publications

publications by categories in reversed chronological order. generated by jekyll-scholar.

2023

  1. MUC16 and TP53 family co-regulate tumor-stromal heterogeneity in pancreatic adenocarcinoma
    Ramakanth Chirravuri-Venkata, Vi Dam, Rama Krishna Nimmakayala, and 8 more authors
    Frontiers in Oncology, 2023
  2. Engineering an ACE2-Derived Fragment as a Decoy for Novel SARS-CoV-2 Virus
    Fabiana Renzi, Austin Seamann, Koelina Ganguly, and 5 more authors
    ACS Pharmacology & Translational Science, 2023
    PDF
  3. Cross-reactivity influences changes in human influenza A virus and Epstein Barr virus specific CD8 memory T cell receptor alpha and beta repertoires between young and old
    Fransenio Clark, Anna Gil, Ishwor Thapa, and 3 more authors
    Frontiers in Immunology, 2023
  4. A Novel HOXA10-Associated 5 Gene-Based Prognostic Signature for Stratification of Short-Term Survivors of Pancreatic Ductal Adenocarcinoma
    Sophia G. Kisling, Pranita Atri, Ashu Shah, and 5 more authors
    Clinical Cancer Research, Jul 2023
  5. Modeling preferential attraction to infected hosts in vector-borne diseases
    Ishwor Thapa, and Dario Ghersi
    Frontiers in Public Health, Jul 2023
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2022

  1. Mucin 5AC–Mediated CD44/ITGB1 Clustering Mobilizes Adipose-Derived Mesenchymal Stem Cells to Modulate Pancreatic Cancer Stromal Heterogeneity
    Koelina Ganguly, Jesse L Cox, Dario Ghersi, and 5 more authors
    Gastroenterology, Jul 2022
  2. Electronic health record (EHR) simulation into biomedical informatics course improves students’ understanding of the impact of EHR documentation burden and usability on clinical workflow
    Martina A Clarke, and Dario Ghersi
    Health and Technology, Jul 2022
  3. Variant calling enhances the identification of cancer cells in single-cell RNA sequencing data
    William Gasper, Francesca Rossi, Matteo Ligorio, and 1 more author
    PLoS computational biology, Jul 2022
    PDF
  4. Cross-Reactive T Cell Response Exists in Chronic Lymphocytic Choriomeningitis Virus Infection upon Pichinde Virus Challenge
    Jasmin Mischke, Sebastian Klein, Austin Seamann, and 5 more authors
    Viruses, Jul 2022
  5. Integrative Analysis of Genetic and Tumor Microenvironment Topology to Delineate Prognostic Subtypes in Mantle Cell Lymphoma
    Sunandini Sharma, Alyssa C Bouska, Alicia Gamboa, and 8 more authors
    Blood, Jul 2022
  6. Cross-reactivity influences changes in human influenza A virus and Epstein Barr virus specific CD8 memory T cell receptor alpha and beta repertoires between young and old
    Fransenio Clark, Anna Gil, Ishwor Thapa, and 3 more authors
    Frontiers in Immunology, Jul 2022

2021

  1. SwarmTCR: a computational approach to predict the specificity of T cell receptors
    Ryan Ehrlich, Larisa Kamga, Anna Gil, and 3 more authors
    BMC bioinformatics, Jul 2021
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  2. Mucin Expression and Splicing Determine Novel Subtypes and Patient Mortality in Pancreatic Ductal AdenocarcinomaPDAC Survival and Subtyping by Mucin Profiling
    Christopher M Thompson, Andrew Cannon, Sean West, and 8 more authors
    Clinical Cancer Research, Jul 2021
  3. Mucin 5 AC Tunes Adipose-Mesenchymal Stem Cells to Regulate Stromal Heterogeneity in Pancreatic Cancer
    K Ganguly, J Cox, D Ghersi, and 2 more authors
    In PANCREAS, Jul 2021
  4. Pre-clinical Assessment of ISOX, A Potential New Therapeutic For Pancreatic Cancer
    P Atri, G Natarajan, P Seshacharyulu, and 8 more authors
    In PANCREAS, Jul 2021
  5. Identifying Molecular Fragments That Drive 7-Dehydrocholesterol Elevation
    Dario Ghersi, and Thiago C Genaro-Mattos
    ACS Pharmacology & Translational Science, Jul 2021
  6. Automatic Extension of Medical Subject Headings (MeSH) Thesaurus to Emerging Research
    William Gasper, Jiahao Ma, Dario Ghersi, and 3 more authors
    In 2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Jul 2021
  7. A new approach for analyzing safety and performance factors in civil infrastructures using correlation networks and population analysis
    Prasad Chetti, Hesham H Ali, Dario Ghersi, and 3 more authors
    In 13th International Workshop on Structural Health Monitoring: Enabling Next-Generation SHM for Cyber-Physical Systems, IWSHM 2021, Jul 2021

2020

  1. Presence and structure-activity relationship of intrinsically disordered regions across mucins
    Joseph Carmicheal, Pranita Atri, Sunandini Sharma, and 7 more authors
    FASEB journal: official publication of the Federation of American Societies for Experimental Biology, Jul 2020
  2. MUCIN-4 (MUC4) is a novel tumor antigen in pancreatic cancer immunotherapy
    Shailendra K Gautam, Sushil Kumar, Vi Dam, and 3 more authors
    In Seminars in immunology, Jul 2020
  3. Epstein-barr virus epitope–major histocompatibility complex interaction combined with convergent recombination drives selection of diverse t cell receptor αand βrepertoires
    Anna Gil, Larisa Kamga, Ramakanth Chirravuri-Venkata, and 5 more authors
    MBio, Jul 2020
  4. Differential mutation spectrum and immune landscape in African Americans versus Whites: A possible determinant to health disparity in head and neck cancer
    Sanjib Chaudhary, Vi Dam, Koelina Ganguly, and 8 more authors
    Cancer letters, Jul 2020
  5. CXCR3 and cognate ligands are associated with immune cell alteration and aggressiveness of pancreatic ductal adenocarcinoma
    Andrew Cannon, Christopher M Thompson, H Carlo Maurer, and 7 more authors
    Clinical Cancer Research, Jul 2020
  6. NEEP: null empirically estimated p-values for high-throughput molecular survival analysis
    Sean West, Hesham Ali, and Dario Ghersi
    Journal of Open Source Software, Jul 2020
  7. PD-L1 checkpoint inhibition narrows the antigen-specific T cell receptor repertoire in chronic lymphocytic choriomeningitis virus infection
    S Klein, D Ghersi, MP Manns, and 3 more authors
    Journal of virology, Jul 2020
  8. Cancer-associated fibroblasts: versatile players in the tumor microenvironment
    Debolina Ganguly, Raghav Chandra, John Karalis, and 8 more authors
    Cancers, Jul 2020
  9. MeSH Indexing Using the Biomedical Citation Network
    William Gasper, Parvathi Chundi, and Dario Ghersi
    In Proceedings of the 11th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics, Jul 2020
  10. Measurement of structural change in co-expression networks from cancer gene expression data
    Qianran Li, Dario Ghersi, Ishwor Thapa, and 3 more authors
    International Journal of Data Mining and Bioinformatics, Jul 2020

2019

  1. Uncovering and characterizing splice variants associated with survival in lung cancer patients
    Sean West, Sushil Kumar, Surinder K Batra, and 2 more authors
    PLoS computational biology, Jul 2019
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  2. Computer modeling of clonal dominance: memory-anti-naive and its curbing by attrition
    Filippo Castiglione, Dario Ghersi, and Franco Celada
    Frontiers in immunology, Jul 2019
    PDF
  3. FunSet: an open-source software and web server for performing and displaying Gene Ontology enrichment analysis
    Matthew L Hale, Ishwor Thapa, and Dario Ghersi
    Bmc Bioinformatics, Jul 2019
    PDF
  4. Pre-clinical development of ISOX; A novel therapy for pancreatic cancer identified utilizing system biology approach (s)
    Pranita Atri, Parthasarathy Seshacharyulu, Satyanaryana Rachagani, and 8 more authors
    Cancer Research, Jul 2019
  5. A novel mechanism for pancreatic cancer stem cell maintenance: PAF1C-independent role of PAF1
    Saswati Karmakar, Sanchita Rauth, Rama Krishna Nimmakayala, and 6 more authors
    Cancer Research, Jul 2019
  6. Influenza A virus (IAV) infection in humans leads to expansion of highly diverse CD8 T cell repertoires cross-reactive with Epstein Barr virus (EBV)
    Anna Gil, Rabi Mishra, InYoung Song, and 3 more authors
    The Journal of Immunology, Jul 2019
  7. CDR3αdrives selection of the immunodominant Epstein Barr virus (EBV) BRLF1-specific CD8 T cell receptor repertoire in primary infection
    Larisa Kamga, Anna Gil, Inyoung Song, and 6 more authors
    PLoS pathogens, Jul 2019
  8. Identifying structural changes in correlation networks models of cancer gene expression by stage
    Qianran Li, Dario Ghersi, Ishwor Thapa, and 3 more authors
    In 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Jul 2019

2018

  1. Biological pathway data formats and standards
    Ramakanth C Venkata, and Dario Ghersi
    In Encyclopedia of Bioinformatics and Computational Biology: ABC of Bioinformatics, Jul 2018
  2. Cluster analysis of biological networks
    Asuda Sharma, Hesham Ali, and Dario Ghersi
    Encyclopedia of Bioinformatics and Computational Biology: ABC of Bioinformatics, Jul 2018
  3. Two critical positions in zinc finger domains are heavily mutated in three human cancer types
    Daniel Munro, Dario Ghersi, and Mona Singh
    PLoS computational biology, Jul 2018
  4. Elucidating the role of MUC5AC-MET axis in breast cancer brain metastasis
    Mohd W Nasser, Shailendra K Gautam, Ranjana Kanchan, and 8 more authors
    Cancer Research, Jul 2018
  5. Biological pathway analysis
    Ramakanth Chirravuri Venkata, and Dario Ghersi
    In Encyclopedia of Bioinformatics and Computational Biology: ABC of Bioinformatics, Jul 2018

2017

  1. Broad TCR repertoire and diverse structural solutions for recognition of an immunodominant CD8+ T cell epitope
    InYoung Song, Anna Gil, Rabinarayan Mishra, and 3 more authors
    Nature structural & molecular biology, Jul 2017
  2. Contribution of the T cell receptor to the generation and maintenance of EBV epitopespecific CD8 T cell responses following primary infection
    Larisa Kamga, Robin Brody, Anita Gautam, and 3 more authors
    The Journal of Immunology, Jul 2017
  3. Unique influenza A cross-reactive memory CD8 T-cell receptor repertoire has a potential to protect against EBV seroconversion
    Levi B Watkin, Rabinarayan Mishra, Anna Gil, and 4 more authors
    Journal of Allergy and Clinical Immunology, Jul 2017
  4. Comparison of a quantum random number generator with pseudorandom number generators for their use in molecular Monte Carlo simulations
    Dario Ghersi, Abhishek Parakh, and Mihaly Mezei
    Journal of computational chemistry, Jul 2017
  5. Analysis of Clinical Significance of MUC4 Isoforms in Pancreatic Cancer Patients Using TCGA RNA-Seq Dataset
    CM Thompson, S Kumar, D Ghersi, and 4 more authors
    In PANCREAS, Jul 2017
  6. A System Biology Approach via Connectivity Mapping (CMAP) to Identify New Therapeutic Targets Against Lethal Pancreatic Cancer
    P Atri, D Ghersi, S Kaur, and 2 more authors
    In PANCREAS, Jul 2017
  7. PD2 Functions as the Master Regulator of Stem Cell Network Genes in Pancreatic Cancer
    S Karmakar, S Barkeer, D Ghersi, and 3 more authors
    In PANCREAS, Jul 2017
  8. Severity of acute infectious mononucleosis correlates with cross-reactive influenza CD8 T-cell receptor repertoires
    Nuray Aslan, Levi B Watkin, Anna Gil, and 6 more authors
    MBio, Jul 2017
  9. Analyzing T cell receptor alpha/beta usage in binding to the pMHC
    Ryan Ehrlich, and Dario Ghersi
    In 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Jul 2017
  10. In-silico analysis of the “memory anti-Naı̈ve” effect in anti-viral cross-reactive responses
    Filippo Castiglione, Dario Ghersi, and Franco Celada
    In 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Jul 2017
  11. Severity of acute infectious mononucleosis correlates with cross-reactive influenza CD8 T-cell receptor repertoires. mBio 8: e01841-17
    N Aslan, LB Watkin, A Gil, and 6 more authors
    Jul 2017

2016

  1. Building towards precision medicine: empowering medical professionals for the next revolution
    Scott McGrath, and Dario Ghersi
    BMC medical genomics, Jul 2016
  2. Identifying enriched drug fragments as possible candidates for metabolic engineering
    Sunandini Sharma, Kritika Karri, Ishwor Thapa, and 2 more authors
    BMC medical genomics, Jul 2016
  3. Recovering Bound Forms of Protein Structures Using the Elastic Network Model and Molecular Interaction Fields
    Dario Ghersi, and Roberto Sanchez
    In Proceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, Jul 2016
  4. Forecasting the spread of mosquito-borne disease using publicly accessible data: a case study in Chikungunya
    Kathryn M Cooper, Dhundy R Bastola, Robin Gandhi, and 4 more authors
    In AMIA Annual Symposium Proceedings, Jul 2016

2014

  1. Interaction-based discovery of functionally important genes in cancers
    Dario Ghersi, and Mona Singh
    Nucleic Acids Research, Jul 2014
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  2. molBLOCKS: decomposing small molecule sets and uncovering enriched fragments
    Dario Ghersi, and Mona Singh
    Bioinformatics, Jul 2014

2013

  1. Disentangling function from topology to infer the network properties of disease genes
    Dario Ghersi, and Mona Singh
    BMC Systems Biology, Jul 2013

2012

  1. Automated identification of binding sites for phosphorylated ligands in protein structures
    Dario Ghersi, and Roberto Sanchez
    Proteins: Structure, Function, and Bioinformatics, Jul 2012

2011

  1. Computer simulations of heterologous immunity: highlights of an interdisciplinary cooperation
    Claudia Calcagno, Roberto Puzone, Yanthe E Pearson, and 5 more authors
    Autoimmunity, Jul 2011
  2. Beyond structural genomics: computational approaches for the identification of ligand binding sites in protein structures
    Dario Ghersi, and Roberto Sanchez
    Journal of structural and functional genomics, Jul 2011
  3. Systematic assessment of accuracy of comparative model of proteins belonging to different structural fold classes
    Suvobrata Chakravarty, Dario Ghersi, and Roberto Sanchez
    Journal of molecular modeling, Jul 2011

2010

  1. Biochemical profiling of histone binding selectivity of the yeast bromodomain family
    Qiang Zhang, Suvobrata Chakravarty, Dario Ghersi, and 4 more authors
    PloS one, Jul 2010

2009

  1. A discrete computer model of the immune system reveals competitive interactions between the humoral and cellular branch and between cross-reacting memory and naı̈ve responses
    Yiming Cheng, Dario Ghersi, Claudia Calcagno, and 3 more authors
    Vaccine, Jul 2009
  2. SITEHOUND-web: a server for ligand binding site identification in protein structures
    Marylens Hernandez, Dario Ghersi, and Roberto Sanchez
    Nucleic acids research, Jul 2009
  3. Improving accuracy and efficiency of blind protein-ligand docking by focusing on predicted binding sites
    Dario Ghersi, and Roberto Sanchez
    Proteins: Structure, Function, and Bioinformatics, Jul 2009
  4. EasyMIFS and SiteHound: a toolkit for the identification of ligand-binding sites in protein structures
    Dario Ghersi, and Roberto Sanchez
    Bioinformatics, Jul 2009
  5. EasyMIFs and SiteHound
    Dario Ghersi, and Roberto Sanchez
    Bioinformatics, Jul 2009

2006

  1. Narrowed TCR repertoire and viral escape as a consequence of heterologous immunity
    Markus Cornberg, Alex T Chen, Lee A Wilkinson, and 8 more authors
    The Journal of clinical investigation, Jul 2006
  2. IFN-induced attrition of CD8 T cells in the presence or absence of cognate antigen during the early stages of viral infections
    Kapil Bahl, Sung-Kwon Kim, Claudia Calcagno, and 5 more authors
    The Journal of Immunology, Jul 2006

2004

  1. CD8 memory T cells: cross-reactivity and heterologous immunity
    Liisa K Selin, Markus Cornberg, Michael A Brehm, and 6 more authors
    In Seminars in immunology, Jul 2004