Browsing SPH Scholarly Articles by Title

Now showing items 2685-2704 of 6362

    • Genome-wide specificities of CRISPR-Cas Cpf1 nucleases in human cells 

      Kleinstiver, Benjamin P.; Tsai, Shengdar Q.; Prew, Michelle S.; Nguyen, Nhu T.; Welch, Moira M.; Lopez, Jose M.; McCaw, Zachary R.; Aryee, Martin J.; Joung, J. Keith (2016)
      The activities and genome-wide specificities of CRISPR-Cas Cpf1 nucleases1 are not well defined. We show that two Cpf1 nucleases from Acidaminococcus sp. BV3L6 and Lachnospiraceae bacterium ND2006 (AsCpf1 and LbCpf1, ...

    • A genome-wide survey of CD4+ lymphocyte regulatory genetic variants identifies novel asthma genes 

      Sharma, Sunita; Zhou, Xiaobo; Thibault, Derek M.; Himes, Blanca; Liu, Andy; Szefler, Stanley J.; Strunk, Robert; Castro, Mario; Hansel, Nadia N.; Diette, Gregory B.; Vonakis, Becky M.; Adkinson, N. Franklin; Avila, Lydiana; Soto-Quiros, Manuel; Barraza-Villareal, Albino; Lemanske, Robert F.; Solway, Julian; Krishnan, Jerry; White, Steven James; Cheadle, Chris; Berger, Alan E.; Fan, Jinshui; Boorgula, Meher Preethi; Nicolae, Dan; Gilliland, Frank; Barnes, Kathleen; London, Stephanie J.; Martinez, Fernando; Ober, Carole; Celedón, Juan C.; Carey, Vincent James; Weiss, Scott Tillman; Raby, Benjamin Alexander (Elsevier BV, 2014)
      Background: Genome-wide association studies have yet to identify the majority of genetic variants involved in asthma. We hypothesized that expression quantitative trait locus (eQTL) mapping can identify novel asthma genes ...

    • A Genome-Wide “Pleiotropy Scan” Does Not Identify New Susceptibility Loci for Estrogen Receptor Negative Breast Cancer 

      Campa, Daniele; Barrdahl, Myrto; Tsilidis, Konstantinos K.; Severi, Gianluca; Diver, W. Ryan; Siddiq, Afshan; Chanock, Stephen; Hoover, Robert N.; Ziegler, Regina G.; Berg, Christine D.; Buys, Saundra S.; Haiman, Christopher A.; Henderson, Brian E.; Schumacher, Fredrick R.; Le Marchand, Loïc; Flesch-Janys, Dieter; Lindström, Sara; Hunter, David J.; Hankinson, Susan E.; Willett, Walter C.; Kraft, Peter; Cox, David G.; Khaw, Kay-Tee; Tjønneland, Anne; Dossus, Laure; Trichopoulos, Dimitrios; Panico, Salvatore; van Gils, Carla H.; Weiderpass, Elisabete; Barricarte, Aurelio; Sund, Malin; Gaudet, Mia M.; Giles, Graham; Southey, Melissa; Baglietto, Laura; Chang-Claude, Jenny; Kaaks, Rudolf; Canzian, Federico (Public Library of Science, 2014)
      Approximately 15–30% of all breast cancer tumors are estrogen receptor negative (ER−). Compared with ER-positive (ER+) disease they have an earlier age at onset and worse prognosis. Despite the vast number of risk variants ...

    • Genomewide association between GLCCI1 and response to glucocorticoid therapy in asthma 

      Tantisira, Kelan; Lasky-Su, Jessica A. Lasky; Harada, Michishige; Murphy, Amy; Litonjua, Augusto Ampil; Himes, Blanca; Lange, Christoph; Lazarus, Ross; Sylvia, Jody; Klanderman, Barbara; Duan, Qing Ling; Qiu, Weiliang; Hirota, Tomomitsu; Martinez, Fernando D.; Mauger, David; Sorkness, Christine; Szefler, Stanley; Lazarus, Stephen C.; Lemanske, Robert F.; Peters, Stephen P.; Lima, John J.; Nakamura, Yusuke; Tamari, Mayumi; Weiss, Scott Tillman (New England Journal of Medicine (NEJM/MMS), 2011)
      Background: The response to treatment for asthma is characterized by wide interindividual variability, with a significant number of patients who have no response. We hypothesized that a genomewide association study would ...

    • Genomewide Association Study for Determinants of HIV-1 Acquisition and Viral Set Point in HIV-1 Serodiscordant Couples with Quantified Virus Exposure 

      Lingappa, Jairam R.; Petrovski, Slavé; Kahle, Erin; Fellay, Jacques; Shianna, Kevin; McElrath, M. Juliana; Thomas, Katherine Bain; Baeten, Jared M.; Celum, Connie; Wald, Anna; de Bruyn, Guy; Mullins, James I.; Nakku-Joloba, Edith; Farquhar, Carey; Essex, Myron Elmer; Donnell, Deborah; Kiarie, James; Haynes, Bart; Goldstein, David (Public Library of Science (PLoS), 2011)
      BACKGROUND: Host genetic factors may be important determinants of HIV-1 sexual acquisition. We performed a genome-wide association study (GWAS) for host genetic variants modifying HIV-1 acquisition and viral control in the ...

    • Genomewide meta‐analysis identifies loci associated with IGF‐I and IGFBP‐3 levels with impact on age‐related traits 

      Teumer, Alexander; Qi, Qibin; Nethander, Maria; Aschard, Hugues; Bandinelli, Stefania; Beekman, Marian; Berndt, Sonja I.; Bidlingmaier, Martin; Broer, Linda; Cappola, Anne; Ceda, Gian Paolo; Chanock, Stephen; Chen, Ming‐Huei; Chen, Tai C.; Chen, Yii‐Der Ida; Chung, Jonathan; Del Greco Miglianico, Fabiola; Eriksson, Joel; Ferrucci, Luigi; Friedrich, Nele; Gnewuch, Carsten; Goodarzi, Mark O.; Grarup, Niels; Guo, Tingwei; Hammer, Elke; Hayes, Richard B.; Hicks, Andrew A.; Hofman, Albert; Houwing‐Duistermaat, Jeanine J.; Hu, Frank; Hunter, David J.; Husemoen, Lise L.; Isaacs, Aaron; Jacobs, Kevin B.; Janssen, Joop A. M. J. L.; Jansson, John‐Olov; Jehmlich, Nico; Johnson, Simon; Juul, Anders; Karlsson, Magnus; Kilpelainen, Tuomas O.; Kovacs, Peter; Kraft, Peter; Li, Chao; Linneberg, Allan; Liu, Yongmei; Loos, Ruth J. F.; Lorentzon, Mattias; Lu, Yingchang; Maggio, Marcello; Magi, Reedik; Meigs, James; Mellström, Dan; Nauck, Matthias; Newman, Anne B.; Pollak, Michael N.; Pramstaller, Peter P.; Prokopenko, Inga; Psaty, Bruce M.; Reincke, Martin; Rimm, Eric B.; Rotter, Jerome I.; Saint Pierre, Aude; Schurmann, Claudia; Seshadri, Sudha; Sjögren, Klara; Slagboom, P. Eline; Strickler, Howard D.; Stumvoll, Michael; Suh, Yousin; Sun, Qi; Zhang, Cuilin; Svensson, Johan; Tanaka, Toshiko; Tare, Archana; Tönjes, Anke; Uh, Hae‐Won; van Duijn, Cornelia M.; van Heemst, Diana; Vandenput, Liesbeth; Vasan, Ramachandran S.; Völker, Uwe; Willems, Sara M.; Ohlsson, Claes; Wallaschofski, Henri; Kaplan, Robert C. (John Wiley and Sons Inc., 2016)
      Summary The growth hormone/insulin‐like growth factor (IGF) axis can be manipulated in animal models to promote longevity, and IGF‐related proteins including IGF‐I and IGF‐binding protein‐3 (IGFBP‐3) have also been implicated ...

    • Genomewide Pattern of Synonymous Nucleotide Substitution in Two Complete Genomes of Mycobacterium tuberculosis 

      Hughes, Austin L.; Friedman, Robert; Murray, Megan Blanche (Centers for Disease Control and Prevention, 2002)
      Comparison of the pattern of synonymous nucleotide substitution between two complete genomes of Mycobacterium tuberculosis at 3,298 putatively orthologous loci showed a mean percent difference per synonymous site of 0.000328 ...

    • Genomic analyses of Neisseria gonorrhoeae reveal an association of the gonococcal genetic island with antimicrobial resistance 

      Harrison, Odile B.; Clemence, Marianne; Dillard, Joseph P.; Tang, Christoph M.; Trees, David; Grad, Yonatan H.; Maiden, Martin C.J. (W.B. Saunders, 2016)
      Summary Objectives: Antimicrobial resistance (AMR) threatens our ability to treat the sexually transmitted bacterial infection gonorrhoea. The increasing availability of whole genome sequence (WGS) data from Neisseria ...

    • Genomic analysis identifies association of Fusobacterium with colorectal carcinoma 

      Kostic, Aleksandar David; Gevers, D.; Pedamallu, Chandra Sekhar; Michaud, Monia; Duke, F.; Earl, A. M.; Ojesina, Akinyemi Ifedapo; Jung, J.; Bass, Adam Joel; Tabernero, J.; Baselga, J.; Liu, C.; Shivdasani, Ramesh Arjun; Ogino, Shuji; Birren, B. W.; Huttenhower, Curtis; Garrett, Wendy S.; Meyerson, Matthew Langer (Cold Spring Harbor Laboratory Press, 2011)
      The tumor microenvironment of colorectal carcinoma is a complex community of genomically altered cancer cells, nonneoplastic cells, and a diverse collection of microorganisms. Each of these components may contribute to ...

    • Genomic Analysis Identifies Targets of Convergent Positive Selection in Drug Resistant Mycobacterium tuberculosis 

      Farhat, Maha R; Shapiro, B Jesse; Kieser, Karen J; Sultana, Razvan; Jacobson, Karen R; Victor, Thomas C; Warren, Robin M; Streicher, Elizabeth M; Calver, Alistair; Sloutsky, Alex; Kaur, Devinder; Posey, Jamie E; Plikaytis, Bonnie; Oggioni, Marco R; Gardy, Jennifer L; Johnston, James C; Rodrigues, Mabel; Tang, Patrick K C; Kato-Maeda, Midori; Borowsky, Mark L; Muddukrishna, Bhavana; Kreiswirth, Barry N; Kurepina, Natalia; Galagan, James; Gagneux, Sebastien; Birren, Bruce; Rubin, Eric J; Lander, Eric S; Sabeti, Pardis C; Murray, Megan (2013)
      Mycobacterium tuberculosis is successfully evolving antibiotic resistance, threatening attempts at tuberculosis epidemic control. Mechanisms of resistance, including the genetic changes favored by selection in resistant ...

    • Genomic Analysis of the Basal Lineage Fungus Rhizopus oryzae Reveals a Whole-Genome Duplication 

      Ma, Li-Jun; Ibrahim, Ashraf S.; Skory, Christopher; Grabherr, Manfred G.; Burger, Gertraud; Butler, Margi; Elias, Marek; Idnurm, Alexander; Lang, B. Franz; Sone, Teruo; Abe, Ayumi; Corrochano, Luis M.; Fu, Jianmin; Hansberg, Wilhelm; Kim, Jung-Mi; Kodira, Chinnappa D.; Koehrsen, Michael J.; Miranda-Saavedra, Diego; O'Leary, Sinead; Ortiz-Castellanos, Lucila; Poulter, Russell; Rodriguez-Romero, Julio; Ruiz-Herrera, José; Shen, Yao-Qing; Zeng, Qiandong; Birren, Bruce W.; Cuomo, Christina A.; Wickes, Brian L.; Calvo, Sarah E; Engels, Reinhard; Galagan, James E; Liu, Bo (Public Library of Science, 2009)
      Rhizopus oryzae is the primary cause of mucormycosis, an emerging, life-threatening infection characterized by rapid angioinvasive growth with an overall mortality rate that exceeds 50%. As a representative of the paraphyletic ...

    • Genomic and Clinical Effects Associated with a Relaxation Response Mind-Body Intervention in Patients with Irritable Bowel Syndrome and Inflammatory Bowel Disease 

      Kuo, Braden; Bhasin, Manoj; Jacquart, Jolene; Scult, Matthew A.; Slipp, Lauren; Riklin, Eric Isaac Kagan; Lepoutre, Veronique; Comosa, Nicole; Norton, Beth-Ann; Dassatti, Allison; Rosenblum, Jessica; Thurler, Andrea H.; Surjanhata, Brian C.; Hasheminejad, Nicole N.; Kagan, Leslee; Slawsby, Ellen; Rao, Sowmya R.; Macklin, Eric A.; Fricchione, Gregory L.; Benson, Herbert; Libermann, Towia A.; Korzenik, Joshua; Denninger, John W. (Public Library of Science, 2015)
      Introduction: Irritable Bowel Syndrome (IBS) and Inflammatory Bowel Disease (IBD) can profoundly affect quality of life and are influenced by stress and resiliency. The impact of mind-body interventions (MBIs) on IBS and ...

    • A genomic and evolutionary approach reveals non-genetic drug resistance in malaria 

      Herman, Jonathan D; Rice, Daniel P; Ribacke, Ulf; Silterra, Jacob; Deik, Amy A; Moss, Eli L; Broadbent, Kate M; Neafsey, Daniel E; Desai, Michael M; Clish, Clary B; Mazitschek, Ralph; Wirth, Dyann F (BioMed Central, 2014)
      Background: Drug resistance remains a major public health challenge for malaria treatment and eradication. Individual loci associated with drug resistance to many antimalarials have been identified, but their epistasis ...

    • Genomic and phenotypic insights from an atlas of genetic effects on DNA methylation 

      Min, Josine L.; Hemani, Gibran; Hannon, Eilis; Dekkers, Koen F.; Castillo-Fernandez, Juan; Luijk, René; Carnero-Montoro, Elena; Lawson, Daniel J.; Burrows, Kimberley; Suderman, Matthew; Bretherick, Andrew D.; Richardson, Tom G.; Klughammer, Johanna; Iotchkova, Valentina; Sharp, Gemma; Al Khleifat, Ahmad; Shatunov, Aleksey; Iacoangeli, Alfredo; McArdle, Wendy L.; Ho, Karen M.; Kumar, Ashish; Söderhäll, Cilla; Soriano-Tárraga, Carolina; Giralt-Steinhauer, Eva; Kazmi, Nabila; Mason, Dan; McRae, Allan F.; Corcoran, David L.; Sugden, Karen; Kasela, Silva; Cardona, Alexia; Day, Felix R.; Cugliari, Giovanni; Viberti, Clara; Guarrera, Simonetta; Lerro, Michael; Gupta, Richa; Bollepalli, Sailalitha; Mandaviya, Pooja; Zeng, Yanni; Clarke, Toni-Kim; Walker, Rosie M.; Schmoll, Vanessa; Czamara, Darina; Ruiz-Arenas, Carlos; Rezwan, Faisal I.; Marioni, Riccardo E.; Lin, Tian; Awaloff, Yvonne; Germain, Marine; Aïssi, Dylan; Zwamborn, Ramona; van Eijk, Kristel; Dekker, Annelot; van Dongen, Jenny; Hottenga, Jouke-Jan; Willemsen, Gonneke; Xu, Cheng-Jian; Barturen, Guillermo; Català-Moll, Francesc; Kerick, Martin; Wang, Carol; Melton, Phillip; Elliott, Hannah R.; Shin, Jean; Bernard, Manon; Yet, Idil; Smart, Melissa; Gorrie-Stone, Tyler; Shaw, Chris; Al Chalabi, Ammar; Ring, Susan M.; Pershagen, Göran; Melén, Erik; Jiménez-Conde, Jordi; Roquer, Jaume; Lawlor, Deborah A.; Wright, John; Martin, Nicholas G.; Montgomery, Grant W.; Moffitt, Terrie E.; Poulton, Richie; Esko, Tõnu; Milani, Lili; Metspalu, Andres; Perry, John R. B.; Ong, Ken K.; Wareham, Nicholas J.; Matullo, Giuseppe; Sacerdote, Carlotta; Panico, Salvatore; Caspi, Avshalom; Arseneault, Louise; Gagnon, France; Ollikainen, Miina; Kaprio, Jaakko; Felix, Janine F.; Rivadeneira, Fernando; Tiemeier, Henning; van IJzendoorn, Marinus H.; Uitterlinden, André G.; Jaddoe, Vincent W. V.; Haley, Chris; McIntosh, Andrew M.; Evans, Kathryn L.; Murray, Alison; Räikkönen, Katri; Lahti, Jari; Nohr, Ellen A.; Sørensen, Thorkild I. A.; Hansen, Torben; Morgen, Camilla S.; Binder, Elisabeth B.; Lucae, Susanne; Gonzalez, Juan Ramon; Bustamante, Mariona; Sunyer, Jordi; Holloway, John W.; Karmaus, Wilfried; Zhang, Hongmei; Deary, Ian J.; Wray, Naomi R.; Starr, John M.; Beekman, Marian; van Heemst, Diana; Slagboom, P. Eline; Morange, Pierre-Emmanuel; Trégouët, David-Alexandre; Veldink, Jan H.; Davies, Gareth E.; de Geus, Eco J. C.; Boomsma, Dorret I.; Vonk, Judith M.; Brunekreef, Bert; Koppelman, Gerard H.; Alarcón-Riquelme, Marta E.; Huang, Rae-Chi; Pennell, Craig E.; van Meurs, Joyce; Ikram, M. Arfan; Hughes, Alun D.; Tillin, Therese; Chaturvedi, Nish; Pausova, Zdenka; Paus, Tomas; Spector, Timothy D.; Kumari, Meena; Schalkwyk, Leonard C.; Visscher, Peter M.; Davey Smith, George; Bock, Christoph; Gaunt, Tom R.; Bell, Jordana T.; Heijmans, Bastiaan T.; Mill, Jonathan; Relton, Caroline L. (Springer Science and Business Media LLC, 2021-09)
      Characterising genetic influences on DNA methylation (DNAm) provides an opportunity to understand mechanisms underpinning gene regulation and disease. Here we describe results of DNA methylation-quantitative trait loci ...

    • Genomic characterization of brain metastases identifies drivers of metastatic lung adenocarcinoma 

      Shih, David; Nayyar, Naema; Bihun, Ivanna; Dagogo-Jack, Ibiayi; Gill, Corey; Aquilanti, Elisa; Bertalan, Mia; Kaplan, Alexander; Chukwueke, Ugonma; Ippen, Franziska; Alvarez-Breckenridge, Christopher; Camarda, Nicholas; Lastrapes, Matthew; McCabe, Devin; Kuter, Ben; Kaufmann, Benjamin; Strickland, Matthew; Martinez-Gutierrez, Juan Carlos; Nagabhushan, Deepika; De Sauvage, Magali; White, Michael; Castro, Brandyn; Hoang, Kaitlin; Kaneb, Andrew; Batchelor, Emily; Paek, Sun Ha; Park, Sun Hye; Martinez-Lage Alvarez, Maria; Berghoff, Anna S.; Merrill, Parker; Gerstner, Elizabeth; Batchelor, Tracy; Frosch, Matthew; Frazier, Ryan P.; Borger, Darrell; Iafrate, Anthony; Johnson, Bruce E.; Santagata, Sandro; Preusser, Matthias; Cahill, Daniel; Carter, Scott; Brastianos, Priscilla (Elsevier BV, 2020-06)

    • Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma 

      Giannakis, Marios; Mu, Xinmeng Jasmine; Shukla, Sachet A.; Qian, Zhi Rong; Cohen, Ofir; Nishihara, Reiko; Bahl, Samira; Cao, Yin; Amin-Mansour, Ali; Yamauchi, Mai; Sukawa, Yasutaka; Stewart, Chip; Rosenberg, Mara; Mima, Kosuke; Inamura, Kentaro; Nosho, Katsuhiko; Nowak, Jonathan A.; Lawrence, Michael S.; Giovannucci, Edward L.; Chan, Andrew T.; Ng, Kimmie; Meyerhardt, Jeffrey A.; Van Allen, Eliezer M.; Getz, Gad; Gabriel, Stacey B.; Lander, Eric S.; Wu, Catherine J.; Fuchs, Charles S.; Ogino, Shuji; Garraway, Levi A. (Cell Press, 2016)
      Summary Large-scale genomic characterization of tumors from prospective cohort studies may yield new insights into cancer pathogenesis. We performed whole-exome sequencing of 619 incident colorectal cancers (CRCs) and ...

    • Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011 

      Grad, Yonatan Hagai; Lipsitch, Marc; Feldgarden, M.; Arachchi, H. M.; Cerqueira, G. C.; Fitzgerald, Michael L.; Godfrey, P.; Haas, Brandon Russell; Murphy, C. I.; Russ, C.; Sykes, Sean; Walker, B. J.; Wortman, J. R.; Young, Sarah; Zeng, Q.; Abouelleil, A.; Bochicchio, J.; Chauvin, S.; DeSmet, T.; Gujja, S.; Mccowan, Caryn Alissa; Montmayeur, A.; Steelman, S.; Frimodt-Moller, J.; Petersen, A. M.; Struve, C.; Krogfelt, K. A.; Bingen, E.; Weill, F.-X.; Lander, Eric Steven; Nusbaum, C.; Birren, B. W.; Hung, Deborah Tan; Hanage, William P. (Proceedings of the National Academy of Sciences, 2012)
      The degree to which molecular epidemiology reveals information about the sources and transmission patterns of an outbreak depends on the resolution of the technology used and the samples studied. Isolates of Escherichia ...

    • The genomic landscape and evolution of endometrial carcinoma progression and abdominopelvic metastasis 

      Gibson, William J.; Hoivik, Erling A.; Halle, Mari K.; Taylor-Weiner, Amaro; Cherniack, Andrew D.; Berg, Anna; Holst, Frederik; Zack, Travis I.; Werner, Henrica M. J.; Staby, Kjersti M.; Rosenberg, Mara; Stefansson, Ingunn M.; Kusonmano, Kanthida; Chevalier, Aaron; Mauland, Karen K.; Trovik, Jone; Krakstad, Camilla; Giannakis, Marios; Hodis, Eran; Woie, Kathrine; Bjorge, Line; Vintermyr, Olav K.; Wala, Jeremiah A.; Lawrence, Michael S.; Getz, Gad; Carter, Scott L.; Beroukhim, Rameen; Salvesen, Helga B. (2016)
      Recent studies have detailed the genomic landscape of primary endometrial cancers, but their evolution into metastases has not been characterized. We performed whole-exome sequencing of 98 tumor biopsies including complex ...

    • Genomic mapping of RNA polymerase II reveals sites of co-transcriptional regulation in human cells 

      Brodsky, Alexander S; Meyer, Clifford; Swinburne, Ian A; Hall, Giles; Keenan, Benjamin J; Liu, Xiaole Shirley; Fox, Edward Alvin; Silver, Pamela A. (BioMed Central, 2005)
      Background: Transcription by RNA polymerase II is regulated at many steps including initiation, promoter release, elongation and termination. Accumulation of RNA polymerase II at particular locations across genes can be ...

    • The genomic origins of asthma 

      Sharma, Sunita; Chhabra, Divya; Kho, Alvin Thong-Juak; Hayden, Lystra P.; Tantisira, Kelan; Weiss, Scott Tillman (BMJ, 2014)
      Lung function tracks from the earliest age that it can be reliably measured. Genome wide association studies (GWAS) suggest that most variants identified for common complex traits are both regulatory in function and active ...