Recent Submissions

  • MRM screening/biomarker discovery with linear ion trap MS: a library of human cancer-specific peptides 

    Yang, Xu; Lazar, Iulia M. (BMC, 2009-03-27)
    Background: The discovery of novel protein biomarkers is essential in the clinical setting to enable early disease diagnosis and increase survivability rates. To facilitate differential expression analysis and biomarker ...
  • Genome Sequences of Three Brucella canis Strains Isolated from Humans and a Dog 

    Canario Viana, Marcus Vinicius; Wattam, Alice Rebecca; Batra, Dhwani Govil; Boisvert, Sebastien; Brettin, Thomas Scott; Frace, Michael; Xia, Fangfang; Azevedo, Vasco; Tiller, Rebekah; Hoffmaster, Alex R. (2017-02)
    Brucella canis is a facultative intracellular pathogen that preferentially infects members of the Canidae family. Here, we report the genome sequencing of two Brucella canis strains isolated from humans and one isolated ...
  • Missing genes in the annotation of prokaryotic genomes 

    Warren, Andrew S.; Archuleta, Jeremy; Feng, Wu-chun; Setubal, João Carlos (BioMed Central, 2010)
    Background: Protein-coding gene detection in prokaryotic genomes is considered a much simpler problem than in intron-containing eukaryotic genomes. However there have been reports that prokaryotic gene finder programs have ...
  • Permanent Draft Genome Sequence of Desulfurococcus amylolyticus Strain Z-533(T), a Peptide and Starch Degrader Isolated from Thermal Springs in the Kamchatka Peninsula and Kunashir Island, Russia 

    Susanti, Dwi; Johnson, Eric F.; Lapidus, Alla; Han, James; Reddy, T. B. K.; Mukherjee, Supratim; Pillay, Manoj; Perevalova, Anna A.; Ivanova, Natalia N.; Woyke, Tanja; Kyrpides, Nikos C.; Mukhopadhyay, Biswarup (2017-04)
    Desulfurococcus amylolyticus Z-533(T), a hyperthermophilic crenarcheon, ferments peptide and starch, generating acetate, isobutyrate, isovalerate, CO2, and hydrogen. Unlike D. amylolyticus Z-1312, it cannot use cellulose ...
  • Complete Genome Sequence of Bordetella pertussis Pelita III, the Production Strain for an Indonesian Whole-Cell Pertussis Vaccine 

    Efendi, Yusuf Sofyan; Susanti, Dwi; Tritama, Erman; Pasier, Michelle Lueders; Putri, Gilang Nadia Niwan; Raharso, Sugeng; Iskandar; Aditiawati, Pingkan; Giri-Rachman, Ernawati Arifin; Mukhopadhyay, Biswarup; Purwantini, Endang (2017-04)
    PT Bio Farma, the sole World Health Organization-approved Indonesian vaccine producer, manufactures a whole-cell whooping cough vaccine (wP) that, as part of a pentavalent diphtheria-tetanus-pertussis/hepatitis B/Haemophilus ...
  • EGR1 recruits TET1 to shape the brain methylome during development and upon neuronal activity 

    Sun, Zhixiong; Xu, Xiguang; He, Jianlin; Murray, Alexander; Sun, Ming-an; Wei, Xiaoran; Wang, Xia; McCoig, Emmarose; Xie, Evan; Jiang, Xi; Li, Liwu; Zhu, Jinsong; Chen, Jianjun; Morozov, Alexei; Pickrell, Alicia M.; Theus, Michelle H.; Xie, Hehuang (2019-08-29)
    Life experience can leave lasting marks, such as epigenetic changes, in the brain. How life experience is translated into storable epigenetic information remains largely unknown. With unbiased data-driven approaches, we ...
  • SIPsmartER delivered through rural, local health districts: adoption and implementation outcomes 

    Porter, Kathleen J.; Brock, Donna J.; Estabrooks, Paul A.; Perzynski, Katelynn M.; Hecht, Erin R.; Ray, Pamela; Kruzliakova, Natalie; Cantrell, Eleanor S.; Zoellner, Jamie M. (2019-09-18)
    Abstract Background SIPsmartER is a 6-month evidenced-based, multi-component behavioral intervention that targets sugar-sweetened beverages among adults. It consists of ...
  • COPASI and its applications in biotechnology 

    Bergmann, Frank T.; Hoops, Stefan; Klahn, Brian; Kummer, Ursula; Mendes, Pedro; Pahle, Juergen; Sahle, Sven (2017-11-10)
    COPASI is software used for the creation, modification, simulation and computational analysis of kinetic models in various fields. It is open-source, available for all major platforms and provides a user-friendly graphical ...
  • Origin and diversification of Xanthomonas citri subsp. citri pathotypes revealed by inclusive phylogenomic, dating, and biogeographic analyses 

    Patané, José S. L.; Martins, Joaquim; Rangel, Luiz T.; Belasque, José; Digiampietri, Luciano A.; Facincani, Agda P.; Ferreira, Rafael M.; Jaciani, Fabrício J.; Zhang, Yunzeng; Varani, Alessandro M.; Almeida, Nalvo F.; Wang, Nian; Ferro, Jesus A.; Moreira, Leandro M.; Setubal, João C. (2019-09-09)
    Abstract Background Xanthomonas citri subsp. citri pathotypes cause bacterial citrus canker, being responsible for severe agricultural losses worldwide. The A pathotype has a ...
  • Improved reference genome of Aedes aegypti informs arbovirus vector control 

    Matthews, Benjamin J.; Dudchenko, Olga; Kingan, Sarah B.; Koren, Sergey; Antoshechkin, Igor; Crawford, Jacob E.; Glassford, William J.; Herre, Margaret; Redmond, Seth N.; Rose, Noah H.; Weedall, Gareth D.; Wu, Yang; Batra, Sanjit S.; Brito-Sierra, Carlos A.; Buckingham, Steven D.; Campbell, Corey L.; Chan, Saki; Cox, Eric; Evans, Benjamin R.; Fansiri, Thanyalak; Filipovic, Igor; Fontaine, Albin; Gloria-Soria, Andrea; Hall, Richard; Joardar, Vinita S.; Jones, Andrew K.; Kay, Raissa G. G.; Kodali, Vamsi K.; Lee, Joyce; Lycett, Gareth J.; Mitchell, Sara N.; Muehling, Jill; Murphy, Michael R.; Omer, Arina D.; Partridge, Frederick A.; Peluso, Paul; Aiden, Aviva Presser; Ramasamy, Vidya; Rasic, Gordana; Roy, Sourav; Saavedra-Rodriguez, Karla; Sharan, Shruti; Sharma, Atashi; Smith, Melissa Laird; Turner, Joe; Weakley, Allison M.; Zhao, Zhilei; Akbari, Omar S.; Black, William C.; Cao, Han; Darby, Alistair C.; Hill, Catherine A.; Johnston, J. Spencer; Murphy, Terence D.; Raikhel, Alexander S.; Sattelle, David B.; Sharakhov, Igor V.; White, Bradley J.; Zhao, Li; Aiden, Erez Lieberman; Mann, Richard S.; Lambrechts, Louis; Powell, Jeffrey R.; Sharakhova, Maria V.; Tu, Zhijian; Robertson, Hugh M.; McBride, Carolyn S.; Hastic, Alex R.; Korlach, Jonas; Neafsey, Daniel E.; Phillippy, Adam M.; Vosshall, Leslie B. (2018-11-22)
    Female Aedes aegypti mosquitoes infect more than 400 million people each year with dangerous viral pathogens including dengue, yellow fever, Zika and chikungunya. Progress in understanding the biology of mosquitoes and ...
  • Risk Assessment in Chinese Hospitalized Patients Comparing the Padua and Caprini Scoring Algorithms 

    Chen, Xiaolan; Pan, Lei; Deng, Hui; Zhang, Jingyuan; Tong, Xinjie; Huang, He; Zhang, Min; He, Jianlin; Caprini, Joseph A.; Wang, Yong (2018-12)
    The current venous thromboembolism (VTE) guidelines recommend all patients to be assessed for the risk of VTE using risk assessment models (RAMs). The study was to evaluate the performance of the Caprini and Padua RAMs ...
  • Environmental stresses induce karyotypic instability in colorectal cancer cells 

    Tan, Zhihao; Chan, Yong Jie Andrew; Chua, Ying Jie Karen; Rutledge, Samuel D.; Pavelka, Norman; Cimini, Daniela; Rancati, Giulia (2019-01)
    Understanding how cells acquire genetic mutations is a fundamental biological question with implications for many different areas of biomedical research, ranging from tumor evolution to drug resistance. While karyotypic ...
  • Divergent age-dependent peripheral immune transcriptomic profile following traumatic brain injury 

    Hazy, Amanda; Bochicchio, Lauren; Oliver, Andrea; Xie, Eric; Geng, Shuo; Brickler, Thomas; Xie, Hehuang; Li, Liwu; Allen, Irving C.; Theus, Michelle H. (2019-06-12)
    The peripheral immune system is a major regulator of the pathophysiology associated with traumatic brain injury (TBI). While age-at-injury influences recovery from TBI, the differential effects on the peripheral immune ...
  • Innate Immunity Induced by the Major Allergen Alt a 1 From the Fungus Alternaria Is Dependent Upon Toll-Like Receptors 2/4 in Human Lung Epithelial Cells 

    Hayes, Tristan; Rumore, Amanda; Howard, Brad; He, Xin; Luo, Mengyao; Wuenschmann, Sabina; Chapman, Martin; Kale, Shiv D.; Li, Liwu; Kita, Hirohito; Lawrence, Christopher B. (2018-07-30)
    Allergens are molecules that elicit a hypersensitive inflammatory response in sensitized individuals and are derived from a variety of sources. Alt a 1 is the most clinically important secreted allergen of the ubiquitous ...
  • Fatgraph models of RNA structure 

    Huang, Fenix; Reidys, Christian; Rezazadegan, Reza (De Gruyter, 2017-02-08)
    In this review paper we discuss fatgraphs as a conceptual framework for RNA structures. We discuss various notions of coarse-grained RNA structures and relate them to fatgraphs. We motivate and discuss the main intuition ...
  • Diminished single-stimulus response in vmPFC to favorite people in children diagnosed with Autism Spectrum Disorder 

    Kishida, Kenneth T.; De Asis-Cruz, Josepheen; Treadwell-Deering, Diane; Liebenow, Brittany; Beauchamp, Michael S.; Montague, P. Read (2019-07)
    From an early age, individuals with autism spectrum disorder (ASD) spend less time engaged in social interaction compared to typically developing peers (TD). One reason behind this behavior may be that the brains of children ...
  • Genomic divergence and adaptive convergence in Drosophila simulans from Evolution Canyon, Israel 

    Kang, Lin; Rashkovetsky, Eugenia; Michalak, Katarzyna; Garner, Harold R.; Mahaney, James E.; Rzigalinski, Beverly A.; Korol, Abraham; Nevo, Eviatar; Michalak, Pawel (2019-06-11)
    Biodiversity refugia formed by unique features of the Mediterranean arid landscape, such as the dramatic ecological contrast of "Evolution Canyon," provide a natural laboratory in which local adaptations to divergent ...
  • Butyrate Protects Mice from Clostridium difficile-Induced Colitis through an HIF-1-Dependent Mechanism 

    Fachi, Jose Luis; Felipe, Jaqueline de Souza; Pral, Lais Passariello; da Silva, Bruna Karadi; Correa, Renan Oliveira; Pereira de Andrade, Mirella Cristiny; da Fonseca, Denise Morais; Basso, Paulo Jose; Saraiva Camara, Niels Olsen; de Sales e Souza, Ericka Lorenna; Martins, Flaviano dos Santos; Sato Guima, Suzana Eiko; Thomas, Andrew Maltez; Setubal, Joao Carlos; Magalhaes, Yuli Thamires; Forti, Fabio Luis; Candreva, Thamiris; Rodrigues, Hosana Gomes; de Jesus, Marcelo Bispo; Consonni, Silvio Roberto; Farias, Alessandro dos Santos; Varga-Weisz, Patrick; Ramirez Vinolo, Marco Aurelio (Cell Press, 2019-04-16)
    Antibiotic-induced dysbiosis is a key factor predisposing intestinal infection by Clostridium difficile. Here, we show that interventions that restore butyrate intestinal levels mitigate clinical and pathological features ...
  • Insights into the Evolution of Longevity from the Bowhead Whale Genome 

    Keane, Michael; Semeiks, Jeremy; Webb, Andrew E.; Li, Yang I.; Quesada, Victor; Craig, Thomas; Madsen, Lone Bruhn; van Dam, Sipko; Brawand, David; Marques, Patricia I.; Michalak, Pawel; Kang, Lin; Bhak, Jong; Yim, Hyung-Soon; Grishin, Nick V.; Nielsen, Nynne Hjort; Heide-Jorgensen, Mads Peter; Oziolor, Elias M.; Matson, Cole W.; Church, George M.; Stuart, Gary W.; Patton, John C.; George, J. Craig; Suydam, Robert; Larsen, Knud; Lopez-Otin, Carlos; O'Connell, Mary J.; Bickham, John W.; Thomsen, Bo; de Magalhaes, Joao Pedro (Cell Press, 2015-01-06)
    The bowhead whale (Balaena mysticetus) is estimated to live over 200 years and is possibly the longest-living mammal. These animals should possess protective molecular adaptations relevant to age-related diseases, particularly ...
  • Same influenza vaccination strategies but different outcomes across US cities? 

    Taylor, Claudia; Marathe, Achla; Beckman, Richard (International Society for Infectious Diseases, 2010-09)
    Objectives: This research aimed to determine if the same influenza vaccination strategies would have the same level of effectiveness when applied to two different US metropolitan areas, Miami and Seattle, where the composition ...

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