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.

Follow

Publications from 2004

Link

A dynein light intermediate chain, D1bLIC, is required for retrograde intraflagellar transport, Yuqing Hou, Gregory J. Pazour, and George B. Witman

Link

Motor function of unconventional myosin, Mitsuo Ikebe, Akira Inoue, So Nishikawa, Kazuaki Homma, Hiroto Tanaka, Atsuko Hikikoshi Iwane, Eisaku Katayama, Reiko Ikebe, and Toshio Yanagida

Link

Pericentrin forms a complex with intraflagellar transport proteins and polycystin-2 and is required for primary cilia assembly, Agata Jurczyk, Adam Scott Gromley, Sambra D. Redick, Jovenal T. San Agustin, George B. Witman, Gregory J. Pazour, Dorien J. M. Peters, and Stephen J. Doxsey

Link

STAT5 is required for thymopoiesis in a development stage-specific manner, Joonsoo Kang, Brian DiBenedetto, Kavitha Narayan, Hang Zhao, Sandy D. Der, and Cynthia A. Chambers

Link

Paralog group 1 hox genes regulate rhombomere 5/6 expression of vhnf1, a repressor of rostral hindbrain fates, in a meis-dependent manner, Choe Seong-Kyu and Charles G. Sagerstrom

Publications from 2003

Link

Phenotype discovery by gene expression profiling: mapping of biological processes linked to BMP-2-mediated osteoblast differentiation, Eva Balint, David S. Lapointe, Hicham Drissi, Caroline M. J. van der Meijden, Daniel W. Young, Andre J. Van Wijnen, Janet L. Stein, Gary S. Stein, and Jane B. Lian

Link

Osteoblast-related transcription factors Runx2 (Cbfa1/AML3) and MSX2 mediate the expression of bone sialoprotein in human metastatic breast cancer cells, George L. Barnes, Amjad Javed, Sylvan M. Waller, Mohammad H. Kamal, Kerri E. Hebert, Mohammad Q. Hassan, Akeila Bellahcene, Andre J. Van Wijnen, Marian F. Young, Jane B. Lian, Gary S. Stein, and Louis C. Gerstenfeld

Link

Mechanism of p38 MAP kinase activation in vivo, Deborah Marie Brancho, Nobuyuki Tanaka, Anja Jaeschke, Juan-Jose Ventura, Nyaya Kelkar, Yoshinori Tanaka, Masanao Kyuuma, Toshikazu Takeshita, Richard A. Flavell, and Roger J. Davis

Link

Regulation of the SHP-2 tyrosine phosphatase by a novel cholesterol- and cell confluence-dependent mechanism, Alison Burkart, Babak Samii, Silvia Corvera, and Howard S. Shpetner

Link

Regulated expression of the Escherichia coli dam gene, Melissa A. Calmann and Martin G. Marinus

Link

Tails of two Tirs: actin pedestal formation by enteropathogenic E. coli and enterohemorrhagic E. coli O157:H7, Kenneth Geno Campellone and John M. Leong

Link

DC3, the 21-kDa subunit of the outer dynein arm-docking complex (ODA-DC), is a novel EF-hand protein important for assembly of both the outer arm and the ODA-DC, Diane M. Casey, Kazuo Inaba, Gregory J. Pazour, Saeko Takada, Ken-ichi Wakabayashi, Curtis G. Wilkerson, Ritsu Kamiya, and George B. Witman

Link

DC3, the smallest subunit of the Chlamydomonas flagellar outer dynein arm-docking complex, is a redox-sensitive calcium-binding protein, Diane M. Casey, Toshiki Yagi, Ritsu Kamiya, and George B. Witman

Link

siRNA function in RNAi: a chemical modification analysis, Ya-Lin Chiu and Tariq M. Rana

Link

Fusion deficiency induced by mutations at the dimer interface in the Newcastle disease virus hemagglutinin-neuraminidase is due to a temperature-dependent defect in receptor binding, Elizabeth Ann Corey, Anne M. Mirza, Elizabeth Levandowsky, and Ronald M. Iorio

Link

Duplication of U3 sequences in the long terminal repeat of mink cell focus-inducing viruses generates redundancies of transcription factor binding sites important for the induction of thymomas, Nancy L. DiFronzo, Marisa Frieder, Scott A. Loiler, Quynh N. Pham, and Christie A. Holland

Link

Membrane recognition and targeting by lipid-binding domains, Jonathan P. DiNitto, Thomas Charles Cronin, and David G. Lambright

Link

Interaction of the growth hormone receptor with cytokine-induced Src homology domain 2 protein in rat adipocytes, Ling Du, G. Peter Frick, Lih-Ruey Tai, Akihiko Yoshimura, and H. Maurice Goodman

Link

Localization of a beta-actin messenger ribonucleoprotein complex with zipcode-binding protein modulates the density of dendritic filopodia and filopodial synapses, Taesun Eom, Laura N. Antar, Robert H. Singer, and Gary J. Bassell

Link

Visualization of single molecules of mRNA in situ, Andrea M. Femino, Kevin E. Fogarty, Lawrence M. Lifshitz, Walter A. Carrington, and Robert H. Singer

Link

Chromatin remodeling activities act on UV-damaged nucleosomes and modulate DNA damage accessibility to photolyase, Helene Gaillard, Daniel J. Fitzgerald, Corey Lewis Smith, Craig L. Peterson, Timothy J. Richmond, and Fritz Thoma

Link

Local ERM activation and dynamic growth cones at Schwann cell tips implicated in efficient formation of nodes of Ranvier, Cheryl L. Gatto, Barbara J. Walker, and Stephen Lambert

Link

A novel human protein of the maternal centriole is required for the final stages of cytokinesis and entry into S phase, Adam Scott Gromley, Agata Jurczyk, James Sillibourne, Ensar Halilovic, Mette M. Mogensen, Irina Groisman, Maureen Blomberg, and Stephen J. Doxsey

Link

Tumor suppressor pRB functions as a co-repressor of the CCAAT displacement protein (CDP/cut) to regulate cell cycle controlled histone H4 transcription, Sunita Gupta, Mai X. Luong, Sylvia A. Bleuming, Angela Miele, Michael Luong, Daniel W. Young, Erik S. Knudsen, Andre J. Van Wijnen, Janet L. Stein, and Gary S. Stein

Link

In vitro analysis of RNA interference in Drosophila melanogaster, Benjamin Haley, Guiliang Tang, and Phillip D. Zamore

Link

Structural basis for endosomal targeting by FYVE domains, Akira Hayakawa, Susan J. Hayes, Deirdre C. Lawe, Eathiraj Sudharshan, Richard A. Tuft, Kevin E. Fogarty, David Lambright, and Silvia Corvera

Link

Genome-wide analysis of mRNAs regulated by the nonsense-mediated and 5' to 3' mRNA decay pathways in yeast, Feng He, Xiangrui Li, Phyllis Spatrick, Ryan Casillo, Shuyun Dong, and Allan Jacobson

Link

Profiling follicle stimulating hormone-induced gene expression changes in normal and malignant human ovarian surface epithelial cells, Shuk-Mei Ho, Kin-Mang Lau, Samuel C. Mok, and Viqar Syed

Link

Correlation between hearing loss and scala media area in guinea pigs with long-standing endolymphatic hydrops, Morgan E. Hott, Martin Graham, Lawrence J. Bonassar, and Cliff A. Megerian

Link

Maintenance of open chromatin and selective genomic occupancy at the cell cycle-regulated histone H4 promoter during differentiation of HL-60 promyelocytic leukemia cells, Hayk Hovhannisyan, Brian C. Cho, Partha Mitra, Martin A. Montecino, Gary S. Stein, Andre J. Van Wijnen, and Janet L. Stein

Link

Chromatin and transcription: histones continue to make their marks, Mariela Jaskelioff and Craig L. Peterson

Link

Rad54p is a chromatin remodeling enzyme required for heteroduplex DNA joint formation with chromatin, Mariela Jaskelioff, Stephen Van Komen, Jocelyn E. Krebs, Patrick Sung, and Craig L. Peterson

Link

Differential gene expression analysis using paraffin-embedded tissues after laser microdissection, Joung-Ok Kim, Hyun-Nam Kim, Mi-Hye Hwang, Hong-In Shin, Shin-Yoon Kim, Rang-Woon Park, Eui-Yun Park, In-San Kim, Andre J. Van Wijnen, Janet L. Stein, Jane B. Lian, Gary S. Stein, and Je-Yong Choi

Link

Alloimmune injury and rejection of human skin grafts on human peripheral blood lymphocyte-reconstituted non-obese diabetic severe combined immunodeficient beta2-microglobulin-null mice, Nicole A. Turgeon, Scott J. Banuelos, Leonard D. Shultz, Bonnie L. Lyons, Neal N. Iwakoshi, Dale L. Greiner, John P. Mordes, Aldo A. Rossini, and Michael C. Appel

Publications from 2002

Link

Expression of estrogen receptor beta in the fetal, neonatal, and prepubertal human prostate, Jason Y. Adams, Irwin Leav, Kin-Mang Lau, Shuk-Mei Ho, and Solveig M.V. Pflueger

Link

SRC-1 and Wnt signaling act together to specify endoderm and to control cleavage orientation in early C. elegans embryos, Yanxia Bei, Jennifer Hogan, Laura A. Berkowitz, Martha C. Soto, Christian Ernest Rocheleau, Ka Ming Pang, John J. Collins, and Craig C. Mello

Link

Increased production of interleukin-8 in primary human monocytes and in human epithelial and endothelial cell lines after dengue virus challenge, Irene Bosch, Kris Xhaja, Luis Estevez, Gregory Raines, Heather J. Melichar, Rajas V. Warke, Marcia V. Fournier, Francis A. Ennis, and Alan L. Rothman

Link

Essential role for the SANT domain in the functioning of multiple chromatin remodeling enzymes, Laurie A. Boyer, Michael R. Langer, Kimberly A. Crowley, Song Tan, John M. Denu, and Craig L. Peterson

Link

Mechanical disruption of individual nucleosomes reveals a reversible multistage release of DNA, Brent D. Brower-Toland, Corey Lewis Smith, Richard C. Yeh, John T. Lis, Craig L. Peterson, and Michelle D. Wang

Link

Naive B lymphocytes undergo homeostatic proliferation in response to B cell deficit, Mark S. Cabatingan, Madelyn R. Schmidt, Ranjan Sen, and Robert T. Woodland

Link

A tyrosine-phosphorylated 12-amino-acid sequence of enteropathogenic Escherichia coli Tir binds the host adaptor protein Nck and is required for Nck localization to actin pedestals, Kenneth Geno Campellone, Andrew Giese, Donald J. Tipper, and John M. Leong

Link

Human cytomegalovirus immediate early proteins and cell growth control, Jonathan Patrick Castillo and Timothy F. Kowalik

Link

Tat stimulates cotranscriptional capping of HIV mRNA, Ya-Lin Chiu, C. Kiong Ho, Nayanendu Saha, Beate Schwer, Stewart Shuman, and Tariq M. Rana

Link

RNAi in human cells: basic structural and functional features of small interfering RNA, Ya-Lin Chiu and Tariq M. Rana

Link

Cooperative nucleotide binding to the human erythrocyte sugar transporter, Erin K. Cloherty, Kara B. Levine, Christopher A. Graybill, and Anthony Carruthers

Link

1,25-(OH)2-vitamin D3 suppresses the bone-related Runx2/Cbfa1 gene promoter, Hicham Drissi, Arlyssa Pouliot, Christian Koolloos, Janet L. Stein, Jane B. Lian, Gary S. Stein, and Andre J. Van Wijnen

Link

Identification of novel protein/DNA interactions within the promoter of the bone-related transcription factor Runx2/Cbfa1, Hicham Drissi, Arlyssa Pouliot, Janet L. Stein, Andre J. Van Wijnen, Gary S. Stein, and Jane B. Lian

Link

Mechanisms for regulation of cellular responsiveness to human IFN-beta1a, Stefan A. Dupont, Susan E. Goelz, Jaya Goyal, and Marie Green

Link

Viral abrogation of stem cell transplantation tolerance causes graft rejection and host death by different mechanisms, Daron Forman, Raymond M. Welsh, Thomas G. Markees, Bruce A. Woda, John P. Mordes, Aldo A. Rossini, and Dale L. Greiner

Link

Cytokine gene expression and protein production in peripheral blood mononuclear cells of children with acute dengue virus infections, Susan J. Gagnon, Masuko Mori, Ichiro Kurane, Sharone Green, David W. Vaughn, Siripen Kalayanarooj, Saroj Suntayakorn, Francis A. Ennis, and Alan L. Rothman

Link

Redirecting retroviral tropism by insertion of short, nondisruptive peptide ligands into envelope, Timothy J. Gollan and Michael R. Green

Link

Selective targeting and inducible destruction of human cancer cells by retroviruses with envelope proteins bearing short peptide ligands, Timothy J. Gollan and Michael R. Green

Link

RNAi (Nematodes: Caenorhabditis elegans), Alla Grishok and Craig C. Mello

Link

Translational control of the embryonic cell cycle, Irina Groisman, Mi-Young Jung, Madathia Sarkissian, Quiping Cao, and Joel D. Richter

Link

Cytokinesis in eukaryotes, David A. Guertin, Susanne Trautmann, and Dannel McCollum

Link

Dma1 prevents mitotic exit and cytokinesis by inhibiting the septation initiation network (SIN), David A. Guertin, Srinivas Venkatram, K. Lance Gould, and Dannel McCollum

Link

A predominantly nuclear protein affecting cytoplasmic localization of beta-actin mRNA in fibroblasts and neurons, Wei Gu, Feng Pan, Honglai Zhang, Gary J. Bassell, and Robert H. Singer

Link

Transcription factors RUNX1/AML1 and RUNX2/Cbfa1 dynamically associate with stationary subnuclear domains, Kimberly Stacy Harrington, Amjad Javed, Hicham Drissi, Sandra Marie McNeil, Jane B. Lian, Janet L. Stein, Andre J. Van Wijnen, Yu-Li Wang, and Gary S. Stein

Link

TGF beta receptor internalization into EEA1-enriched early endosomes: role in signaling to Smad2, Susan J. Hayes, Anil Chawla, and Silvia Corvera

Link

The death domain kinase RIP protects thymocytes from tumor necrosis factor receptor type 2-induced cell death, Nicole M. Hermance, Sarah R. Oikemus, Elizabeth D. Kilpatrick, Leslie A. Cunningham, and Michelle Kelliher

Link

DNA microarrays in prostate cancer, Shuk-Mei Ho and Kin-Mang Lau

Link

Cytokinesis: myosin spots the ring, Ming-Chin Hou and Dannel McCollum

Link

Mob2p interacts with the protein kinase Orb6p to promote coordination of cell polarity with cell cycle progression, Ming-Chin Hou, David J. Wiley, Fulvia Verde, and Dannel McCollum

Link

N-methyl-D-aspartate receptor signaling results in Aurora kinase-catalyzed CPEB phosphorylation and alpha CaMKII mRNA polyadenylation at synapses, Yi-Shuian Huang, Mi-Young Jung, Madathia Sarkissian, and Joel D. Richter

Link

DOC-2/DAB2 is the binding partner of myosin VI, Akira Inoue, Osamu Sato, Kazuaki Homma, and Mitsuo Ikebe

Link

Integrated channel plasticity contributes to alcohol tolerance in neurohypophysial terminals, Thomas K. Knott, Alejandro M. Dopico, Govindan Dayanithi, Jose R. Lemos, and Steven N. Treistman

Link

Novel functional interactions between Trk kinase and p75 neurotrophin receptor in neuroblastoma cells, Mahesh B. Lachyankar, Peter J. Condon, Marie-Claire Daou, Asit K. De, John B. Levine, Axel Obermeier, and Alonzo H. Ross

Link

Meis family proteins are required for hindbrain development in the zebrafish, Choe Seong-Kyu, Nikolaos Vlachakis, and Charles G. Sagerstrom

Publications from 2001

Link

The Snail protein family regulates neuroblast expression of inscuteable and string, genes involved in asymmetry and cell division in Drosophila, Shovon Imtiaz Ashraf and Y. Tony Ip

Link

Differential regulation of the two principal Runx2/Cbfa1 n-terminal isoforms in response to bone morphogenetic protein-2 during development of the osteoblast phenotype, Chaitali Banerjee, Amjad Javed, Je-Yong Choi, Jack Green, Vicki Rosen, Andre J. Van Wijnen, Janet L. Stein, Jane B. Lian, and Gary S. Stein

Link

Absence of Dbp2p alters both nonsense-mediated mRNA decay and rRNA processing, Andrew T. Bond, David A. Mangus, Feng He, and Allan Jacobson

Link

Nicotinamide adenine dinucleotide (NAD) and its metabolites inhibit T lymphocyte proliferation: role of cell surface NAD glycohydrolase and pyrophosphatase activities, Rita Bortell, Joel Moss, Robert C. McKenna, Mark R. Rigby, Dena Niedzwiecki, Linda A. Stevens, Walter A. Patton, John P. Mordes, Dale L. Greiner, and Aldo A. Rossini

Link

Levels of Art2+ cells but not soluble Art2 protein correlate with expression of autoimmune diabetes in the BB rat, Rita Bortell, Debra J. Waite, Barbara J. Whalen, Derrick James Todd, Jean H. Leif, Elena Lesma, Joel Moss, John P. Mordes, Aldo A. Rossini, and Dale L. Greiner

Link

Cell-cycle arrest in TrkA-expressing NIH3T3 cells involves nitric oxide synthase, Dylan A. Bulseco, Wojciech Poluha, Christopher M. Schonhoff, Marie-Claire Daou, Peter J. Condon, and Alonzo H. Ross

Link

xid mice reveal the interplay of homeostasis and Bruton's tyrosine kinase-mediated selection at multiple stages of B cell development, Michael P. Cancro, Alex P. Sah, Sherri L. Levy, David M. Allman, Madelyn R. Schmidt, and Robert T. Woodland

Link

Injection molding of chondrocyte/alginate constructs in the shape of facial implants, Sophia C. N. Chang, Jon A. Rowley, Geoffrey Tobias, Nicholas G. Genes, Amit K. Roy, David J. Mooney, Charles A. Vacanti, and Lawrence J. Bonassar

Link

Memory CD8+ T cells in heterologous antiviral immunity and immunopathology in the lung, Hong D. Chen, Armando E. Fraire, Isabelle Joris, Michael A. Brehm, Raymond M. Welsh, and Liisa K. Selin

Link

HIV-1 Tat protein interacts with mammalian capping enzyme and stimulates capping of TAR RNA, Ya-Lin Chiu, Elizabeth Coronel, C. Kiong Ho, Stewart Shuman, and Tariq M. Rana

Link

Multivalent endosome targeting by homodimeric EEA1, John J. Dumas, Eric Lee Merithew, Eathiraj Sudharshan, Deepa Rajamani, Susan J. Hayes, Deirdre C. Lawe, Silvia Corvera, and David G. Lambright

Link

Expression of the osteoblast differentiation factor RUNX2 (Cbfa1/AML3/Pebp2alpha A) is inhibited by tumor necrosis factor-alpha, Linda C. Gilbert, Xiaofei He, Paul K. Farmer, Janet Rubin, Hicham Drissi, Andre J. Van Wijnen, Jane B. Lian, Gary S. Stein, and Mark S. Nanes

Link

Pteridine reductase mechanism correlates pterin metabolism with drug resistance in trypanosomatid parasites, David G. Gourley, Alexander W. Schuttelkopf, Gordon A. Leonard, James Luba, Larry W. Hardy, Stephen M. Beverley, and William N. Hunter

Link

Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing, Alla Grishok, Amy E. Pasquinelli, Darryl Conte Jr., Na Li, Susan Parrish, Ilho Ha, David L. Baillie, Andrew Z. Fire, Gary Ruvkun, and Craig C. Mello

Link

Interaction between the noncatalytic region of Sid1p kinase and Cdc14p is required for full catalytic activity and localization of Sid1p, David A. Guertin and Dannel McCollum

Link

CCAAT/enhancer-binding proteins (C/EBP) beta and delta activate osteocalcin gene transcription and synergize with Runx2 at the C/EBP element to regulate bone-specific expression, Soraya E. Gutierrez, Amjad Javed, Daniel K. Tennant, Monique van Rees, Martin A. Montecino, Gary S. Stein, Janet L. Stein, and Jane B. Lian

Link

Motor function and regulation of myosin X, Kazuaki Homma, Junya Saito, Reiko Ikebe, and Mitsuo Ikebe

Link

The core of the motor domain determines the direction of myosin movement, Kazuaki Homma, Misako Yoshimura, Junya Saito, Reiko Ikebe, and Mitsuo Ikebe

Link

Skin allograft maintenance in a new synchimeric model system of tolerance, Neal N. Iwakoshi, Thomas G. Markees, Nicole A. Turgeon, Thomas B. Thornley, Amy Cuthbert, Jean Leif, Nancy E. Phillips, John P. Mordes, Dale L. Greiner, and Aldo A. Rossini

Link

Human RAD52 exhibits two modes of self-association, Wasantha Ranatunga, Doba Jackson, Janice A. Lloyd, Anthony L. Forget, Kendall L. Knight, and Gloria E. O. Borgstahl

Publications from 2000

Link

A profound deficiency in thymic progenitor cells in mice lacking Jak3, Allison Michelle Baird, Julie Ann Lucas, and Leslie J. Berg

Link

Functional delineation of three groups of the ATP-dependent family of chromatin remodeling enzymes, Laurie A. Boyer, Colin Logie, Edgar Bonte, Peter B. Becker, Paul A. Wade, Alan P. Wolffe, Carl Wu, Anthony N. Imbalzano, and Craig L. Peterson

Link

Actin-related proteins (Arps): conformational switches for chromatin-remodeling machines, Laurie A. Boyer and Craig L. Peterson

Link

Roles of the histone H2A-H2B dimers and the (H3-H4)(2) tetramer in nucleosome remodeling by the SWI-SNF complex, Laurie A. Boyer, Xiao Shao, Richard H. Ebright, and Craig L. Peterson

Link

Role of human cytomegalovirus immediate-early proteins in cell growth control, Jonathan Patrick Castillo, Andrew D. Yurochko, and Timothy F. Kowalik

Link

JNK1 is required for T cell-mediated immunity against Leishmania major infection, Stephanie L. Constant, Chen Dong, Derek D. Yang, Mark Allen Wysk, Roger J. Davis, and Richard A. Flavell

Link

The kinetic mechanism of the hairpin ribozyme in vivo: influence of RNA helix stability on intracellular cleavage kinetics, Christine Patricia Donahue, Ramesh S. Yadava, Steven M. Nesbitt, and Martha J. Fedor

Link

Transcriptional autoregulation of the bone related CBFA1/RUNX2 gene, Hicham Drissi, Quyen Luc, A. Rauf Shakoori, Susana Chuva De Sousa Lopes, Je-Yong Choi, Anne Terry, Ming Hu, Stephen N. Jones, James C. Neil, Jane B. Lian, Janet L. Stein, Andre J. Van Wijnen, and Gary S. Stein

Link

Molecular determinants that mediate selective activation of p38 MAP kinase isoforms, Herve Enslen, Deborah Marie Brancho, and Roger J. Davis

Link

A role for the lissencephaly gene LIS1 in mitosis and cytoplasmic dynein function, Nicole E. Faulkner, Denis L. Dujardin, Chin-Yin Tai, Kevin T. Vaughan, Christopher B. O'Connell, Yu-Li Wang, and Richard B. Vallee

Link

Modified intranuclear organization of regulatory factors in human acute leukemias: reversal after treatment, Jeffrey A. Gordon, Shirwin M. Pockwinse, F. Marc Stewart, Peter J. Quesenberry, Tatsuya Nakamura, Carlo M. Croce, Jane B. Lian, Janet L. Stein, Andre J. Van Wijnen, and Gary S. Stein

Link

Genetic requirements for inheritance of RNAi in C. elegans, Alla Grishok, Hiroaki Tabara, and Craig C. Mello