Works

Skip to main content

Part of the Bioinformatics Commons

2023

DeepHTLV: a Deep Learning Framework for Detecting Human T-Lymphotrophic Virus 1 Integration Sites, Johnathan Jia, Johnathan Jia
Dissertations and Theses (Open Access)

Adipocytes and Innate Immunity in Systemic Sclerosis, Nancy Wareing
Dissertations and Theses (Open Access)

Gene Expression–Based Algorithms for the Identification of Drug Combinations in Personalized Medicine, Lon Fong
Dissertations and Theses (Open Access)

2022

The Role of the Hypoxia-Inducible Factor 2 in Pancreatic Cancer: Mechanisms of Tumor Immunosuppression and Intestinal Radioprotection, Carolina Garcia Garcia
Dissertations and Theses (Open Access)

Genomewide CRISPR/Cas9 Screen Identifies Network of Protein Complexes that Regulate TRIM24, Lalit Patel
Dissertations and Theses (Open Access)

HAPLOTYPE-INFORMED ALLELIC IMBALANCE DETECTION FROM RNA IN CANCER, Zuhal Ozcan
Dissertations and Theses (Open Access)

Decoding Copy Number Substructure and Evolution from Single Cell Genomics, Darlan Conterno Minussi
Dissertations and Theses (Open Access)

COMPUTATIONAL APPROACHES TO UNDERSTAND CHEMORESISTANCE & TUMOR EVOLUTION USING LONGITUDINAL CLINICAL DATA AND LINEAGE TRACING, Sahil Seth
Dissertations and Theses (Open Access)

EXPLOITING CHEMOGENETIC AND GENETIC INTERACTIONS IN HUMAN CELLS AS AN AVENUE FOR NEW THERAPEUTIC OPPORTUNITIES, Medina Colic
Dissertations and Theses (Open Access)

An Investigation of Epigenetic Mechanisms Driving the Biology of Head and Neck Squamous Cell Carcinoma, Scot Carson Callahan
Dissertations and Theses (Open Access)

INVESTIGATING THE ECOLOGY AND EVOLUTION OF NORMAL BREAST TISSUES AND BREAST CANCER WITH SINGLE CELL GENOMICS, Tapsi Kumar, Tapsi Kumar
Dissertations and Theses (Open Access)

2021

Unveiling global roles of G-quadruplexes and G4-22 in human genetics, Ruth Barros De Paula
Dissertations and Theses (Open Access)

Impact of Intratumor Heterogeneity and the Tumor Microenvironment in Shaping Tumor Evolution and Response to Therapy, Akash Mitra
Dissertations and Theses (Open Access)

Rare variant association studies in Crohn’s Disease and Colorectal Cancer: methods and applications, Jiun-Sheng Chen
Dissertations and Theses (Open Access)

DISCOVERY OF NOVEL UBIQUITIN- AND METHYLATION-DEPENDENT INTERACTIONS USING PROTEIN DOMAIN MICROARRAYS, Jianji Chen
Dissertations and Theses (Open Access)

Computational Approaches to Delineate Transcriptional and Functional Heterogeneity in Pancreatic Cancer, Sanjana Srinivasan
Dissertations and Theses (Open Access)

BIASES AND BLIND-SPOTS IN GENOME-WIDE CRISPR-CAS9 KNOCKOUT SCREENS, Merve Dede
Dissertations and Theses (Open Access)

2020

DECODING THE EVOLUTIONARY RESPONSE TO PROSTATE CANCER THERAPY USING PLASMA GENOME SEQUENCING, Naveen Ramesh
Dissertations and Theses (Open Access)

INVESTIGATION OF PROLIFERATION SUPPRESSORS IN GENETIC FITNESS SCREENS, Walter Frank Lenoir IV
Dissertations and Theses (Open Access)

DEVELOPMENT OF COMPUTATIONAL TOOLS TO TARGET MICRORNA, Luo Song
Dissertations and Theses (Open Access)

A CONTEXT-FORWARD IN VIVO FUNCTIONAL GENOMICS PLATFORM FOR TARGET DISCOVERY AND ESTABLISHING VULNERABILITY CONTEXT IN PANCREATIC CANCER, Johnathon Rose, Johnathon Lynn Rose
Dissertations and Theses (Open Access)

PUTATIVE ROLES OF CD200 IN THE LEUKEMOGENESIS AND IMMUNE EVASION OF LEUKEMIA STEM CELLS, Shelley Herbrich
Dissertations and Theses (Open Access)

IDENTIFICATION OF TRIM24 DOMAIN ESSENTIALITY IN PRIMARY TRIM24COE CARCINOSARCOMA CELL LINES, Cem Dede
Dissertations and Theses (Open Access)

UNDERSTANDING INTERCELLULAR SIGNALING DURING LUNG INJURY-REPAIR, Margo Patricia Cain
Dissertations and Theses (Open Access)

Table-to-Text: Generating Descriptive Text for Scientific Tables from Randomized Controlled Trials, Qiang Wei
Dissertations (Open Access)

2019

VaxInsight: an artificial intelligence system to access large-scale public perceptions of vaccination from social media, Jingcheng Du
Dissertations (Open Access)

MOLECULAR CONSEQUENCES OF HIGH TAZ EXPRESSION IN GLIOMAS, Visweswaran Ravikumar
Dissertations and Theses (Open Access)

P53R245W MUTATION ELICITS METASTATIC PHENOTYPE IN PTEN DEFICIENT PROSTATE CANCER, Ky Pham
Dissertations and Theses (Open Access)

Utilizing Temporal Information in The EHR for Developing a Novel Continuous Prediction Model, Kang Lin Hsieh
Dissertations (Open Access)

Design and Architecture of an Ontology-driven Dialogue System for HPV Vaccine Counseling, Amith Faheem Muhammad
Dissertations (Open Access)

COMPUTATIONAL GENOMIC MODELS FOR SPATIO-TEMPORAL INVESTIGATION OF EARLY LUNG CANCER PATHOLOGY, Smruthy Sivakumar
Dissertations and Theses (Open Access)

Data collection curated with an application ontology describes the methods and results upon performing an ex-vivo voltage-clamp assay on outer hair cells of the mammalian cochlea, Brenda Farrell, Jason Bengtson
BCM Research Data

2018

Improving dbNSFP, Mingyao Lu
Dissertations and Theses (Open Access)

Targeting PH domain proteins for cancer therapy, Zhi Tan
Dissertations and Theses (Open Access)

PREDICTION OF 1P/19Q CODELETION STATUS IN DIFFUSE GLIOMA PATIENTS USING PREOPERATIVE MULTIPARAMETRIC MAGNETIC RESONANCE IMAGING, Donnie Kim
Dissertations and Theses (Open Access)

GENOMIC AND TRANSCRIPTOMIC LANDSCAPE OF COLORECTAL PREMALIGNANCY, Kyle Chang
Dissertations and Theses (Open Access)

Omics Approaches to Uncover Germline and Somatic Variation Underlying Inherited Sarcomagenesis, Justin Wong
Dissertations and Theses (Open Access)

Comparing Attributional and Relational Similarity as a Means to Identify Clinically Relevant Drug-gene Relationships, Safa Fathiamini
Dissertations (Open Access)

Ontology-Based Clinical Information Extraction Using SNOMED CT, Jun Li
Dissertations (Open Access)

Computational insights into the generation of chromosomal copy number changes, Yihua Liu
Dissertations and Theses (Open Access)

INVESTIGATING THE IMPACT OF INTRAGENIC DNA METHYLATION ON GENE EXPRESSION, AND THE CLINICAL IMPLICATIONS ON TUMOR CELLS AND ASSOCIATED STROMA, Michael McGuire
Dissertations and Theses (Open Access)

Using the Literature to Identify Confounders, Scott Malec
Dissertations (Open Access)

2017

Computational Identification of Noncoding Driver Mutations Based on Impact on RNA Processing, Kevin Zhu
Dissertations and Theses (Open Access)

INTEGRATIVE CANCER IMMUNOGENOMIC ANALYSIS OF SERIAL MELANOMA BIOPSIES REVEALS CORRELATES OF RESPONSE AND RESISTANCE TO SEQUENTIAL CTLA-4 AND PD-1 BLOCKADE TREATMENT, Whijae Roh
Dissertations and Theses (Open Access)

Impact of Terminology Mapping on Population Health Cohorts IMPaCt, Barbara A. Berkovich
Dissertations (Open Access)

NON-CODING RNAS IDENTIFY THE INTRINSIC MOLECULAR SUBTYPES OF MUSCLE-INVASIVE BLADDER CANCER, Andrea E. Ochoa
Dissertations and Theses (Open Access)

Statistical Methods for Two Problems in Cancer Research: Analysis of RNA-seq Data from Archival Samples and Characterization of Onset of Multiple Primary Cancers, Jialu Li
Dissertations and Theses (Open Access)

Understanding Patient Safety Reports via Multi-label Text Classification and Semantic Representation, Chen Liang
Dissertations (Open Access)

A Life Cycle Approach to the Development and Validation of an Ontology of the U.S. Common Rule (45 C.F.R. § 46), Francis Manion
Dissertations (Open Access)

Improving Syntactic Parsing of Clinical Text Using Domain Knowledge, Min Jiang
Dissertations (Open Access)

2016

Development Of An In Silico Kir Genotyping Algorithm And Its Application To Population And Cancer Immunogenetic Analyses, Howard Rosoff
Dissertations and Theses (Open Access)

DataGauge: A Model-Driven Framework for Systematically Assessing the Quality of Clinical Data for Secondary Use, Jose Franck DiazVasquez
Dissertations (Open Access)

GENOMIC DRIVERS OF CUTANEOUS SQUAMOUS CELL CARCINOMA DEVELOPMENT, Vida Chitsazzadeh
Dissertations and Theses (Open Access)

Investigating Metastatic Lineage in Colorectal Cancer by Single Cell DNA Sequencing, Marco Leung
Dissertations and Theses (Open Access)

Accurate mutation annotation and functional prediction enhance the applicability of -omics data in precision medicine, Tenghui Chen
Dissertations and Theses (Open Access)

Implications of Computational Cognitive Models for Information Retrieval, Joshua Caleb Goodwin
Dissertations (Open Access)

Validation of Case Finding Algorithms for Hepatocellular Cancer From Administrative Data and Electronic Health Records Using Natural Language Processing., Yvonne Sada, Jason Hou, Peter Richardson, Hashem El-Serag, Jessica Davila
BCM Faculty Publications

2015

Process Mining of Medication Revisions in Electronic Health Records, Deevakar Rogith
Dissertations (Open Access)

Detection of Genes Influencing Chronic and Mendelian Disease via Loss-Of-Function Variation, Alexander H. Li
Dissertations and Theses (Open Access)

Germline Mutation Detection in Next Generation Sequencing Data and TP53 Mutation Carrier Probability Estimation for Li-Fraumeni Syndrome, Gang Peng
Dissertations and Theses (Open Access)

IDENTIFICATION OF FAMILIAL WILMS TUMOR PREDISPOSITION GENES USING WHOLE GENOME SEQUENCING, Timothy B. Palculict
Dissertations and Theses (Open Access)

COMPUTATIONAL MODELING OF RNA-SMALL MOLECULE AND RNA-PROTEIN INTERACTIONS, Lu Chen
Dissertations and Theses (Open Access)

Investigating the Interaction of AURKA and UBE2C in Colorectal Cancer Cells, Apurva M. Hegde
Dissertations and Theses (Open Access)

Designing for Practice Development in a Social Learning System: Communicating Norms and Vicarious Experience, Claire Loe
Dissertations (Open Access)

MEASURING SINGLE CELL RESPONSES TO LAPATINIB IN A HETEROGENEOUS POPULATION, Preety Priya
Dissertations and Theses (Open Access)

2014

Named Entity Recognition in Chinese Clinical Text, Jianbo Lei
Dissertations (Open Access)

Mapping the Human Vasculature by In Vivo Phage Display, Julianna Bronk
Dissertations and Theses (Open Access)

GENETIC PREDICTORS OF METABOLIC SIDE EFFECTS OF DIURETIC THERAPY, Jorge L. Del Aguila
Dissertations and Theses (Open Access)

Genomic Characterization of Polyps in Familial Adenomatous Polyposis Patients and Identification of Candidate Chemopreventive Drugs, Francis A. San Lucas
Dissertations and Theses (Open Access)

Integrating Domain Knowledge to Improve Signal Detection from Electronic Health Records for Pharmacovigilance, Ning Shang
Dissertations (Open Access)

THE ASSOCIATION BETWEEN THE IL-1 PATHWAY, Isaac C. Wun
Dissertations and Theses (Open Access)

p53 MAINTAINS HEPATIC CELL IDENTITY DURING LIVER REGENERATION, Zeynep Hande Coban Akdemir
Dissertations and Theses (Open Access)

STRUCTURE BASED PREDICTION OF DRUG-PROTEIN INTERACTIONS AT ALLOSTERIC SITES: TOWARDS DIRECT INHIBITION OF THE RAS ONCOGENE, Harrison Hocker
Dissertations and Theses (Open Access)

2013

INTRODUCING A NOVEL METHOD FOR GENETIC ANALYSIS OF AUTISM SPECTRUM DISORDER, sepideh nouri
Dissertations and Theses (Open Access)

Attributing Meaning to Online Social Network Analysis for Tailored Socio-Behavioral Support Systems, Sahiti Myneni
Dissertations (Open Access)

Development and Evaluation of an Ontology-Based Quality Metrics Extraction System, Sina Madani
Dissertations (Open Access)

RNA-SEQUENCING APPLICATIONS: GENE EXPRESSION QUANTIFICATION AND METHYLATOR PHENOTYPE IDENTIFICATION, Guoshuai Cai
Dissertations and Theses (Open Access)

Radiomics of NSCLC: Quantitative CT Image Feature Characterization and Tumor Shrinkage Prediction, Luke Hunter
Dissertations and Theses (Open Access)

THE NATURAL AND ORTHOGONAL INTERACTION (NOIA) MODELS FOR QUANTITATIVE TRAITS (QTs) AND COMPLEX DISEASES, Feifei Xiao
Dissertations and Theses (Open Access)

GENOME-WIDE PROFILING UNVEILS CRITICIAL FUNCTIONS OF p53 IN HUMAN EMBRYONIC STEM CELLS, Kadir C. Akdemir
Dissertations and Theses (Open Access)

DEVELOPMENT OF NOVEL METHODS TO MINIMIZE THE IMPACT OF SEQUENCING ERRORS IN THE NEXT-GENERATION SEQUENCING DATA ANALYSIS, Xiaofeng Zheng
Dissertations and Theses (Open Access)

2012

A STUDY ON THE FUNCTION OF 14-3-3SIGMA IN REGULATING CANCER ENERGY METABOLISM, Liem M. Phan, Liem M. Phan
Dissertations and Theses (Open Access)

Systems Biology Approaches to Probe Gene Regulation in Bacteria, Diogo F. Troggian Veiga
Dissertations and Theses (Open Access)

2011

A Method for Representing Contextualized Information (MeRCI) to Improve Situational Awareness Among Electronic Message Brokering System Dashboard Users, Arunkumar Srinivasan
Dissertations (Open Access)

2010

NETWORK TOPOLOGY IN HUMAN PROTEIN INTERACTION DATA PREDICTS FUNCTIONAL ASSOCIATION, HUA LI
Dissertations and Theses (Open Access)

SURVIVAL PREDICTION FOR BRAIN TUMOR PATIENTS USING GENE EXPRESSION DATA, Vinicius Bonato
Dissertations and Theses (Open Access)

2009

BIOMEDICAL LANGUAGE UNDERSTANDING AND EXTRACTION (BLUE-TEXT): A MINIMAL SYNTACTIC, SEMANTIC METHOD, Parsa Mirhaji
Dissertations (Open Access)