Publications from 2005
Cutting edge: MHC class II-restricted killing in vivo during viral infection, Evan Robert Jellison, Sung-Kwon Kim, and Raymond M. Welsh
Lymphocyte enhancer-binding factor 1 (Lef1) inhibits terminal differentiation of osteoblasts, Rachel A. Kahler, Mario Galindo, Jane B. Lian, Gary S. Stein, Andre J. Van Wijnen, and Jennifer J. Westendorf
Four novel RUNX2 mutations including a splice donor site result in the cleidocranial dysplasia phenotype, Hyo-Jin Kim, Soon-Hyeun Nam, Hyun-Jung Kim, Hyo-Sang Park, Hyun-Mo Ryoo, Shin-Yoon Kim, Tae-Joon Cho, Seung-Gon Kim, Suk-Chul Bae, In-San Kim, Janet L. Stein, Andre J. Van Wijnen, Gary S. Stein, Jane B. Lian, and Je-Yong Choi
Private specificities of CD8 T cell responses control patterns of heterologous immunity, Sung-Kwon Kim, Markus Cornberg, Xiaoting Z. Wang, Hong D. Chen, Liisa K. Selin, and Raymond M. Welsh
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
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
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
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
PTEN enters the nucleus by diffusion, Fenghua Liu, Stefan R. Wagner, Robert B. Campbell, Jeffrey A. Nickerson, Celia A. Schiffer, and Alonzo H. Ross
Passenger-strand cleavage facilitates assembly of siRNA into Ago2-containing RNAi enzyme complexes, Christian B. Matranga, Yukihide Tomari, Chanseok Shin, David P. Bartel, and Phillip D. Zamore
Plant RNA interference in vitro, Christian B. Matranga and Phillip D. Zamore
Analysis of global gene expression and double-strand-break formation in DNA adenine methyltransferase- and mismatch repair-deficient Escherichia coli, Jennifer L. Robbins-Manke, Zoran Z. Zdraveski, Martin G. Marinus, and John M. Essigmann
Variable Meis-dependence among paralog group-1 Hox proteins, Choe Seong-Kyu and Charles G. Sagerstrom
Design of HIV-1 protease inhibitors active on multidrug-resistant virus, Dominique L. N. G. S Surleraux, Herman A. De Kock, Wim G. Verschueren, Geert M. E. Pille, Louis J. R. Maes, Anik Peeters, Sandrine Vendeville, Sandra De Meyer, Hilde Azijn, Rudi Pauwels, Marie-Pierre de Bethune, Nancy M. King, Moses Prabu-Jeyabalan, Celia A. Schiffer, and Piet B. T. P. Wigerinck
Discovery and selection of TMC114, a next generation HIV-1 protease inhibitor, Dominique L. N. G. S Surleraux, Abdellah Tahri, Wim G. Verschueren, Geert M. E. Pille, Herman A. De Kock, Tim H. M. Jonckers, Anik Peeters, Sandra De Meyer, Hilde Azijn, Rudi Pauwels, Marie-Pierre de Bethune, Nancy M. King, Moses Prabu-Jeyabalan, Celia A. Schiffer, and Piet B. T. P. Wigerinck
Perspective: machines for RNAi, Yukihide Tomari and Phillip D. Zamore
Ribo-gnome: the big world of small RNAs, Phillip D. Zamore and Benjamin Haley
Publications from 2004
Helicobacter pylori activates the early growth response 1 protein in gastric epithelial cells, M.M.M. Abdel-Latif, H. J. Windle, Katherine A. Fitzgerald, Y. S. Ang, D. Ni Eidhin, M. Li-Weber, K. Sabra, and Daniel J. Kelleher
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
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
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
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
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
Conventional transport assays underestimate sugar transport rates in human red cells, David M. Blodgett and Anthony Carruthers
The SANT domain: a unique histone-tail-binding module, Laurie A. Boyer, Robert R. Latek, and Craig L. Peterson
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
MutS inhibits RecA-mediated strand exchange with platinated DNA substrates, Melissa A. Calmann and Martin G. Marinus
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
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
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
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
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
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
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
A peptidyl transferase ribozyme capable of combinatorial peptide synthesis, Zhiyong Cui, Lele Sun, and Biliang Zhang
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
Stress induction and mitochondrial localization of Oxr1 proteins in yeast and humans, Nathan Andrew Elliott and Michael R. Volkert
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
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
Xrcc3 is recruited to DNA double strand breaks early and independent of Rad51, Anthony L. Forget, Brian Thomas Bennett, and Kendall L. Knight
KCNE3 truncation mutants reveal a bipartite modulation of KCNQ1 K+ channels, Steven D. Gage and William R. Kobertz
Effect of substrate mechanics on chondrocyte adhesion to modified alginate surfaces, Nicholas G. Genes, Jon A. Rowley, David J. Mooney, and Lawrence J. Bonassar
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
Conformational changes of lysozyme refolding intermediates and implications for aggregation and renaturation, Zhenyu Gu, Xiaonan Zhu, Shaowei Ni, Zhiguo Su, and Hai-Meng Zhou
Kinetic analysis of the RNAi enzyme complex, Benjamin Haley and Phillip D. Zamore
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
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
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
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
A dynein light intermediate chain, D1bLIC, is required for retrograde intraflagellar transport, Yuqing Hou, Gregory J. Pazour, and George B. Witman
Sequence-specific inhibition of small RNA function, Gyorgy Hutvagner, Martin J. Simard, Craig C. Mello, and Phillip D. Zamore
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
Association of a novel human immunodeficiency virus type 1 protease substrate cleft mutation, L23I, with protease inhibitor therapy and in vitro drug resistance, Elizabeth Johnston, Mark A. Winters, Soo-Yon Rhee, Thomas C. Merigan, Celia A. Schiffer, and Robert W. Shafer
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
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
Combating susceptibility to drug resistance: lessons from HIV-1 protease, Nancy M. King, Moses Prabu-Jeyabalan, Ellen A. Nalivaika, and Celia A. Schiffer
Structural and thermodynamic basis for the binding of TMC114, a next-generation human immunodeficiency virus type 1 protease inhibitor, Nancy M. King, Moses Prabu-Jeyabalan, Ellen A. Nalivaika, Piet B. T. P. Wigerinck, Marie-Pierre de Bethune, and Celia A. Schiffer
Identification of residues important for DNA binding in the full-length human Rad52 protein, Janice A. Lloyd, Dharia A. McGrew, and Kendall L. Knight
Spontaneous and cisplatin-induced recombination in Escherichia coli, Anetta Nowosielska, Melissa A. Calmann, Zoran Z. Zdraveski, John M. Essigmann, and Martin G. Marinus
Structural basis for coevolution of a human immunodeficiency virus type 1 nucleocapsid-p1 cleavage site with a V82A drug-resistant mutation in viral protease, Moses Prabu-Jeyabalan, Ellen A. Nalivaika, Nancy M. King, and Celia A. Schiffer
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
A single Argonaute protein mediates both transcriptional and posttranscriptional silencing in Schizosaccharomyces pombe, Alla A. Sigova, Nicholas R. Rhind, and Phillip D. Zamore
RISC assembly defects in the Drosophila RNAi mutant armitage, Yukihide Tomari, Tingting Du, Benjamin Haley, Dianne S. Schwarz, Ryan Bennett, Heather A. Cook, Birgit S. Koppetsch, William E. Theurkauf, and Phillip D. Zamore
A protein sensor for siRNA asymmetry, Yukihide Tomari, Christian B. Matranga, Benjamin Haley, Natalia Julia Martinez, and Phillip D. Zamore
Publications from 2003
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
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
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
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
Regulated expression of the Escherichia coli dam gene, Melissa A. Calmann and Martin G. Marinus
Tails of two Tirs: actin pedestal formation by enteropathogenic E. coli and enterohemorrhagic E. coli O157:H7, Kenneth Geno Campellone and John M. Leong
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
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
siRNA function in RNAi: a chemical modification analysis, Ya-Lin Chiu and Tariq M. Rana
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
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
Selective silencing by RNAi of a dominant allele that causes amyotrophic lateral sclerosis, Hongliu Ding, Dianne S. Schwarz, Alex Carl Keene, El Bachir Affar, Laura Fenton, Xugang Xia, Yang Shi, Phillip D. Zamore, and Zuoshang Xu
Membrane recognition and targeting by lipid-binding domains, Jonathan P. DiNitto, Thomas Charles Cronin, and David G. Lambright
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
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
Visualization of single molecules of mRNA in situ, Andrea M. Femino, Kevin E. Fogarty, Lawrence M. Lifshitz, Walter A. Carrington, and Robert H. Singer
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
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
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
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
Inhibition of aggregation by media selection, sample loading and elution in size exclusion chromatographic refolding of denatured bovine carbonic anhydrase B, Zhenyu Gu, Xiaonan Zhu, Shaowei Ni, Haimeng Zhou, and Zhiguo Su
In vitro analysis of RNA interference in Drosophila melanogaster, Benjamin Haley, Guiliang Tang, and Phillip D. Zamore
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
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
Covariation of amino acid positions in HIV-1 protease, Noah G. Hoffman, Celia A. Schiffer, and Ronald I. Swanstrom
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
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
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
Chromatin and transcription: histones continue to make their marks, Mariela Jaskelioff and Craig L. Peterson
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
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
Structure-based prediction of potential binding and nonbinding peptides to HIV-1 protease, Nese Kurt, Turkan Haliloglu, and Celia A. Schiffer
Cooperative fluctuations of unliganded and substrate-bound HIV-1 protease: a structure-based analysis on a variety of conformations from crystallography and molecular dynamics simulations, Nese Kurt, Walter Robert Peter Scott, Celia A. Schiffer, and Turkan Haliloglu
The role of human alkyladenine glycosylase in cellular resistance to the chloroethylnitrosoureas, Qiong Li, Steven E. Wright, Zdenka Matijasevic, Wincha Chong, David B. Ludlum, and Michael R. Volkert
Role of SeqA and Dam in Escherichia coli gene expression: a global/microarray analysis, Anders Lobner-Olesen, Martin G. Marinus, and Flemming G. Hansen
A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes, Richard J. Roberts and Martin G. Marinus