Adam Zemla

Department of Family Medicine, Medical University of Gdańsk, Dębinki 2, 80-211 Gdańsk, Poland; Department of Cardiac Surgery, Ceynowa Hospital, Wejherowo, Poland.

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December 2018

Sendai virus intra-host population dynamics and host immunocompetence influence viral virulence during passage.

Authors:

José Peña Haiyin Chen-Harris Jonathan E Allen Mona Hwang Maher Elsheikh Shalini Mabery Helle Bielefeldt-Ohmann Adam T Zemla Richard A Bowen Monica K Borucki

Virus Evol 2016 Jan 9;2(1):vew008. Epub 2016 Apr 9.

Lawrence Livermore National Laboratory, Livermore, CA, USA.

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January 2016

Microbial mercury methylation in Antarctic sea ice.

Authors:

Caitlin M Gionfriddo Michael T Tate Ryan R Wick Mark B Schultz Adam Zemla Michael P Thelen Robyn Schofield David P Krabbenhoft Kathryn E Holt John W Moreau

Nat Microbiol 2016 08 1;1(10):16127. Epub 2016 Aug 1.

School of Earth Sciences, University of Melbourne, Parkville, Victoria 3010, Australia.

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August 2016

Identification of Genome-Wide Mutations in Ciprofloxacin-Resistant F. tularensis LVS Using Whole Genome Tiling Arrays and Next Generation Sequencing.

Authors:

Crystal J Jaing Kevin S McLoughlin James B Thissen Adam Zemla Shea N Gardner Lisa M Vergez Feliza Bourguet Shalini Mabery Viacheslav Y Fofanov Heather Koshinsky Paul J Jackson

PLoS One 2016;11(9):e0163458. Epub 2016 Sep 26.

Physical Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, United States of America.

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September 2016

Light Regimes Shape Utilization of Extracellular Organic C and N in a Cyanobacterial Biofilm.

Authors:

Rhona K Stuart Xavier Mayali Amy A Boaro Adam Zemla R Craig Everroad Daniel Nilson Peter K Weber Mary Lipton Brad M Bebout Jennifer Pett-Ridge Michael P Thelen

mBio 2016 06 28;7(3). Epub 2016 Jun 28.

Lawrence Livermore National Laboratory, Livermore, California, USA

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June 2016

Identification of a novel drug lead that inhibits HCV infection and cell-to-cell transmission by targeting the HCV E2 glycoprotein.

Authors:

Reem R Al Olaby Laurence Cocquerel Adam Zemla Laure Saas Jean Dubuisson Jost Vielmetter Joseph Marcotrigiano Abdul Ghafoor Khan Felipe Vences Catalan Alexander L Perryman Joel S Freundlich Stefano Forli Shoshana Levy Rod Balhorn Hassan M Azzazy

PLoS One 2014 30;9(10):e111333. Epub 2014 Oct 30.

Department of Chemistry, The American University in Cairo, New Cairo, Egypt.

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December 2015

GeneSV - an Approach to Help Characterize Possible Variations in Genomic and Protein Sequences.

Authors:

Adam Zemla Tanya Kostova Rodion Gorchakov Evgeniya Volkova David W C Beasley Jane Cardosa Scott C Weaver Nikos Vasilakis Pejman Naraghi-Arani

Bioinform Biol Insights 2014 Jan 8;8:1-16. Epub 2014 Jan 8.

Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA.

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January 2014

Rapid countermeasure discovery against Francisella tularensis based on a metabolic network reconstruction.

Authors:

Sidhartha Chaudhury Mohamed Diwan M Abdulhameed Narender Singh Gregory J Tawa Patrik M D'haeseleer Adam T Zemla Ali Navid Carol E Zhou Matthew C Franklin Jonah Cheung Michael J Rudolph James Love John F Graf David A Rozak Jennifer L Dankmeyer Kei Amemiya Simon Daefler Anders Wallqvist

PLoS One 2013 21;8(5):e63369. Epub 2013 May 21.

Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command, Fort Detrick, Maryland, United States of America.

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December 2013

A strain of Yersinia pestis with a mutator phenotype from the Republic of Georgia.

Authors:

Chythanya Rajanna Gary Ouellette Mohammed Rashid Adam Zemla Mark Karavis Carol Zhou Tamara Revazishvili Brady Redmond Lauren McNew Lela Bakanidze Paata Imnadze Bryan Rivers Evan W Skowronski Kevin P O'Connell Alexander Sulakvelidze Henry S Gibbons

FEMS Microbiol Lett 2013 Jun 17;343(2):113-20. Epub 2013 Apr 17.

Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.

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June 2013

The role of viral population diversity in adaptation of bovine coronavirus to new host environments.

Authors:

Monica K Borucki Jonathan E Allen Haiyin Chen-Harris Adam Zemla Gilda Vanier Shalini Mabery Clinton Torres Pamela Hullinger Tom Slezak

PLoS One 2013 7;8(1):e52752. Epub 2013 Jan 7.

Lawrence Livermore National Laboratory, Livermore, CA, USA.

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July 2013

Computational analysis of pathogen-borne metallo β-lactamases reveals discriminating structural features between B1 types.

Authors:

Eithon Cadag Elizabeth Vitalis Kristin P Lennox Carol L Ecale Zhou Adam T Zemla

BMC Res Notes 2012 Feb 14;5:96. Epub 2012 Feb 14.

Global Security Computing Applications Division, Lawrence Livermore National Laboratory, Livermore, 94550 CA, USA.

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February 2012

A semi-quantitative, synteny-based method to improve functional predictions for hypothetical and poorly annotated bacterial and archaeal genes.

Authors:

Alexis P Yelton Brian C Thomas Sheri L Simmons Paul Wilmes Adam Zemla Michael P Thelen Nicholas Justice Jillian F Banfield

PLoS Comput Biol 2011 Oct 20;7(10):e1002230. Epub 2011 Oct 20.

Department of Environmental Science, Policy, and Management, University of California, Berkeley, California, United States of America.

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October 2011

StralSV: assessment of sequence variability within similar 3D structures and application to polio RNA-dependent RNA polymerase.

Authors:

Adam T Zemla Dorothy M Lang Tanya Kostova Raul Andino Carol L Ecale Zhou

BMC Bioinformatics 2011 Jun 2;12:226. Epub 2011 Jun 2.

Global Security Computing Applications Division, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA.

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June 2011

Practical applications of structural genomics technologies for mutagen research.

Authors:

Adam Zemla Brent W Segelke

Mutat Res 2011 Jun 21;722(2):165-70. Epub 2010 Dec 21.

Global Security Computing Applications Division, Lawrence Livermore National Laboratory, Livermore, CA 94551 0808, USA.

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June 2011

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea.

Nature 2009 Dec;462(7276):1056-60

DOE Joint Genome Institute, Walnut Creek, California 94598, USA.

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December 2009

Amino acid and structural variability of Yersinia pestis LcrV protein.

Authors:

Andrey P Anisimov Svetlana V Dentovskaya Evgeniy A Panfertsev Tat'yana E Svetoch Pavel Kh Kopylov Brent W Segelke Adam Zemla Maxim V Telepnev Vladimir L Motin

Infect Genet Evol 2010 Jan 14;10(1):137-45. Epub 2009 Oct 14.

State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Moscow Region, Russia.

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January 2010

The other 90% of the protein: assessment beyond the Calphas for CASP8 template-based and high-accuracy models.

Authors:

Daniel A Keedy Christopher J Williams Jeffrey J Headd W Bryan Arendall Vincent B Chen Gary J Kapral Robert A Gillespie Jeremy N Block Adam Zemla David C Richardson Jane S Richardson

Proteins 2009 ;77 Suppl 9:29-49

Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA.

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January 2010

SpaK/SpaR two-component system characterized by a structure-driven domain-fusion method and in vitro phosphorylation studies.

Authors:

Anu Chakicherla Carol L Ecale Zhou Martha Ligon Dang Virginia Rodriguez J Norman Hansen Adam Zemla

PLoS Comput Biol 2009 Jun 5;5(6):e1000401. Epub 2009 Jun 5.

Computing Applications and Research Department, Lawrence Livermore National Laboratory, Livermore, California, United States of America.

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June 2009

Community genomic and proteomic analyses of chemoautotrophic iron-oxidizing "Leptospirillum rubarum" (Group II) and "Leptospirillum ferrodiazotrophum" (Group III) bacteria in acid mine drainage biofilms.

Authors:

Daniela S Aliaga Goltsman Vincent J Denef Steven W Singer Nathan C VerBerkmoes Mark Lefsrud Ryan S Mueller Gregory J Dick Christine L Sun Korin E Wheeler Adam Zemla Brett J Baker Loren Hauser Miriam Land Manesh B Shah Michael P Thelen Robert L Hettich Jillian F Banfield

Appl Environ Microbiol 2009 Jul 8;75(13):4599-615. Epub 2009 May 8.

University of California-Berkeley, 94720, USA.

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July 2009

Identification of a thermo-regulated glutamine-binding protein from Yersinia pestis.

Authors:

Monique Cosman Joseph B Pesavento Adam Zemla Peter T Beernink Rod Balhorn Daniel Barsky

Protein Pept Lett 2008 ;15(9):887-94

Lawrence Livermore National Laboratory, Livermore, CA 94551, USA.

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December 2008

Characterization of cytochrome 579, an unusual cytochrome isolated from an iron-oxidizing microbial community.

Authors:

Steven W Singer Clara S Chan Adam Zemla Nathan C VerBerkmoes Mona Hwang Robert L Hettich Jillian F Banfield Michael P Thelen

Appl Environ Microbiol 2008 Jul 9;74(14):4454-62. Epub 2008 May 9.

Chemistry Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA.

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July 2008

Structural re-alignment in an immunogenic surface region of ricin A chain.

Authors:

Adam T Zemla Carol L Ecale Zhou

Bioinform Biol Insights 2008 Feb 1;2:5-13. Epub 2008 Feb 1.

Computational Biology for Countermeasures Group, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA.

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February 2008

STRALCP--structure alignment-based clustering of proteins.

Authors:

Adam Zemla Brian Geisbrecht Jason Smith Marisa Lam Bonnie Kirkpatrick Mark Wagner Tom Slezak Carol Ecale Zhou

Nucleic Acids Res 2007 26;35(22):e150. Epub 2007 Nov 26.

Computing Applications and Research, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA.

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January 2008

Selective high-affinity ligand antibody mimics for cancer diagnosis and therapy: initial application to lymphoma/leukemia.

Authors:

Rod Balhorn Saphon Hok Patricia A Burke Felice C Lightstone Monique Cosman Adam Zemla Gary Mirick Julie Perkins Arutselvan Natarajan Michele Corzett Sally J DeNardo Huguette Albrecht Jeff P Gregg Gerry L DeNardo

Clin Cancer Res 2007 Sep;13(18 Pt 2):5621s-5628s

Chemistry, Materials and Life Sciences and Computations, Lawrence Livermore National Laboratory, Livermore, California, 94550, USA.

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September 2007

MannDB - a microbial database of automated protein sequence analyses and evidence integration for protein characterization.

Authors:

Carol L Ecale Zhou Marisa W Lam Jason R Smith Adam T Zemla Matthew D Dyer Thomas A Kuczmarski Elizabeth A Vitalis Thomas R Slezak

BMC Bioinformatics 2006 Oct 17;7:459. Epub 2006 Oct 17.

Lawrence Livermore National Laboratory, Pathogen Bio-informatics, Livermore, CA, USA.

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October 2006

Antibody elbow angles are influenced by their light chain class.

Authors:

Robyn L Stanfield Adam Zemla Ian A Wilson Bernhard Rupp

J Mol Biol 2006 Apr 25;357(5):1566-74. Epub 2006 Jan 25.

Department of Molecular Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA.

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April 2006

A non-cleavable UmuD variant that acts as a UmuD' mimic.

Authors:

Penny J Beuning Sharotka M Simon Adam Zemla Daniel Barsky Graham C Walker

J Biol Chem 2006 Apr 6;281(14):9633-40. Epub 2006 Feb 6.

Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

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April 2006

Computational approaches for identification of conserved/unique binding pockets in the A chain of ricin.

Authors:

Carol L Ecale Zhou Adam T Zemla Diana Roe Malin Young Marisa Lam Joseph S Schoeniger Rod Balhorn

Bioinformatics 2005 Jul 19;21(14):3089-96. Epub 2005 May 19.

Lawrence Livermore National Laboratory 7000 E. Avenue, Livermore, CA 94550, USA.

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July 2005

The crystal structures of EAP domains from Staphylococcus aureus reveal an unexpected homology to bacterial superantigens.

Authors:

Brian V Geisbrecht Brent Y Hamaoka Benjamin Perman Adam Zemla Daniel J Leahy

J Biol Chem 2005 Apr 3;280(17):17243-50. Epub 2005 Feb 3.

Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.

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April 2005

Mycobacterium tuberculosis RmlC epimerase (Rv3465): a promising drug-target structure in the rhamnose pathway.

Authors:

Katherine A Kantardjieff Chang Yub Kim Cleo Naranjo Geoffry S Waldo Timothy Lekin Brent W Segelke Adam Zemla Min S Park Thomas C Terwilliger Bernhard Rupp

Acta Crystallogr D Biol Crystallogr 2004 May 21;60(Pt 5):895-902. Epub 2004 Apr 21.

Department of Chemistry and Biochemistry and W M Keck Foundation Center for Molecular Structure, California State University Fullerton, Fullerton, CA 92834, USA.

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May 2004