, Sandra Pauli, Sean P. Ryder, and Rafal Ciosk

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Structural insights into early folding events using continuous-flow time-resolved SAXS, Sagar V. Kathuria, Liang Guo, Rita Graceffa, Raul Barrea, R. Paul Nobrega, C. Robert Matthews, Tom Irving, and Osman Bilsel

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Long-term Trends in Short-term Outcomes in Acute Myocardial Infarction, Hoa L. Nguyen, Jane S. Saczynski, Joel M. Gore, Molly E. Waring, Darleen M. Lessard, Jorge L. Yarzebski, George W. Reed, Frederick A. Spencer, Shu-Xia Li, and Robert J. Goldberg

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Xenopus laevis oocytes infected with multi-drug-resistant bacteria: implications for electrical recordings, Denice O'Connell, Karen Mruk, Jessica M. Rocheleau, and William R. Kobertz

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Dynamics of preferential substrate recognition in HIV-1 protease: redefining the substrate envelope, Aysegul Ozen, Turkan Haliloglu, and Celia A. Schiffer

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Conformational lability in the class II MHC 3-10 helix and adjacent extended strand dictate HLA-DM susceptibility and peptide exchange, Corrie A. Painter, Maria P. Negroni, Kathy A. Kellersberger, Zarixia Zavala-Ruiz, James E. Evans, and Lawrence J. Stern

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Molecular mechanisms of viral and host cell substrate recognition by hepatitis C virus NS3/4A protease, Keith P. Romano, Jennifer M. Laine, Laura M. Deveau, Hong Cao, Francesca Massi, and Celia A. Schiffer

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MicroRNA Expression Data Reveals a Signature of Kidney Damage following Ischemia Reperfusion Injury, Michael D. Shapiro, Jessamyn Bagley, Jeff Latz, Jonathan G. Godwin, Xupeng Ge, Stefan G. Tullius, and John Iacomini

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Translocation channel gating kinetics balances protein translocation efficiency with signal sequence recognition fidelity, Steven F. Trueman, Elisabet C. Mandon, and Reid Gilmore

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A quantitative RNA code for mRNA target selection by the germline fate determinant GLD-1, Jane E. Wright, Dimos Gaidatzis, Mathias Senften, Brian M. Farley, Eric Westhof, Sean P. Ryder, and Rafal Ciosk

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Quaking regulates Hnrnpa1 expression through its 3' UTR in oligodendrocyte precursor cells, Nancy R. Zearfoss, Carina C. Clingman, Brian M. Farley, Lisa M. McCoig, and Sean P. Ryder

Publications from 2010

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Molecular Basis for Drug Resistance in HIV-1 Protease, Akbar Ali, Rajintha M. Bandaranayake, Yufeng Cai, Nancy M. King, Madhavi Kolli, Seema Mittal, Jennifer E. Foulkes-Murzycki, Madhavi N. L. Nalam, Ellen A. Nalivaika, Aysegul Ozen, Moses Prabu-Jeyabalan, Kelly Thayer, and Celia A. Schiffer

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The effect of clade-specific sequence polymorphisms on HIV-1 protease activity and inhibitor resistance pathways, Rajintha M. Bandaranayake, Madhavi Kolli, Nancy M. King, Ellen A. Nalivaika, Annie Heroux, Junko Kakizawa, Wataru Sugiura, and Celia A. Schiffer

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Decomposing the energetic impact of drug resistant mutations in HIV-1 protease on binding DRV, Yufeng Cai and Celia A. Schiffer

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Acute Modulation of Sugar Transport in Brain Capillary Endothelial Cell Cultures during Activation of the Metabolic Stress Pathway, Anthony J. Cura and Anthony Carruthers

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Evaluating the substrate-envelope hypothesis: structural analysis of novel HIV-1 protease inhibitors designed to be robust against drug resistance, Madhavi N. L. Nalam, Akbar Ali, Michael D. Altman, G. S. Kiran Kumar Reddy, Sripriya Chellappan, Visvaldas Kairys, Aysegul Ozen, Hong Cao, Michael K. Gilson, Bruce Tidor, Tariq M. Rana, and Celia A. Schiffer

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Drug resistance against HCV NS3/4A inhibitors is defined by the balance of substrate recognition versus inhibitor binding, Keith P. Romano, Akbar Ali, William E. Royer, and Celia A. Schiffer

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Discovery of a novel function for human Rad51: maintenance of the mitochondrial genome, Jay M. Sage, Otto S. Gildemeister, and Kendall L. Knight

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Crystal structure of the APOBEC3G catalytic domain reveals potential oligomerization interfaces., Shivender Shandilya, Madhavi N. L. Nalam, Ellen A. Nalivaika, Phillip J. Gross, Johnathan C. Valesano, Keisuke Shindo, Ming Li, Mary Munson, William E. Royer, Elena Harjes, Takahide Kono, Hiroshi Matsuo, Reuben S. Harris, Mohan Somasundaran, and Celia A. Schiffer

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Therapeutic targeting of C-terminal binding protein in human cancer, Michael W. Straza, Seema Paliwal, Ramesh C. Kovi, Barur R. Rajeshkumar, Peter Trenh, Daniel Parker, Giles F. Whalen, Stephen Lyle, Celia A. Schiffer, and Steven R. Grossman

Publications from 2009

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A convergence of rRNA and mRNA quality control pathways revealed by mechanistic analysis of nonfunctional rRNA decay, Sarah E. Cole, Frederick J. laRiviere, Christopher N. Merrikh, and Melissa J. Moore

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Discovery of a novel activator of KCNQ1-KCNE1 K channel complexes., Karen Mruk and William R. Kobertz

Publications from 2008

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Modulation of N-type Calcium Channel Activity by G-proteins and Protein Kinase C, Curtis F. Barrett and Ann R. Rittenhouse

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Amphetamine-induced decreases in dopamine transporter surface expression are protein kinase C-independent, Ekaterina Boudanova, Deanna M. Navaroli, and Haley E. Melikian

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RNA target specificity of the embryonic cell fate determinant POS-1, Brian M. Farley, John M. Pagano, and Sean P. Ryder

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Zinc binding modulates the entire folding free energy surface of human Cu,Zn superoxide dismutase., Can Kayatekin, Jill A. Zitzewitz, and C. Robert Matthews

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Model for the peptide-free conformation of class II MHC proteins, Corrie A. Painter, Anthony Cruz, Gustavo E. Lopez, Lawrence J. Stern, and Zarixia Zavala-Ruiz

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Non-obese diabetic-recombination activating gene-1 (NOD-Rag1 null) interleukin (IL)-2 receptor common gamma chain (IL2r gamma null) null mice: a radioresistant model for human lymphohaematopoietic engraftment, Todd Pearson, Leonard D. Shultz, David M. Miller, Marie A. King, Joseph Laning, William Fodor, Amy Cuthbert, Lisa M. Burzenski, Bruce Gott, Bonnie L. Lyons, Oded Foreman, Aldo A. Rossini, and Dale L. Greiner

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Class II major histocompatibility complex tetramer staining: progress, problems, and prospects, Sabrina S. Vollers and Lawrence J. Stern

Publications from 2007

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Coordinated regulation of Toll-like receptor and NOD2 signaling by K63-linked polyubiquitin chains, Derek W. Abbott, Yibin Yang, Jessica E. Hutti, Swetha Madhavarapu, Michelle A. Kelliher, and Lewis C. Cantley

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Microsecond hydrophobic collapse in the folding of Escherichia coli dihydrofolate reductase, an alpha/beta-type protein, Munehito Arai, Elena Kondrashkina, Can Kayatekin, C. Robert Matthews, Masahiro Iwakura, and Osman Bilsel

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Phosphorylation at serine 208 of the 1alpha,25-dihydroxy Vitamin D3 receptor modulates the interaction with transcriptional coactivators, Gloria Arriagada, Roberto Paredes, Juan Olate, Andre J. Van Wijnen, Jane B. Lian, Gary S. Stein, Janet L. Stein, Sergio Onate, and Martin A. Montecino

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Mass spectrometry analysis of HIV-1 Vif reveals an increase in ordered structure upon oligomerization in regions necessary for viral infectivity, Jared R. Auclair, Karin M. Green, Shivender Shandilya, James E. Evans, Mohan Somasundaran, and Celia A. Schiffer

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Structural basis of GLUT1 inhibition by cytoplasmic ATP, David M. Blodgett, Julie Kelley De Zutter, Kara B. Levine, Pusha Karim, and Anthony Carruthers

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Enterohaemorrhagic and enteropathogenic Escherichia coli Tir proteins trigger a common Nck-independent actin assembly pathway, Michael John Brady, Kenneth Geno Campellone, Megha Ghildiyal, and John M. Leong

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Crystallization and preliminary X-ray analysis of a domain in the Runx2 transcription factor that interacts with the 1alpha,25 dihydroxy vitamin D3 receptor, Carola Bruna, Gloria Arriagada, Jane B. Lian, Gary S. Stein, Marta Bunster, Jose Martinez-Oyanedel, and Martin A. Montecino

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The 1alpha,25-dihydroxy Vitamin D3 receptor preferentially recruits the coactivator SRC-1 during up-regulation of the osteocalcin gene, Loreto Carvallo, Berta Henriquez, Juan Olate, Andre J. Van Wijnen, Jane B. Lian, Gary S. Stein, Sergio Onate, Janet L. Stein, and Martin A. Montecino

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Quantitative analysis of RNA-mediated protein-protein interactions in living cells by FRET, Ya-Lin Chiu, Hong Cao, and Tariq M. Rana

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Mutations in the stalk of the measles virus hemagglutinin protein decrease fusion but do not interfere with virus-specific interaction with the homologous fusion protein, Elizabeth Ann Corey and Ronald M. Iorio

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Altered selectivity of parathyroid hormone (PTH) and PTH-related protein (PTHrP) for distinct conformations of the PTH/PTHrP receptor, Thomas Dean, Jean-Pierre Vilardaga, John T. Potts, and Thomas James Gardella

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TALE-family homeodomain proteins regulate endodermal sonic hedgehog expression and pattern the anterior endoderm, Philip J. Diiorio, Kristen Alexa, Seong-Kyu Choe, Letitiah Etheridge, and Charles G. Sagerstrom

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Identification of tau stem loop RNA stabilizers, Christine Patricia Donahue, Jake Ni, Eriks Rozners, Marcie A. Glicksman, and Michael S. Wolfe

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YRA1 autoregulation requires nuclear export and cytoplasmic Edc3p-mediated degradation of its pre-mRNA, Shuyun Dong, Chunfang Li, Daniel Zenklusen, Robert H. Singer, Allan Jacobson, and Feng He

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Tec kinases in T cell and mast cell signaling, Martin Felices, Markus Falk, Yoko Kosaka, and Leslie J. Berg

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Endoplasmic reticulum stress signaling in pancreatic beta-cells, Sonya G. Fonseca, Kathryn L. Lipson, and Fumihiko Urano

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The human Rad51 K133A mutant is functional for DNA double-strand break repair in human cells, Anthony L. Forget, Matthew S. Loftus, Dharia A. McGrew, Brian Thomas Bennett, and Kendall L. Knight