Browsing HMS Scholarly Articles by Title

Now showing items 3183-3202 of 17922

    • Comprehensive Approach to Improving Maternal Health and Achieving MDG 5: Report from the Mountains of Lesotho 

      Satti, Hind Elkheir; Motsamai, Sophie; Chetane, Palesa; Marumo, Leshoboro; Barry, Donna; Riley, Jennifer; McLaughlin, Megan Marie; Seung, Kwonjune Justin; Mukherjee, Joia Stapleton (Public Library of Science, 2012)
      Background: Although it is now widely recognized that reductions in maternal mortality and improvements in women's health cannot be achieved through simple, vertical strategies, few programs have provided successful models ...

    • A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing 

      Alioto, Tyler S.; Buchhalter, Ivo; Derdak, Sophia; Hutter, Barbara; Eldridge, Matthew D.; Hovig, Eivind; Heisler, Lawrence E.; Beck, Timothy A.; Simpson, Jared T.; Tonon, Laurie; Sertier, Anne-Sophie; Patch, Ann-Marie; Jäger, Natalie; Ginsbach, Philip; Drews, Ruben; Paramasivam, Nagarajan; Kabbe, Rolf; Chotewutmontri, Sasithorn; Diessl, Nicolle; Previti, Christopher; Schmidt, Sabine; Brors, Benedikt; Feuerbach, Lars; Heinold, Michael; Gröbner, Susanne; Korshunov, Andrey; Tarpey, Patrick S.; Butler, Adam P.; Hinton, Jonathan; Jones, David; Menzies, Andrew; Raine, Keiran; Shepherd, Rebecca; Stebbings, Lucy; Teague, Jon W.; Ribeca, Paolo; Giner, Francesc Castro; Beltran, Sergi; Raineri, Emanuele; Dabad, Marc; Heath, Simon C.; Gut, Marta; Denroche, Robert E.; Harding, Nicholas J.; Yamaguchi, Takafumi N.; Fujimoto, Akihiro; Nakagawa, Hidewaki; Quesada, Víctor; Valdés-Mas, Rafael; Nakken, Sigve; Vodák, Daniel; Bower, Lawrence; Lynch, Andrew G.; Anderson, Charlotte L.; Waddell, Nicola; Pearson, John V.; Grimmond, Sean M.; Peto, Myron; Spellman, Paul; He, Minghui; Kandoth, Cyriac; Lee, Semin; Zhang, John; Létourneau, Louis; Ma, Singer; Seth, Sahil; Torrents, David; Xi, Liu; Wheeler, David A.; López-Otín, Carlos; Campo, Elías; Campbell, Peter J.; Boutros, Paul C.; Puente, Xose S.; Gerhard, Daniela S.; Pfister, Stefan M.; McPherson, John D.; Hudson, Thomas J.; Schlesner, Matthias; Lichter, Peter; Eils, Roland; Jones, David T. W.; Gut, Ivo G. (Nature Publishing Group, 2015)
      As whole-genome sequencing for cancer genome analysis becomes a clinical tool, a full understanding of the variables affecting sequencing analysis output is required. Here using tumour-normal sample pairs from two different ...

    • Comprehensive cellular‐resolution atlas of the adult human brain 

      Ding, Song‐Lin; Royall, Joshua J.; Sunkin, Susan M.; Ng, Lydia; Facer, Benjamin A.C.; Lesnar, Phil; Guillozet‐Bongaarts, Angie; McMurray, Bergen; Szafer, Aaron; Dolbeare, Tim A.; Stevens, Allison; Tirrell, Lee; Benner, Thomas; Caldejon, Shiella; Dalley, Rachel A.; Dee, Nick; Lau, Christopher; Nyhus, Julie; Reding, Melissa; Riley, Zackery L.; Sandman, David; Shen, Elaine; van der Kouwe, Andre; Varjabedian, Ani; Write, Michelle; Zollei, Lilla; Dang, Chinh; Knowles, James A.; Koch, Christof; Phillips, John W.; Sestan, Nenad; Wohnoutka, Paul; Zielke, H. Ronald; Hohmann, John G.; Jones, Allan R.; Bernard, Amy; Hawrylycz, Michael J.; Hof, Patrick R.; Fischl, Bruce; Lein, Ed S. (John Wiley and Sons Inc., 2016)
      ABSTRACT Detailed anatomical understanding of the human brain is essential for unraveling its functional architecture, yet current reference atlases have major limitations such as lack of whole‐brain coverage, relatively ...

    • Comprehensive comparative analysis of RNA sequencing methods for degraded or low input samples 

      Adiconis, Xian; Borges-Rivera, Diego; Satija, Rahul; DeLuca, David S.; Busby, Michele A.; Berlin, Aaron M.; Sivachenko, Andrey; Thompson, Dawn Anne; Wysoker, Alec; Fennell, Timothy; Gnirke, Andreas; Pochet, Nathalie; Regev, Aviv; Levin, Joshua Z. (2013)
      RNA-Seq is an effective method to study the transcriptome, but can be difficult to apply to scarce or degraded RNA from fixed clinical samples, rare cell populations, or cadavers. Recent studies have proposed several methods ...

    • Comprehensive confocal endomicroscopy of the esophagus in vivo 

      Kang, Dongkyun; Schlachter, Simon C.; Carruth, Robert W.; Kim, Minkyu; Wu, Tao; Tabatabaei, Nima; Vacas-Jacques, Paulino; Shishkov, Milen; Woods, Kevin; Sauk, Jenny S.; Leung, John; Nishioka, Norman S.; Tearney, Guillermo J. (© Georg Thieme Verlag KG, 2014)
      Background and study aims: Biopsy sampling error can be a problem for the diagnosis of certain gastrointestinal tract diseases. Spectrally-encoded confocal microscopy (SECM) is a high-speed reflectance confocal microscopy ...

    • Comprehensive Definition of the SigH Regulon of Mycobacterium tuberculosis Reveals Transcriptional Control of Diverse Stress Responses 

      Sharp, Jared D.; Singh, Atul K.; Park, Sang Tae; Lyubetskaya, Anna; Peterson, Matthew W.; Gomes, Antonio L. C.; Potluri, Lakshmi-Prasad; Raman, Sahadevan; Galagan, James E.; Husson, Robert N. (Public Library of Science, 2016)
      Expression of SigH, one of 12 Mycobacterium tuberculosis alternative sigma factors, is induced by heat, oxidative and nitric oxide stresses. SigH activation has been shown to increase expression of several genes, including ...

    • Comprehensive Dissection of PDGF-PDGFR Signaling Pathways in PDGFR Genetically Defined Cells 

      Wu, Erxi; Palmer, Nathan; Tian, Ze; Moseman, Annie P.; Galdzicki, Michal; Wang, Xuetao; Berger, Bonnie; Zhang, Hongbing; Kohane, Isaac Samuel (Public Library of Science, 2008)
      Despite the growing understanding of PDGF signaling, studies of PDGF function have encountered two major obstacles: the functional redundancy of PDGFRα and PDGFRβ in vitro and their distinct roles in vivo. Here we used ...

    • Comprehensive DNA Methylation Analysis Reveals a Common Ten-Gene Methylation Signature in Colorectal Adenomas and Carcinomas 

      Patai, Árpád V.; Valcz, Gábor; Hollósi, Péter; Kalmár, Alexandra; Péterfia, Bálint; Patai, Árpád; Wichmann, Barnabás; Spisák, Sándor; Barták, Barbara Kinga; Leiszter, Katalin; Tóth, Kinga; Sipos, Ferenc; Kovalszky, Ilona; Péter, Zoltán; Miheller, Pál; Tulassay, Zsolt; Molnár, Béla (Public Library of Science, 2015)
      Microarray analysis of promoter hypermethylation provides insight into the role and extent of DNA methylation in the development of colorectal cancer (CRC) and may be co-monitored with the appearance of driver mutations. ...

    • Comprehensive Essentiality Analysis of the Mycobacterium tuberculosis Genome via Saturating Transposon Mutagenesis 

      DeJesus, Michael A.; Gerrick, Elias R.; Xu, Weizhen; Park, Sae Woong; Long, Jarukit E.; Boutte, Cara C.; Rubin, Eric J.; Schnappinger, Dirk; Ehrt, Sabine; Fortune, Sarah M.; Sassetti, Christopher M.; Ioerger, Thomas R. (American Society for Microbiology, 2017)
      ABSTRACT For decades, identifying the regions of a bacterial chromosome that are necessary for viability has relied on mapping integration sites in libraries of random transposon mutants to find loci that are unable to ...

    • Comprehensive Evaluation of Peripheral Nerve Regeneration in the Acute Healing Phase Using Tissue Clearing and Optical Microscopy in a Rodent Model 

      Jung, Yookyung; Ng, Joanna H.; Keating, Cameron P.; Senthil-Kumar, Prabhu; Zhao, Jie; Randolph, Mark A.; Winograd, Jonathan M.; Evans, Conor L. (Public Library of Science, 2014)
      Peripheral nerve injury (PNI), a common injury in both the civilian and military arenas, is usually associated with high healthcare costs and with patients enduring slow recovery times, diminished quality of life, and ...

    • Comprehensive evaluation of serum microRNAs as biomarkers in multiple sclerosis 

      Regev, Keren; Paul, Anu; Healy, Brian; von Glenn, Felipe; Diaz-Cruz, Camilo; Gholipour, Taha; Mazzola, Maria Antonietta; Raheja, Radhika; Nejad, Parham; Glanz, Bonnie I.; Kivisakk, Pia; Chitnis, Tanuja; Weiner, Howard L.; Gandhi, Roopali (Lippincott Williams & Wilkins, 2016)
      Objective: To identify circulating microRNAs (miRNAs) linked to disease stage and disability in multiple sclerosis (MS). Methods: Sera from 296 participants including patients with MS, other neurologic diseases (Alzheimer ...

    • Comprehensive Expression of Wnt Signaling Pathway Genes during Development and Maturation of the Mouse Cochlea 

      Geng, Ruishuang; Noda, Teppei; Mulvaney, Joanna F.; Lin, Vincent Y. W.; Edge, Albert S. B.; Dabdoub, Alain (Public Library of Science, 2016)
      Background: In the inner ear Wnt signaling is necessary for proliferation, cell fate determination, growth of the cochlear duct, polarized orientation of stereociliary bundles, differentiation of the periotic mesenchyme, ...

    • Comprehensive Genetic Assessment of a Functional TLR9 Promoter Polymorphism: No Replicable Association with Asthma or Asthma-Related Phenotypes 

      Avila, Lydiana; Hawrylowicz, Catherine M; Lange, Nancy Elizabeth; Zhou, Xiaobo; Su, Jessica Ann Lasky; Himes, Blanca Elena; Lazarus, Ross; Raby, Benjamin Alexander; Litonjua, Augusto Ampil; Soto-Quiros, Manuel; Celedon, Juan C (BioMed Central, 2011)
      Background: Prior studies suggest a role for a variant (rs5743836) in the promoter of toll-like receptor 9 (TLR9) in asthma and other inflammatory diseases. We performed detailed genetic association studies of the functional ...

    • Comprehensive genomic analyses associate UGT8 variants with musical ability in a Mongolian population 

      Park, Hansoo; Lee, Seungbok; Kim, Hyun-Jin; Ju, Young Seok; Shin, Jong-Yeon; Hong, Dongwan; von Grotthuss, Marcin; Lee, Dong-Sung; Park, Changho; Kim, Jennifer; Kim, Boram; Yoo, Yun Joo; Cho, Sung-Il; Sung, Joohon; Lee, Charles; Kim, Jong-Il; Seo, Jeong-Sun (BMJ Publishing Group, 2012)
      Background: Musical abilities such as recognising music and singing performance serve as means for communication and are instruments in sexual selection. Specific regions of the brain have been found to be activated by ...

    • Comprehensive Identification of Host Modulators of HIV-1 Replication using Multiple Orthologous RNAi Reagents 

      Zhu, Jian; Davoli, Teresa; Perriera, Jill M.; Chin, Christopher R.; Gaiha, Gaurav D.; John, Sinu P.; Sigiollot, Frederic D.; Gao, Geng; Xu, Qikai; Qu, Hongjing; Pertel, Thomas; Sims, Jennifer S.; Smith, Jennifer A.; Baker, Richard E.; Maranda, Louise; Ng, Aylwin; Elledge, Stephen J.; Brass, Abraham L. (2016)
      SUMMARY RNAi screens have implicated hundreds of host proteins as HIV-1 dependency factors (HDFs). While informative, these early studies overlap poorly due to false positives and false negatives. To ameliorate these issues, ...

    • Comprehensive identification of translation start sites by tetracycline-inhibited ribosome profiling 

      Nakahigashi, Kenji; Takai, Yuki; Kimura, Michiko; Abe, Nozomi; Nakayashiki, Toru; Shiwa, Yuh; Yoshikawa, Hirofumi; Wanner, Barry L.; Ishihama, Yasushi; Mori, Hirotada (Oxford University Press, 2016)
      Tetracycline-inhibited ribosome profiling (TetRP) provides a powerful new experimental tool for comprehensive genome-wide identification of translation initiation sites in bacteria. We validated TetRP by confirming the ...

    • Comprehensive Imaging of Gastroesophageal Biopsy Samples by Spectrally Encoded Confocal Microscopy 

      Kang, DongKyun; Suter, Melissa; Boudoux, Caroline; Yoo, Hongki; Yachimski, Patrick S.; Puricelli, William P.; Nishioka, Norman Shizuaki; Mino-Kenudson, Mari; Lauwers, Gregory Y.; Bouma, Brett; Tearney, Guillermo James (Elsevier BV, 2010)
      Background: Spectrally encoded confocal microscopy (SECM) is a high-speed reflectance confocal microscopy technique that has the potential to be used for acquiring comprehensive images of the entire distal esophagus ...

    • Comprehensive metabolome analyses reveal N-acetylcysteine-responsive accumulation of kynurenine in systemic lupus erythematosus: implications for activation of the mechanistic target of rapamycin 

      Perl, Andras; Hanczko, Robert; Lai, Zhi-Wei; Oaks, Zachary; Kelly, Ryan; Borsuk, Rebecca; Asara, John M.; Phillips, Paul E. (Springer US, 2015)
      Systemic lupus erythematosus (SLE) patients exhibit depletion of the intracellular antioxidant glutathione and downstream activation of the metabolic sensor, mechanistic target of rapamycin (mTOR). Since reversal of ...

    • Comprehensive Microscopy of the Esophagus in Human Patients with Optical Frequency Domain Imaging 

      Suter, Melissa; Vakoc, Benjamin; Yachimski, Patrick S.; Shishkov, Milen Stefanov; Lauwers, Gregory Y.; Mino-Kenudson, Mari; Bouma, Brett; Nishioka, Norman Shizuaki; Tearney, Guillermo James (Elsevier BV, 2008)
      Background: Optical coherence tomography (OCT) is a cross-sectional, high-resolution imaging modality that has been shown to accurately differentiate esophageal specialized intestinal metaplasia (SIM) from gastric cardia ...

    • Comprehensive molecular characterization of gastric adenocarcinoma 

      Bass, Adam J.; Thorsson, Vesteinn; Shmulevich, Ilya; Reynolds, Sheila M.; Miller, Michael; Bernard, Brady; Hinoue, Toshinori; Laird, Peter W.; Curtis, Christina; Shen, Hui; Weisenberger, Daniel J.; Schultz, Nikolaus; Shen, Ronglai; Weinhold, Nils; Kelsen, David P.; Bowlby, Reanne; Chu, Andy; Kasaian, Katayoon; Mungall, Andrew J.; Robertson, A. Gordon; Sipahimalani, Payal; Cherniack, Andrew; Getz, Gad; Liu, Yingchun; Noble, Michael S.; Pedamallu, Chandra; Sougnez, Carrie; Taylor-Weiner, Amaro; Akbani, Rehan; Lee, Ju-Seog; Liu, Wenbin; Mills, Gordon B.; Yang, Da; Zhang, Wei; Pantazi, Angeliki; Parfenov, Michael; Gulley, Margaret; Piazuelo, M. Blanca; Schneider, Barbara G.; Kim, Jihun; Boussioutas, Alex; Sheth, Margi; Demchok, John A.; Rabkin, Charles S.; Willis, Joseph E.; Ng, Sam; Garman, Katherine; Beer, David G.; Pennathur, Arjun; Raphael, Benjamin J.; Wu, Hsin-Ta; Odze, Robert; Kim, Hark K.; Bowen, Jay; Leraas, Kristen M.; Lichtenberg, Tara M.; Weaver, Stephanie; McLellan, Michael; Wiznerowicz, Maciej; Sakai, Ryo; Lawrence, Michael S.; Cibulskis, Kristian; Lichtenstein, Lee; Fisher, Sheila; Gabriel, Stacey B.; Lander, Eric S.; Ding, Li; Niu, Beifang; Ally, Adrian; Balasundaram, Miruna; Birol, Inanc; Brooks, Denise; Butterfield, Yaron S. N.; Carlsen, Rebecca; Chu, Justin; Chuah, Eric; Chun, Hye-Jung E.; Clarke, Amanda; Dhalla, Noreen; Guin, Ranabir; Holt, Robert A.; Jones, Steven J.M.; Lee, Darlene; Li, Haiyan A.; Lim, Emilia; Ma, Yussanne; Marra, Marco A.; Mayo, Michael; Moore, Richard A.; Mungall, Karen L.; Nip, Ka Ming; Schein, Jacqueline E.; Tam, Angela; Thiessen, Nina; Beroukhim, Rameen; Carter, Scott L.; Cherniack, Andrew D.; Cho, Juok; DiCara, Daniel; Frazer, Scott; Gehlenborg, Nils; Heiman, David I.; Jung, Joonil; Kim, Jaegil; Lin, Pei; Meyerson, Matthew; Ojesina, Akinyemi I.; Pedamallu, Chandra Sekhar; Saksena, Gordon; Schumacher, Steven E.; Stojanov, Petar; Tabak, Barbara; Voet, Doug; Rosenberg, Mara; Zack, Travis I.; Zhang, Hailei; Zou, Lihua; Protopopov, Alexei; Santoso, Netty; Lee, Semin; Zhang, Jianhua; Mahadeshwar, Harshad S.; Tang, Jiabin; Ren, Xiaojia; Seth, Sahil; Yang, Lixing; Xu, Andrew W.; Song, Xingzhi; Xi, Ruibin; Bristow, Christopher A.; Hadjipanayis, Angela; Seidman, Jonathan; Chin, Lynda; Park, Peter J.; Kucherlapati, Raju; Ling, Shiyun; Rao, Arvind; Weinstein, John N.; Kim, Sang-Bae; Lu, Yiling; Mills, Gordon; Bootwalla, Moiz S.; Lai, Phillip H.; Triche, Timothy; Van Den Berg, David J.; Baylin, Stephen B.; Herman, James G.; Murray, Bradley A.; Askoy, B. Arman; Ciriello, Giovanni; Dresdner, Gideon; Gao, Jianjiong; Gross, Benjamin; Jacobsen, Anders; Lee, William; Ramirez, Ricardo; Sander, Chris; Senbabaoglu, Yasin; Sinha, Rileen; Sumer, S. Onur; Sun, Yichao; Thorsson, Vésteinn; Iype, Lisa; Kramer, Roger W.; Kreisberg, Richard; Rovira, Hector; Tasman, Natalie; Ng, Santa Cruz Sam; Haussler, David; Stuart, Josh M.; Verhaak, Roeland G.W.; Leiserson, Mark D. M.; Taylor, Barry S.; Black, Aaron D.; Carney, Julie Ann; Gastier-Foster, Julie M.; Helsel, Carmen; McAllister, Cynthia; Ramirez, Nilsa C.; Tabler, Teresa R.; Wise, Lisa; Zmuda, Erik; Penny, Robert; Crain, Daniel; Gardner, Johanna; Lau, Kevin; Curely, Erin; Mallery, David; Morris, Scott; Paulauskis, Joseph; Shelton, Troy; Shelton, Candace; Sherman, Mark; Benz, Christopher; Lee, Jae-Hyuk; Fedosenko, Konstantin; Manikhas, Georgy; Potapova, Olga; Voronina, Olga; Belyaev, Smitry; Dolzhansky, Oleg; Rathmell, W. Kimryn; Brzezinski, Jakub; Ibbs, Matthew; Korski, Konstanty; Kycler, Witold; ŁaŸniak, Radoslaw; Leporowska, Ewa; Mackiewicz, Andrzej; Murawa, Dawid; Murawa, Pawel; Spychała, Arkadiusz; Suchorska, Wiktoria M.; Tatka, Honorata; Teresiak, Marek; Abdel-Misih, Raafat; Bennett, Joseph; Brown, Jennifer; Iacocca, Mary; Rabeno, Brenda; Kwon, Sun-Young; Kemkes, Ariane; Curley, Erin; Alexopoulou, Iakovina; Engel, Jay; Bartlett, John; Albert, Monique; Park, Do-Youn; Dhir, Rajiv; Luketich, James; Landreneau, Rodney; Janjigian, Yelena Y.; Cho, Eunjung; Ladanyi, Marc; Tang, Laura; McCall, Shannon J.; Park, Young S.; Cheong, Jae-Ho; Ajani, Jaffer; Camargo, M. Constanza; Alonso, Shelley; Ayala, Brenda; Jensen, Mark A.; Pihl, Todd; Raman, Rohini; Walton, Jessica; Wan, Yunhu; Eley, Greg; Mills Shaw, Kenna R.; Tarnuzzer, Roy; Wang, Zhining; Yang, Liming; Zenklusen, Jean Claude; Davidsen, Tanja; Hutter, Carolyn M.; Sofia, Heidi J.; Burton, Robert; Chudamani, Sudha; Liu, Jia (2014)
      Gastric cancer is a leading cause of cancer deaths, but analysis of its molecular and clinical characteristics has been complicated by histological and aetiological heterogeneity. Here we describe a comprehensive molecular ...