School of Systems Biology

All Items

• Assessing a Correlation between Predicted Protein Stability and Antibiotic Resistance of Beta-Lactamase Enzymes

  SARINA LI, SHARANYA TUMMA, Iosif Vaisman

• Extracellular Vesicles derived from Cancer demonstrate Autophagosome Properties

  Daivik Siddhi, Marissa Howard, James Erickson, Heather Branscome, Dr. Amanda Haymond, Dr. Virginia Espina, Dr. Fatah Kashanchi, Dr. Lance Liotta

• Advancing Scientific Communication about Cancer Research: How to Develop Inhibitors for PD-1 and PD-L1 and Why It Is So Important

  SIRI NIKKU, Rachel Carter, Amanda Haymond

• Analysis of Bacterial Microbiome and Human Proteome for Lung Cancer Characterization via Affinity Nanoparticles and De Novo Assisted Database Search Mass Spectrometry

  RAYMOND DEL VECCHIO, Rayan Alhammad, Ruben Magni, Alessandra Luchini

• Analysis of CFTR Gene Mutations in Cystic Fibrosis

  PRANAV PREM, Iosif Vaisman

• Application of Nylon Affinity Nets to Capture Tuberculosis Extracellular Vesicles and Identify Protein Biomarkers

  VIDHI SHARMA, MERICA PATRICIA TALLEY, Ahana Byne, Barbara Birkaya, Alessandra Luchini

• Assessing the Immunogenicity of DNA Scaffolding for Hybrid Molecular Modalities in THP-1 Cells

  Hanna Sovinski, Jessica Roman, Alessandra Luchini, Lance Liotta, Remi Veneziano, Amanda Haymond

• AutoMute2.0 to Predict Disease-Causing and Neutral Mutations in Human Transmembrane Proteins

  Abhinav Pappu, Dr. Iosif I. Vaisman

• BERT Feature Embeddings Fused With Physiochemical Feature Representations Yields More Accurate and Versatile Model for Prediction of Blood Brain Barrier Penetrating Peptides

  MYTHREYA DHARANI, Iosif Vaisman

• Binding of indolicidin to the DMPC bilayer using molecular dynamics simulations

  KUBER GOHIL, Christopher Lockhart

• Capturing Exosomes in Urine using a Polyamide 6 - Affinity Net

  ADYA MISRA, AZADA SAMADI, Rocio Cornero, Alessandra Luchini

• Characterization of Large EVs From Breast Cancer Cells

  Christopher Pishvaian, Yuriy Kim, Dr. Lance Liotta, Dr. Fatah Kashanchi

• Characterization of the Saliva Microbiome in Women with Suspicious Mammograms

  EMRE NALBANTOGLU, Ngoc Vuong, Ruben Magni, Virginia Espina, Lance Liotta, Alessandra Luchini

• Characterizing Interactions Between PD-1 and PD-L1 in Cell-Based Models of Ovarian Cancer and Investigating the Effect of Chemotherapy on Cancer-Derived Exosomes

  SIRI NIKKU, Amanda Haymond

• Computational Model of Vaccination Effects for COVID-19

  SHAWN KIM, Marissa Howard, Lance Liotta

• Computational Model to Analyze Calcium Imbalances in Cells Affected by Alzheimer's Disease

  RIYA DEV, Aman Ullah

• Computational study on the transmission of COVID-19 in Virginia using SIQR Model

  Benoy Sen, Dr. Aman Ullah

• Creation of Printable Protein Models from Atomic Coordinates

  Maxwell Meytin, Dr. Iosif Vaisman

• Data Analysis of Genetic Variability in Alzheimer's Affected Brains

  AKANKSHA TIBREWALA, Aman Ullah

• Data Analysis of Genetic Variability in Alzheimer’s Affected Brains

  Akanksha Tibrewala, Dr. Aman Ullah

• De novo drug design for a protein binding site

  MUHAMMAD CHAWLA, Christopher Lockhart

• Deciphering Age-Associated Gene Expression Patterns in Colon Cancer: Implications for Older Patients' Risk and Survival

  ERIKA LI, NAVNEETH MURAL, Eric Twum, Aman Ullah

• Development of a Model for Ductal Carcinoma in Situ Progression Using the Processing Visualization Software

  MEERA GUPTA, Marissa Howard, Lance Liotta

• Differential Gene Expression Analysis of Alzheimer & Type 1 Diabetic Patients

  SARA ABOUELNAGA, KAAN EGUZ, Brenda Ngo, Aman Ullah

• Effect of Extracellular Vesicles from HTLV-1 Infected Cells on Recipient Uninfected Cells

  ARNAV SUBEDI, Fatah Kashanchi

• Effect of TAR Binding Molecules on HIV-1 Proviral Transcription

  Rhea Tammireddi, Dr. Pooja Khatkar, Dr. Fatah Kashanchi

• Evaluating Reduced and Oxidized Abeta Peptides Using Machine Learning

  Kuber Gohil; Dr. Christopher Lockhart

• Evaluating the Viability of Saliva-based Sampling in COVID-19 Diagnostic Tests Compared to Nasopharyngeal (NP) and Oropharyngeal Swabs (OP)

  JASMINE LAOUDI, Dr. Fatah Kashanchi, Mahla Dehbandi

• Evaluation of differential G-protein subunit markers for HIV latent infection in Jurkat and A3R5.7 cells

  SAMUEL LI, LUKE MEHTA, Linda Chillin, Sameer Tiwari, Yuntao Wu

• Exploring Drug Resistance in Breast Cancer Using a Boolean Model

  KEERTANA YALAMANCHILI, Saleet Jafri

• Exploring Drug Resistance in Gastrointestinal Cancer Using a Network Model

  SREENIDHI SANKARARAMAN, Saleet Jafri

• Extracellular Vesicles from HTLV-1 Infected Cells Induce Secretion of Proinflammatory Cytokines in Recipient Blood Brain Barrier Cells

  Jamie Nelson, Daniel Pinto, James Erickson, Heather Branscome, Dr. Fatah Kashanchi

• HIV-1 Transcription Inhibition Using Small RNA-Binding Molecules

  MAYA PASHAI, Yuriy Kim, Anastasia Williams, Fatah Kashanchi

• Identification of substrates for Francisella novicida chitinases in order to characterize the importance of chitinase in biofilm formation

  Samuel Littman, Alex Irizarry, Dr. Monique Van Hoek

• IF EVs: a new molecular measurement of mitochondrial health

  LINDA HUANG, ANJU ADVANI, EMMA MATHEW, LAYLA HASANZADAH, Olivia Montemurro, Angela Rojas, Purva Gade, Marissa Howard, Lance Liotta

• Incorporating COVID-19 Ion Channel Adaptations to Understand Immune Response

  Vaibhav Gurunathan, Dr. Saleet Jafri

• Incorporating Ryanodine Receptor Calcium Release Channels into a Computational Model of Calcium Concentration in T-Lymphocytes

  VICKY CHEN, Saleet Jafri

• Investigating Viral Entry Routes and the Impact of SARS-CoV-2 on the Central Nervous System

  KRISHNA PAHWA, SAUMAN DAS, ELIZABETH MCCLOUGH, Fatah Kashanchi

• Machine Learning Approaches and Methods for Discriminating B-Cell Epitopes, specifically in COVID-19 Spike Proteins

  David Mastro, Dr. Iosif Vaisman

• Machine Learning Models of CHI3L1 Mutant Pathogenicity using Computational Mutagenesis

  ALEXANDRA CARAUS, Iosif Vaisman

• Modeling Future Spread of COVID-19 in Different U.S. States in Light of Disparate Vaccination Rates and the Delta Variant's Rise

  DANIEL LEVERETT, Saleet Jafri

• Modeling the Effect of Gene Expression Variation on T cell Activation and Differentiation

  VAIBHAV GURUNATHAN, Saleet Jafri

• Network analysis of replica exchange simulations

  MARÍA JOSÉ DÍAZ DELGADO, Christopher Lockhart

• Novel Role for Phosphorylated Merlin and Mitophagy Triggered PINK-1 in Neurofibromatosis Type 2 Meniningiomas

  EMMA MATHEW, Angela Rojas, ANJU ADVANI, LAYLA HASANZADAH, LINDA HUANG, Purva Gade, Marissa Howard, Ali Andalibi, Lance Liotta

• Optimization of Nucleo-Cytosol Separation to capture EZH2 subcellular localization in Non-Small Cell Lung Cancers

  LENA HASAN, RUSUL ABDULRAZZAQ, AANYA KOLLI, Abduljalil Alsubaie, Mariaelena Pierobon

• Oral Fluid Drug Testing: What Interferes With These On-Site Kits?

  VALERIE CRUZ ORTIZ, Sydney Andes, Paul Russo, Sally Rucker, Virginia Espina

• Plants Could Provide a New Dimension to Crime Scene Analysis

  TIMOTHY STOCKER, Paul Russo, Weidong Zhou, Virginia Espina

• Predicting optimal catalytic temperature of enzymes using Graph Convolutional Networks

  LUKE MEI, Iosif Vaisman

• Protect or potentiate: The Role of Common Medications in Response to Radiotherapy

  Sydney Andes, Dr. Justin Davis, Daniel Pinto, Dr. Fatah Kaschanchi, Dr. Claudius Mueller, Dr. Virginia Espina

• Proteomics Profiling Around the AMPK-AKT Signaling Pathway Using the Reverse Phase Array Technology Reveals a Predictive Model for Both Recurrence and Overall Survival in NSCLC as well as Drug Sensitivity in Ovarian Cancer

  CODY JONES, Emanuel F Petricoin

• RexDash: A Comprehensive Dashboard for Analyzing the Technical Performance of Replica Exchange Molecular Dynamics Simulations

  SOHAM JAIN, Christopher Lockhart

• RNA-Sequence Analysis of the mdx Mouse Model of Duchenne Muscular Dystrophy

  BHAVYA BODDU, Aman Ullah

• Saliva Genotyping Using the 96.96 IFC with SNP Type Assays

  AURORA RICHARD, SHREYES AIER, Cade Skislak, Amy Young, Lance Liotta

• Secretory Mitophagy Exports p53: A new pro-tumor survival mechanism.

  LAYLA HASANZADAH, ANJU ADVANI, EMMA MATHEW, LINDA HUANG, Angela Rojas, Purva Gade, Marissa Howard, Lance Liotta

• Sequence-based Models of Antimicrobial Peptide Stability

  JASMINE MA, Iosif Vaisman

• Testing Ab Initio Designed Antimicrobial Peptides Against Multi-Drug Resistant Acinetobacter baumannii

  Gabriel Ascoli, Fahad Alsaab, Dr. Monique Van Hoek

• The Effect of Cannabidiol and HU308 on Extracellular Vesicle Populations of HIV-1 Infected Monocytes

  Vivian Gao, Anastasia Williams, Yuriy Kim, Dr. Fatah Kashanchi

• The Use of CBD and HU308 in HIV-1 Infected cells and their response to M1

  SABRINA ROJAS, Anastasia Williams, Fatah Kashanchi

• The Use of Mass Spectrometry to Determine Fatal Intoxication of Synthetic Cannabinoids, Baclofen, and PGAs through Body Matrices in Forensic Toxicology

  ADELAIDE GANNON, Emanuel F Petricoin

• The α7 Nicotinic Acetylcholine Receptor: Computational Modeling of Channel Gating

  SOHINI BANERJEE, Aman Ullah

• Therapeutics and Vaccines in the Fight Against COVID-19

  HARRISH GANESH, ALEX KASHANCHI, Fatah Kashanchi, Anastasia Williams

• Tumor Suppressor Merlin Offers a New Therapeutic Strategy for HER2-Low Breast Cancer

  ANJU ADVANI, LAYLA HASANZADAH, EMMA MATHEW, LINDA HUANG, Angela Rojas, Purva Gade, Marissa Howard, Lance Liotta

• Using a Convolutional Neural Network to Classify Nanobodies on Neutralizing Ability Using Sequence Data for SARS-Cov-2

  NITHYA VINODH, losif Vaisman

• Vaccine Effect of Extracellular Vesicles from HTLV-1 Infected Cells

  Jacob Yu, Yuriy Kim, Anastasia Williams, Dr. Fatah Kashanchi