1.
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.
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.
φ X216, 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.
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.
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.
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 |
7.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
A comparative genomics perspective on the genetic content of the alkaliphilic haloarchaeon Natrialba magadii ATCC 43099T
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.
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.
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.
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.
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.
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.
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.