Browsing SPH Scholarly Articles by Title

Now showing items 2692-2711 of 6362

    • 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 ...

    • Genomic profiling distinguishes familial multiple and sporadic multiple meningiomas 

      Engler, David A; Roy, Jennifer; Shen, Yiping; Nunes, Fabio Pereira; Stemmer-Rachamimov, Anat; James, Marianne F.; Mohapatra, Gayatry; Plotkin, Scott Randall; Betensky, Rebecca Aubrey; Ramesh, Vijaya; Gusella, James Francis (BioMed Central, 2009)
      Background: Meningiomas may occur either as familial tumors in two distinct disorders, familial multiple meningioma and neurofibromatosis 2 (NF2), or sporadically, as either single or multiple tumors in individuals with ...

    • Genomic Screening in Family-Based Association Testing 

      Murphy, Amy; McQueen, Matthew B; Su, Jessica Ann Lasky; Kraft, Peter; Lazarus, Ross; Laird, Nan M.; Lange, Christoph; Van Steen, Kristel (BioMed Central, 2005)
      Due to the recent gains in the availability of single-nucleotide polymorphism data, genome-wide association testing has become feasible. It is hoped that this additional data may confirm the presence of disease susceptibility ...

    • Genomic Sites of Human Immunodeficiency Virus Type 2 (HIV-2) Integration: Similarities to HIV-1 In Vitro and Possible Differences In Vivo 

      MacNeil, A.; Sankale, J.-L.; Meloni, S; Sarr, A. D.; Mboup, S.; Kanki, Phyllis Jean (American Society for Microbiology, 2006)
      Retroviruses have distinct preferences in integration site selection in the host cell genome during in vitro infection, with human immunodeficiency virus type 1 (HIV-1) integration strongly favoring transcriptional units. ...

    • Genomics of Loa loa, a Wolbachia-free filarial parasite of humans 

      Desjardins, Christopher A.; Cerqueira, Gustavo C.; Goldberg, Jonathan M.; Hotopp, Julie C. Dunning; Haas, Brian J.; Zucker, Jeremy; Ribeiro, Jose’ M.C.; Saif, Sakina; Levin, Joshua Z.; Fan, Lin; Zeng, Qiandong; Russ, Carsten; Wortman, Jennifer R.; Fink, Doran L.; Birren, Bruce W.; Nutman, Thomas B. (2014)
      Loa loa, the African eyeworm, is a major filarial pathogen of humans. Unlike most filariae, Loa loa does not contain the obligate intracellular Wolbachia endosymbiont. We describe the 91.4 Mb genome of Loa loa, and the ...

    • Genotype vs. Phenotype and the Rise of Non-Communicable Diseases: The Importance of Lifestyle Behaviors During Childhood 

      Wu, Brian W; Skidmore, Paula M; Orta, Olivia R; Faulkner, James; Lambrick, Danielle; Signal, Leigh; Williams, Michelle A; Stoner, Lee (Cureus, 2016)
      Despite continued research and growing public awareness, the incidence of non-communicable diseases (NCD) continues to accelerate. While a person may have a genetic predisposition to certain NCDs, the rapidly changing ...

    • Genotypic and Functional Impact of HIV-1 Adaptation to Its Host Population during the North American Epidemic 

      Cotton, Laura A.; Kuang, Xiaomei T.; Le, Anh Q.; Carlson, Jonathan M.; Chan, Benjamin; Chopera, Denis R.; Brumme, Chanson J.; Markle, Tristan J.; Martin, Eric; Shahid, Aniqa; Anmole, Gursev; Mwimanzi, Philip; Nassab, Pauline; Penney, Kali A.; Rahman, Manal A.; Milloy, M.-J.; Schechter, Martin T.; Markowitz, Martin; Carrington, Mary; Walker, Bruce D.; Wagner, Theresa; Buchbinder, Susan; Fuchs, Jonathan; Koblin, Beryl; Mayer, Kenneth H.; Harrigan, P. Richard; Brockman, Mark A.; Poon, Art F. Y.; Brumme, Zabrina L. (Public Library of Science, 2014)
      HLA-restricted immune escape mutations that persist following HIV transmission could gradually spread through the viral population, thereby compromising host antiviral immunity as the epidemic progresses. To assess the ...

    • Genotyping Analyses of Tuberculosis Cases in U.S.- and Foreign-Born Massachusetts Residents 

      Sharnprapai, Sharon; Miller, Ann C.; Suruki, Robert; Corkren, Edward; Etkind, Sue; Driscoll, Jeffrey; McGarry, Michael; Nardell, Edward Anthony (Centers for Disease Control and Prevention, 2002)
      We used molecular genotyping to further understand the epidemiology and transmission patterns of tuberculosis (TB) in Massachusetts. The study population included 983 TB patients whose cases were verified by the Massachusetts ...