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ABCC Publications

Ex vivo activation of CD4+ T-cells from donors on suppressive ART can lead to sustained production of infectious HIV-1 from a subset of infected cells

Bui JK, Halvas EK, Fyne E, Sobolewski MD, Koontz D, Shao W, Luke B, Hong FF, Kearney MF, Mellors JW
Published: 02/01/2017

Somatic Genomics and Clinical Features of Lung Adenocarcinoma: A Retrospective Study

Shi J, Hua X, Zhu B, Ravichandran S, Wang M, Nguyen C, Brodie SA, Palleschi A, Alloisio M, Pariscenti G, Jones K, Zhou W, Bouk AJ, Boland J, Hicks B, Risch A, Bennett H, Luke BT, Song L, Duan J, Liu P, Kohno T, Chen Q, Meerzaman D, Marconett C, Laird-Offringa I, Mills I, Caporaso NE, Gail MH, Pesatori AC, Consonni D, Bertazzi PA, Chanock SJ, Landi MT
Published: 12/01/2016

Ultrasensitive single-genome sequencing: accurate, targeted, next generation sequencing of HIV-1 RNA

Boltz VF, Rausch J, Shao W, Hattori J, Luke B, Maldarelli F, Mellors JW, Kearney MF, Coffin JM
Published: 12/01/2016

Whole exome sequencing in families with CLL detects a variant in Integrin ? 2 associated with disease susceptibility

Lynn R. Goldin, Mary L. McMaster, Melissa Rotunno, Sarah E. M. Herman, Kristine Jones, Bin Zhu, Joseph Boland, Laurie Burdett, Belynda Hicks, Sarangan Ravichandran, Brian T. Luke, Meredith Yeager, Laura Fontaine, Alisa M. Goldstein, Stephen J. Chanock, Margaret A. Tucker, Adrian Wiestner, Gerald Martiand Neil E. Caporaso
Published: 11/01/2016

Comparative proteomics of a model MCF10A-KRasG12V cell line reveals a distinct molecular signature of the KRasG12V cell surface

Ye X, Chan KC, Waters AM, Bess M, Harned A, Wei BR, Loncarek J, Luke BT, Orsburn BC, Hollinger BD, Stephens RM, Bagni R, Martinko A, Wells JA, Nissley DV, McCormick F, Whiteley G, Blonder J
Published: 11/01/2016

The NIH Protein Capture Reagents Program (PCRP): a standardized protein affinity reagent toolbox

Blackshaw S, Venkataraman A, Irizarry J, Yang K, Anderson S, Campbell E, Gatlin CL, Freeman NL, Basavappa R, Stewart R, Loss MA, Pino I, Zhu H, Bader JS
Published: 09/01/2016

Identification of extracellular miRNA in archived serum samples by next-generation sequencing from RNA extracted using multiple methods

Gautam A, Kumar R, Dimitrov G, Hoke A, Hammamieh R, Jett M
Published: 08/01/2016

Retrovirus Integration Database (RID): a public database for retroviral insertion sites into host genomes

Shao W, Shan J, Kearney MF, Wu X, Maldarelli F, Mellors JW, Luke B, Coffin JM, Hughes SH.
Published: 07/01/2016

APOBEC3 proteins can copackage and comutate HIV-1 genomes

Desimmie BA, Burdick RC, Izumi T, Doi H, Shao W, Alvord WG, Sato K, Koyanagi Y, Jones S, Wilson E, Hill S, Maldarelli F, Hu WS, Pathak VK
Published: 07/01/2016

Whole exome sequencing in families at high risk for Hodgkin lymphoma: identification of a predisposing mutation in the KDR gene

Rotunno M, McMaster ML, Boland J, Bass S, Zhang X, Burdett L, Hicks B, Ravichandran S, Luke BT, Yeager M, Fontaine L, Hyland PL, Goldstein AM, NCI DCEG Cancer Sequencing Working Group., NCI DCEG Cancer Genomics Research Laboratory., Chanock SJ, Caporaso NE, Tucker MA, Goldin LR
Published: 07/01/2016

The C/EBP? protein is stabilized by estrogen receptor ? activity, inhibits SNAI2 expression and associates with good prognosis in breast cancer

Mendoza-Villanueva D, Balamurugan K, Ali HR, Kim SR, Sharan S, Johnson RC, Merchant AS, Caldas C, Landberg G, Sterneck E
Published: 05/01/2016

GTF2E2 Mutations Destabilize the General Transcription Factor Complex TFIIE in Individuals with DNA Repair-Proficient Trichothiodystrophy

Kuschal C, Botta E, Orioli D, Digiovanna JJ, Seneca S, Keymolen K, Tamura D, Heller E, Khan SG, Caligiuri G, Lanzafame M, Nardo T, Ricotti R, Peverali FA, Stephens R, Zhao Y, Lehmann AR, Baranello L, Levens D, Kraemer KH, Stefanini M
Published: 04/07/2016

The transition from the open minimum to the ring minimum on the ground state and on the lowest excited state of like symmetry in ozone: A configuration interaction study

Theis D, Ivanic J, Windus TL, Ruedenberg K
Published: 03/01/2016

Identification of IL-23p19 as an endothelial proinflammatory peptide that promotes gp130-STAT3 signaling

Espígol-Frigolé G, Planas-Rigol E, Ohnuki H, Salvucci O, Kwak H, Ravichandran S, Luke B, Cid MC, Tosato G
Published: 03/01/2016

Clonally expanded CD4+ T cells can produce infectious HIV-1 in vivo

Simonetti FR, Sobolewski MD, Fyne E, Shao W, Spindler J, Hattori J, Anderson EM, Watters SA, Hill S, Wu X, Wells D, Su L, Luke B, Halvas EK, Besson G, Penrose KJ, Yang Z, Kwan RW, Van Waes C, Uldrick T, Citrin D, Kovacs J, Polis M, Rehm C, Gorelick R, Piatak M Jr, Keele B, Kearney MF, Coffin JM, Hughes SH, Mellors JW, Maldarelli F
Published: 02/01/2016

Infrared Spectroscopy and Structure of (NO)n Clusters

Hoshina H, Slipchenko M, Prozument K, Verma D, Schmidt MW, Ivanic J, Vilesov AF
Published: 02/01/2016

Towards Better Precision Medicine: PacBio Single-Molecule Long Reads Resolve the Interpretation of HIV Drug Resistant Mutation Profiles at Explicit Quasispecies (Haplotype) Level

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
Published: 01/01/2016

Distinguishing highly similar gene isoforms with a clustering-based bioinformatics analysis of PacBio single-molecule long reads

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 da W
Published: 01/01/2016

Deep sequencing of HPV16 genomes: A new high-throughput tool for exploring the carcinogenicity and natural history of HPV16 infection

Michael Cullen, JosephF.Boland, Mark Schiffman, Xijun Zhang, Nicolas Wentzensen,Qi Yang, Zigui Chen, Kai Yu , Jason Mitchell, David Roberson, Sara Bass, Laurie Burdette,Moara Machado , Sarangan Ravichandran , Luke BT , Mitchell J. Machiela, MarkAndersen,Matt Osentoski , Michael Laptewicz , Sholom Wacholder , Ashlie Feldman,  Tina Raine-Bennett,Thomas Lorey , Philip E.Castle , Meredith Yeager , Robert D.Burk, Lisa Mirabello
Published: 12/01/2015

Whole-exome sequencing reveals a C-terminal germline variant in CEBPA-associated acute myeloid leukemia: 45-year follow-up of a large family

Pathak A, Seipel K, Pemov A, Dewan R, Brown C, Ravichandran S, Luke BT, Malasky M, Suman S, Yeager M, Cancer Genomics Research Laboratory ND, Cancer Sequencing Working Group ND, Parry DM, Gatti RA, Caporaso NE, Mulvihill J, Goldin LR, Pabst T, McMaster ML, Stewart DR
Published: 12/01/2015

Elevated plasma viral loads in romidespin treated SIV-infected rhesus macaques on suppressive combination antiretroviral therapy

Del Prete GQ, Oswald K, Lara A, Shoemaker R, Smedley J, Macallister R, Coalter V, Wiles A, Wiles R, Li Y, Fast R, Kiser R, Lu B, Zheng J, Alvord WG, Trubey CM, Piatak M Jr, Deleage C, Keele BF, Estes JD, Hesselgesser J, Geleziunas R, Lifson JD
Published: 12/01/2015

LEDGF/p75 interacts with mRNA splicing factors and targets HIV-1 integration to highly spliced genes

Singh PK, Plumb MR, Ferris AL, Iben JR, Wu X, Fadel HJ, Luke BT, Esnault C, Poeschla EM, Hughes SH, Kvaratskhelia M, Levin HL
Published: 11/01/2015

Reactive Species Involved in the Regioselective Photooxidation of Heptamethine Cyanines

Nani RR, Kelley JA, Ivanic J, Schnermann MJ
Published: 11/01/2015

Histone H3 Lysine 27 demethylases Jmjd3 and Utx are required for T-cell differentiation

Sugata Manna, Jong Kyong Kim, Catherine Baugé, Margaret Cam, Yongmei Zhao, Jyoti Shetty, Melanie S. Vacchio, Ehydel Castro, Bao Tran, Lino Tessarollo & Rémy Bosselut
Published: 09/02/2015

The Proto-oncogene Transcription Factor Ets1 Regulates Neural Crest Development through Histone Deacetylase 1 to Mediate Output of Bone Morphogenetic Protein Signaling

Wang C, Kam RK, Shi W, Xia Y, Chen X, Cao Y, Sun J, Du Y, Lu G, Chen Z, Chan WY, Chan SO, Deng Y, Zhao H
Published: 09/01/2015

The Somatic Autosomal Mutation Matrix in Cancer Genomes

Temiz NA, Donohue DE, Albino Bacolla, Karen M. Vasquez, David N. Cooper, Mudunuri U, Ivanic J, Cer RZ, Yi M, Stephens RM, Collins JR, Luke BT
Published: 08/01/2015

AVIA v2.0: annotation, visualization and impact analysis of genomic variants and genes

Vuong H, Che A, Ravichandran S, Luke BT, Collins JR, Mudunuri US
Published: 08/01/2015

Juvenile myelomonocytic leukemia due to a germline CBL Y371C mutation: 35?year follow?up of a large family,

Pathak A, Pemov A, McMaster ML, Dewan R, Ravichandran S, Pak E, Dutra A, Lee HJ, Vogt A, Zhang X, Yeager M, Anderson S, Kirby M; NCI DCEG Cancer Genomics Research Laboratory; NCI DCEG Cancer Sequencing Working Group, Caporaso N,Greene MH, Goldin LR, Stewart DR.
Published: 07/01/2015

APOL1 toxin, innate immunity, and kidney injury

Limou S, Dummer PD, Nelson GW, Kopp JB, Winkler CA
Published: 07/01/2015

Can structural features of kinase receptors provide clues on selectivity and inhibition? A molecular modeling study

Ravichandran S, Luke BT, Collins JR
Published: 04/01/2015

Acute and Chronic Plasma Metabolomic and Liver Transcriptomic Stress Effects in a Mouse Model with Features of Post-Traumatic Stress Disorder

Gautam A, D'Arpa P, Donohue DE, Muhie S, Chakraborty N, Luke BT, Grapov D, Carroll EE, Meyerhoff JL, Hammamieh R, Jett M
Published: 01/01/2015

BCL11A is a triple-negative breast cancer gene with critical functions in stem and progenitor cells

Khaled WT, Choon Lee S, Stingl J, Chen X, Raza Ali H, Rueda OM, Hadi F, Wang J, Yu Y, Chin SF, Stratton M, Futreal A, Jenkins NA, Aparicio S, Copeland NG, Watson CJ, Caldas C, Liu P
Published: 01/01/2015

Specific HIV integration sites are linked to clonal expansion and persistence of infected cells

Maldarelli F, Wu X, Su L, Simonetti FR, Shao W, Hill S, Spindler J, Ferris AL, Mellors JW, Kearney MF, Coffin JM, Hughes SH
Published: 07/11/2014

PAPNC, a novel method to calculate nucleotide diversity from large scale next generation sequencing data

Shao W, Kearney MF, Boltz VF, Spindler JE, Mellors JW, Maldarelli F, Coffin JM.
Published: 07/01/2014

An Example of Genetically Distinct HIV Type 1 Variants in Cerebrospinal Fluid and Plasma During Suppressive Therapy

Dahl V, Gisslen M, Hagberg L, Peterson J, Shao W, Spudich S, Price RW, Palmer S
Published: 05/01/2014

Rare missense variants in POT1 predispose to familial cutaneous malignant melanoma

Shi J, Yang XR, Ballew B, Rotunno M, Calista D, Fargnoli MC, Ghiorzo P, Bressac-de Paillerets B, Nagore E, Avril MF, Caporaso NE, McMaster ML, Cullen M, Wang Z, Zhang X, NCI DCEG Cancer Sequencing Working Group, NCI DCEG Cancer Genomics Research Laboratory, French Familial Melanoma Study Group, Bruno W, Pastorino L, Queirolo P, Banuls-Roca J, Garcia-Casado Z, Vaysse A, Mohamdi H, Riazalhosseini Y, Foglio M, Jouenne F, Hua X, Hyland PL, Yin J, Vallabhaneni H, Chai W, Minghetti P, Pellegrini C, Ravichandran S, Eggermont A, Lathrop M, Peris K, Scarra GB, Landi G, Savage SA, Sampson JN, He J, Yeager M, Goldin LR, Demenais F, Chanock SJ, Tucker MA, Goldstein AM, Liu Y, Landi MT
Published: 05/01/2014

Aminolysis of an N-diazeniumdiolated amidine as an approach to diazeniumdiolated ammonia

Biswas D, Hrabie JA, Saavedra JE, Cao Z, Keefer LK, Ivanic J, Holland RJ
Published: 05/01/2014

Covalent bonds are created by the drive of electron waves to lower their kinetic energy through expansion

Schmidt MW, Ivanic J, Ruedenberg K
Published: 05/01/2014

Mutations in HIV-1 RT affect the errors made in a single cycle of viral replication

Abram ME, Ferris AL, Das K, Quinoñes O, Shao W, Tuske S, Alvord WG, Arnold E, Hughes SH
Published: 04/23/2014

Pharmacophore model of the quercetin binding site of the SIRT6 protein

Ravichandran S, Singh N, Donnelly D, Migliore M, Johnson P, Fishwick C, Luke BT, Martin B, Maudsley S, Fugmann SD, Moaddel R
Published: 04/01/2014

Lack of detectable HIV-1 molecular evolution during suppressive antiretroviral therapy

Kearney MF, Spindler J, Shao W, Yu S, Anderson EM, O'Shea A, Rehm C, Poethke C, Kovacs N, Mellors JW, Coffin JM, Maldarelli F
Published: 03/01/2014

The identification of a novel SIRT6 modulator from Trigonella foenum-graecum using ligand fishing with protein coated magnetic beads

Singh N, Ravichandran S, Spelman K, Fugmann SD, Moaddel R
Published: 03/01/2014

The HIV-1 reservoir in eight patients on long-term suppressive antiretroviral therapy is stable with few genetic changes over time

Josefsson L, von Stockenstrom S, Faria NR, Sinclair E, Bacchetti P, Killian M, Epling L, Tan A, Ho T, Lemey P, Shao W, Hunt PW, Somsouk M, Wylie W, Douek DC, Loeb L, Custer J, Hoh R, Poole L, Deeks SG, Hecht F, Palmer S
Published: 12/01/2013

Homology-mediated end-capping as a primary step of sister chromatid fusion in the breakage-fusion-bridge cycles

Marotta M, Chen X, Watanabe T, Faber PW, Diede SJ, Tapscott S, Tubbs R, Kondratova A, Stephens R, Tanaka H
Published: 11/01/2013

HIV populations are large and accumulate high genetic diversity in a nonlinear fashion

Maldarelli F, Kearney M, Palmer S, Stephens R, Mican J, Polis MA, Davey RT, Kovacs J, Shao W, Rock-Kress D, Metcalf JA, Rehm C, Greer SE, Lucey DL, Danley K, Alter H, Mellors JW, Coffin JM
Published: 09/01/2013

Evaluation of sequence ambiguities of the HIV-1 pol gene as a method to identify recent HIV-1 infection in transmitted drug resistance surveys

Andersson E, Shao W, Bontell I, Cham F, Cuong do D, Wondwossen A, Morris L, Hunt G, Sönnerborg A, Bertagnolio S, Maldarelli F, Jordan MR
Published: 08/01/2013

Decoding nitric oxide release rates of amine-based diazeniumdiolates

Wang YN, Collins J, Holland RJ, Keefer LK, Ivanic J
Published: 08/01/2013

Synthesis and characterization of a SIRT6 open tubular column: predicting deacetylation activity using frontal chromatography

Singh N, Ravichandran S, Norton DD, Fugmann SD, Moaddel R
Published: 05/01/2013

Analysis of 454 sequencing error rate, error sources, and artifact recombination for detection of Low-frequency drug resistance mutations in HIV-1 DNA

Shao W, Boltz VF, Spindler JE, Kearney MF, Maldarelli F, Mellors JW, Stewart C, Volfovsky N, Levitsky A, Stephens RM, Coffin JM
Published: 02/01/2013

Knowledge and theme discovery across very large biological data sets using distributed queries: a prototype combining unstructured and structured data

Mudunuri US, Khouja M, Repetski S, Venkataraman G, Che A, Luke BT, Girard FP, Stephens RM
Published: 01/01/2013

Guanine holes are prominent targets for mutation in cancer and inherited disease

Bacolla A, Temiz NA, Yi M, Ivanic J, Cer RZ, Donohue DE, Ball EV, Mudunuri US, Wang G, Jain A, Volfovsky N, Luke BT, Stephens RM, Cooper DN, Collins JR, Vasquez KM
Published: 01/01/2013

Non-B DB v2.0: a database of predicted non-B DNA-forming motifs and its associated tools

Cer RZ, Donohue DE, Mudunuri US, Temiz NA, Loss MA, Starner NJ, Halusa GN, Volfovsky N, Yi M, Luke BT, Bacolla A, Collins JR, Stephens RM
Published: 01/01/2013

Trypsin-mediated 18O/16O labeling for biomarker discovery

Ye X, Chan KC, Prieto DA, Luke BT, Johann DJ Jr, Stockwin LH, Newton DL, Blonder J
Published: 01/01/2013

Single cell analysis of lymph node tissue from HIV-1 infected patients reveals that the majority of CD4+ T-cells contain one HIV-1 DNA molecule

Josefsson L, Palmer S, Faria NR, Lemey P, Casazza J, Ambrozak D, Kearney M, Shao W, Kottilil S, Sneller M, Mellors J, Coffin JM, Maldarelli F
Published: 01/01/2013

High-level theoretical study of the NO dimer and tetramer: has the tetramer been observed?

Ivanic J, Schmidt MW, Luke B
Published: 12/01/2012

Ultrasensitive allele-specific PCR reveals rare preexisting drug-resistant variants and a large replicating virus population in macaques infected with a simian immunodeficiency virus containing human immunodeficiency virus reverse transcriptase

Boltz VF, Ambrose Z, Kearney MF, Shao W, Kewalramani VN, Maldarelli F, Mellors JW, Coffin JM
Published: 12/01/2012

Bcl11a is essential for lymphoid development and negatively regulates p53

Yu Y, Wang J, Khaled W, Burke S, Li P, Chen X, Yang W, Jenkins NA, Copeland NG, Zhang S, Liu P
Published: 12/01/2012

A molecular model of the enantioselective liquid chromatographic separation of (R,S)-ifosfamide and its N-dechloroethylated metabolites on a teicoplanin aglycon chiral stationary phase

Ravichandran S, Collins JR, Singh N, W Wainer I
Published: 12/01/2012

Efficient targeted gene disruption in Xenopus embryos using engineered transcription activator-like effector nucleases (TALENs)

Lei Y, Guo X, Liu Y, Cao Y, Deng Y, Chen X, Cheng CH, Dawid IB, Chen Y, Zhao H
Published: 10/01/2012

Hematopoietic precursor cells isolated from patients on long-term suppressive HIV therapy did not contain HIV-1 DNA

Josefsson L, Eriksson S, Sinclair E, Ho T, Killian M, Epling L, Shao W, Lewis B, Bacchetti P, Loeb L, Custer J, Poole L, Hecht FM, Palmer S
Published: 07/01/2012

Setbp1 promotes the self-renewal of murine myeloid progenitors via activation of Hoxa9 and Hoxa10

Oakley K, Han Y, Vishwakarma BA, Chu S, Bhatia R, Gudmundsson KO, Keller J, Chen X, Vasko V, Jenkins NA, Copeland NG, Du Y
Published: 06/01/2012

Proteomic profiling of H-Ras-G12V induced hypertrophic cardiomyopathy in transgenic mice using comparative LC-MS analysis of thin fresh-frozen tissue sections

Wei BR, Simpson RM, Johann DJ, Dwyer JE, Prieto DA, Kumar M, Ye X, Luke B, Shive HR, Webster JD, Hoover SB, Veenstra TD, Blonder J
Published: 03/01/2012

The role of methylation in the intrinsic dynamics of B- and Z-DNA

Temiz NA, Donohue DE, Bacolla A, Luke BT, Collins JR
Published: 01/01/2012

Post-digestion ¹?O exchange/labeling for quantitative shotgun proteomics of membrane proteins

Ye X, Luke BT, Johann DJ Jr, Chan KC, Prieto DA, Ono A, Veenstra TD, Blonder J
Published: 01/01/2012

Multiple sources of contamination in samples from patients reported to have XMRV infection

Kearney MF, Spindler J, Wiegand A, Shao W, Anderson EM, Maldarelli F, Ruscetti FW, Mellors JW, Hughes SH, Le Grice SF, Coffin JM
Published: 01/01/2012

Rapid and efficient reprogramming of somatic cells to induced pluripotent stem cells by retinoic acid receptor gamma and liver receptor homolog 1

Wang W, Yang J, Liu H, Lu D, Chen X, Zenonos Z, Campos LS, Rad R, Guo G, Zhang S, Bradley A, Liu P
Published: 11/01/2011

Single genome sequencing of HIV-1 gag and protease resistance mutations at virologic failure during the OK04 trial of simplified versus standard maintenance therapy

McKinnon JE, Delgado R, Pulido F, Shao W, Arribas JR, Mellors JW
Published: 01/01/2011

Reprogramming of T cells to natural killer-like cells upon Bcl11b deletion

Li P, Burke S, Wang J, Chen X, Ortiz M, Lee SC, Lu D, Campos L, Goulding D, Ng BL, Dougan G, Huntly B, Gottgens B, Jenkins NA, Copeland NG, Colucci F, Liu P
Published: 07/01/2010