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 2005

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The bone-related Zn finger transcription factor Osterix promotes proliferation of mesenchymal cells, Yeon-Ju Kim, Hyun-Nam Kim, Eui-Kyun Park, Byung-Heon Lee, Hyun-Mo Ryoo, Shin-Yoon Kim, In-San Kim, Janet L. Stein, Jane B. Lian, Gary S. Stein, Andre J. Van Wijnen, and Je-Yong Choi

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Haem repression of the housekeeping 5-aminolaevulinic acid synthase gene in the hepatoma cell line LMH, Sridevi Kolluri, Timothy J. Sadlon, Brian K. May, and Herbert L. Bonkovsky

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Bone marrow microenvironmental changes in aged mice compromise V(D)J recombinase activity and B cell generation, Joseph E. Labrie, Lisa A. Borghesi, and Rachel M. Gerstein

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Properties of the human erythrocyte glucose transport protein are determined by cellular context, Kara B. Levine, Trista K. Robichaud, Stephanie Hamill, Lisa A. Sultzman, and Anthony Carruthers

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Variable Meis-dependence among paralog group-1 Hox proteins, Choe Seong-Kyu and Charles G. Sagerstrom

Publications from 2004

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Smad function and intranuclear targeting share a Runx2 motif required for osteogenic lineage induction and BMP2 responsive transcription, Faiza Afzal, Jitesh Pratap, Kosei Ito, Yoshiaki Ito, Janet L. Stein, Andre J. Van Wijnen, Gary S. Stein, Jane B. Lian, and Amjad Javed

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Unconstrained steps of myosin VI appear longest among known molecular motors, M. Yusuf Ali, Kazuaki Homma, Atsuko Hikikoshi Iwane, Kengo Adachi, Hiroyasu Itoh, Kazuhiko Kinosita, Toshio Yanagida, and Mitsuo Ikebe

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High ER stress in beta-cells stimulates intracellular degradation of misfolded insulin, Jenny R. Allen, Linh X. Nguyen, Karen E.G. Sargent, Kathryn L. Lipson, Anthony Hackett, and Fumihiko Urano

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A faux 3'-UTR promotes aberrant termination and triggers nonsense-mediated mRNA decay, Nadia Amrani, Robin Ganesan, Stephanie Kervestin, David A. Mangus, Shubhendu Ghosh, and Allan Jacobson

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Worniu, a Snail family zinc-finger protein, is required for brain development in Drosophila, Shovon Imtiaz Ashraf, Atish Ganguly, John Roote, and Y. Tony Ip

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Conventional transport assays underestimate sugar transport rates in human red cells, David M. Blodgett and Anthony Carruthers

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The SANT domain: a unique histone-tail-binding module, Laurie A. Boyer, Robert R. Latek, and Craig L. Peterson

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Functional characterization of a human histone gene cluster duplication, Corey D. Braastad, Hayk Hovhannisyan, Andre J. Van Wijnen, Janet L. Stein, and Gary S. Stein

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Clustering of Nck by a 12-residue Tir phosphopeptide is sufficient to trigger localized actin assembly, Kenneth Geno Campellone, Susannah Rankin, Tony Pawson, Marc W. Kirschner, Donald J. Tipper, and John M. Leong

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EspFU is a translocated EHEC effector that interacts with Tir and N-WASP and promotes Nck-independent actin assembly, Kenneth Geno Campellone, Douglas Robbins, and John M. Leong

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Identification of genes that synergize with Cbfb-MYH11 in the pathogenesis of acute myeloid leukemia, Lucio H. Castilla, Paola N. Perrat, Natalia Julia Martinez, Sean F. Landrette, R. Keys, Sarah R. Oikemus, J. Flanegan, Susan Ann Heilman, Lisa Garrett, A. Dutra, S. Anderson, German A. Pihan, L. Wolff, and Pu P. Liu

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Structural basis of heteromeric smad protein assembly in TGF-beta signaling, Benoy Maramparambil Chacko, Bin Y. Qin, Ashutosh Tiwari, Genbin Shi, Suvana S. Lam, Lawrence J. Hayward, Mark De Caestecker, and Kai Lin

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Visualizing a correlation between siRNA localization, cellular uptake, and RNAi in living cells, Ya-Lin Chiu, Akbar Ali, Chia-ying Chu, Hong Cao, and Tariq M. Rana

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Inhibition of human immunodeficiency virus type 1 replication by RNA interference directed against human transcription elongation factor P-TEFb (CDK9/CyclinT1), Ya-Lin Chiu, Hong Cao, Jean-Marc Jacque, Mario Stevenson, and Tariq M. Rana

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Structural determinants of phosphoinositide selectivity in splice variants of Grp1 family PH domains, Thomas Charles Cronin, Jonathan P. DiNitto, Michael P. Czech, and David G. Lambright

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A peptidyl transferase ribozyme capable of combinatorial peptide synthesis, Zhiyong Cui, Lele Sun, and Biliang Zhang

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Structure, exchange determinants, and family-wide rab specificity of the tandem helical bundle and Vps9 domains of Rabex-5, Anna M. Delprato, Eric Lee Merithew, and David G. Lambright

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Stress induction and mitochondrial localization of Oxr1 proteins in yeast and humans, Nathan Andrew Elliott and Michael R. Volkert

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Regulation of cerebellar neuronal migration and neurite outgrowth by thyroxine and 3,3',5'-triiodothyronine, Alan P. Farwell, Susan A. Dubord-Tomasetti, Andrzej Z. Pietrzykowski, Stanley J. Stachelek, and Jack L. Leonard

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Imaging cocaine-induced changes in the mesocorticolimbic dopaminergic system of conscious rats, Marcelo Febo, Annabell C. Segarra, Jeffrey R. Tenney, Mathew E. Brevard, Timothy Q. Duong, and Craig F. Ferris

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Xrcc3 is recruited to DNA double strand breaks early and independent of Rad51, Anthony L. Forget, Brian Thomas Bennett, and Kendall L. Knight

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KCNE3 truncation mutants reveal a bipartite modulation of KCNQ1 K+ channels, Steven D. Gage and William R. Kobertz

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Effect of substrate mechanics on chondrocyte adhesion to modified alginate surfaces, Nicholas G. Genes, Jon A. Rowley, David J. Mooney, and Lawrence J. Bonassar

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The vitamin D response element in the distal osteocalcin promoter contributes to chromatin organization of the proximal regulatory domain, Soraya E. Gutierrez, Jilin Liu, Amjad Javed, Martin A. Montecino, Gary S. Stein, Jane B. Lian, and Janet L. Stein

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Kinetic analysis of the RNAi enzyme complex, Benjamin Haley and Phillip D. Zamore

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Dlx3 transcriptional regulation of osteoblast differentiation: temporal recruitment of Msx2, Dlx3, and Dlx5 homeodomain proteins to chromatin of the osteocalcin gene, Mohammad Q. Hassan, Amjad Javed, Maria I. Morasso, Jeremy Karlin, Martin A. Montecino, Andre J. Van Wijnen, Gary S. Stein, Janet L. Stein, and Jane B. Lian

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The repressor function of snail is required for Drosophila gastrulation and is not replaceable by Escargot or Worniu, Kirugaval Hemavathy, Xiaodi Hu, Shovon Imtiaz Ashraf, Stephen J. Small, and Y. Tony Ip

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Fabrication of tissue engineered tympanic membrane patches using computer-aided design and injection molding, Morgan E. Hott, Cliff A. Megerian, Rich Beane, and Lawrence J. Bonassar

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Initiation of cytokinesis is controlled through multiple modes of regulation of the Sid2p-Mob1p kinase complex, Ming-Chin Hou, David A. Guertin, and Dannel McCollum

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

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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

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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

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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

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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

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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

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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

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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

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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

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

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

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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

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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

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

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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

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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

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

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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

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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

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

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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

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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

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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

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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

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

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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

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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

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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

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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

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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

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

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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

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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

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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

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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

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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

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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

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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

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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

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

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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

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

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

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

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

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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

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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

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

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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

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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

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

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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

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

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

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

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

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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

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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

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

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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

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

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

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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

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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

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

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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