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ABCS Publications

Integration in or near oncogenes plays only a minor role in determining the in vivo distribution of HIV integration sites before or during suppressive antiretroviral therapy

Coffin J, Bale M, Wells D, Guo S, Luke B, Zerbato J, Sobelewski M, Sia T, Shao W, Wu X, Maldarelli F, Kearney MF, Mellors JW,  Hughes SH
Journal: PLoS Pathog; Published: 04/01/2021

A multi-center cross-platform single-cell RNA sequencing reference dataset

Chen X, Yang C, Chen W, Zhao Y, Farmer A, Tran B, Furtak V, Moos M Jr., Xiao W, Wang C
Journal: Sci Data; Published: 02/02/2021

Ubiquitination of MHC Class II by March-I regulates dendritic cell fitness

Kim HJ, Bandola-Simon J, Ishido S, Wong NW, Koparde VN, Cam M, Roche PA
Journal: J Immunol; Published: 02/01/2021

Mitochondrial DNA alterations underlie an irreversible shift to aerobic glycolysis in fumarate hydratase–deficient renal cancer

Crooks DR, Maio N, Lang M, Ricketts CJ, Vocke CD, Gurram S, Turan S, Kim YY, Cawthon GM, Sohelian F, De Val Alda N, Pfeiffer RM, Jailwala P, Tandon M, Tran B, Fan TWM, Lane AN, Ried T, Wangsa D, Malayeri AA, Merino MJ, Yang Y, Meier JL, Ball MW,  Rouault TA, Srinivasan R, Linehan WM
Journal: Sci Signal; Published: 01/05/2021

Cross-resistance of cisplatin selected cells to anti-microtubule agents: Role of general survival mechanisms

Patel RP, Kuhn S, Yin D, Hotz J, Maher FA, Robey RW, Gottesman MM, Horibata S
Journal: Transl Oncol; Published: 01/01/2021

Antibody-mediated depletion of viral reservoirs is limited in SIV-infected macaques treated early with antiretroviral therapy

Swanstrom AE, Immonen TT, Oswald K, Pyle C, Thomas JA, Bosche WJ, Silipino L, Hull M, Newman L, Coalter V, Wiles A, Wiles R, Kiser J, Morcock DR, Shoemaker R, Fast R, Breed MW, Kramer J, Donohue D, Malys T, Fennessey CM, Trubey CM, Deleage C, Estes JD, Lifson JD, Keele BF, Del Prete GQ
Journal: J Clin Invest; Published: 01/01/2021

A multi-center study benchmarking single-cell RNA sequencing technologies using reference samples

Chen W?, Zhao Y?, Chen X?, Yang Z?, Xu X,Bi Y, Chen V, Li J, Choi H, Ernest B, Tran B, Mehta MKumar P, Moos M Jr, Farmer A, Mir A, Mehra U, Li J, Xiao W, Wang C
Journal: Nat Biotechnol; Published: 12/21/2020

AVIA 3.0: interactive portal for genomic variant and sample level analysis

Reardon HV, Che A, Luke BT, Ravichandran S, Collins JR, Mudunuri US
Journal: Bioinformatics; Published: 12/01/2020

Antigenic re-stimulation of virus-specific memory CD8 T Cells requires days of lytic protein accumulation for maximal cytotoxic capacity

Migueles SA, Rogan DC, Gavil NV, Kelly EP, Toulmin SA, Wang LT, Lack J, Ward AJ, Pryal PF, Ludwig AK, Medina RG, Apple BJ, Toumanios CN, Poole AL, Rehm CA, Jones SE, Liang CJ, Connors M
Journal: J Virol; Published: 11/09/2020

Inborn errors of Type I IFN immunity in patients with life-threatening COVID-19

Zhang Q, Bastard P, Liu Z, Le Pen J, Moncada-Velez M, Chen J, Ogishi M, Sabli IKD, Hodeib S, Korol C, Rosain J, Bilguvar K, Ye J, Bolze A, Bigio B, Yang R, Arias AA, Zhou Q, Zhang Y, Onodi F, Korniotis S, Karpf L, Philippot Q, Chbihi M, Bonnet-Madin L, Dorgham K, Smith N, Schneider WM, Razooky BS, Hoffmann HH, Michailidis E, Moens L, Han JE, Lorenzo L, Bizien L, Meade P, Neehus AL, Ugurbil AC, Corneau A, Kerner G, Zhang P, Rapaport F, Seeleuthner Y, Manry J, Masson C, Schmitt Y, Schlüter A, Le Voyer T, Khan T, Li J, Fellay J, Roussel L, Shahrooei M, Alosaimi MF, Mansouri D, Al-Saud H, Al-Mulla F, Almourfi F, Al-Muhsen SZ, Alsohime F, Al Turki S, Hasanato R, van de Beek D, Biondi A, Bettini LR, D'Angio' M, Bonfanti P, Imberti L, Sottini A, Paghera S, Quiros-Roldan E, Rossi C, Oler AJ, Tompkins MF, Alba C, Vandernoot I, Goffard JC, Smits G, Migeotte I, Haerynck F, Soler-Palacin P, Martin-Nalda A, Colobran R, Morange PE, Keles S, Çölkesen F, Ozcelik T, Yasar KK, Senoglu S, Karabela ?N, Rodríguez-Gallego C, Novelli G, Hraiech S, Tandjaoui-Lambiotte Y, Duval X, Laouénan C, COVID-STORM Clinicians., COVID Clinicians., Imagine COVID Group., French COVID Cohort Study Group., CoV-Contact Cohort., Amsterdam UMC Covid-19 Biobank., COVID Human Genetic Effort., NIAID-USUHS/TAGC COVID Immunity Group., Snow AL, Dalgard CL, Milner JD, Vinh DC, Mogensen TH, Marr N, Spaan AN, Boisson B, Boisson-Dupuis S, Bustamante J, Puel A, Ciancanelli MJ, Meyts I, Maniatis T, Soumelis V, Amara A, Nussenzweig M, García-Sastre A, Krammer F, Pujol A, Duffy D, Lifton RP, Zhang SY, Gorochov G, Béziat V, Jouanguy E, Sancho-Shimizu V, Rice CM, Abel L, Notarangelo LD, Cobat A, Su HC, Casanova JL, Lack J, et al
Journal: Science; Published: 10/23/2020

Analysis of SARS-CoV-2 ORF3a structure reveals chloride binding sites

Marquez-Miranda V, Rojas M, Duarte Y, Diaz-Franulic I, Holmgren M, Cachau R, Gonzalez-Nilo FD
Journal: biorXiv; Published: 10/22/2020

HIV-1 viremia not suppressible by antiretroviral therapy can originate from large T cell clones producing infectious virus

Halvas EK, Joseph KW, Brandt LD, Guo S, Sobolewski MD, Jacobs JL, Tumiotto C, Bui JK, Cyktor JC, Keele BF, Morse GD, Bale MJ, Shao W, Kearney MF, Coffin JM, Rausch JW, Wu X, Hughes SH, Mellors JW
Journal: J Clin Invest; Published: 10/01/2020

A germline 1;3 translocation disrupting the VHL gene: a novel genetic cause for von Hippel-Lindau

Ricketts CJ, Vocke CD, Lang M, Chen X, Zhao Y, Tran B, Tandon M, Schmidt LS, Ball MW, Linehan WM
Journal: J Med Genet; Published: 10/01/2020

Serological responses to human virome define clinical outcomes of Italian patients infected with SARS-CoV-2

Wang L, Candia J, Ma L, Zhao Y, Imberti L, Sottini A, Dobbs K, Lisco A, Sereti I, Su HC, Notarangelo LD, Wang XW
Journal: Cell; Published: 09/07/2020

Novel, abundant Drosha isoforms are deficient in miRNA processing in cancer cells

Dai L, Hallmark L, Bofill De Ros X, Crouch H, Chen S, Shi T , Yang A, Lian C, Zhao Y, Tran B, Gu S
Journal: RNA Biol; Published: 08/30/2020

Identification of potential modulators of Osteosarcoma metastasis by high throughput cellular screening of natural products

Long SA, Huang S, Kambala A, Ren L, Wilson J, Goetz M, Hao X, Yang X, Goncharova EI, Jia L, LeBlanc A, Khanna C, Henrich CJ, Beutler JA
Journal: Chem Biol Drug Des; Published: 07/14/2020

In search of genetic factors predisposing to familial hairy cell leukemia (HCL): exome-sequencing of four multiplex HCL pedigrees

Pemov A, Pathak A, Jones SJ, Dewan R, Merberg J, Karra S, Kim J, Arons E, Ravichandran S, Luke BT, Suman S, Yeager M, NCI DCEG Cancer Genomics Research Laboratory., Dyer MJS, Lynch HT, Greene MH, Caporaso NE, Kreitman RJ, Goldin LR, Spinelli JJ, Brooks-Wilson A, McMaster ML, Stewart DR
Journal: Leukemia; Published: 07/01/2020

A viral exposure signature defines early onset of hepatocellular carcinoma

Liu J, Tang W, Budhu A, Forgues M, Hernandez MO, Candia J, Kim Y, Bowman ED, Ambs S, Zhao Y, Tran B, Wu X, Koh C, Surana P, Liang TJ, Guarnera M, Mann D, Rajaure M, Greten TF, Wang Z, Yu H, Wang XW
Journal: Cell; Published: 07/01/2020

Using iCn3D and the World Wide Web for structure-based collaborative research: Analyzing molecular interactions at the root of COVID-19

Youkharibache P, Cachau R, Madej T, Wang J
Journal: biorXiv; Published: 07/01/2020

Optimization for sequencing and analysis of degraded FFPE-RNA samples

Levin Y, Talsania K, Tran B, Shetty J, Zhao Y, Mehta M
Journal: JoVE; Published: 06/08/2020

Induction of DNMT3B by PGE2 and IL6 at distant metastatic sites promotes epigenetic modification and breast cancer colonization

So JY, Skrypek N, Yang HH, Merchant AS, Nelson GW, Chen WD, Ishii H, Chen JM, Hu G, Achyut BR, Yoon EC, Han L, Huang C, Cam MC, Zhao K, Lee MP, Yang L
Journal: Cancer Res; Published: 06/01/2020

Impact of losing hRpn13 Pru or UCHL5 on proteasome clearance of ubiquinated proteins and RA190 cytoxicity

Osei-Amponsa V, Sridharan V, Tandon M, Evans CN, Klarmann K, Cheng KT, Lack J, Chari R, Walters KJ
Journal: Mol Cell Biol; Published: 05/01/2020

Impact of cyanine conformational restraint in the near-infrared range

Matikonda SS, Hammersley G, Kumari N, Grabenhorst L, Glembockyte V, Tinnefeld P, Ivanic J, Levitus M, Schnermann MJ
Journal: J Org Chem; Published: 05/01/2020

Author Correction: Safety and feasibility of anti-CD19 CAR T cells with fully human binding domains in patients with B-cell lymphoma

Brudno JN, Lam N, Vanasse D, Shen YW, Rose JJ, Rossi J, Xue A, Bot A, Scholler N, Mikkilineni L, Roschewski M, Dean R, Cachau R, Youkharibache P, Patel R, Hansen B, Stroncek DF, Rosenberg SA, Gress RE, Kochenderfer JN
Journal: Nat Med; Published: 05/01/2020

Recent developments in the general atomic and molecular electronic structure system

Barca GMJ, Bertoni C, Carrington L, Datta D, De Silva N, Deustua JE, Fedorov DG, Gour JR, Gunina AO, Guidez E, Harville T, Irle S, Ivanic J, Kowalski K, Leang SS, Li H, Li W, Lutz JJ, Magoulas I, Mato J, Mironov V, Nakata H, Pham BQ, Piecuch P, Poole D, Pruitt SR, Rendell AP, Roskop LB, Ruedenberg K, Sattasathuchana T, Schmidt MW, Shen J, Slipchenko L, Sosonkina M, Sundriyal V, Tiwari A, Vallejo JLG, Westheimer B, Wloch M, Xu P, Zahariev F, Gordon MS
Journal: J Chem Phys; Published: 04/21/2020

Repurposing the Pummerer rearrangement: determination of methionine sulfoxides in peptides

Woodroofe CC, Ivanic J, Monti S, Levine RL, Swenson RE
Journal: Chembiochem; Published: 02/01/2020

Safety and feasibility of anti-CD19 CAR T cells with fully human binding domains in patients with B-cell lymphoma

Brudno JN, Lam N, Vanasse D, Shen YW, Rose JJ, Rossi J, Xue A, Bot A, Scholler N, Mikkilineni L, Roschewski M, Dean R, Cachau R, Youkharibache P, Patel R, Hansen B, Stroncek DF, Rosenberg SA, Gress RE, Kochenderfer JN
Journal: Nat Med; Published: 02/01/2020

Intact HIV proviruses persist in children seven to nine years after initiation of antiretroviral therapy in the first year of life

Katusiime MG, Halvas EK, Wright I, Joseph K, Bale MJ, Kirby-McCullough B, Engelbrecht S, Shao W, Hu W-S, Cotton M, Mellors JW, Kearney MF, van Zyl GU
Journal: J Virol; Published: 01/31/2020

Impact of antiretroviral therapy duration on HIV-1 infection of T Cells within anatomic sites

Lee E, von Stockenstrom S, Morcilla V, Odevall L, Hiener B, Shao W, Hartogensis W, Bacchetti P, Milush J, Liegler T, Sinclair E, Hatano H, Hoh R , Somsouk M, Hunt P, Boritz E, Douek D, Fromentin R, Chomont N, Deeks SG, Hecht FM, Palmer S 
Journal: J Virol; Published: 01/17/2020

HIV proviral sequence database: a new public database for near full-length HIV proviral sequences and their meta-analyses

Shao W, Shan J, Hu WS, Halvas EK, Mellors JW, Coffin JM, Kearney MF.
Journal: AIDS Res Hum Retroviruses; Published: 01/01/2020

Combined HIV-1 sequence and integration site analysis informs viral dynamics and allows reconstruction of replicating viral ancestors

Patro SC, Brandt LD, Bale MJ, Halvas EK, Joseph KW, Shao W, Wu X, Guo S, Murrell B, Wiegand A, Spindler J, Raley C, Hautman C, Sobolewski M, Fennessey CM, Hu WS, Luke B, Hasson JM, Niyongabo A, Capoferri AA, Keele BF, Milush J, Hoh R, Deeks SG, Maldarelli F, Hughes SH, Coffin JM, Rausch JW, Mellors JW, Kearney MF
Journal: Proc Natl Acad Sci U S A; Published: 12/17/2019

Single-Cell Profiling Defines Transcriptomic Signatures Specific to Tumor-Reactive versus Virus-Responsive CD4+T Cells

Magen A, Nie J, Ciucci T, Tamoutounour S, Zhao Y, Mehta M, Tran B, McGavern DB, Hannenhalli S, Bosselut R 
Journal: Cell Rep; Published: 12/01/2019

Electrostatically driven Guanidinium interactions domains that control hydrogel-mediated protein delivery in vivo

Miller SE, Yamada Y, Patel N, Suarez E, Andrews C, Tau S, Luke BT, Cachau RE, Schneider JP
Journal: ACS Central Science; Published: 11/27/2019

Contribution of SLC22A12 on hypouricemia and its clinical significance for screening purposes

Cha DH, Gee HY, Cachau R, Choi JM, Park D, Jee SH, Ryu S, Kim KK, Won HH, Limou S, Myung W, Winkler CA, Cho SK
Journal: Sci Rep; Published: 10/01/2019

Linked dual-class HIV resistance mutations are associated with treatment failure

Boltz VF, Shao W, Bale MJ, Halvas EK, Luke B, McIntyre JA, Schooley RT, Lockman S, Currier JS, Sawe F, Hogg E, Hughes MD, Kearney MF, Coffin JM, Mellors JW
Journal: JCI Insight; Published: 10/01/2019

Assessment of Coagulation Homeostasis in Blunt, Penetrating, and Thermal Trauma: Guidance for a Multicenter Systems Biology Approach

Shupp JW, Brummel-Ziedins KE, Cohen MJ, Freeman K, Hammamieh R, Mudunuri US, Orfeo T, Moffatt LT, Brownstein BH, Mann KG, Jett M, Pusateri AE
Journal: Shock; Published: 10/01/2019

The upcoming subatomic resolution revolution

Cachau RE, Zhu J, Nicklaus MC
Journal: Curr Opin Struct Biol; Published: 10/01/2019

A Thpok-directed transcriptional circuitry promotes Bcl6 and Maf expression to orchestrate T follicular helper differentiation

Vacchio MS, Ciucci T, Gao Y, Watanabe M, Balmaceno-Criss M, McGinty MT, Huang A, Xiao Q, McConkey C, Zhao Y, Shetty J, Tran B, Pepper M, Vahedi G, Jenkins MK, McGavern DB, Bosselut R
Journal: Immunity; Published: 09/01/2019

TLR7 agonist administration to SIV-infected macaques receiving early initiated cART does not induce plasma viremia

Del Prete GQ, Alvord WG, Li Y, Deleage C, Nag M, Oswald K, Thomas JA, Pyle C, Bosche WJ, Coalter V, Wiles A, Wiles R, Berkemeier B, Hull M, Chipriano E, Silipino L, Fast R, Kiser J, Kiser R, Malys T, Kramer J, Breed MW, Trubey CM, Estes JD, Barnes TL, Hesselgesser J, Geleziunas R, Lifson JD
Journal: JCI Insight; Published: 06/01/2019

Clones of infected cells arise early in HIV-infected individuals

Coffin JM, Wells DW, Zerbato JM, Kuruc JD, Guo S, Luke BT, Eron JJ, Bale M, Spindler J, Simonetti FR, Hill S, Kearney MF, Maldarelli F, Wu X, Mellors JW, Hughes SH
Journal: JCI Insight; Published: 06/01/2019

Associations of CDH1 germline variant location and cancer phenotype in families with hereditary diffuse gastric cancer (HDGC)

Lo W, Zhu B, Sabesan A, Wu HH, Powers A, Sorber RA, Ravichandran S, Chen I, McDuffie LA, Quadri HS, Beane JD, Calzone K, Miettinen MM, Hewitt SM, Koh C, Heller T, Wacholder S, Rudloff U
Journal: J Med Genet; Published: 06/01/2019

Robustness of RNA sequencing on older formalin-fixed paraffin-embedded tissue from high-grade ovarian serous adenocarcinomas

Zhao Y, Mehta M, Walton A, Talsania K, Levin Y, Shetty J, Gillanders EM, Tran B, Carrick D
Journal: PLoS One; Published: 05/07/2019

Relationship between human leukocyte antigen alleles and risk of Kaposi's sarcoma in Cameroon

Cornejo Castro EM, Morrison B, Marshall V, Labo N, Miley W, Clements N, Nelson G, Ndom P, Stolka K, Hemmingway-Goday JJ, Abassora M, Gao X, Smith JS, Carrington M, Whitby D
Journal: Genes Immun; Published: 05/01/2019

The Natural Product Butylcycloheptyl Prodiginine Binds Pre-miR-21, Inhibits Dicer-Mediated Processing of Pre-miR-21, and Blocks Cellular Proliferation

Matarlo JS, Krumpe LRH, Heinz WF, Oh D, Shenoy SR, Thomas CL, Goncharova EI, Lockett SJ, O'Keefe BR
Journal: Cell Chem Biol; Published: 05/01/2019

Genome Assembly and Annotation of the Trichoplusia ni Tni-FNL Insect Cell Line Enabled by Long-Read Technologies 

Talsania K, Mehta M, Raley C, Kriga K, Gowda S, Grose C, Drew M, Roberts V, Kwong T, Burkett S, Oeser S, Stephens R, Soppet D, Chen X, Kumar P, German O, Smimova T,  Hautman CShetty J, Tran B, Zhao YEsposito D
Journal: Genes (Basel); Published: 01/01/2019

The emergence and functional fitness of memory CD4+ T cells require the transcription factor Thpok

Ciucci T, Vacchio MS, Gao Y, Tomassoni Ardori F, Candia J, Mehta M, Zhao Y, Tran B, Pepper M, Tessarollo L, McGavern DB, Bosselut R
Journal: Immunity; Published: 01/01/2019

A novel pathway of LPS uptake through syndecan-1 leading to pyroptotic cell death

Yokoyama S, Cai Y, Murata M, Tomita T, Yoneda M, Xu L, Pilon AL, Cachau RE, Kimura S
Journal: Elife; Published: 12/01/2018

NPHS2 V260E is a frequent cause of steroid-resistant nephrotic syndrome in Black South African children

Asharam K, Bhimma R, David VA, Coovadia HM, Qulu WP, Naicker T, Gillies CE, Vega-Warner V, Johnson RC, Limou S, Kopp JB, Sampson M, Nelson GW, Winkler CA
Journal: Kidney Int Rep; Published: 11/01/2018

PanoromiX: a time-course network medicine platform integrating molecular assays and pathophenotypic data

Yang R, Watson D, Williams J, Kumar R, Campbell R, Mudunuri U, Hammamieh R, Jett M
Journal: BMC Bioinformatics; Published: 11/01/2018

Plasma metabolomic profiling of a ketamine and placebo crossover trial of major depressive disorder and healthy control subjects

Moaddel R, Shardell M, Khadeer M, Lovett J, Kadriu B, Ravichandran S, Morris PJ, Yuan P, Thomas CJ, Gould TD, Ferrucci L, Zarate CA
Journal: Psychopharmacology (Berl); Published: 10/01/2018

Fetal-not maternal APOL1 genotype associated with risk for preeclampsia in those with African ancestry

Reidy KJ, Hjorten RC, Simpson CL, Rosenberg AZ, Rosenblum SD, Kovesdy CP, Tylabsky FA, Myrie J, Ruiz BL, Haque S, Mozhui K, Nelson GW, David VA, Yang X, Suzuki M, Jacob J, Reznik SE, Kaskel FJ, Kopp JB, Winkler CA, Davis RL
Journal: Am J Hum Genet; Published: 09/01/2018

Defining the conditional basis of silicon phthalocyanine near-IR ligand exchange

Anderson ED, Sova S, Ivanic J, Kelly L, Schnermann MJ
Journal: Phys Chem Chem Phys; Published: 07/04/2018

Hybrid correlation energy (HyCE): an approach based on separate evaluations of internal and external components

Ivanic J, Schmidt MW
Journal: J Phys Chem A; Published: 06/14/2018

Direct molecular dissection of tumor parenchyma from tumor stroma in tumor xenograft using mass spectrometry–based glycoproteomics

Ye X, Luke BT, Wei B, Kaczmarczyk JA, Loncarek J,  Dwyer JE, Simpson MR, Johann DJ, Saul RG, Nissley DV, McCormick F, Whiteley GR, Blonder J
Journal: Oncotarget; Published: 05/01/2018

Genetics and Pathogenesis of Diffuse Large B-Cell Lymphoma

Schmitz R, Wright GW, Huang DW, Johnson CA, Phelan JD, Wang JQ, Roulland S, Kasbekar M, Young RM, Shaffer AL, Hodson DJ, Xiao W, Yu X, Yang Y, Zhao H, Xu W, Liu X, Zhou B, Du W, Chan WC, Jaffe ES, Gascoyne RD, Connors JM, Campo E, Lopez-Guillermo A, Rosenwald A, Ott G, Delabie J, Rimsza LM, Tay Kuang Wei K, Zelenetz AD, Leonard JP, Bartlett NL, Tran B, Shetty J, Zhao Y, Soppet DR, Pittaluga S, Wilson WH, Staudt LM
Journal: N Engl J Med; Published: 04/01/2018

Synthesis and biological evaluation of fluorescent bryostatin analogues

Cummins TJ, Kedei N, Czikora A, Lewin NE, Kirk S, Petersen ME, McGowan KM, Chen JQ, Luo X, Johnson RC, Ravichandran S, Blumberg PM, Keck GE
Journal: Chembiochem; Published: 04/01/2018

Natural polyphenols as sirtuin 6 modulators

Rahnasto-Rilla M, Tyni J, Huovinen M, Jarho E, Kulikowicz T, Ravichandran S, A Bohr V, Ferrucci L, Lahtela-Kakkonen M, Moaddel R
Journal: Sci Rep; Published: 03/01/2018

Single cell analysis reveals cancer stem cell heterogeneity in hepatocellular carcinoma

Zheng H, Pomyen Y, Hernandez MO, Li C, Livak F, Tang W, Dang H, Greten TF, Davis JL, Zhao Y, Mehta M, Levin Y, Shetty J, Tran B, Budhu A, Wang XW
Journal: Hepatol; Published: 01/01/2018

Ca2+ -sensor neurocalcin ? and hormone ANF Modulate ANF-RGC activity by diverse pathways: role of the signaling helix domain

Duda T, Pertzev A, Ravichandran S, Sharma RK
Journal: Front Mol Neurosci; Published: 01/01/2018

The evolutionary landscape of chronic lymphocytic leukemia treated with ibrutinib targeted therapy

Landau DA, Sun C, Rosebrock D, Herman SEM, Fein J, Sivina M, Underbayev C, Liu D, Hoellenriegel J, Ravichandran S, Farooqui MZH, Zhang W, Cibulskis C, Zviran A, Neuberg DS, Livitz D, Bozic I, Leshchiner I, Getz G, Burger JA, Wiestner A, Wu CJ
Journal: Nat Commun; Published: 12/01/2017

The full transcription map of mouse papillomavirus type 1 (MmuPV1) in mouse wart tissues

Xue XY, Majerciak V, Uberoi A, Kim BH, Gotte D, Chen X, Cam M, Lambert PF, Zheng ZM
Journal: PLoS Pathog; Published: 11/01/2017

No evidence of HIV replication in children on antiretroviral therapy

Van Zyl GU, Katusiime MG, Wiegand A, McManus WR, Bale MJ, Halvas EK, Luke B, Boltz VF, Spindler J, Laughton B, Engelbrecht S, Coffin JM, Cotton MF, Shao W, Mellors JW, Kearney MF
Journal: J Clin Invest; Published: 10/01/2017

Control of regulatory T cell differentiation by the transcription factors Thpok and LRF

Carpenter AC, Wohlfert E, Chopp LB, Vacchio MS, Nie J, Zhao YShetty J, Xiao Q, Deng C, Tran B, Cam M, Gaida MM, Belkaid Y, Bosselut R 
Journal: J Immunol; Published: 09/01/2017

Control of regulatory T cell differentiation by the transcription factors Thpok and LRF

Carpenter AC, Wohlfert E, Chopp LB, Vacchio MS, Nie J, Zhao Y, Shetty J, Xiao Q, Deng C, Tran B, Cam M, Gaida MM, Belkaid Y, Bosselut R
Journal: J Immunol; Published: 09/01/2017

Conformational energy range of ligands in protein crystal structures: the difficult quest for accurate understanding

Peach ML, Cachau RE, Nicklaus MC
Journal: J Mol Recognit; Published: 08/01/2017

Transcriptomic profiling and quantitative high-throughput (qHTS) drug screening of CDH1 deficient hereditary diffuse gastric cancer (HDGC) cells identify treatment leads for familial gastric cancer

Chen I, Mathews-Greiner L, Li D, Abisoye-Ogunniyan A, Ray S, Bian Y, Shukla V, Zhang X, Guha R, Thomas C, Gryder B, Zacharia A, Beane JD, Ravichandran S, Ferrer M, Rudloff U
Journal: J Transl Med; Published: 05/01/2017

A mouse recapitulating APOL1-associated kidney disease

Winkler CA, Nelson GW
Journal: Nat Med; Published: 04/01/2017

In vivo activation of duocarmycin-antibody conjugates by near-infrared light

Nani RR, Gorka AP, Nagaya T, Yamamoto T, Ivanic J, Kobayashi H, Schnermann MJ
Journal: ACS Cent Sci; Published: 04/01/2017

Proviruses with identical sequences comprise a large fraction of the replication-competent HIV reservoir 

Bui JK, Sobolewski MD, Keele BF, Spindler J, Musick A, Wiegand A, Luke BT, Shao W, Hughes SH, Coffin JM, Kearney MF, Mellors JW  
Journal: PLoS Pathog; Published: 03/01/2017

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
Journal: PLoS Pathog; Published: 02/01/2017

Membrane Guanylate Cyclase catalytic Subdomain: Structure and Linkage with Calcium Sensors and Bicarbonate

Ravichandran S, Duda T, Pertzev A, Sharma RK
Journal: Front Mol Neurosci; Published: 01/01/2017

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
Journal: PLoS Med; 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
Journal: Retrovirology; Published: 12/01/2016

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
Journal: Oncotarget; Published: 11/01/2016

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

Goldin LR, McMaster ML, Rotunno M, Herman SEM, Jones K, Zhu B, Boland J, Burdett L, Hicks B, Ravichandran S,  Luke BT, Yeager M, Fontaine L, Goldstein AM, Chanock SJ, Tucker MA, Wiestner A, Martland G, Caporaso NE
Journal: Blood; 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
Journal: Nat Methods; 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
Journal: Mol Biol Rep; Published: 08/01/2016

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
Journal: Nucleic Acids Res; 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
Journal: Haematologica; Published: 07/01/2016

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.
Journal: Retrovirology; 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
Journal: Oncogene; 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
Journal: Am J Hum Genet; 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
Journal: J Chem Phys; 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
Journal: Sci Signal; Published: 03/01/2016

Infrared Spectroscopy and Structure of (NO)n Clusters

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

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
Journal: Proc Natl Acad Sci U S A; Published: 02/01/2016

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
Journal: BioData Min; Published: 01/01/2016

Towards better precision medicine:  PacBio single-molecular long reads resold 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
Journal: J Data Mining Genomics Proteomics; Published: 01/01/2016

Common Genetic Variants Found in HLA and KIR Immune Genes in Autism Spectrum Disorder

Torres AR, Sweeten TL, Johnson RC, Odell D, Westover JB, Bray-Ward P, Ward DC, Davies CJ, Thomas AJ, Croen LA, Benson M
Journal: Front Neurosci; 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
Journal: Papillomavirus Res; 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
Journal: Haematologica; 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
Journal: Antimicrob Agents Chemother; 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
Journal: Genes Dev; Published: 11/01/2015

Reactive Species Involved in the Regioselective Photooxidation of Heptamethine Cyanines

Nani RR, Kelley JA, Ivanic J, Schnermann MJ
Journal: Chem Sci; 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
Journal: Nat Commun; 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
Journal: J Biol Chem; Published: 09/01/2015

A population-structured HIV epidemic in Israel: roles of risk and ethnicity

Grossman Z, Avidor B, Mor Z, Chowers M, Levy I, Shahar E, Riesenberg K, Sthoeger Z, Maayan S, Shao W, Lorber M, Olstein-Pops K, Elbirt D, Elinav H, Asher I, Averbuch D, Istomin V, Gottesman BS, Kedem E, Girshengorn S, Kra-Oz Z, Shemer Avni Y, Radian Sade S, Turner D, Maldarelli F
Journal: PLoS One; Published: 08/24/2015

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
Journal: Hum Genet; 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
Journal: Bioinformatics; Published: 08/01/2015

Longitudinal genetic characterization reveals that cell proliferation maintains a persistent HIV Type 1 DNA pool during effective HIV therapy

von Stockenstrom S, Odevall L, Lee E, Sinclair E, Bacchetti P, Killian M, Epling L, Shao W, Hoh R, Ho T, Faria NR, Lemey P, Albert J, Hunt P, Loeb L, Pilcher C, Poole L, Hatano H, Somsouk M, Douek D, Boritz E, Deeks SG, Hecht FM, Palmer S
Journal: J Infect Dis; 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.
Journal: Hum Genet; Published: 07/01/2015

APOL1 toxin, innate immunity, and kidney injury

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

New insights into the enzymatic mechanism of human chitotriosidase (CHIT1) catalytic domain by atomic resolution X-ray diffraction and hybrid QM/MM

Fadel F, Zhao Y, Cachau R, Cousido-Siah A, Ruiz FX, Harlos K, Howard E, Mitschler A, Podjarny A
Journal: Acta Crystallogr D Biol Crystallogr; 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
Journal: J Mol Graph Model; Published: 04/01/2015

ALDsuite: Dense marker MALD using principalcomponents of ancestral linkage disequilibrium

Johnson RC, Nelson GW, Zagury J-F, Winkler CA
Journal: BMC Genet; Published: 03/01/2015

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
Journal: PLoS One; 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
Journal: Nat Commun; 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
Journal: Science; 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.
Journal: J Virol Methods.; 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
Journal: J Infect Dis; 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
Journal: Nat Genet; 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
Journal: J Org Chem; 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
Journal: J Chem Phys; 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
Journal: J Virol; 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
Journal: J Mol Graph Model; 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
Journal: PLoS Pathog; 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
Journal: J Chromatogr B Analyt Technol Biomed Life Sci; Published: 03/01/2014

Enigma prevents Cbl-c-mediated ubiquitination and degradation of RETMEN2A

Kales SC, Nau MM, Merchant AS, Lipkowitz S
Journal: PLoS One; Published: 01/01/2014

Identification of gene signatures used to recognize biological characteristics of gastric cancer upon gene expression data

Yan Z, Luke BT, Tsang SX, Xing R, Pan Y, Liu Y, Wang J, Geng T, Li J, Lu Y
Journal: Biomark Insights; Published: 01/01/2014

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
Journal: Proc Natl Acad Sci U S A; 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
Journal: Nucleic Acids Res; Published: 11/01/2013

Nanoinformatics knowledge infrastructures: bringing efficient information management to nanomedical research

de la Iglesia D, Cachau RE, García-Remesal M, Maojo V
Journal: Comput Sci Discov; 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
Journal: J Virol; 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
Journal: Infect Genet Evol; Published: 08/01/2013

Decoding nitric oxide release rates of amine-based diazeniumdiolates

Wang YN, Collins J, Holland RJ, Keefer LK, Ivanic J
Journal: J Phys Chem A; 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
Journal: Anal Biochem; 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
Journal: Retrovirology; 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
Journal: PLoS One; 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
Journal: PLoS Genet; 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
Journal: Nucleic Acids Res; 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
Journal: Methods Mol Biol; 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
Journal: PLoS Pathog; Published: 01/01/2013

Nanoinformatics workshop report: Current resources, community needs, and the proposal of a collaborative framework for data sharing and information integration

Harper SL, Hutchison JE, Baker N, Ostraat M, Tinkle S, Steevens J, Hoover MD, Adamick J, Rajan K, Gaheen S, Cohen Y, Nel A, Cachau RE, Tuominen M
Journal: Comput Sci Discov; 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
Journal: J Chem Phys; 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
Journal: J Virol; 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
Journal: J Exp Med; 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
Journal: J Chromatogr A; Published: 12/01/2012

Genes affected by mouse mammary tumor virus (MMTV) proviral insertions in mouse mammary tumors are deregulated or mutated in primary human mammary tumors

Callaha R, Mudunuri U, Bargo S, Raafat A, McCurdy D, Boulanger C, Lowther W, Stephens R, Luke BT, Stewart C, Wu X, Munroe D, Smith GH.
Journal: Oncotarget; Published: 10/18/2012

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
Journal: Proc Natl Acad Sci U S A; 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
Journal: J Infect Dis; 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
Journal: Blood; Published: 06/01/2012

Nanoinformatics: developing new computing applications for nanomedicine

Maojo V, Fritts M, Martin-Sanchez F, De la Iglesia D, Cachau RE, Garcia-Remesal M, Crespo J, Mitchell JA, Anguita A, Baker N, Barreiro JM, Benitez SE, De la Calle G, Facelli JC, Ghazal P, Geissbuhler A, Gonzalez-Nilo F, Graf N, Grangeat P, Hermosilla I, Hussein R, Kern J, Koch S, Legre Y, Lopez-Alonso V, Lopez-Campos G, Milanesi L, Moustakis V, Munteanu C, Otero P, Pazos A, Perez-Rey D, Potamias G, Sanz F, Kulikowski C
Journal: Comput Sci Eng; Published: 06/01/2012

Searching for non-B DNA-forming motifs using nBMST (non-B DNA motif search tool)

Cer RZ, Bruce KH, Donohue DE, Temiz NA, Mudunuri US, Yi M, Volfovsky N, Bacolla A, Luke BT, Collins JR, Stephens RM
Journal: Curr Protoc Hum Genet; Published: 04/01/2012

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
Journal: J Proteome Res; Published: 03/01/2012

Study of interaction energies between the PAMAM dendrimer and nonsteroidal anti-inflammatory drug using a distributed computational strategy and experimental analysis by ESI-MS/MS

Avila-Salas F, Sandoval C, Caballero J, Guiñez-Molinos S, Santos LS, Cachau RE, González-Nilo FD
Journal: J Phys Chem B; Published: 02/01/2012

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

Temiz NA, Donohue DE, Bacolla A, Luke BT, Collins JR
Journal: PLoS One; 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
Journal: Methods Mol Biol; 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
Journal: PLoS One; Published: 01/01/2012

Nanoinformatics: a new area of research in nanomedicine

Maojo V, Fritts M, de la Iglesia D, Cachau RE, Garcia-Remesal M, Mitchell JA, Kulikowski C
Journal: Int J Nanomedicine; 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
Journal: Proc Natl Acad Sci U S A; Published: 11/01/2011

Supramolecular complexes of quantum dots and a polyamidoamine (PAMAM)-folate derivative for molecular imaging of cancer cells

Geraldo DA, Duran-Lara EF, Aguayo D, Cachau RE, Tapia J, Esparza R, Yacaman MJ, Gonzalez-Nilo FD, Santos LS
Journal: Anal Bioanal Chem; Published: 04/01/2011

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
Journal: Antivir Ther; Published: 01/01/2011

Non-B DB: a database of predicted non-B DNA-forming motifs in mammalian genomes

Cer RZ, Bruce KH, Mudunuri US, Yi M, Volfovsky N, Luke BT, Bacolla A, Collins JR, Stephens RM
Journal: Nucleic Acids Res; Published: 01/01/2011

Nanoinformatics: an emerging area of information technology at the intersection of bioinformatics, computational chemistry and nanobiotechnology

González-Nilo F, Pérez-Acle T, Guínez-Molinos S, Geraldo DA, Sandoval C, Yévenes A, Santos LS, Laurie VF, Mendoza H, Cachau RE
Journal: Biol Res; 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
Journal: Science; Published: 07/01/2010

Optimized method for computing (18)O/(16)O ratios of differentially stable-isotope labeled peptides in the context of postdigestion (18)O exchange/labeling

Ye X, Luke BT, Johann DJ Jr, Ono A, Prieto DA, Chan KC, Issaq HJ, Veenstra TD, Blonder J
Journal: Anal Chem; Published: 07/01/2010

The zinc-dependent protease activity of the botulinum neurotoxins

Lebeda FJ, Cer RZ, Mudunuri U, Stephens R, Singh BR, Adler M
Journal: Toxins (Basel); Published: 05/01/2010

Euprosterna elaeasa virus genome sequence and evolution of the Tetraviridae family: emergence of bipartite genomes and conservation of the VPg signal with the dsRNA Birnaviridae family

Zeddam JL, Gordon KH, Lauber C, Alves CA, Luke BT, Hanzlik TN, Ward VK, Gorbalenya AE
Journal: Virology; Published: 02/01/2010

Temporal characteristics of botulinum neurotoxin therapy

Lebeda FJ, Cer RZ, Stephens RM, Mudunuri U
Journal: Expert Rev Neurother; Published: 01/01/2010

Development of a high-throughput cell-based reporter assay to identify stabilizers of tumor suppressor Pdcd4

Blees JS, Schmid T, Thomas CL, Baker AR, Benson L, Evans JR, Goncharova EI, Colburn NH, McMahon JB, Henrich CJ:
Journal: J Biomol Screen; Published: 01/01/2010