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Work published with BioMed Central, Chemistry Central and SpringerOpen by researchers at Los Alamos National Laboratory

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1.

Research article   Open Access

Transcriptome profiling reveals links between ParS/ParR, MexEF-OprN, and quorum sensing in the regulation of adaptation and virulence in Pseudomonas aeruginosa

Dongping Wang, Candace Seeve, Leland S Pierson, Elizabeth A Pierson BMC Genomics 2013, 14:618 (13 September 2013)

Abstract | Full text | PDF | PubMed

2.

Review   Open Access Highly Accessed

Modeling the within-host dynamics of HIV infection

Alan S Perelson, Ruy M Ribeiro BMC Biology 2013, 11:96 (3 September 2013)

Abstract | Full text | PDF | PubMed |  Editor’s summary

Alan Perelson and Ruy Ribeiro explain how differential equations that model the dynamics of HIV replication in its human host have led to important quantitative insights into the biology of HIV infection.

3.

Software   Open Access Highly Accessed

A multiple-alignment based primer design algorithm for genetically highly variable DNA targets

Johanna Brodin, Mohan Krishnamoorthy, Gayathri Athreya, Will Fischer, Peter Hraber, Cheryl Gleasner, Lance Green, Bette Korber, Thomas Leitner BMC Bioinformatics 2013, 14:255 (21 August 2013)

Abstract | Full text | PDF | PubMed

4.

Research   Open Access

Novel microstructure quantification framework for databasing, visualization, and analysis of microstructure data

Stephen R Niezgoda, Anand K Kanjarla, Surya R Kalidindi Integrating Materials and Manufacturing Innovation 2013, 2:3 (2 July 2013)

Abstract | Full text | PDF

5.

Methodology   Open Access

Elastomeric microparticles for acoustic mediated bioseparations

Leah M Johnson, Lu Gao, C Shields IV, Margret Smith, Kirill Efimenko, Kevin Cushing, Jan Genzer, Gabriel P López Journal of Nanobiotechnology 2013, 11:22 (28 June 2013)

Abstract | Full text | PDF | PubMed

6.

Research   Open Access

Ammonia-oxidizing archaea and bacteria are structured by geography in biological soil crusts across North American arid lands

Yevgeniy Marusenko, Scott T Bates, Ian Anderson, Shannon L Johnson, Tanya Soule, Ferran Garcia-Pichel Ecological Processes 2013, 2:9 (26 April 2013)

Abstract | Full text | PDF

7.

Research   Open Access Highly Accessed

Dynamic electrophoretic fingerprinting of the HIV-1 envelope glycoprotein

Daniel J Stieh, Joshua L Phillips, Paul M Rogers, Deborah F King, Gianguido C Cianci, Simon A Jeffs, Sandrasegaram Gnanakaran, Robin J Shattock Retrovirology 2013, 10:33 (20 March 2013)

Abstract | Full text | PDF | PubMed

8.

Research article   Open Access Highly Accessed

Draft genome sequence of the rubber tree Hevea brasiliensis

Ahmad Yamin Abdul Rahman, Abhilash O Usharraj, Biswapriya B Misra, Gincy P Thottathil, Kandakumar Jayasekaran, Yun Feng, Shaobin Hou, Su Yean Ong, Fui Ling Ng, Ling Sze Lee, Hock Siew Tan, Muhd Khairul Luqman Muhd Sakaff, Beng Soon Teh, Bee Khoo, Siti Suriawati Badai, Nurohaida Ab Aziz, Anton Yuryev, Bjarne Knudsen, Alexandre Dionne-Laporte, Nokuthula P Mchunu, Qingyi Yu, Brennick J Langston, Tracey Allen K Freitas, Aaron G Young, Rui Chen, Lei Wang, Nazalan Najimudin, Jennifer A Saito, Maqsudul Alam BMC Genomics 2013, 14:75 (2 February 2013)

Abstract | Full text | PDF | PubMed |  Editor’s summary

The draft genome of the rubber tree Hevea brasiliensis is almost 80% repetitive DNA with 12.7% of genes models identified being unique to this species, including key rubber biosynthesis and disease resistance genes

9.

Research article   Open Access

The genome of Pelobacter carbinolicus reveals surprising metabolic capabilities and physiological features

Muktak Aklujkar, Shelley A Haveman, Raymond DiDonato, Olga Chertkov, Cliff S Han, Miriam L Land, Peter Brown, Derek R Lovley BMC Genomics 2012, 13:690 (10 December 2012)

Abstract | Full text | PDF | PubMed

10.

Research article   Open Access

φX216, a P2-like bacteriophage with broad Burkholderia pseudomallei and B. mallei strain infectivity

Brian H Kvitko, Christopher R Cox, David DeShazer, Shannon L Johnson, Kent J Voorhees, Herbert P Schweizer BMC Microbiology 2012, 12:289 (7 December 2012)

Abstract | Full text | PDF | PubMed

11.

Nano Express   Open Access

Tuning of defects in ZnO nanorod arrays used in bulk heterojunction solar cells

Diana C Iza, David Muñoz-Rojas, Quanxi Jia, Brian Swartzentruber, Judith L MacManus-Driscoll Nanoscale Research Letters 2012, 7:655 (27 November 2012)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

12.

Research   Open Access Highly Accessed

Impact of immune escape mutations on HIV-1 fitness in the context of the cognate transmitted/founder genome

Hongshuo Song, Jeffrey W Pavlicek, Fangping Cai, Tanmoy Bhattacharya, Hui Li, Shilpa S Iyer, Katharine J Bar, Julie M Decker, Nilu Goonetilleke, Michael KP Liu, Anna Berg, Bhavna Hora, Mark S Drinker, Josh Eudailey, Joy Pickeral, M Moody, Guido Ferrari, Andrew McMichael, Alan S Perelson, George M Shaw, Beatrice H Hahn, Barton F Haynes, Feng Gao Retrovirology 2012, 9:89 (30 October 2012)

Abstract | Full text | PDF | PubMed |  Editor’s summary

This paper reveals a broad spectrum of fitness costs to CTL escape mutations in HIV-1l genomes, similar to recent findings reported for neutralizing antibody escape mutations. The findings highlight the extraordinary plasticity and adaptive potential of the HIV-1 genome.

13.

Research   Open Access

Literature mining of protein-residue associations with graph rules learned through distant supervision

KE Ravikumar, Haibin Liu, Judith D Cohn, Michael E Wall, Karin Verspoor Journal of Biomedical Semantics 2012, 3(Suppl 3):S2 (5 October 2012)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central | 1 comment

14.

Research   Open Access Highly Accessed

HIV-1 subtype C superinfected individuals mount low autologous neutralizing antibody responses prior to intrasubtype superinfection

Debby Basu, Colleen S Kraft, Megan K Murphy, Patricia J Campbell, Tianwei Yu, Peter T Hraber, Carmela Irene, Abraham Pinter, Elwyn Chomba, Joseph Mulenga, William Kilembe, Susan A Allen, Cynthia A Derdeyn, Eric Hunter Retrovirology 2012, 9:76 (20 September 2012)

Abstract | Full text | PDF | PubMed |  Editor’s summary

This work suggests that the lack of development of IgG antibodies, as reflected in autologous NAbs as well as gp120 and V1V2 binding antibodies to the primary infection virus, combined with potentially competing, non-protective IgA antibodies, may increase susceptibility to superinfection in the context of settings where a single HIV-1 subtype predominates.

15.

Poster presentation   Open Access

Stability and neutralization capacity of a novel mosaic HIV-1 gp140 trimer in a guinea pig model

JP Nkolola, JM Kovacs, B Korber, B Chen, M Seaman, D Barouch Retrovirology 2012, 9(Suppl 2):P299 (13 September 2012)

Full text | PDF

16.

Poster presentation   Open Access

Comparison of the depth of vaccine-elicited HIV-1 Env epitope-specific CD8+ T lymphocyte responses

SL Hulot, BT Korber, G Pantaleo, J Tartaglia, B Jacobs, B Perdiguero, CE Gomez, M Esteban, N Letvin, MS Seaman, B Haynes, S Santra Retrovirology 2012, 9(Suppl 2):P288 (13 September 2012)

Full text | PDF

17.

Poster presentation   Open Access

Intrasubtype C superinfected individuals mount delayed and low-titer autologous neutralizing antibody responses prior to superinfection

D Basu, C Kraft, P Campbell, M Murphy, T Yu, P Hraber, E Chomba, J Mulenga, W Kilembe, S Allen, C Derdeyn, E Hunter Retrovirology 2012, 9(Suppl 2):P159 (13 September 2012)

Full text | PDF

18.

Poster presentation   Open Access

Sequential exposure to specific antibody escape mutations may program neutralization breadth during subtype A HIV-1 infection

MK Murphy, L Yue, R Pan, S Boliar, A Sethi, E Karita, SA Allen, E Cormier, JE Robinson, S Gnanakaran, E Hunter, X Kong, CA Derdeyn Retrovirology 2012, 9(Suppl 2):P104 (13 September 2012)

Full text | PDF

19.

Oral presentation   Open Access

Full-length HIV-1 immunogens induce greater T lymphocyte responses to conserved epitopes than conserved-region-only HIV-1 immunogens in monkeys

KE Stephenson, A SanMiguel, NL Simmons, K Smith, JJ Szinger, BT Korber, DH Barouch Retrovirology 2012, 9(Suppl 2):O70 (13 September 2012)

Full text | PDF

20.

Research article   Open Access Highly Accessed

Rapid phylogenetic and functional classification of short genomic fragments with signature peptides

Joel Berendzen, William J Bruno, Judith D Cohn, Nicolas W Hengartner, Cheryl R Kuske, Benjamin H McMahon, Murray A Wolinsky, Gary Xie BMC Research Notes 2012, 5:460 (28 August 2012)

Abstract | Full text | PDF | PubMed

21.

Research article   Open Access

Genetic diversity within the genus Francisella as revealed by comparative analyses of the genomes of two North American isolates from environmental sources

Shivakumara Siddaramappa, Jean F Challacombe, Jeannine M Petersen, Segaran Pillai, Cheryl R Kuske BMC Genomics 2012, 13:422 (24 August 2012)

Abstract | Full text | PDF | PubMed

22.

Methodology article   Open Access

Specification, annotation, visualization and simulation of a large rule-based model for ERBB receptor signaling

Matthew S Creamer, Edward C Stites, Meraj Aziz, James A Cahill, Chin Tan, Michael E Berens, Haiyong Han, Kimberley J Bussey, Daniel D Von Hoff, William S Hlavacek, Richard G Posner BMC Systems Biology 2012, 6:107 (22 August 2012)

Abstract | Full text | PDF | PubMed

23.

Research   Open Access

A coarse-grained model for synergistic action of multiple enzymes on cellulose

Andrea Asztalos, Marcus Daniels, Anurag Sethi, Tongye Shen, Paul Langan, Antonio Redondo, Sandrasegaram Gnanakaran Biotechnology for Biofuels 2012, 5:55 (1 August 2012)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

24.

Oral presentation   Open Access

Oxygen dynamics during in vitro seizures

Yina Wei, Ghanim Ullah, Justin Ingram, Steven Schiff BMC Neuroscience 2012, 13(Suppl 1):O20 (16 July 2012)

Full text | PDF

25.

Software review   Open Access Highly Accessed

Automatic Fortran to C++ conversion with FABLE

Ralf W Grosse-Kunstleve, Thomas C Terwilliger, Nicholas K Sauter, Paul D Adams Source Code for Biology and Medicine 2012, 7:5 (28 May 2012)

Abstract | Full text | PDF | PubMed

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