Welcome! My name is Vishal Koparde ( pronouced as We-shall Co-Par-Day ).
I actively contribute code to numerous repos:
- CCR Collaborative Bioinformatics Resource
- RNA Biology Lab
- CCR Genetics Branch
- NCI Pangea
- NIDAP
- Vaccine Branch
- abcsFrederick
| Title | Publication | Year | DOI |
|---|---|---|---|
| Tumor-Intrinsic Epigenetic States Uncover a Stem-Like SCLC Predictive of Chemoimmunotherapy Failure | Journal of Clinical Oncology | Submitted | TBD |
| Chromatin Accessibility Profiling Reveals a Stem-Like Subtype of Small Cell Lung Cancer with Poor Prognosis and Resistance to Chemoimmunotherapy | Cancer Discovery | Accepted | TBD |
| Sp Transcription Factors Establish the Signaling Environment in the Neuromesodermal Progenitor Niche During Axial Elongation | eLife | Preprint Available | https://doi.org/10.1101/2025.06.03.657492 |
| Immune Niche Formation Reveals Mechanisms of Tumor Dormancy and Targeting Opportunities | Nature Cancer | 2026 (preprint) | https://doi.org/10.21203/rs.3.rs-8167536/v1 |
| OA01.01: Tumor-Intrinsic Epigenetic States Uncover a Stem-Like SCLC Predictive of Chemoimmunotherapy Failure | Journal of Thoracic Oncology | 2026 | https://doi.org/10.1016/j.jtho.2026.103996 |
| Immune Niche Formation in Engineered Mouse Models Reveals Mechanisms of Tumor Dormancy | bioRxiv | 2025 | https://doi.org/10.1101/2025.04.16.649000. |
| Expression of IMPACT curtails metabolic plasticity and augments NK cell killing to abrogate metastatic growth | Cancer Discovery | 2025 | https://doi.org/10.1158/2159-8290.CD-24-1055 |
| Transfer RNA acetylation regulates in vivo mammalian stress signaling | Science Advances | 2025 | https://doi.org/10.1126/sciadv.ads2923 |
| Noncanonical circRNA biogenesis driven by alpha and gamma herpesviruses | EMBOJ | 2025 | https://doi.org/10.1038/s44318-025-00398-0 |
| Loss of tumor suppressors promotes a non-cell-autonomous inflammatory response and enhances LAG3+T cell mediated immune suppression | Nat. Comms. | 2024 | https://doi.org/10.1038/s41467-024-50262-8 |
| DNAJC9 prevents CENP-A mislocalization and chromosomal instability by maintaining the fidelity of histone supply chains | EMBOJ | 2024 | https://doi.org/10.1038/s44318-024-00093-6 |
| Interferon induced circRNAs escape herpesvirus host shutoff and suppress lytic infection | EMBO Rep. | 2024 | https://doi.org/10.1038/s44319-023-00051-z |
| Chromatin accessibility landscape of human triple-negative breast cancer cell lines reveals variation by patient donor ancestry | Cancer Research Communications | 2023 | https://doi.org/10.1158/2767-9764.CRC-23-0236 |
| SMYD3 represses tumor-intrinsic interferon response in HPV-negative squamous cell carcinoma of the head and neck | Cell Reports | 2023 | https://doi.org/10.1016/j.celrep.2023.112823 |
| The transcription factor EGR2 controls homing and pathogenicity of TH17 cells in the central nervous system | Nature Immunology | 2023 | https://doi.org/10.1038/s41590-023-01553-7 |
| Transcriptional landscape of Kaposi sarcoma tumors identifies unique immunologic signatures and key determinants of angiogenesis | Journal of Translational Medicine | 2023 | https://doi.org/10.1186/s12967-023-04517-5 |
| A virus-induced circular RNA maintains latent infection of Kaposi’s sarcoma herpesvirus | PNAS | 2023 | https://doi.org/10.1073/pnas.2212864120 |
| Antisense transcription from lentiviral gene targeting linked to an integrated stress response in colorectal cancer cells | Molecular Therapy | 2022 | https://doi.org/10.1016/j.omtn.2022.05.029 |
| Unique roles of vaginal Megasphaera phylotypes in reproductive health | Microbial Genomics | 2021 | https://doi.org/10.1099/mgen.0.000526 |
| PERK signaling through C/EBPδ contributes to ER stress-induced expression of immunomodulatory and tumor promoting chemokines by cancer cells | Cell Death & Disease | 2021 | https://doi.org/10.1038/s41419-021-04318-y |
| Ubiquitination of MHC Class II by March-I Regulates Dendritic Cell Fitness | The Journal of Immunology | 2021 | https://doi.org/10.4049/jimmunol.2000975 |
| Characterizing expression and regulation of gamma-herpesviral circular RNAs | Frontiers in microbiology | 2021 | https://doi.org/10.3389/fmicb.2021.670542 |
| Identifying and characterizing virus-encoded circular RNAs | Methods | 2021 | https://doi.org/10.1016/j.ymeth.2021.03.004 |
| Loss of myeloid-specific lamin A/C drives lung metastasis through Gfi-1 and C/EBPε-mediated granulocytic differentiation | Molecular carcinogenesis | 2020 | https://doi.org/10.1002/mc.23147 |
| Racioethnic diversity in the dynamics of the vaginal microbiome during pregnancy | Nature medicine | 2019 | https://doi.org/10.1038/s41591-019-0465-8 |
| The vaginal microbiome and preterm birth | Nature medicine | 2019 | https://doi.org/10.1038/s41591-019-0450-2 |
| Multi-omic Microbiome Profiles in the Female Reproductive Tract in Early Pregnancy | Infectious Microbes & Diseases | 2019 | https://doi.org/10.1097/IM9.0000000000000007 |
| Head and neck squamous cancer progression is marked by CLIC4 attenuation in tumor epithelium and reciprocal stromal upregulation of miR-142-3p, a novel post-transcriptional regulator of CLIC4 | Oncotarget | 2019 | https://doi.org/10.18632/oncotarget.27387 |
| Rbfox1 up-regulation impairs BDNF-dependent hippocampal LTP by dysregulating TrkB isoform expression levels | Elife | 2019 | https://doi.org/10.7554/eLife.49673.001 |
| Single chromosome aneuploidy induces genome-wide perturbation of nuclear organization and gene expression | Neoplasia | 2019 | https://doi.org/10.1016/j.neo.2019.02.003 |
| Genomic comparison of Trypanosoma conorhini and Trypanosoma rangeli to Trypanosoma cruzi strains of high and low virulence | BMC genomics | 2018 | https://doi.org/10.1186/s12864-018-5112-0 |
| Towards Predicting Graft Vs Host Disease from Predicted Tissue Specific Minor Histocompatibility Antigens | Blood | 2018 | https://doi.org/10.1182/blood-2018-99-119783 |
| Determining the quantitative principles of T cell response to antigenic disparity in stem cell transplantation | Frontiers in immunology | 2018 | https://doi.org/10.3389/fimmu.2018.02284 |
| ONC201 kills breast cancer cells in vitro by targeting mitochondria | Oncotarget | 2018 | https://doi.org/10.18632/oncotarget.24862 |
| Discovery of Kaposi's sarcoma herpesvirus-encoded circular RNAs and a human antiviral circular RNA | Proceedings of the National Academy of Sciences | 2018 | https://doi.org/10.1073/pnas.1816183115 |
| MEEPTOOLS: a maximum expected error based FASTQ read filtering and trimming toolkit | International Journal of Computational Biology and Drug Design | 2017 | https://doi.org/10.1504/IJCBDD.2017.085409 |
| Dynamical system modeling to simulate donor T cell response to whole exome sequencing-derived recipient peptides: Understanding randomness in alloreactivity incidence following stem cell transplantation | PLoS One | 2017 | https://doi.org/10.1371/journal.pone.0187771 |
| Cytomegalovirus Antigenic Mimicry of Human Alloreactive Peptides: Exploring Cross-Reactivity As a Potential Trigger for Graft Versus Host Disease | Biology of Blood and Marrow Transplantation | 2017 | https://doi.org/10.1016/j.bbmt.2016.12.649 |
| Whole Exome Sequencing to Determine the Likelihood of Graft Versus Host Disease in Stem Cell Transplant Donor-Recipient Pairs | Biology of Blood and Marrow Transplantation | 2017 | https://doi.org/10.1016/j.bbmt.2016.12.650 |
| Whole Exome Sequencing and in silico Determination of the Magnitude of Alloreactive Antigen Presentation on HLA DRB1 in Allogeneic Stem Cell Transplant Recipients | Biology of Blood and Marrow Transplantation | 2017 | https://doi.org/10.1016/j.bbmt.2016.12.339 |
| Sequence homology between HLA-bound cytomegalovirus and human peptides: A potential trigger for alloreactivity | PloS one | 2017 | https://doi.org/10.1371/journal.pone.0178763 |
| Dynamical System Modeling to Simulate Donor T Cell Response to Whole Exome Sequencing-Derived Recipient Peptides Demonstrates Different Alloreactivity Potential in HLA-Matched and-Mismatched Donor–Recipient Pairs | Biology of Blood and Marrow Transplantation | 2016 | https://doi.org/10.1016/j.bbmt.2015.11.1103 |
| MeFiT: merging and filtering tool for illumina paired-end reads for 16S rRNA amplicon sequencing | BMC bioinformatics | 2016 | https://doi.org/10.1186/s12859-016-1358-1 |
| Comparison of Lactobacillus crispatus isolates from Lactobacillus-dominated vaginal microbiomes with isolates from microbiomes containing bacterial vaginosis-associated bacteria | Microbiology | 2016 | https://doi.org/10.1099/mic.0.000238 |
| Identification of a gene in Mycoplasma hominis associated with preterm birth and microbial burden in intraamniotic infection | American journal of obstetrics and gynecology | 2015 | https://doi.org/10.1016/j.ajog.2015.01.032 |
| 3d interaction homology: The structurally known rotamers of tyrosine derive from a surprisingly limited set of information‚Äêrich hydropathic interaction environments described by maps | Proteins: Structure, Function, and Bioinformatics | 2015 | https://doi.org/10.1002/prot.24813 |
| Exome Sequencing Derived Alloreactivity Potential May Predict Gvhd in Allogeneic Stem Cell Transplantation | Blood | 2015 | https://doi.org/10.1182/blood.V126.23.3078.3078 |
| Peptides Derived from the CMV Proteome Mimic Unique Stem Cell Transplant Recipient Specific Peptides: Possible Role in Eliciting a Pro-Gvh T Cell Response | Blood | 2015 | https://doi.org/10.1182/blood.V126.23.4285.4285 |
| Understanding Water and Its Many Roles in Biological Structure: Ways to Exploit a Resource for Drug Discovery | Computer-Aided Drug Discovery | 2015 | https://doi.org/10.1007/7653_2015_58 |
| Whole exome sequencing to estimate alloreactivity potential between donors and recipients in stem cell transplantation | British journal of haematology | 2014 | https://doi.org/10.1111/bjh.12898 |
| BOTUX: Bayesian-like operational taxonomic unit examiner | International journal of computational biology and drug design | 2014 | https://doi.org/10.1504/IJCBDD.2014.061652 |
| Stem cell transplantation as a dynamical system: are clinical outcomes deterministic? | Frontiers in immunology | 2014 | https://doi.org/10.3389/fimmu.2014.00613 |
| Differences in vaginal microbiome in African American women versus women of European ancestry | Microbiology | 2014 | https://doi.org/10.1099/mic.0.081034-0 |
| In silico derivation of HLA-specific alloreactivity potential from whole exome sequencing of stem-cell transplant donors and recipients: understanding the quantitative immunobiology of allogeneic transplantation | Frontiers in immunology | 2014 | https://doi.org/10.3389/fimmu.2014.00529 |
| Applying an empirical hydropathic forcefield in refinement may improve low-resolution protein X-ray crystal structures | PLoS One | 2011 | https://doi.org/10.1371/journal.pone.0015920 |
| Phase transformations during sintering of titania nanoparticles | ACS nano | 2008 | https://doi.org/10.1021/nn800092m |
| Sintering of titanium dioxide nanoparticles: a comparison between molecular dynamics and phenomenological modeling | Journal of Nanoparticle Research | 2008 | https://doi.org/10.1007/s11051-007-9342-3 |
| Molecular dynamics study of water adsorption on TiO2 nanoparticles | The Journal of Physical Chemistry C | 2007 | https://doi.org/10.1021/jp0666380 |
| Molecular dynamics simulation of titanium dioxide nanoparticle sintering | The Journal of Physical Chemistry B | 2005 | https://doi.org/10.1021/jp054667p |