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Submissions from 2014

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SNPlice: Variants that Modulate Intron-retention from RNA-sequencing Data, Prakriti Mudvari, Mercedeh Movassagh, Kamran Kowsari, Ali Seyfi, Maria Kokkinaki, Nathan J. Edwards, Nady Golestaneh, and Anelia Horvath

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Structure-function analysis of hepatitis C virus envelope glycoproteins E1 and E2, Aparajita Nayak, Nagarajan Pattabiraman, Numrah Fadra, Radoslav Goldman, and Raja Mazumder

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Human germline and pan-cancer variomes and their distinct functional profiles, Yang Pan, Konstantinos Karagiannis, Haichen Zhang, Hayley Dingerdissen, Amirhossein Shamsaddini, Quan Wan, Vahan Simonyan, and Raja Mazumder

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Understanding the mechanism of glucose-induced relief of Rgt1-mediated repression in yeast, Adhiraj Roy, David Jouandot, Kyu Hong Cho, and Jeong-Ho Kim

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Glucose starvation-induced turnover of the yeast glucose transporter Hxt1, Adhiraj Roy, Yong-Bae Kim, Kyu Hong Cho, and Jeong-Ho Kim

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Cytosolic functions of MORC2 in lipogenesis and adipogenesis, Beatriz Sanchez-Solana, Da-Qiang Li, and Rakesh Kumar

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HIVE-hexagon: High-performance, parallelized sequence alignment for next-generation sequencing data analysis, Luis Santana-Quintero, Hayley Dingerdissen, Jean Thierry-Mieg, Raja Mazumder, and Vahan Simonyan

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Census-based rapid and accurate metagenome taxonomic profiling, Amirhossein Shamsaddini, Yang Pan, W. Evan Johnson, Konstantinos Krampis, Mariya Shcheglovitova, Vahan Simonyan, Amy Zanne, and Raja Mazumder

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Alpha-asarone protects endothelial cells from injury by angiotensin II, Ha-Xia Shi, Jiajun Yang, Tao Yang, Yong-Liang Xue, Jun Liu, Ya-Juan Li, Dan-Dan Zhang, Ji-Wen Zhu, and Ka Bian

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Drugs for macular degeneration, price discrimination, and Medicare's responsibility to overpay, Jonathan Silver

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High-performance integrated virtual environment (HIVE) tools and applications for big data analysis, Vahan Simonyan and Raja Mazumder

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Increased copy number of the DLX4 homeobox gene in breast axillary lymph node metastasis, Clarissa Torresan, Marcia M.C. Oliveira, Silma R.F. Pereira, Enilze M.S.F. Ribeiro, Catalin Marian, Yuriy Gusev, Rubens S. Lima, Cicero A. Urban, Patricia A. Berg, Bassem R. Haddad, Iglenir J. Cavalli, and Luciane R. Cavalli

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Adverse signaling of scavenger receptor class B1 and PGC1s in alcoholic hepatosteatosis and steatohepatitis and protection by betain in rat, Ravi Varatharajalu, Mamatha Garige, Leslie A. Leckey, Jaime Arellanes-Robledo, Karina Reyes-Gordillo, Ruchi Shah, and M. Raj Lakshman

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ERK3 promotes endothelial cell functions by upregulating SRC-3/SP1-mediated VEGFR2 expression, Wei Wang, Ka Bian, Sreeram Vallabhaneni, Bin Zhang, Ray-Chang Wu, Bert W. O'Malley, and Weiwen Long

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MiR-34a regulates therapy resistance by targeting HDAC1 and HDAC7 in breast cancer, Mei-Yi Wu, Junjiang Fu, Xiuli Xiao, Jingbo Wu, and Ray-Chang Wu

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A framework for organizing cancer-related variations from existing databases, publications and NGS data using a High-performance Integrated Virtual Environment (HIVE), Tsung-Jung Wu, Amirhossein Shamsaddini, Yang Pan, Krista Smith, Daniel J. Chrichton, Vahan Simonyan, and Raja Mazumder

Effects of rutaecarpine on inflammatory cytokines in insulin resistant primary skeletal muscle cells, J Yang, X. Nie, H. Shi, Y. Zhang, J. Zhang, Y. Yuan, and Ka Bian

Submissions from 2013

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Fibrogenic actions of acetaldehyde are β-catenin dependent but Wingless independent: A critical role of nucleoredoxin and reactive oxygen species in human hepatic stellate cells, Jaime Arellanes-Robledo, Karina Reyes-Gordillo, Ruchi Shah, Jose Alfredo Dominguez-Rosales, Zamira Hernandez-Nazara, Francesco Ramirez, Marcos Rojkind, and M. Raj Lakshman

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Community annotation and the evolution of cooperation: How patience matters, Atin Basuchoudhary, Vahan Simoyan, and Raja Mazumder

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CKAP2 ensures chromosomal stability by maintaining the integrity of microtubule nucleation sites, Chanelle M. Case, Dan L. Sackett, Danny Wangsa, Tatiana S. Karpova, James G. McNally, Thomas Ried, and Jordi Camps

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A positive feedback loop regulates the expression of polycomb group protein BMI1 via WNT signaling pathway, Joon-Ho Cho, Manjari Dimri, and Goberdhan P. Dimri

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The prince and the pauper: Which one is real?: The problem of secondary mutation during mutagenesis in Streptococcus pyogenes, Kyu Hong Cho, Jordan O. Wright, Juan P. Svencionis, and Jeong-Ho Kim

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Biphasic regulation of myosin light chain phosphorylation by p21-activated kinase modulates intestinal smooth muscle contractility, Ji Chu, Ngoc T. Pham, Nicole Olate, Karina Kislitsyna, Mary-Claire Day, Phillip A. LeTourneau, Alex Kots, Randolph H. Stewart, Glen A. Laine, Charles S. Cox Jr., and Karen Uray

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Clinical and technical factors associated with skin intrinsic fluorescence in subjects with type 1 diabetes from the Diabetes Control and Complications Trial/Epidemiology of Diabetes Interventions and Complications study, Patricia A. Cleary, Barbara H. Braffett, Trevor J. Orchard, Timothy J. Lyons, John D. Maynard, Catherine C. Cowie, Rose A. Gubitosi-Klug, Jeff F. Way, Karen L. Anderson, Annette Barnie, and Stephan Villavicencio

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Metastasis tumor-associated protein 2 enhances metastatic behavior and is associated with poor outcomes in estrogen receptor-negative breast cancer., Kyle R. Covington, Lauren Brusco, Ines Barone, Anna Tsimelzon, Jennifer Selever, Arnoldo Corona-Rodriguez, Powel Brown, Rakesh Kumar, Susan G. Hilsenbeck, and Suzanne A.W. Fuqua

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Erratum to: Development and evaluation of a decision aid for BRCA carriers with breast cancer, Julie Culver, Deborah MacDonald, Andrea Thornton, Sharon Sand, Marcia Grant, Deborah Bowen, Harry Burke, Nellie Garcia, Kelly Metcalfe, and Jeffrey Weitzel

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Mechanism and consequence of the autoactivation of p38α mitogen-activated protein kinase promoted by TAB1, Gina F. DeNicola, Eva D. Martin, Apirat Chaikuad, Rekha Bassi, James Clark, Luigi Martino, Sharwari Verma, Pierre Sicard, Renee Tata, R. Andrew Atkinson, Stefan Knapp, Maria R. Conte, and Michael S. Marber

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MicroRNA-141 regulates BMI1 expression and induces senescence in human diploid fibroblasts, Manjari Dimri, Jeremy D. Carroll, Joon-Ho Cho, and Goberdhan P. Dimri

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Proteome-wide analysis of nonsynonymous single-nucleotide variations in active sites of human proteins, Hayley Dingerdissen, Mona Motwani, Konstantinos Karagiannis, Vahan Simonyan, and Raja Mazumder

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RNA sequencing of cancer reveals novel splicing alterations, Jeyanthy Eswaran, Anelia Horvath, Sucheta Godbole, Sirigiri Divijendra Natha Reddy, Prakriti Mudvari, Kazufumi Ohshiro, Dinesh Cyanam, Sujit S. Nair, Suzanne A.W. Fuqua, Kornelia Polyak, Liliana D. Florea, and Rakesh Kumar

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DNA homologous recombination factor SFR1 physically and functionally interacts with estrogen receptor alpha, Yuxin Feng, David Singleton, Chun Guo, Amanda Gardner, Suresh Pakala, Rakesh Kumar, Elwood Jensen, Jinsong Zhang, and Sohaib Khan

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Angiotensin (5-8) modulates nociception at the rat periaqueductal gray via the NO-sGC pathway and an endogenous opioid, L. M. Guethe, A. Pelegrini-da Silva, K. G. Borelli, M. A. Juliano, G. G. Pelosi, J. B. Pesquero, C. Silva, F. M.A. Correa, Ferid Murad, W. A. Prado, and A. R. Martins

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A comprehensive, multi-scale dynamical model of ErbB receptor signal transduction in human mammary epithelial cells, Tomas Helikar, Naomi Kochi, Bryan Kowal, Manjari Dimri, Mayumy Naramura, Srikumar M. Raja, Vimla Band, Hamid Band, and Jim A. Rogers

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Novel insights into breast cancer genetic variance through RNA sequencing, Anelia Horvath, Suresh B. Pakala, Prakriti Mudvari, Sirigiri Divijendra Natha Reddy, Kazufumi Ohshiro, Sandra Casimiro, Ricardo Pires, Suzanne A.W. Fuqua, Masakazu Toi, Luis Costa, Sujit S. Nair, Saraswati Sukumar, and Rakesh Kumar

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From genes to environment: using integrative genomics to build a "systems-level" understanding of autism spectrum disorders, Valerie Wailin Hu

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The Expanding Genomic Landscape of Autism: Discovering the 'Forest' Beyond the 'Trees', Valerie Wailin Hu

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Developing a Predictive Gene Classifier for Autism Spectrum Disorders Based upon Differential Gene Expression Profiles of Phenotype Subgroups, Valerie Wailin Hu and Yinglei Lai

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Colorimetric detection of senescence-associated β galactosidase, Koji Itahana, Yoko Itahana, and Goberdhan P. Dimri

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Acidic nucleoplasmic DNA-binding protein (And-1) controls chromosome congression by regulating the assembly of centromere protein A (CENP-A) at centromeres, Aimee Jaramillo-Lambert, Jing Hao, Haijie Xiao, Yongming Li, Zhiyong Han, and Wenge Zhu

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The clinical isolate Pseudomonas aeruginosa MMA83 carries two copies of the blaNDM-1 gene in a novel genetic context., Branco Jovcic, Zorica Lepsanovic, Jelena Begovic, Bojan Rakonjac, Jelena Perovanovic, Ljubisa Topisirovic, and Milan Kojic

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SNVDis: A proteome-wide analysis service for evaluating nsSNVs in protein functional sites and pathways, Konstantinos Karagiannis, Vahan Simonyan, and Raja Mazumder

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Laminin-111-derived peptides and cancer, Yamato Kikkawa, Kentaro Hozumi, Fumihiko Katagiri, Motoyoshi Nomizu, Hynda K. Kleinman, and Jennifer E. Koblinski

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The glucose signaling network in yeast, Jeong-Ho Kim, Adhiraj Roy, David Jouandot, and Kyu Hong Cho

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CYP2E1, oxidative stress, post-translational modifications and lipid metabolism, M. Raj Lakshman, Mamatha Garige, Maokai A. Gong, Leslie A. Leckey, Ravi Varatharajalu, Robert S. Redman, Devanshi Seth, Paul S. Haber, Kenneth Hirsch, Richard Amdur, and Ruchi Shah

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Structure-based comparative analysis and prediction of N-linked glycosylation sites in evolutionarily distant eukaryotes, Phuc Vinh Nguyen Lam, Radoslav Goldman, Konstantinos Karagiannis, Tejas Narsule, Vahan Simonyan, Valerii Soika, and Raja Mazumder

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The MORC family: New epigenetic regulators of transcription and DNA damage response, Da-Qiang Li, Sujit S. Nair, and Rakesh Kumar

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Metastasis-associated protein 1 is an integral component of the circadian molecular machinery, Da-Qiang Li, Suresh B. Pakala, Sirigiri Divijendra Natha Reddy, Shaohua Peng, Seetharaman Balasenthil, Chu-Xia Deng, Cheng Chi Lee, Michael A. Rea, and Rakesh Kumar

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Mg-supplementation attenuates ritonavir-induced hyperlipidemia, oxidative stress, and cardiac dysfunction in rats, I. Tong Mak, Jay H. Kramer, Xi Chen, Joanna J. Chmielinska, Christopher F. Spurney, and William B. Weglicki

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Derailed estrogen signaling and breast cancer: An authentic couple, Bramanandam Manavathi, Oindrilla Dey, Vijay Narsihma Reddy Gajulapalli, Raghavendra Singh Bhatia, Suresh Bugide, and Rakesh Kumar

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Identification of novel gene targets and functions of p21-activated kinase 1 during DNA damage by gene expression profiling, Mona Motwani, Da-Qiang Li, Anelia Horvath, and Rakesh Kumar

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Extraction of molecular features through exome to transcriptome alignment, Prakriti Mudvari, Kamran Kowsari, Charles Cole, Raja Mazumder, and Anelia Horvath

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Genomic insights into triple-negative and HER2-positive breast cancers using isogenic model systems, Prakriti Mudvari, Kazufumi Ohshiro, Vasudha S. Nair, Anelia Horvath, and Rakesh Kumar

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A core chromatin remodeling factor instructs global chromatin signaling through multivalent reading of nucleosome codes, Sujit S. Nair, Da-Qiang Li, and Rakesh Kumar

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Comparative lipid profiles of milk bank breast milk and infant formulas, Anya Oleynik, Tatiana Eliseeva, and Jack Y. Vanderhoek

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MTA1 promotes STAT3 transcription and pulmonary metastasis in breast cancer, Suresh B. Pakala, Suresh K. Rayala, Rui-An Wang, Kazufumi Ohshiro, Prakriti Mudvari, Sirigiri Divijendra Natha Reddy, Yi Zheng, Ricardo Pires, Sandra Casimiro, M. Radhakrishna Pillai, Luis Costa, and Rakesh Kumar

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PFI-1, a highly selective protein interaction inhibitor, targeting BET bromodomains., Sarah Picaud, David Da Costa, Angeliki Thanasopoulou, Panagis Filippakopoulos, Paul V. Fish, Martin Philpott, Oleg Fedorov, Paul Brennan, Mark E. Bunnage, Dafydd R. Owen, James E. Bradner, Phillippe Taniere, Brendan O'Sullivan, Susanne Muller, Juerg Schwaller, Tatjana Stankovic, and Stefan Knapp

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VBP15: Preclinical characterization of a novel anti-inflammatory delta 9,11 steroid, Erica K.M. Reeves, Eric P. Hoffman, Kanneboyina Nagaraju, Jesse M. Damsker, and John M. McCall

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Mth1 regulates the interaction between the Rgt1 repressor and the Ssn6-Tup1 corepressor complex by modulating PKA-dependent phosphorylation of Rgt1, Adhiraj Roy, Yong Jae Shin, Kyu Hong Cho, and Jeong-Ho Kim

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Construction of yeast strains useful for screening drugs that inhibit glucose uptake and glycolysis, Adhiraj Roy, Yong Jae Shin, and Jeong-Ho Kim

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Differential recruitment of coregulators to the RORA promoter adds another layer of complexity to gene (dys)regulation by sex hormones in autism, Tewarit Sarachana and Valerie Wailin Hu

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Genome-wide identification of transcriptional targets of RORA reveals direct regulation of multiple genes associated with autism spectrum disorder, Tewarit Sarachana and Valerie Wailin Hu

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Role of microRNAs in Autism Spectrum Disorder, T Sarachana and V W. Hu

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TGF-β1 up-regulates the expression of PDGF-β receptor mRNA and induces a delayed PI3K-, AKT-, and p70S6K-dependent proliferative response in activated hepatic stellate cells, Ruchi Shah, Karina Reyes-Gordillo, Jaime Arellanes-Robledo, Carmen G. Lechuga, Zamira Hernandez-Nazara, Adam Cotty, Marcus Rojkind, and M. Raj Lakshman

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Evidence for a novel mechanism of the PAK1 interaction with the Rho-GTPases Cdc42 and Rac, Yong Jae Shin, Eun Hye Kim, Adhiraj Roy, and Jeong-Ho Kim

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Protein kinase CK2 phosphorylates and activates p21-activated kinase 1, Yong Jae Shin, Yong-Bae Kim, and Jeong-Ho Kim

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A novel stratification method in linkage studies to address inter- and intra-family heterogeneity in autism, Zohreh Talebizadeh, Dan E. Arking, and Valerie Wailin Hu

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Novel regulatory small RNAs in Streptococcus pyogenes, Rafael A. Tesorero, Ning Yu, Jordan O. Wright, Juan P. Svencionis, Qiang Cheng, Jeong-Ho Kim, and Kyu Hong Cho

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Draft genome sequences of Burkholderia cenocepacia ET12 lineage strains K56-2 and BC7, John J. Varga, Liliana Losada, Adrian M. Zelazny, Maria Kim, Jamison McCorrison, Lauren Brinkac, Elizabeth P. Sampaio, David E. Greenberg, Indresh Singh, Cheryl Heiner, Meredith Ashby, William C. Nierman, Steven M. Holland, and Joanna B. Goldberg

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ARID4A and ARID4B regulate male fertility, a functional link to the AR and RB pathways, Ray-Chang Wu, Ming Jiang, Arthur L. Beaudet, and Mei-Yi Wu

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[Study on in vitro anti-inflammatory activity of total flavonoids from Glycyrrhizae Radix et Rhizoma and its ingredients]., Xiao-Lu Yang, Duo Liu, Ka Bian, and Dan-Dan Zhang

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SRC-3 coactivator regulates cell resistance to cytotoxic stress via TRAF4-mediated p53 destabilization, Ping Yi, Weiya Xia, Ray-Chang Wu, David M. Lonard, Mien-Chie Hung, and Bert W. O'Malley

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Human cytomegalovirus inhibits apoptosis by proteasome-mediated degradation of bax at endoplasmic reticulum-mitochondrion contacts, Aiping Zhang, Richard L. Hildreth, and Anamaris M. Colberg-Poley

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Effects of different extracting fractions from Mori Ramulus and their combinations on inflammatory mediators in macrophage, D. D. Zhang, N. Tang, X. D. Hua, and Ka Bian

Submissions from 2012

Therapeutic management of the hallux rigidus, A Aggarwal, S Kumar, and R. Kumar

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Development of an analytical HPLC methodology to study the effects of thymosin β4 on actin in sputum of cystic fibrosis patients, Mahnaz Badamchian, Ali A. Damavandy, and Allan L. Goldstein

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Expression of p14 ARF, p15 INK4b, p16 INK4a and skp2 increases during esophageal squamous cell cancer progression, Peng Bai, Xue Xiao, Juan Zou, Lin Cui, Tri M. Bui-Nguyen, Jinsong Liu, Jianguo Xiao, Bin Chang, Jin Wu, and He Wang

Expression of p14 ARF, p15 INK4b, p16 INK4a and skp2 increases during esophageal squamous cell cancer progression, P Bai, X Xiao, J Zou, L Cui, and TM Bui Nguyen

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The Role of MicroRNAs in the Management of Liver Cancer ., Krishna K. Banaudha and Mukesh Verma

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NOS-2 signaling and cancer therapy, Ka Bian, Farshid Ghassemi, Alex Sotolongo, Alan Siu, Lauren Shauger, Alex Kots, and Ferid Murad

NOS-2 signaling and cancer therapy, K Bian, F Ghassemi, A Sotolongo, A Siu, and L Shauger

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Cryptococcus gattii Comparative Genomics and Transcriptomics: A NIH/NIAID White Paper, V. Chaturvedi and William C. Nierman

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Hydrogen peroxide alters splicing of soluble guanylyl cyclase and selectively modulates expression of splicing regulators in human cancer cells, Gilbert J. Cote, Wen Zhu, Anthony Thomas, Emil Martin, Ferid Murad, and Iraida G. Sharina

Hydrogen Peroxide alters splicing of soluble Guanylyl cyclase and selectively modulates expression of splicing regulators in human cancer cells, GJ Cote, W Zhu, A Thomas, E Martin, and F Murad

Transcriptomic landscape of breast cancers through mRNA sequencing, J Eswaran, D Cyanam, P Mudvari, SDN Reddy, and SB Pakala

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Transcriptomic landscape of breast cancers through mRNA sequencing, Jeyanthy Eswaran, Dinesh Cyanam, Prakriti Mudvari, Sirigiri Divijendra Natha Reddy, Suresh Pakala, Sujit S. Nair, Liliana Florea, Suzanne A.W. Fuqua, Sucheta Godbole, and Rakesh Kumar

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The Global Cancer Genomics Consortium: Interfacing genomics and cancer medicine, Jeyanthy Eswaran, Sudeep Gupta, Amit Dutt, Masakazu Toi, M. Radhakrishna Pillai, Luis Costa, Stefan Knapp, Rajendra Badwe, and Rakesh Kumar

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Molecular pathways: targeting p21-activated kinase 1 signaling in cancer--opportunities, challenges, and limitations, Jeyanthy Eswaran, Da-Qiang Li, Anil Shah, and Rakesh Kumar

The Global Cancer Genomics Consortium: Interfacing genomics and cancer medicine, J Eswaran, S Gupta, A Dutt, M Toi, and MR Pillai

Molecular pathways: Targeting p21-activated kinase 1 signaling in cancer - Opportunities, challenges, and limitations, J Eswaran, D. Li, and R Kumar

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The bromodomain interaction module, Panagis Filippakopoulos and Stefan Knapp

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Histone recognition and large-scale structural analysis of the human bromodomain family, Panagis Filippakopoulos, Sarah Picaud, Maria Mangos, Tracy Keates, Jean-Philippe Lambert, Dalia Barsyte-Lovejoy, Ildiko Felletar, Rudolf Volkmer, Susanne Muller, Tony Pawson, Anne-Claude Gingras, Cheryl H. Arrowsmith, and Stefan Knapp

The bromodomain interaction module, P Knapp, S Filippakopoulos

Histone recognition and large-scale structural analysis of the human bromodomain family, P Filippakopoulos, S Picaud, M Mangos, T Keates, and J. Lambert

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Recent advances in biocuration: Meeting report from the Fifth International Biocuration Conference, Pascale Gaudet, Cecilia Arighi, Frederic Bastian, Alex Bateman, Judith A. Blake, Raja Mazumder, and +17 additional authors

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Biocuration virtual issue 2012., Pascale Gaudet and Raja Mazumder

Biocuration virtual issue 2012, P Gaudet and R Mazumder

Thymosin ?4: A multi-functional regenerative peptide. Basic properties and clinical applications, AL Goldstein, E Hannappel, G Sosne, and HK Kleinman

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Introduction for thymosins in health and disease, Allan L. Goldstein and Enrico Garaci

Advances in the regenerativeproperties and clinical applications of Thymosin β4, Allan L. Goldstein, Ewald Hannappel, and J. R. Sa-Reed

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Thymosin β4: a multi-functional regenerative peptide. Basic properties and clinical applications, Allan L. Goldstein, Ewald Hannappel, Gabriel Sosne, and Hynda K. Kleinman