1. Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas.
    Daniel J Brat, Roel G W Verhaak, Kenneth D Aldape, W K Alfred Yung, Sofie R Salama, Lee A D Cooper, Esther Rheinbay, C Ryan Miller, Mark Vitucci, Olena Morozova, A Gordon Robertson, Houtan Noushmehr, Peter W Laird, Andrew D Cherniack, Rehan Akbani, Jason T Huse, Giovanni Ciriello, Laila M Poisson, Jill S Barnholtz-Sloan, Mitchel S Berger, Cameron Brennan, Rivka Colen, Howard Colman, Adam E Flanders, Caterina Giannini, Mia Grifford, Antonio Iavarone, Rajan Jain, Isaac Joseph, Jaegil Kim, Katayoon Kasaian, Tom Mikkelsen, Bradley A Murray, Brian Patrick O'Neill, Lior Pachter, Donald W Parsons, Carrie Sougnez, Erik P Sulman, Scott R Vandenberg, Erwin G Van Meir, Andreas von Deimling, Hailei Zhang, Daniel Crain, Kevin Lau, David Mallery, Scott Morris, Joseph Paulauskis, Robert Penny, Troy Shelton, Mark Sherman, Peggy Yena, Aaron Black, Jay Bowen, Katie Dicostanzo, Julie Gastier-Foster, Kristen M Leraas, Tara M Lichtenberg, Christopher R Pierson, Nilsa C Ramirez, Cynthia Taylor, Stephanie Weaver, Lisa Wise, Erik Zmuda, Tanja Davidsen, John A Demchok, Greg Eley, Martin L Ferguson, Carolyn M Hutter, Kenna R Mills Shaw, Bradley A Ozenberger, Margi Sheth, Heidi J Sofia, Roy Tarnuzzer, Zhining Wang, Liming Yang, Jean Claude Zenklusen, Brenda Ayala, Julien Baboud, Sudha Chudamani, Mark A Jensen, Jia Liu, Todd Pihl, Rohini Raman, Yunhu Wan, Ye Wu, Adrian Ally, J Todd Auman, Miruna Balasundaram, Saianand Balu, Stephen Baylin, Rameen Beroukhim, Moiz S Bootwalla, Reanne Bowlby, Christopher A Bristow, Denise Brooks, Yaron Butterfield, Rebecca Carlsen, Scott Carter, Lynda Chin, Andy Chu, Eric Chuah, Kristian Cibulskis, Amanda Clarke, Simon G Coetzee, Noreen Dhalla, Tim Fennell, Sheila Fisher, Stacey Gabriel, Gad Getz, Richard Gibbs, Ranabir Guin, Angela Hadjipanayis, D Neil Hayes, Toshinori Hinoue, Katherine Hoadley, Robert A Holt, Alan P Hoyle, Stuart R Jefferys, Steven Jones, Corbin D Jones, Raju Kucherlapati, Phillip H Lai, Eric Lander, Semin Lee, Lee Lichtenstein, Yussanne Ma, Dennis T Maglinte, Harshad S Mahadeshwar, Marco A Marra, Michael Mayo, Shaowu Meng, Matthew L Meyerson, Piotr A Mieczkowski, Richard A Moore, Lisle E Mose, Andrew J Mungall, Angeliki Pantazi, Michael Parfenov, Peter J Park, Joel S Parker, Charles M Perou, Alexei Protopopov, Xiaojia Ren, Jeffrey Roach, Thaís Sabedot, Jacqueline Schein, Steven E Schumacher, Jonathan G Seidman, Sahil Seth, Hui Shen, Janae V Simons, Payal Sipahimalani, Matthew G Soloway, Xingzhi Song, Huandong Sun, Barbara Tabak, Angela Tam, Donghui Tan, Jiabin Tang, Nina Thiessen, Timothy Triche, David J Van Den Berg, Umadevi Veluvolu, Scot Waring, Daniel J Weisenberger, Matthew D Wilkerson, Tina Wong, Junyuan Wu, Liu Xi, Andrew W Xu, Lixing Yang, Travis I Zack, Jianhua Zhang, B Arman Aksoy, Harindra Arachchi, Chris Benz, Brady Bernard, Daniel Carlin, Juok Cho, Daniel DiCara, Scott Frazer, Gregory N Fuller, Gao, Nils Gehlenborg, David Haussler, David I Heiman, Lisa Iype, Anders Jacobsen, Zhenlin Ju, Sol Katzman, Hoon Kim, Theo Knijnenburg, Richard Bailey Kreisberg, Michael S Lawrence, William Lee, Kalle Leinonen, Pei Lin, Shiyun Ling, Wenbin Liu, Yingchun Liu, Yuexin Liu, Yiling Lu, Gordon Mills, Sam Ng, Michael S Noble, Evan Paull, Arvind Rao, Sheila Reynolds, Gordon Saksena, Zack Sanborn, Chris Sander, Nikolaus Schultz, Yasin Senbabaoglu, Ronglai Shen, Ilya Shmulevich, Rileen Sinha, Josh Stuart, Onur Sumer, Yichao Sun, Natalie Tasman, Barry S Taylor, Doug Voet, Nils Weinhold, John N Weinstein, Da Yang, Kosuke Yoshihara, Siyuan Zheng, Wei Zhang, Lihua Zou, Ty Abel, Sara Sadeghi, Mark L Cohen, Jenny Eschbacher, Eyas M Hattab, Aditya Raghunathan, Matthew J Schniederjan, Dina Aziz, Gene Barnett, Wendi Barrett, Darell Bigner, Lori Boice, Cathy Brewer, Chiara Calatozzolo, Benito Campos, Carlos Gilberto Carlotti, Timothy A Chan, Lucia Cuppini, Erin Curley, Stefania Cuzzubbo, Karen Devine, Francesco DiMeco, Rebecca Duell, J Bradley Elder, Ashley Fehrenbach, Gaetano Finocchiaro, William Friedman, Jordonna Fulop, Johanna Gardner, Beth Hermes, Christel Herold-Mende, Christine Jungk, Ady Kendler, Norman Lehman, Eric Lipp, Ouida Liu, Randy Mandt, Mary McGraw, Roger Mclendon, Christopher McPherson, Luciano Neder, Phuong Nguyen, Ardene Noss, Raffaele Nunziata, Quinn T Ostrom, Cheryl Palmer, Alessandro Perin, Bianca Pollo, Alexander Potapov, Olga Potapova, W Kimryn Rathmell, Daniil Rotin, Lisa Scarpace, Cathy Schilero, Kelly Senecal, Kristen Shimmel, Vsevolod Shurkhay, Suzanne Sifri, Rosy Singh, Andrew E Sloan, Kathy Smolenski, Susan M Staugaitis, Ruth Steele, Leigh Thorne, Daniela P C Tirapelli, Andreas Unterberg, Mahitha Vallurupalli, Yun Wang, Ronald Warnick, Felicia Williams, Yingli Wolinsky, Sue Bell, Mara Rosenberg, Chip Stewart, Franklin Huang, Jonna L Grimsby, Amie J Radenbaugh, and Jianan Zhang

    New England Journal of Medicine 372(26):2481 (2015) PMID 26061751

    Diffuse low-grade and intermediate-grade gliomas (which together make up the lower-grade gliomas, World Health Organization grades II and III) have highly variable clinical behavior that is not adequately predicted on the basis of histologic class. Some are indolent; others quickly progress to g...
  2. Development of a robust classifier for quality control of reverse-phase protein arrays.

    PMID 25380958 PMCID PMC4375399

    High-throughput reverse-phase protein array (RPPA) technology allows for the parallel measurement of protein expression levels in approximately 1000 samples. However, the many steps required in the complex protocol (sample lysate preparation, slide printing, hybridization, washing and amplified ...
  3. [Construction of novel thioredoxin fusion protein expression system and the production of recombinant Lf-CATH2].

    Chinese Journal of Biotechnology/Shengwu Gongch... 31(3):403 (2015) PMID 26204761

    The objective of this study was to construct an improved thioredoxin fusion protein expression system, and express the cathelicidin-derived peptide, Lf-CATH2. The improved fusion vector Lf-CATH2-pET32α(-TS) was successfully constructed by firstly deleting the thrombin site and S tag from the pET...
  4. Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks.

    Genome Research 25(2):257 (2015) PMID 25378249 PMCID PMC4315299

    We introduce a method for simultaneous prediction of microRNA-target interactions and their mediated competitive endogenous RNA (ceRNA) interactions. Using high-throughput validation assays in breast cancer cell lines, we show that our integrative approach significantly improves on microRNA-targ...
  5. Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks.

    Genome Research 25(2):257 (2015) PMID 25378249 PMCID PMC4315299

    We introduce a method for simultaneous prediction of microRNA-target interactions and their mediated competitive endogenous RNA (ceRNA) interactions. Using high-throughput validation assays in breast cancer cell lines, we show that our integrative approach significantly improves on microRNA-targ...
  6. Erratum to: Modeling precision treatment of breast cancer.

    Genome biology 16(1):95 (2015) PMID 25962591 PMCID PMC4426644

    During the type-setting of the final version of the article [1] some of the additional files were swapped. The correct files are republished in this Erratum.
  7. Decoupling of the PI3K Pathway via Mutation Necessitates Combinatorial Treatment in HER2+ Breast Cancer.

    PLoS ONE 10(7):e0133219 (2015) PMID 26181325 PMCID PMC4504492

    We report here on experimental and theoretical efforts to determine how best to combine drugs that inhibit HER2 and AKT in HER2+ breast cancers. We accomplished this by measuring cellular and molecular responses to lapatinib and the AKT inhibitors (AKTi) GSK690693 and GSK2141795 in a panel of 22...
  8. α-Tubulin acetylation elevated in metastatic and basal-like breast cancer cells promotes microtentacle formation, adhesion, and invasive migration.

    Cancer Research 75(1):203 (2015) PMID 25503560 PMCID PMC4350791

    Metastatic cases of breast cancer pose the primary challenge in clinical management of this disease, demanding the identification of effective therapeutic strategies that remain wanting. In this study, we report that elevated levels of α-tubulin acetylation are a sufficient cause of metastatic p...
  9. Integrated analysis reveals microRNA networks coordinately expressed with key proteins in breast cancer.

    Genome Medicine 7(1):21 (2015) PMID 25873999 PMCID PMC4396592

    The role played by microRNAs in the deregulation of protein expression in breast cancer is only partly understood. To gain insight, the combined effect of microRNA and mRNA expression on protein expression was investigated in three independent data sets. Protein expression was modeled as a multi...
  10. Corrigendum: A pan-cancer proteomic perspective on The Cancer Genome Atlas.

    Nature Communications 6:4852 (2015) PMID 25629879

  11. α-Tubulin acetylation elevated in metastatic and basal-like breast cancer cells promotes microtentacle formation, adhesion, and invasive migration.

    Cancer Research 75(1):203 (2015) PMID 25503560 PMCID PMC4350791

    Metastatic cases of breast cancer pose the primary challenge in clinical management of this disease, demanding the identification of effective therapeutic strategies that remain wanting. In this study, we report that elevated levels of α-tubulin acetylation are a sufficient cause of metastatic p...
  12. Corrigendum: A pan-cancer proteomic perspective on The Cancer Genome Atlas.

    Nature Communications 6:4852 (2015) PMID 25629879

  13. Purification and characterization of a novel defensin from the salivary glands of the black fly, Simulium bannaense.

    Parasites & Vectors 8:71 (2015) PMID 25649358 PMCID PMC4324660

    Black flies (Diptera: Simuliidae) are haematophagous insects that can cause allergic reactions and act as vectors of pathogens. Although their saliva has been thought to contain a diverse array of physiologically active molecules, little information is available on antimicrobial factors in black...
  14. Novel Cathelicidins from Pigeon Highlights Evolutionary Convergence in Avain Cathelicidins and Functions in Modulation of Innate Immunity.

    Scientific reports 5:11082 (2015) PMID 26194630 PMCID PMC4508531

    Cathelicidins are short cationic host defense peptides and play a central role in host innate immune system. Here we identified two novel cathelicidins, Cl-CATH2 and 3, from Columba livia. Evolutionary analysis of avian cathelicidins via phylogenetic tree and Ka/Ks calculations supported the pos...
  15. Copy Number Gain of hsa-miR-569 at 3q26.2 Leads to Loss of TP53INP1 and Aggressiveness of Epithelial Cancers.

    Cancer Cell 26(6):863 (2014) PMID 25490449

    Small noncoding miRNAs represent underexplored targets of genomic aberrations and emerging therapeutic targets. The 3q26.2 amplicon is among the most frequent genomic aberrations in multiple cancer lineages including ovarian and breast cancers. We demonstrate that hsa-miR-569 (hereafter designat...
  16. Copy Number Gain of hsa-miR-569 at 3q26.2 Leads to Loss of TP53INP1 and Aggressiveness of Epithelial Cancers.

    Cancer Cell 26(6):863 (2014) PMID 25490449 PMCID PMC4261159

    Small noncoding miRNAs represent underexplored targets of genomic aberrations and emerging therapeutic targets. The 3q26.2 amplicon is among the most frequent genomic aberrations in multiple cancer lineages including ovarian and breast cancers. We demonstrate that hsa-miR-569 (hereafter designat...
  17. Copy number gain of hsa-miR-569 at 3q26.2 leads to loss of TP53INP1 and aggressiveness of epithelial cancers.

    Cancer Cell 26(6):863 (2014) PMID 25490449 PMCID PMC4261159

    Small noncoding miRNAs represent underexplored targets of genomic aberrations and emerging therapeutic targets. The 3q26.2 amplicon is among the most frequent genomic aberrations in multiple cancer lineages including ovarian and breast cancers. We demonstrate that hsa-miR-569 (hereafter designat...
  18. Copy Number Gain of hsa-miR-569 at 3q26.2 Leads to Loss of TP53INP1 and Aggressiveness of Epithelial Cancers.

    Cancer Cell 26(6):863 (2014) PMID 25490449

    Small noncoding miRNAs represent underexplored targets of genomic aberrations and emerging therapeutic targets. The 3q26.2 amplicon is among the most frequent genomic aberrations in multiple cancer lineages including ovarian and breast cancers. We demonstrate that hsa-miR-569 (hereafter designat...
  19. Copy Number Gain of hsa-miR-569 at 3q26.2 Leads to Loss of TP53INP1 and Aggressiveness of Epithelial Cancers

    Cancer Cell 26(6):863 (2014)

    Small noncoding miRNAs represent underexplored targets of genomic aberrations and emerging therapeutic targets. The 3q26.2 amplicon is among the most frequent genomic aberrations in multiple cancer lineages including ovarian and breast cancers. We demonstrate that hsa-miR-569 (hereafte...
  20. Copy number gain of hsa-miR-569 at 3q26.2 leads to loss of TP53INP1 and aggressiveness of epithelial cancers.

    Cancer Cell 26(6):863 (2014) PMID 25490449 PMCID PMC4261159

    Small noncoding miRNAs represent underexplored targets of genomic aberrations and emerging therapeutic targets. The 3q26.2 amplicon is among the most frequent genomic aberrations in multiple cancer lineages including ovarian and breast cancers. We demonstrate that hsa-miR-569 (hereafter designat...