Browsing HMS Scholarly Articles by Title

Now showing items 7080-7099 of 17922

    • Genomic Analysis of Plasma Cell-Free DNA in Patients With Cancer 

      Oxnard, Geoffrey Raymond; Paweletz, Cloud; Sholl, Lynette Marie (American Medical Association (AMA), 2016)
      The increased importance of cancer genotyping in guiding cancer treatment has created a need for efficient methods for genomic analysis of patients’ cancers. This increased dependence on DNA-based tumor genotyping assays ...

    • 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 Analysis of the Evolution of Fluoroquinolone Resistance in Mycobacterium tuberculosis Prior to Tuberculosis Diagnosis 

      Zhang, Danfeng; Gomez, James; Chien, Jung-Yien; Haseley, Nathan; Desjardins, Christopher; Earl, Ashlee; Hsueh, Po-Ren; Hung, Deborah (American Society for Microbiology, 2016)
      Fluoroquinolones (FQs) are effective second-line drugs for treating antibiotic-resistant tuberculosis (TB) and are being considered for use as first-line agents. Because FQs are used to treat a range of infections, in a ...

    • Genomic Analysis of the Hydrocarbon-Producing, Cellulolytic, Endophytic Fungus Ascocoryne sarcoides 

      Sboner, Andrea; Kodira, Chinnappa; Egholm, Michael; Church, George McDonald; Gianoulis, Tara A.; Griffin, Meghan A.; Spakowicz, Daniel J.; Dunican, Brian F.; Alpha, Cambria J.; Sismour, A. Michael; Gerstein, Mark B.; Strobel, Scott A. (Public Library of Science, 2012)
      The microbial conversion of solid cellulosic biomass to liquid biofuels may provide a renewable energy source for transportation fuels. Endophytes represent a promising group of organisms, as they are a mostly untapped ...

    • 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 functional analyses of Mycobacterium tuberculosis strains implicate ald in D-cycloserine resistance 

      Desjardins, Christopher A.; Cohen, Keira A.; Munsamy, Vanisha; Abeel, Thomas; Maharaj, Kashmeel; Walker, Bruce J.; Shea, Terrance P.; Almeida, Deepak V.; Manson, Abigail L.; Salazar, Alex; Padayatchi, Nesri; O’Donnell, Max R.; Mlisana, Koleka P.; Wortman, Jennifer; Birren, Bruce W.; Grosset, Jacques; Earl, Ashlee M.; Pym, Alexander S. (2016)
      A more complete understanding of the genetic basis of drug resistance in Mycobacterium tuberculosis is critical for prompt diagnosis and optimal treatment, particularly for toxic second-line drugs like D-cycloserine. Here, ...

    • Genomic and Functional Analysis of ICEPdaSpa1, a Fish-Pathogen-Derived SXT-Related Integrating Conjugative Element That Can Mobilize a Virulence Plasmid 

      Osorio, Carlos R.; Marrero, Joeli; Wozniak, Rachel F.; Lemos, Manuel L.; Burrus, Vincent; Waldor, Matthew K. (American Society for Microbiology, 2008)
      Integrating conjugative elements (ICEs) are self-transmissible mobile elements that transfer between bacteria via conjugation and integrate into the host chromosome. SXT and related ICEs became prevalent in Asian Vibrio ...

    • A genomic case study of mixed fibrolamellar hepatocellular carcinoma 

      Griffith, O. L.; Griffith, M.; Krysiak, K.; Magrini, V.; Ramu, A.; Skidmore, Z. L.; Kunisaki, J.; Austin, R.; McGrath, S.; Zhang, J.; Demeter, R.; Graves, T.; Eldred, J. M.; Walker, J.; Larson, D. E.; Maher, C. A.; Lin, Y.; Chapman, W.; Mahadevan, A.; Miksad, R.; Nasser, I.; Hanto, D. W.; Mardis, E. R. (Oxford University Press, 2016)
      Background: Mixed fibrolamellar hepatocellular carcinoma (mFL-HCC) is a rare liver tumor defined by the presence of both pure FL-HCC and conventional HCC components, represents up to 25% of cases of FL-HCC, and has been ...

    • Genomic characterization of non-O1, non-O139 Vibrio cholerae reveals genes for a type III secretion system 

      Dziejman, Michelle; Serruto, Davide; Tam, Vincent C.; Sturtevant, Derek; Diraphat, Pornphan; Faruque, Shah M.; Rahman, M. Hasibur; Heidelberg, John F.; Decker, Jeremy; Li, Li; Montgomery, Kate T.; Grills, George; Kucherlapati, Raju; Mekalanos, John J. (National Academy of Sciences, 2005)
      Non-O1, non-O139 Vibrio cholerae can cause gastroenteritis and extraintestinal infections, but, unlike O1 and O139 strains of V. cholerae, little is known about the virulence gene content of non-O1, non-O139 strains and ...

    • 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 Counter-Stress Changes Induced by the Relaxation Response 

      Dusek, Jeffery A.; Otu, Hasan H; Wohlhueter, Ann L.; Bhasin, Manoj; Zerbini, Luiz F.; Joseph, Marie G.; Benson, Herbert; Libermann, Towia Aron (Public Library of Science, 2008)
      Background: Mind-body practices that elicit the relaxation response (RR) have been used worldwide for millennia to prevent and treat disease. The RR is characterized by decreased oxygen consumption, increased exhaled nitric ...

    • Genomic data in the All of Us Research Program 

      Bick, Alexander G.; Metcalf, Ginger A.; Mayo, Kelsey R.; Lichtenstein, Lee; Rura, Shimon; Carroll, Robert J.; Musick, Anjene; Linder, Jodell E.; Jordan, I. King; Nagar, Shashwat Deepali; Sharma, Shivam; Meller, Robert; Basford, Melissa; Boerwinkle, Eric; Cicek, Mine S.; Doheny, Kimberly F.; Eichler, Evan E.; Gabriel, Stacey; Gibbs, Richard A.; Glazer, David; Harris, Paul A.; Jarvik, Gail P.; Philippakis, Anthony; Rehm, Heidi L.; Roden, Dan M.; Thibodeau, Stephen N.; Topper, Scott; Blegen, Ashley L.; Wirkus, Samantha J.; Wagner, Victoria A.; Meyer, Jeffrey G.; Cicek, Mine S.; Muzny, Donna M.; Venner, Eric; Mawhinney, Michelle Z.; Griffith, Sean M. L.; Hsu, Elvin; Ling, Hua; Adams, Marcia K.; Walker, Kimberly; Hu, Jianhong; Doddapaneni, Harsha; Kovar, Christie L.; Murugan, Mullai; Dugan, Shannon; Khan, Ziad; Boerwinkle, Eric; Lennon, Niall J.; Austin-Tse, Christina; Banks, Eric; Gatzen, Michael; Gupta, Namrata; Henricks, Emma; Larsson, Katie; McDonough, Sheli; Harrison, Steven M.; Kachulis, Christopher; Lebo, Matthew S.; Neben, Cynthia L.; Steeves, Marcie; Zhou, Alicia Y.; Smith, Joshua D.; Frazar, Christian D.; Davis, Colleen P.; Patterson, Karynne E.; Wheeler, Marsha M.; McGee, Sean; Lockwood, Christina M.; Shirts, Brian H.; Pritchard, Colin C.; Murray, Mitzi L.; Vasta, Valeria; Leistritz, Dru; Richardson, Matthew A.; Buchan, Jillian G.; Radhakrishnan, Aparna; Krumm, Niklas; Ehmen, Brenna W.; Schwartz, Sophie; Aster, M. Morgan T.; Cibulskis, Kristian; Haessly, Andrea; Asch, Rebecca; Cremer, Aurora; Degatano, Kylee; Shergill, Akum; Gauthier, Laura D.; Lee, Samuel K.; Hatcher, Aaron; Grant, George B.; Brandt, Genevieve R.; Covarrubias, Miguel; Banks, Eric; Able, Ashley; Green, Ashley E.; Carroll, Robert J.; Zhang, Jennifer; Condon, Henry R.; Wang, Yuanyuan; Dillon, Moira K.; Albach, C. H.; Baalawi, Wail; Choi, Seung Hoan; Wang, Xin; Rosenthal, Elisabeth A.; Ramirez, Andrea H.; Lim, Sokny; Nambiar, Siddhartha; Ozenberger, Bradley; Wise, Anastasia L.; Lunt, Chris; Ginsburg, Geoffrey S.; Denny, Joshua C. (Springer Science and Business Media LLC, 2024-02-19)
      Comprehensively mapping the genetic basis of human disease across diverse individuals is a longstanding goal for the field of human genetics.1-4 The All of Us Research Program is a longitudinal cohort aiming to enroll a ...

    • Genomic discovery and clonal tracking in multiple myeloma by cell free DNA sequencing 

      Guo, Guangwu; Raje, Noopur; Seifer, Charles; Kloeber, Jake; Meyerson, Matthew Langer; Munshi, Nikhil C; Knoechel, Birgit; Lohr, Jens Guenter (Nature Publishing Group, 2018)

    • Genomic DNA Sequences from Mastodon and Woolly Mammoth Reveal Deep Speciation of Forest and Savanna Elephants 

      Green, Richard E.; Georgiadis, Nicholas J.; Roca, Alfred L.; Hofreiter, Michael; Penny, David; Rohland, Nadin; Reich, David Emil; Mallick, Swapan; Meyer, Matthias (Public Library of Science, 2010)
      To elucidate the history of living and extinct elephantids, we generated 39,763 bp of aligned nuclear DNA sequence across 375 loci for African savanna elephant, African forest elephant, Asian elephant, the extinct American ...

    • Genomic DNA transposition induced by human PGBD5 

      Henssen, Anton G; Henaff, Elizabeth; Jiang, Eileen; Eisenberg, Amy R; Carson, Julianne R; Villasante, Camila M; Ray, Mondira; Still, Eric; Burns, Melissa; Gandara, Jorge; Feschotte, Cedric; Mason, Christopher E; Kentsis, Alex (eLife Sciences Publications, Ltd, 2015)
      Transposons are mobile genetic elements that are found in nearly all organisms, including humans. Mobilization of DNA transposons by transposase enzymes can cause genomic rearrangements, but our knowledge of human genes ...

    • Genomic imprinting of Xist by maternal H3K27me3 

      Inoue, Azusa; Jiang, Lan; Lu, Falong; Zhang, Yi (Cold Spring Harbor Laboratory, 2017-10-01)
      Maternal imprinting at the Xist gene is essential to achieve paternal allele-specific imprinted X-chromosome inactivation (XCI) in female mammals. However, the mechanism underlying Xist imprinting is unclear. Here we show ...

    • Genomic insights into the formation of human populations in East Asia 

      Reich, David (Springer Science and Business Media LLC, 2021-02-22)
      The deep population history of East Asia remains poorly understood due to a lack of ancient DNA data and sparse sampling of present-day people. We report genome-wide data from 166 East Asians dating to 6000 BCE – 1000 CE ...

    • Genomic investigation of etiologic heterogeneity: methodologic challenges 

      Begg, Colin B; Seshan, Venkatraman E; Zabor, Emily C; Furberg, Helena; Arora, Arshi; Shen, Ronglai; Maranchie, Jodi K; Nielsen, Matthew E; Rathmell, W Kimryn; Signoretti, Sabina; Tamboli, Pheroze; Karam, Jose A; Choueiri, Toni K; Hakimi, A Ari; Hsieh, James J (BioMed Central, 2014)
      Background: The etiologic heterogeneity of cancer has traditionally been investigated by comparing risk factor frequencies within candidate sub-types, defined for example by histology or by distinct tumor markers of interest. ...

    • 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 ...