Selective Bibliography of Bao Tran
Sequencing Facility, NCI

"New Advancements in Next-Generation Sequencing Approaches Address a Variety of Biological Questions"
Wednesday, December 20, 2017

1.  Ma L, Chen Z, Huang da W, Kutty G, Ishihara M, Wang H, Abouelleil A, Bishop L, Davey E, Deng R, Deng X, Fan L, Fantoni G, Fitzgerald M, Gogineni E, Goldberg JM, Handley G, Hu X, Huber C, Jiao X, Jones K, Levin JZ, Liu Y, Macdonald P, Melnikov A, Raley C, Sassi M, Sherman BT, Song X, Sykes S, Tran B, Walsh L, Xia Y, Yang J, Young S, Zeng Q, Zheng X, Stephens R, Nusbaum C, Birren BW, Azadi P, Lempicki RA, Cuomo CA, Kovacs JA
Genome analysis of three Pneumocystis species reveals adaptation mechanisms to life exclusively in mammalian hosts
Nature Communications 7:10740 Feb 22 2016

2.  Huang DW, Raley C, Jiang MK, Zheng X, Liang D, Rehman MT, Highbarger HC, Jiao X, Sherman B, Ma L, Chen X, Skelly T, Troyer J, Stephens R, Imamichi T, Pau A, Lempicki RA, Tran B, Nissley D, Lane HC, Dewar RL
Towards Better Precision Medicine: PacBio Single-Molecule Long Reads Resolve the Interpretation of HIV Drug Resistant Mutation Profiles at Explicit Quasispecies (Haplotype) Level
Journal of Data Mining in Genomics & Proteomics 7 (1):182 Jan 2016

3.  Liang M, Raley C, Zheng X, Kutty G, Gogineni E, Sherman BT, Sun Q, Chen X, Skelly T, Jones K, Stephens R, Zhou B, Lau W, Johnson C, Imamichi T, Jiang M, Dewar R, Lempicki RA, Tran B, Kovacs JA, Huang DW
Distinguishing highly similar gene isoforms with a clustering-based bioinformatics analysis of PacBio single-molecule long reads
BioData Mining 9:13 2016

4.  Manna S, Kim JK, Bauge C, Cam M, Zhao Y, Shetty J, Vacchio MS, Castro E, Tran B, Tessarollo L, Bosselut R
Histone H3 Lysine 27 demethylases Jmjd3 and Utx are required for T-cell differentiation
Nature Communications 6:8152 Sep 02 2015

5.  Yu W, McIntosh C, Lister R, Zhu I, Han Y, Ren J, Landsman D, Lee E, Briones V, Terashima M, Leighty R, Ecker JR, Muegge K
Genome-wide DNA methylation patterns in LSH mutant reveals de-repression of repeat elements and redundant epigenetic silencing pathways
Genome Research 24 (10):1613-23 Oct 2014

6.  Jiao X, Zheng X, Ma L, Kutty G, Gogineni E, Sun Q, Sherman BT, Hu X, Jones K, Raley C, Tran B, Munroe DJ, Stephens R, Liang D, Imamichi T, Kovacs JA, Lempicki RA, Huang DW
A Benchmark Study on Error Assessment and Quality Control of CCS Reads Derived from the PacBio RS
Journal of Data Mining in Genomics & Proteomics 4 (3):Jul 31 2013

7.  Shaw AK, Halpern AL, Beeson K, Tran B, Venter JC, Martiny JB
It's all relative: ranking the diversity of aquatic bacterial communities
Environmental Microbiology 10 (9):2200-10 Sep 2008

8.  Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, Yooseph S, Wu D, Eisen JA, Hoffman JM, Remington K, Beeson K, Tran B, Smith H, Baden-Tillson H, Stewart C, Thorpe J, Freeman J, Andrews-Pfannkoch C, Venter JE, Li K, Kravitz S, Heidelberg JF, Utterback T, Rogers YH, Falcon LI, Souza V, Bonilla-Rosso G, Eguiarte LE, Karl DM, Sathyendranath S, Platt T, Bermingham E, Gallardo V, Tamayo-Castillo G, Ferrari MR, Strausberg RL, Nealson K, Friedman R, Frazier M, Venter JC
The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific
PLoS Biology 5 (3):e77 Mar 2007

9.  Nelson KE, Fouts DE, Mongodin EF, Ravel J, DeBoy RT, Kolonay JF, Rasko DA, Angiuoli SV, Gill SR, Paulsen IT, Peterson J, White O, Nelson WC, Nierman W, Beanan MJ, Brinkac LM, Daugherty SC, Dodson RJ, Durkin AS, Madupu R, Haft DH, Selengut J, Van Aken S, Khouri H, Fedorova N, Forberger H, Tran B, Kathariou S, Wonderling LD, Uhlich GA, Bayles DO, Luchansky JB, Fraser CM
Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this species
Nucleic Acids Research 32 (8):2386-95 2004

10.  Buell CR, Joardar V, Lindeberg M, Selengut J, Paulsen IT, Gwinn ML, Dodson RJ, Deboy RT, Durkin AS, Kolonay JF, Madupu R, Daugherty S, Brinkac L, Beanan MJ, Haft DH, Nelson WC, Davidsen T, Zafar N, Zhou L, Liu J, Yuan Q, Khouri H, Fedorova N, Tran B, Russell D, Berry K, Utterback T, Van Aken SE, Feldblyum TV, D'Ascenzo M, Deng WL, Ramos AR, Alfano JR, Cartinhour S, Chatterjee AK, Delaney TP, Lazarowitz SG, Martin GB, Schneider DJ, Tang X, Bender CL, White O, Fraser CM, Collmer A
The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000
Proceedings of the National Academy of Sciences of the United States of America 100 (18):10181-6 Sep 02 2003

created 11/20/17