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Submissions from 2017

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PTPRO represses ERBB2-driven breast oncogenesis by dephosphorylation and endosomal internalization of ERBB2., H Dong, L Ma, J Gan, W Lin, Rakesh Kumar, and +9 additional authors

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Distribution bias analysis of germline and somatic single-nucleotide variations that impact protein functional site and neighboring amino acids, Y Pan, C Yan, Y Hu, Y Fan, Qing Pan, Q Wan, J Torcivia-Rodriguez, and Raja Mazumder

Submissions from 2016

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Ly6E/K Signaling to TGFβ Promotes Breast Cancer Progression, Immune Escape, and Drug Resistance., Midrar AlHossiny, Linlin Luo, William R Frazier, Noriko Steiner, Yuriy Gusev, Bhaskar V. S. Kallakury, Eric Glasgow, Karen Creswell, Subha Madhavan, Rakesh Kumar, Geeta Upadhyay, and Rakesh Kumar

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Lean body mass and risk of incident atrial fibrillation in post-menopausal women., Farnaz Azarbal, Marcia L Stefanick, Themistocles L Assimes, JoAnn E Manson, Jennifer W Bea, Wenjun Li, Lisa W. Martin, and +7 additional authors

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Presence of a Prophage Determines Temperature-Dependent Capsule Production in Streptococcus pyogenes., Leslie Brown, Jeong-Ho Kim, and Kyu Hong Cho

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Soluble Guanylate Cyclase Modulators, BAY 41-2272 and BAY 60-2770 Inhibited Human and Rabbit Prostate Contractility., Fabiano B. Calmasini, Eduardo C. Alexandre, Fabio Henrique Silva, Gilberto De Nucci, Edson Antunes, Carlos A. D'Ancona, and Fabíola Z. Mónica

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Computational clustering for viral reference proteomes., Chuming Chen, Hongzhan Huang, Raja Mazumder, and + 6 more

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Cancer Genomics and Biology 2015 – Meeting Report, Louis W.C. Chow, Luis Costa, Bin-Tean Teh, Da-Qiang Li, Gu Feng, Rakesh Kumar, and +10 additional authors

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Pubcast and Genecast: Browsing and explor-ing publications and associated curated con-tent in biology through mobile devices., Scott Goldweber, Jamal Theodore, John John Torcivia-Rodriguez, Vahan Simonyan, and Raja Mazumder

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NLRX1 Sequesters STING to Negatively Regulate the Interferon Response, Thereby Facilitating the Replication of HIV-1 and DNA Viruses., Haitao Guo, Renate König, Meng Deng, Maximilian Riess, Jinyao Mo, Anamaris M. Colberg-Poley, and +20 more

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Teaching and learning of medical biochemistry according to clinical realities: A case study., Joshua M Jabaut, Ramzi Dudum, Samantha L Margulies, Akshita Mehta, and Zhiyong Han

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A miR-200c/141-BMI1 autoregulatory loop regulates oncogenic activity of BMI1 in cancer cells., Mingu Kang, Manjari Dimri, and Goberdhan P. Dimri

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Thymosin β4 Promotes Dermal Healing., H K Kleinman and G Sosne

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Structure, expression and functions of MTA genes, Rakesh Kumar and Rui-An Wang

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Control of PD-L1 expression by oncogenic activation of the AKT–mTOR pathway in non–small cell lung cancer, Kristin J. Lastwika, Willie Wilson, Qing Kay Li, Jeffrey Norris, Haiying Xu, Sharon R. Ghazarian, Hiroshi Kitagawa, Shigeru Kawabata, Janis M. Taube, Sheng Yao, Linda N. Liu, Joell J. Gills, and Phillip A. Dennis

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And-1 is required for homologous recombination repair by regulating DNA end resection, Yongming Li, Zongzhu Li, Zhiyong Han, and Wenge Zhu

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MOF Acetylates the Histone Demethylase LSD1 to Suppress Epithelial-to-Mesenchymal Transition., Huacheng Luo, Anitha K Shenoy, Xuehui Li, Yue Jin, Lihua Jin, Edward Seto, and +10 additional authors

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Distinct lymphocyte antigens 6 (Ly6) family members Ly6D, Ly6E, Ly6K and Ly6H drive tumorigenesis and clinical outcome., Linlin Luo, Peter McGarvey, Subha Madhavan, Rakesh Kumar, Yuriy Gusev, and Geeta Upadhyay

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DiMeX: A Text Mining System for Mutation-Disease Association Extraction., A S M Ashique Mahmood, Tsung-Jung Wu, Raja Mazumder, and K Vijay-Shanker

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The Endothelium-Dependent Nitric Oxide-cGMP Pathway., F Z. Mónica, K Bian, and F Murad

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RNA2DNAlign: nucleotide resolution allele asymmetries through quantitative assessment of RNA and DNA paired sequencing data., Mercedeh Movassagh, Nawaf Alomran, Prakriti Mudvari, Merve Dede, Cem Dede, Kamran Kowsari, Paula Restrepo, Edmund Cauley, Sonali Bahl, Muzi Li, Wesley Waterhouse, Krasimira Tsaneva-Atanasova, Nathan Edwards, and Anelia Horvath

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Rutaecarpine ameliorates hyperlipidemia and hyperglycemia in fat-fed, streptozotocin-treated rats via regulating the IRS-1/PI3K/Akt and AMPK/ACC2 signaling pathways., Xu-Qiang Nie, Huai-Hong Chen, Jian-Yong Zhang, Yu-Jing Zhang, Jian-Wen Yang, Hui-Jun Pan, Wen-Xia Song, Ferid Murad, Yu-Qi He, and Ka Bian

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Potential role of p21 Activated Kinase 1 (PAK1) in the invasion and motility of oral cancer cells., Muraleedharan Parvathy, Sreeharshan Sreeja, Rakesh Kumar, and M. Radhakrishna Pillai

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Oxidative stress, cellular senescence and ageing, Akshaj Pole, Manjari Dimri, and Goberdhan P. Dimri

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Low-ω3 Fatty Acid and Soy Protein Attenuate Alcohol-Induced Fatty Liver and Injury by Regulating the Opposing Lipid Oxidation and Lipogenic Signaling Pathways., Karina Reyes-Gordillo, Ruchi Shah, Ravi Varatharajalu, Mamatha Garige, Leslie C. Leckey, and M. Raj Lakshman

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The glucose metabolite methylglyoxal inhibits expression of the glucose transport genes by inactivating the cell surface glucose sensors Rgt2 and Snf3 in yeast, Adhiraj Roy, Salman Hashmi, Zerui Li, Angela Dement, Kyu Hong Cho, and Jeong-Ho Kim

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Molecular and behavioral profiling of Dbx1-derived neurons in the arcuate, lateral and ventromedial hypothalamic nuclei., Katie Sokolowski, Tuyen Tran, Shigeyuki Esumi, Yasmin Kamal, Livio Oboti, Julieta Lischinsky, Meredith Goodrich, Andrew Lam, Margaret Carter, Yasushi Nakagawa, and Joshua Corbin

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Thymosin Beta 4: A Potential Novel Therapy for Neurotrophic Keratopathy, Dry Eye, and Ocular Surface Diseases., G Sosne, D Rimmer, H K. Kleinman, and G Ousler

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Epigenetic regulation of soluble guanylate cyclase (sGC) β1 in breast cancer cells., Alex Sotolongo, Fabiola Zakia Mónica, Alex Kots, Haijie Xiao, Jun Liu, Edward Seto, Ka Bian, and Ferid Murad

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Protective Role of Dietary Curcumin in the Prevention of the Oxidative Stress Induced by Chronic Alcohol with respect to Hepatic Injury and Antiatherogenic Markers, Ravi Varatharajalu, Mamatha Garige, Leslie C Leckey, Karina Reyes-Gordillo, Ruchi Shah, and M. Raj Lakshman

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Identification of genes that are essential to restrict genome duplication to once per cell division., Alex Vassilev, Chrissie Y. Lee, Boris Vassilev, Wenge Zhu, Pinar Ormanoglu, Scott E. Martin, and Melvin L. DePamphilis

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A Sensitive and Flexible Assay for Determining Histone Deacetylase 1 (HDAC1) Activity., Mei-Yi Wu and Ray-Chang Wu

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Inhibition of nuclear factor-kappa B enhances the tumor growth of ovarian cancer cell line derived from a low-grade papillary serous carcinoma in p53-independent pathway, Xue Xiao, Gong Yang, Peng Bai, Shunping Gui, Tri M. Bui Nguyen, and +8 additional authors

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Impact of germline and somatic missense variations on drug binding sites., C Yan, N Pattabiraman, J Goecks, P Lam, A Nayak, Y Pan, J Torcivia-Rodriguez, A Voskanian, Q Wan, and Raja Mazumder

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Stabilizing the cold plasma-stimulated medium by regulating medium’s composition, Dayun Yan, Niki Nourmohammadi, Ka Bian, Ferid Murad, Jonathan H. Sherman, and Michael Keidar

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Effects of Viola yedoensis Makino anti-itching compound on degranulation and cytokine generation in RBL-2H3 mast cells., Hai-Rong Zeng, Bing Wang, Zhen Zhao, Qi Zhang, Mei-Yun Liang, Ya-Qi Yao, Ka Bian, and Wei-Rong Zhang

Submissions from 2015

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Epigenetic biomarkers in liver cancer, Krishna K. Banaudha and Mukesh Verma

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What is next in nitric oxide research? From cardiovascular system to cancer biology, Ka Bian and Ferid Murad

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Design of a Novel 3D Printed Bioactive Nanocomposite Scaffold for Improved Osteochondral Regeneration., Nathan J Castro, Romil Patel, and Lijie Grace Zhang

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Cold Plasma Accelerates the Uptake of Gold Nanoparticles Into Glioblastoma Cells, Xiaoqian Cheng, Kenan Rajjoub, Jonathan H. Sherman, Jerome Canady, Nina Recek, Dayun Yan, Ka Bian, Ferid Murad, and Michael Keidar

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MicroRNA-31 is a transcriptional target of histone deacetylase inhibitors and a regulator of cellular senescence, Joon-Ho Cho, Manjari Dimri, and Goberdhan P. Dimri

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Cis-encoded non-coding antisense RNAs in streptococci and other low GC Gram (+) bacterial pathogens, Kyu Hong Cho and Jeong-Ho Kim

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Targeting metastatic breast cancer: problems and potential [version 1; referees: 5 approved], Sarah Deasy, Karol Szczepanek, and Kent Hunter

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PLK1 inhibition downregulates polycomb group protein BMI1 via modulation of the miR-200c/141 cluster, Manjari Dimri, Joon-Ho Cho, Mingu Kang, and Goberdhan P. Dimri

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A transgenic resource for conditional competitive inhibition of conserved Drosophila microRNAs., Tudor A Fulga, Elizabeth M McNeill, Richard Binari, Julia Yelick, Alexandra Blanche, Matthew Booker, Bruno R Steinkraus, Michael Schnall-Levin, Yong Zhao, Todd DeLuca, Fernando Bejarano, Zhe Han, Eric C Lai, Dennis P Wall, Norbert Perrimon, and David Van Vactor

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TopBP1 Governs Hematopoietic Stem/Progenitor Cells Survival in Zebrafish Definitive Hematopoiesis., Lei Gao, Dantong Li, Ke Ma, Wenjuan Zhang, Tao Xu, Wenge Zhu, and +12 additional authors

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Advances in the basic and clinical applications of thymosin β4., Allan L Goldstein and Hynda K Kleinman

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And-1 coordinates with Claspin for efficient Chk1 activation in response to replication stress., Jing Hao, Christelle de Renty, Yongming Li, Haijie Xiao, Michael G Kemp, Zhiyong Han, Melvin L DePamphilis, and Wenge Zhu

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Investigation of sex differences in the expression of RORA and its transcriptional targets in the brain as a potential contributor to the sex bias in autism, Valerie Wailin Hu, Tewarit Sarachana, Rachel M. Sherrard, and Kristen M. Kocher

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The Role of the Pleckstrin Homology Domain-Containing Protein CKIP-1 in Activation of p21-activated Kinase 1 (PAK1), Yong-Bae Kim, Yong Jae Shin, Adhiraj Roy, and Jeong-Ho Kim

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Advantages of distributed and parallel algorithms that leverage Cloud Computing platforms for large-scale genome assembly, Phil Kumari, Raja Mazumder, Vahan Simonyan, and Konstantinos Krampis

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Synergy between NAFLD and AFLD and potential biomarkers., M. Raj Lakshman, Ruchi Shah, Karina Reyes-Gordillo, and Ravi Varatharajalu

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Unravelling the Complexity and Functions of MTA Coregulators in Human Cancer., Da-Qiang Li and Rakesh Kumar

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Prolonged Fasting Identifies Heat Shock Protein 10 as a Sirtuin 3 Substrate: Elucidating a New Mechanism Linking Mitochondrial Protein Acetylation to Fatty Acid Oxidation Enzyme Folding and Function, Zhongping Lu, Yong Chen, Angel M. Aponte, Valentina Battaglia, Marjan Gucek, and Michael N. Sack

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EGFR-TKI, erlotnib, causes hypomagnesemia, oxidative stress and cardiac dysfunction: Attentuation by NK-1 receptor blockade, I. Tong Mak, Jay H. Kramer, Joanna J. Chmielinska, Christopher F. Spurney, and William B. Weglicki

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Vitamin D deficiency in patients with intestinal malabsorption syndromes – think in and outside the gut, Samantha L. Margulies, Divya Kurian, Mark S. Elliott, and Zhiyong Han

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MTA1 regulation of ERβ pathway in salivary gland carcinoma cells., Kazufumi Ohshiro and Rakesh Kumar

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Is there pandemic vitamin D deficiency in the black population? A review of evidence, Ria S. Roberts, Fafa Huberta Koudoro, Mark S. Elliott, and Zhiyong Han

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Assessing Glucose Uptake through the Yeast Hexose Transporter 1 (Hxt1), Adhiraj Roy, Angela D. Dement, Kyu Hong Cho, and Jeong-Ho Kim

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The Genus Cerion (Gastropoda: Cerionidae) in the Florida Keys., Yesha Shrestha, Herman H. Wirshing, and M. G. Harasewych

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Primary Mechanisms of Thymosin β4 Repair Activity in Dry Eye Disorders and Other Tissue Injuries, Gabriel Sosne and Hynda K. Kleinman

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The global cancer genomics consortium's symposium: new era of molecular medicine and epigenetic cancer medicine - cross section of genomics and epigenetics, Masakazu Toi, M. Radhakrishna Pillai, Sudeep Gupta, Rajendra Badwe, Maria Carmo-Fonseca, Luis Costa, Loius W.C. Chow, Stefan Knapp, and Rakesh Kumar

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Viral non-coding RNA inhibits HNF4α expression in HCV associated hepatocellular carcinoma., Zhao Wang, Kristin Ceniccola, Liliana Florea, Bi-Dar Wang, Norman H Lee, and Ajit Kumar

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HCV infection-associated hepatocellular carcinoma in humanized mice., Zhao Wang, Ningbin Wu, Abeba Tesfaye, Stephen Feinstone, and Ajit Kumar

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BioXpress: an integrated RNA-seq-derived gene expression database for pan-cancer analysis., Quan Wan, Hayley Dingerdissen, Yu Fan, Naila Gulzar, Yang Pan, Tsung-Jung Wu, Cheng Yan, Haichen Zhang, and Raja Mazumder

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Androgen Receptor Coactivator ARID4B Is Required for the Function of Sertoli Cells in Spermatogenesis., Ray-Chang Wu, Yang Zeng, I-Wen Pan, and Mei-Yi Wu

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AR Coactivator ARID4B is Required for the Function of Sertoli Cells in Spermatogenesis., Ray-Chang Wu, Yang Zeng, I-Wen Pan, and Mei-Yi Wu

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Generating a focused view of disease ontology cancer terms for pan-cancer data integration and analysis., Tsung-Jung Wu, Lynn M. Schriml, Qing-Rong Chen, Maureen Colbert, Daniel J. Crichton, Raja Mazumder, Ying Hu, and + 10 more

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Anti-Inflammatory Effect of 1,3,5,7-Tetrahydroxy-8-isoprenylxanthone Isolated from Twigs of Garcinia esculenta on Stimulated Macrophage., Dan-Dan Zhang, Hong Zhang, Yuan-Zhi Lao, Rong Wu, Jin-Wen Xu, Ferid Murad, Ka Bian, and Hong-Xi Xu

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UBTD1 induces cellular senescence through an UBTD1-Mdm2/p53 positive feedback loop., Xiao-Wei Zhang, Xiao-Feng Wang, Su-Jie Ni, Wei Qin, Li-Qin Zhao, Rui-Xi Hua, You-Wei Lu, Jin Li, Goberdhan P. Dimri, and Wei-Jian Guo

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The importance of GLP-1 and PYY in resistant starch's effect on body fat in mice., June Zhou, Roy J Martin, Anne M Raggio, Li Shen, Kathleen McCutcheon, and Michael J Keenan

Submissions from 2014

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Single-nucleotide variations in cardiac arrhythmias: Prospects for genomics and proteomics based biomarker discovery and diagnostics, Ayman Abunimer, Krista Smith, Tsung-Jung Wu, Phuc Lam, Vahan Simonyan, and Raja Mazumder

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Germ-line variants of human N-methylpurine DNA glycosylase show impaired DNA repair activity and facilitate 1,N6 ethenoadenine induced mutations., Sanjay Adhikari, Mahandranauth A. Chetram, Jordan Woodrick, Partha S. Mitra, Praveen V. Manthena, Pooja Khatkar, Sivanesan Dakshanamurthy, Monica Dixon, Soumendra K. Karmahapatra, Nikhil K. Nuthalapati, Suhani Gupta, Ganga Narasimhan, Raja Mazumder, Christopher A. Loffredo, Aykut Uren, and Rabindra Roy

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Matrigel: From discovery and ECM mimicry to assays and models for cancer research, Gabriel Benton, Irina Arnoutova, Jay George, Hynda K. Kleinman, and Jennifer E. Koblinski

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sGC-cGMP signaling: Target for anticancer therapy, Ka Bian and Ferid Murad

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The ​oestrogen receptor alpha-regulated lncRNA ​NEAT1 is a critical modulator of prostate cancer, Dimple Chakravarty, Andrea Sboner, Sujit S. Nair, Eugenia Giannopoulou, Ruohan Li, and +16 additional authors

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The effect of tuning cold plasma composition on glioblastoma cell viability, Xiaoqian Cheng, Jonathan H. Sherman, William Murphy, Edward Ratovitski, Jerome Canady, and Michael Keidar

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Mg supplementation protects against ritonavir-mediated endothelial oxidative stress and hepatic eNOS downregulation, Xi Chen and I. Tong Mak

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Non-synonymous variations in cancer and their effects on the human proteome: workflow for NGS data biocuration and proteome-wide analysis of TCGA data, Charles Cole, Konstantinos Krampis, Konstantinos Karagiannis, Jonas Almeida, William J. Faison, Mona Motwani, Quan Wan, Anton Golikov, Yang Pan, Vahan Simonyan, and Raja Mazumder

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The global cancer genomics consortium's third annual symposium: From oncogenomics to cancer care, Luis Costa, Sandra Casimiro, Sudeep Gupta, Stefan Knapp, M. Radhakrishna Pillai, Mazakazu Toi, Rajendra Badwe, Maria Carmo-Fonesca, and Rakesh Kumar

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Discrete conformations of epitope II on the hepatitis C virus E2 protein for antibody-mediated neutralization and nonneutralization, Lu Deng, Li Ma, Lilin Zhong, Hailing Yan, Zhong Zhao, Evi Struble, Stephen Feinstone, Harvey Alter, and Pei Zhang

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Cancer and the ageing process, Manjari Dimri and Goberdhan P. Dimri

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A framework for application of metabolic modeling in yeast to predict the effects of nsSNV in human orthologs, Hayley Dingerdissen, Daniel S. Weaver, Peter D. Karp, Yang Pan, Vahan Simonyan, and Raja Mazumder

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Whole genome single-nucleotide variation profile-based phylogenetic tree building methods for analysis of viral, bacterial and human genomes, William J. Faison, Alexandre Rostovtsev, Eduardo Castro-Nallar, Keith Crandall, Konstantin Chumakov, Vahan Simonyan, and Raja Mazumder

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Frontiers in Autism Research : New Horizons for Diagnosis and Treatment, Valerie Wailin Hu

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Role of hepatitis C virus inducted osteopontin in epithelial to mesenchymal transition, migration, and invasion of hepatocytes, Jawed Iqbal, Steven McRae, Thi Mai, Krishna Banaudha, Mehuli Sarkar-Dutta, and Gulam Waris

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Novel modulators of hepatosteatosis, inflammation and fibrogenesis., M Raj Lakshman, Karina Reyes-Gordillo, Ravi Varatharajalu, Jaime Arellanes-Robledo, Leslie C Leckey, Mamatha Garige, and Ruchi Shah

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MTA family of proteins in DNA damage response: mechanistic insights and potential applications, Da-Qiang Li, Yinlong Yang, and Rakesh Kumar

Advance in studies on molecular mechanisms of cisplatin resistance and intervention with traditional Chinese medicines, L. Liu and Ka Bian

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Role of MTA1 in head and neck cancers, Hezlin Marzook, S. Deivendran, Rakesh Kumar, and M. Radhakrishna Pillai

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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