Data Science and Information Technology Program (DSITP)

ABCS Publications

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

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

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

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

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

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

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

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

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

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

Genetics and Pathogenesis of Diffuse Large B-Cell Lymphoma

Single cell analysis reveals cancer stem cell heterogeneity in hepatocellular carcinoma

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

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

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

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

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

A mouse recapitulating APOL1-associated kidney disease

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

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

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

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

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

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

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

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

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

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

APOBEC3 proteins can copackage and comutate HIV-1 genomes

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

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

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

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

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

Infrared Spectroscopy and Structure of (NO)n Clusters

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

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

Towards better precision medicine:  PacBio single-molecular long reads resold the interpretation of HIV drug resistant mutation profiles at explicit quasispecies (haplotype) level

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

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

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

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

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

Reactive Species Involved in the Regioselective Photooxidation of Heptamethine Cyanines

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

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

The Somatic Autosomal Mutation Matrix in Cancer Genomes

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

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

APOL1 toxin, innate immunity, and kidney injury

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

ALDsuite: Dense marker MALD using principalcomponents of ancestral linkage disequilibrium

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

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

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

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

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

Rare missense variants in POT1 predispose to familial cutaneous malignant melanoma

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

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

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

Pharmacophore model of the quercetin binding site of the SIRT6 protein

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

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

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

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

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

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

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

Decoding nitric oxide release rates of amine-based diazeniumdiolates

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

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

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

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

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

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

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

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

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

Bcl11a is essential for lymphoid development and negatively regulates p53

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

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

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

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

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

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

Post-digestion ¹⁸O exchange/labeling for quantitative shotgun proteomics of membrane proteins

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

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

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

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