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	1.	Research article 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
	2.	Research article *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
	3.	Research article *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
	4.	Nano Express 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
	5.	Research 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.
	6.	Research 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 \| 1 comment
	7.	Research 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.
	8.	Poster presentation 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
	9.	Poster presentation 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
	10.	Poster presentation 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
	11.	Poster presentation 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
	12.	Oral presentation 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
	13.	Research article 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
	14.	Research article *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
	15.	Methodology article 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
	16.	Research 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
	17.	Oral presentation *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
	18.	Software review 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
	19.	Research article *A comparative genomics perspective on the genetic content of the alkaliphilic haloarchaeon Natrialba magadii* ATCC 43099^T** Shivakumara Siddaramappa, Jean F Challacombe, Rosana E DeCastro, Friedhelm Pfeiffer, Diego E Sastre, María I Giménez, Roberto A Paggi, John C Detter, Karen W Davenport, Lynne A Goodwin, Nikos Kyrpides, Roxanne Tapia, Samuel Pitluck, Susan Lucas, Tanja Woyke, Julie A Maupin-Furlow BMC Genomics 2012, 13:165 (4 May 2012) Abstract \| Full text \| PDF \| PubMed
	20.	Research Timing and source of subtype-C HIV-1 superinfection in the newly infected partner of Zambian couples with disparate viruses Colleen S Kraft, Debby Basu, Paulina A Hawkins, Peter T Hraber, Elwyn Chomba, Joseph Mulenga, William Kilembe, Naw H Khu, Cynthia A Derdeyn, Susan A Allen, Olivier Manigart, Eric Hunter Retrovirology 2012, 9:22 (20 March 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary In this subtype-C discordant couple cohort, superinfection, during the first year after HIV-1 infection of the previously negative partner, occurred at a rate similar to primary infection (13.6% [95% CI 5.2-34.8] vs 7.8% [7.1-8.6]). While limited intra-couple superinfection may in part reflect continued condom usage within couples, this and our lack of detecting newly superinfected individuals after one year of primary infection raises the possibility that immunological resistance to intra-subtype superinfection may develop over time in subtype C infected individuals.
	21.	Research article *A structural model of the E. coli* PhoB Dimer in the transcription initiation complex** Chang-Shung Tung, Benjamin H McMahon BMC Structural Biology 2012, 12:3 (20 March 2012) Abstract \| Full text \| PDF \| PubMed
	22.	Research Definition of the viral targets of protective HIV-1-specific T cell responses Beatriz Mothe, Anuska Llano, Javier Ibarrondo, Marcus Daniels, Cristina Miranda, Jennifer Zamarreño, Vanessa Bach, Rosario Zuniga, Susana Pérez-Álvarez, Christoph T Berger, Maria C Puertas, Javier Martinez-Picado, Morgane Rolland, Marilu Farfan, James J Szinger, William H Hildebrand, Otto O Yang, Victor Sanchez-Merino, Chanson J Brumme, Zabrina L Brumme, David Heckerman, Todd M Allen, James I Mullins, Guadalupe Gómez, Philip J Goulder, Bruce D Walker , Jose M Gatell, Bonaventura Clotet, Bette T Korber, Jorge Sanchez, Christian Brander et al. Journal of Translational Medicine 2011, 9:208 (7 December 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	23.	Research article *Horizontal gene transfer in Histophilus somni* and its role in the evolution of pathogenic strain 2336, as determined by comparative genomic analyses** Shivakumara Siddaramappa, Jean F Challacombe, Alison J Duncan, Allison F Gillaspy, Matthew Carson, Jenny Gipson, Joshua Orvis, Jeremy Zaitshik, Gentry Barnes, David Bruce, Olga Chertkov, J Chris Detter, Cliff S Han, Roxanne Tapia, Linda S Thompson, David W Dyer, Thomas J Inzana BMC Genomics 2011, 12:570 (23 November 2011) Abstract \| Full text \| PDF \| PubMed
	24.	Research article *An attenuated strain of Bacillus anthracis* (CDC 684) has a large chromosomal inversion and altered growth kinetics** Richard T Okinaka, Erin P Price, Spenser R Wolken, Jeffrey M Gruendike, Wai Chung, Talima Pearson, Gary Xie, Chris Munk, Karen K Hill, Jean Challacombe, Bruce E Ivins, James M Schupp, Stephen M Beckstrom-Sternberg, Arthur Friedlander, Paul Keim BMC Genomics 2011, 12:477 (30 September 2011) Abstract \| Full text \| PDF \| PubMed
	25.	Research article Complete genome sequence of the filamentous anoxygenic phototrophic bacterium Chloroflexus aurantiacus Kuo-Hsiang Tang, Kerrie Barry, Olga Chertkov, Eileen Dalin, Cliff S Han, Loren J Hauser, Barbara M Honchak, Lauren E Karbach, Miriam L Land, Alla Lapidus, Frank W Larimer, Natalia Mikhailova, Samuel Pitluck, Beverly K Pierson, Robert E Blankenship BMC Genomics 2011, 12:334 (29 June 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The genome sequence of the filamentous anoxygenic phototrophic bacterium Chloroflexus aurantiacus shows numerous distinctive features that may shine light on the origin and early evolution of photosynthesis.