​​​​​​​
​​​​​​​​​​​​
​​ ​​​​​​​​
​​
  • 2018
    • Publication History PA-14-156-2017-2018
      BrainSuite: Software for Analysis and Visualization of Multimodal Brain Imaging Data...
      Read more
    • Publication History PA-14-155-2017-2018
      Boosting the Translational Impact of Scientific Competitions by Ensemble Learning...
      Read more
    • Commentary on the Integration of Model Sharing and Reproducibility Analysis to Scholarly Publishing Workflow in Computational Biomechanics
      As part of a special issue on model sharing and reproducibility in IEEE Transactions on Biomedical Engineering, two manuscripts on computational biomechanics were submitted: A. Rajagopal et al., IEEE Trans. Biomed. Eng., 2016 and A. Schmitz and D. Piovesan, IEEE Trans. Biomed. Eng., 2016. Models us...
      Read more
  • 2017
    • Genome-Scale Architecture of Small Molecule Regulatory Networks and the Fundamental Trade-Off between Regulation and Enzymatic Activity
      Abstract Metabolic flux is in part regulated by endogenous small molecules that modulate the catalytic activity of an enzyme, e.g., allosteric inhibition. In contrast to transcriptional regulation of enzymes, technical limitations have hindered the production of a genome-scale atlas of small mol...
      Read more
    • LEARNING PARSIMONIOUS ENSEMBLES FOR UNBALANCED COMPUTATIONAL GENOMICS PROBLEMS.
      Abstract Prediction problems in biomedical sciences are generally quite difficult, partially due to incomplete knowledge of how the phenomenon of interest is influenced by the variables and measurements used for prediction, as well as a lack of consensus regarding the ideal predictor(s) for spec...
      Read more
    • Analysis of Protein Phosphorylation and Its Functional Impact on Protein-Protein Interactions via Text Mining of the Scientific Literature.
      Abstract Post-translational modifications (PTMs) are one of the main contributors to the diversity of proteoforms in the proteomic landscape. In particular, protein phosphorylation represents an essential regulatory mechanism that plays a role in many biological processes. Protein kinases, the e...
      Read more
    • iPTMnet: Integrative Bioinformatics for Studying PTM Networks.
      Abstract Protein post-translational modification (PTM) is an essential cellular regulatory mechanism, and disruptions in PTM have been implicated in disease. PTMs are an active area of study in many fields, leading to a wealth of PTM information in the scientific literature. There is a need for ...
      Read more
    • Mechanisms to protect the privacy of families when using the transmission disequilibrium test in genome-wide association studies.
      Abstract Motivation: Inappropriate disclosure of human genomes may put the privacy of study subjects and of their family members at risk. Existing privacy-preserving mechanisms for Genome-Wide Association Studies (GWAS) mainly focus on protecting individual information in case-control studie...
      Read more
    • Using machine learning to identify air pollution exposure profiles associated with early cognitive skills among U.S. children.
      Abstract Data-driven machine learning methods present an opportunity to simultaneously assess the impact of multiple air pollutants on health outcomes. The goal of this study was to apply a two-stage, data-driven approach to identify associations between air pollutant exposure profiles and child...
      Read more
    • Using machine learning to identify air pollution exposure profiles associated with early cognitive skills among U.S. children.
      Abstract Data-driven machine learning methods present an opportunity to simultaneously assess the impact of multiple air pollutants on health outcomes. The goal of this study was to apply a two-stage, data-driven approach to identify associations between air pollutant exposure profiles and child...
      Read more
    • Translational high-dimensional drug Interaction discovery and validation using health record databases and pharmacokinetics models.
      Abstract Polypharmacy increases the risk of drug-drug interactions (DDI's). Combining epidemiological studies with pharmacokinetic modeling, we detected and evaluated high-dimensional DDI's among thirty frequent drugs. Multi-drug combinations that increased risk of myopathy were identified in th...
      Read more
    • Robust Fusion of Diffusion MRI Data for Template Construction.
      Abstract Construction of brain templates is generally carried out using a two-step procedure involving registering a population of images to a common space and then fusing the aligned images to form a template. In practice, image registration is not perfect and simple averaging of the images wil...
      Read more
    • Sepsis reconsidered: Identifying novel metrics for behavioral landscape characterization with a high-performance computing implementation of an agent-based model
      Abstract OBJECTIVES: Sepsis affects nearly 1 million people in the United States per year, has a mortality rate of 28-50% and requires more than $20 billion a year in hospital costs. Over a quarter century of research has not yielded a single reliable diagnostic test or a directed therapeuti...
      Read more
    • LMO1 Synergizes with MYCN to Promote Neuroblastoma Initiation and Metastasis
      Abstract A genome-wide association study identified LMO1, which encodes an LIM-domain-only transcriptional cofactor, as a neuroblastoma susceptibility gene that functions as an oncogene in high-risk neuroblastoma. Here we show that dβh promoter-mediated expression of LMO1 in zebrafish synergizes...
      Read more
    • Long-term patient reported outcomes following radiation therapy for oropharyngeal cancer: cross-sectional assessment of a prospective symptom survey in patients ≥65 years old.
      Abstract BACKGROUND: Given the potential for older patients to experience exaggerated toxicity and symptoms, this study was performed to characterize patient reported outcomes in older patients following definitive radiation therapy (RT) for oropharyngeal cancer (OPC). METHODS: Cancer...
      Read more
    • Determination of disease phenotypes and pathogenic variants from exome sequence data in the CAGI 4 gene panel challenge
      Abstract The use of gene panel sequence for diagnostic and prognostic testing is now widespread, but there are so far few objective tests of methods to interpret these data. We describe the design and implementation of a gene panel sequencing data analysis pipeline (VarP) and its assessment in a...
      Read more
    • Ensemble variant interpretation methods to predict enzyme activity and assign pathogenicity in the CAGI4 NAGLU (Human N-acetyl-glucosaminidase) and UBE2I (Human SUMO-ligase) challenges.
      Abstract CAGI (Critical Assessment of Genome Interpretation) conducts community experiments to determine the state of the art in relating genotype to phenotype. Here, we report results obtained using newly developed ensemble methods to address two CAGI4 challenges: enzyme activity for population...
      Read more
    • Best Practices for HPC Center
      Worldwide Best Practices in Partnerships between HPC Centers and Industrial Users Sponsored by: The National Center for Supercomputing Applications (NCSA) ...
      Read more
    • Perspectives on Research in Artificial Intelligence and Artificial General Intelligence Relevant to DoD
      JASON report of January 2017...
      Read more
    • Dose-volume correlates of mandibular osteoradionecrosis in Oropharynx cancer patients receiving intensity-modulated radiotherapy: Results from a case-matched comparison.
      Abstract PURPOSE: To determine dosimetric parameters associated with osteoradionecrosis (ORN) in oropharyngeal cancer (OPC) patients in the IMRT era. MATERIAL AND METHODS: Subsequent to institutional review board approval, we identified ORN in OPC patients treated with IMRT from 2002 ...
      Read more
    • Patterns-of-failure guided biological target volume definition for head and neck cancer patients: FDG-PET and dosimetric analysis of dose escalation candidate subregions.
      BACKGROUND: To identify the radio-resistant subvolumes in pretreatment FDG-PET by mapping the spatial location of the origin of tumor recurrence after IMRT for head-and-neck squamous cell cancer to the pretreatment FDG-PET/CT. METHODS: Patients with local/regional recurrence after IMRT w...
      Read more
    • Final Report of a Prospective Randomized Trial to Evaluate the Dose-Response Relationship for Postoperative Radiation Therapy and Pathologic Risk Groups in Patients With Head and Neck Cancer.
      Abstract PURPOSE: To present the long-term and final report of a phase 3 trial designed to assess dose-response relationship for postoperative radiation therapy (PORT) and pathologic risk groups in head and neck cancer. METHODS AND MATERIALS: Patients who underwent primary surgery for...
      Read more
    • Machine Learning-Assisted Network Inference Approach to Identify a New Class of Genes that Coordinate the Functionality of Cancer Networks.
      Abstract Emerging evidence indicates the existence of a new class of cancer genes that act as "signal linkers" coordinating oncogenic signals between mutated and differentially expressed genes. While frequently mutated oncogenes and differentially expressed genes, which we term Class I cancer ge...
      Read more
    • Quantitative pretreatment CT volumetry: Association with oncologic outcomes in patients with T4a squamous carcinoma of the larynx.
      Abstract BACKGROUND: The purpose of this study was to determine the impact of CT-determined pretreatment primary tumor volume on survival and disease control in T4a laryngeal squamous cell carcinoma (SCC). METHODS: We retrospectively reviewed 124 patients with T4a laryngeal cancer fro...
      Read more
    • Population and allelic variation of A-to-I RNA editing in human transcriptomes.
      BACKGROUND: A-to-I RNA editing is an important step in RNA processing in which specific adenosines in some RNA molecules are post-transcriptionally modified to inosines. RNA editing has emerged as a widespread mechanism for generating transcriptome diversity. However, there remain significa...
      Read more
    • PRESAGE: PRivacy-preserving gEnetic testing via SoftwAre Guard Extension.
      Abstract BACKGROUND: Advances in DNA sequencing technologies have prompted a wide range of genomic applications to improve healthcare and facilitate biomedical research. However, privacy and security concerns have emerged as a challenge for utilizing cloud computing to handle sensitive genom...
      Read more
    • Embarrassingly Parallel Acceleration of Global Tractography via Dynamic Domain Partitioning.
      Abstract Global tractography estimates brain connectivity by organizing signal-generating fiber segments in an optimal configuration that best describes the measured diffusion-weighted data, promising better stability than local greedy methods with respect to imaging noise. However, global tract...
      Read more
    • Covariate selection with group lasso and doubly robust estimation of causal effects.
      Abstract The efficiency of doubly robust estimators of the average causal effect (ACE) of a treatment can be improved by including in the treatment and outcome models only those covariates which are related to both treatment and outcome (i.e., confounders) or related only to the outcome. However...
      Read more
    • Spatio-angular consistent construction of neonatal diffusion MRI atlases.
      Abstract Atlases constructed using diffusion-weighted imaging are important tools for studying human brain development. Atlas construction is in general a two-step process involving spatial registration and fusion of individual images. The focus of most studies so far has been on improving the a...
      Read more
    • Joint prediction of longitudinal development of cortical surfaces and white matter fibers from neonatal MRI.
      Abstract The human brain can be modeled as multiple interrelated shapes (or a multishape), each for characterizing one aspect of the brain, such as the cortex and white matter pathways. Predicting the developing multishape is a very challenging task due to the contrasting nature of the developme...
      Read more
    • Robust Construction of Diffusion MRI Atlases with Correction for Inter-Subject Fiber Dispersion.
      Abstract Construction of brain atlases is generally carried out using a two-step procedure involving registering a population of images to a common space and then fusing the aligned images to form an atlas. In practice, image registration is not perfect and simple averaging of the images will bl...
      Read more
    • Denoising Diffusion-Weighted Images Using Grouped Iterative Hard Thresholding of Multi-Channel Framelets.
      Abstract Noise in diffusion-weighted (DW) images increases the complexity of quantitative analysis and decreases the reliability of inferences. Hence, to improve analysis, it is often desirable to remove noise and at the same time preserve relevant image features. In this paper, we propose a tig...
      Read more
    • The Journal of molecular diagnostics: JmMD
      Abstract A national workgroup convened by the Centers for Disease Control and Prevention identified principles and made recommendations for standardizing the description of sequence data contained within the variant file generated during the course of clinical next-generation sequence analysis f...
      Read more
    • Analysis of Transcriptional Variability in a Large Human iPSC Library Reveals Genetic and Non-genetic Determinants of Heterogeneity.
      Abstract Variability in induced pluripotent stem cell (iPSC) lines remains a concern for disease modeling and regenerative medicine. We have used RNA-sequencing analysis and linear mixed models to examine the sources of gene expression variability in 317 human iPSC lines from 101 individuals. We...
      Read more
    • Critical Role for GAB2 in Neuroblastoma Pathogenesis through the Promotion of SHP2/MYCN Cooperation.
      Abstract Growing evidence suggests a major role for Src-homology-2-domain-containing phosphatase 2 (SHP2/PTPN11) in MYCN-driven high-risk neuroblastoma, although biologic confirmation and a plausible mechanism for this contribution are lacking. Using a zebrafish model of MYCN-overexpressing neur...
      Read more
    • Image mosaicking using SURF features of line segments.
      Abstract In this paper, we present a novel image mosaicking method that is based on Speeded-Up Robust Features (SURF) of line segments, aiming to achieve robustness to incident scaling, rotation, change in illumination, and significant affine distortion between images in a panoramic series. Our ...
      Read more
    • Joint Agency Assessment of the Responses to the Request for Information (RFI) on “Science Drivers Requiring Capable Exascale High Performance Computing”
      PLEASE CLICK ON THE PDF FILE ON THE FRONT PAGE This report provides a joint assessment by the National Institutes of Health (NIH), Department of Energy (DOE) and National Science Foundation (NSF) of the scientific and engineering research community's science drivers requiring capable exascale ...
      Read more
    • Antigenic Determinants of Der p 1: Specificity and Cross-Reactivity Associated with IgE Antibody Recognition
      ...
      Read more
    • Crystal Structure of StnA for the Biosynthesis of Antitumor Drug Streptonigrin Reveals a Unique Substrate Binding Mode
      ...
      Read more
    • UniProt: the universal protein knowledgebase.
      Abstract The UniProt knowledgebase is a large resource of protein sequences and associated detailed annotation. The database contains over 60 million sequences, of which over half a million sequences have been curated by experts who critically review experimental and predicted data for each prot...
      Read more
    • Optimization and Control of Agent-Based Models in Biology: A Perspective.
      Abstract Agent-based models (ABMs) have become an increasingly important mode of inquiry for the life sciences. They are particularly valuable for systems that are not understood well enough to build an equation-based model. These advantages, however, are counterbalanced by the difficulty of ana...
      Read more
    • Algorithm 971: An Implementation of a Randomized Algorithm for Principal Component Analysis.
      Abstract Recent years have witnessed intense development of randomized methods for low-rank approximation. These methods target principal component analysis and the calculation of truncated singular value decompositions. The present article presents an essentially black-box, foolproof implementa...
      Read more
  • 2016
    • BioNetGen 2.2: advances in rule-based modeling.
      ...
      Read more
    • Sharing brain mapping statistical results with the neuroimaging data model.
      ...
      Read more
    • Improving Estimation of Fiber Orientations in Diffusion MRI Using Inter-Subject Information Sharing.
      Abstract Diffusion magnetic resonance imaging is widely used to investigate diffusion patterns of water molecules in the human brain. It provides information that is useful for tracing axonal bundles and inferring brain connectivity. Diffusion axonal tracing, namely tractography, relies on local...
      Read more
    • Breast Imaging in the Era of Big Data: Structured Reporting and Data Mining.
      Abstract OBJECTIVE: The purpose of this article is to describe structured reporting and the development of large databases for use in data mining in breast imaging. CONCLUSION: The results of millions of breast imaging examinations are reported with structured tools based on the BI-RA...
      Read more
    • A network-based phenotype mapping approach to identify genes that modulate drug response phenotypes.
      Abstract To better address the problem of drug resistance during cancer chemotherapy and explore the possibility of manipulating drug response phenotypes, we developed a network-based phenotype mapping approach (P-Map) to identify gene candidates that upon perturbed can alter sensitivity to drug...
      Read more
    • Optimization and Control of Agent-Based Models in Biology: A Perspective
      ...
      Read more
    • Identification of multi-loci hubs from 4C-seq demonstrates the functional importance of simultaneous interactions.
      Abstract Use of low resolution single cell DNA FISH and population based high resolution chromosome conformation capture techniques have highlighted the importance of pairwise chromatin interactions in gene regulation. However, it is unlikely that associations involving regulatory elements act i...
      Read more
    • Diagnosis of Alzheimer's Disease Using View-Aligned Hypergraph Learning with Incomplete Multi-modality Data.
      Abstract Effectively utilizing incomplete multi-modality data for diagnosis of Alzheimer's disease (AD) is still an area of active research. Several multi-view learning methods have recently been developed to deal with missing data, with each view corresponding to a specific modality or a combin...
      Read more
    • Tight Graph Framelets for Sparse Diffusion MRI q-Space Representation.
      Abstract In diffusion MRI, the outcome of estimation problems can often be improved by taking into account the correlation of diffusion-weighted images scanned with neighboring wavevectors in q-space. For this purpose, we propose in this paper to employ tight wavelet frames constructed on non-fl...
      Read more
    • A Hybrid Multishape Learning Framework for Longitudinal Prediction of Cortical Surfaces and Fiber Tracts Using Neonatal Data.
      Abstract Dramatic changes of the human brain during the first year of postnatal development are poorly understood due to their multifold complexity. In this paper, we present the first attempt to jointly predict, using neonatal data, the dynamic growth pattern of brain cortical surfaces (collect...
      Read more
    • XQ-NLM: Denoising Diffusion MRI Data via x-q Space Non-Local Patch Matching.
      Abstract Noise is a major issue influencing quantitative analysis in diffusion MRI. The effects of noise can be reduced by repeated acquisitions, but this leads to long acquisition times that can be unrealistic in clinical settings. For this reason, post-acquisition denoising methods have been w...
      Read more
    • Stability-Weighted Matrix Completion of Incomplete Multi-modal Data for Disease Diagnosis.
      Abstract Effective utilization of heterogeneous multi-modal data for Alzheimer's Disease (AD) diagnosis and prognosis has always been hampered by incomplete data. One method to deal with this is low-rank matrix completion (LRMC), which simultaneous imputes missing data features and target values...
      Read more
    • Construction of Neonatal Diffusion Atlases via Spatio-Angular Consistency.
      Abstract Atlases constructed using diffusion-weighted imaging (DWI) are important tools for studying human brain development. Atlas construction is in general a two-step process involving image registration and image fusion. The focus of most studies so far has been on improving registration thu...
      Read more
    • Augmenting Surgery via Multi-scale Modeling and Translational Systems Biology in the Era of Precision Medicine: A Multidisciplinary Perspective.
      Abstract In this era of tremendous technological capabilities and increased focus on improving clinical outcomes, decreasing costs, and increasing precision, there is a need for a more quantitative approach to the field of surgery. Multiscale computational modeling has the potential to bridge th...
      Read more
    • Multi-scale Modeling in Clinical Oncology: Opportunities and Barriers to Success.
      Hierarchical processes spanning several orders of magnitude of both space and time underlie nearly all cancers. Multi-scale statistical, mathematical, and computational modeling methods are central to designing, implementing and assessing treatment strategies that account for these hierarchies....
      Read more
    • Multiscale Modeling in the Clinic: Drug Design and Development.
      Abstract A wide range of length and time scales are relevant to pharmacology, especially in drug development, drug design and drug delivery. Therefore, multiscale computational modeling and simulation methods and paradigms that advance the linkage of phenomena occurring at these multiple scales ...
      Read more
    • Quantitative human cell encyclopedia
      Scientists gathered to discuss the necessity, feasibility, and challenges of generating a quantitative catalog of the components in human cells that is essential for our understanding of human physiology in health and disease and to support future breakthroughs in treating diseases. This report sum...
      Read more
    • Council on Library and Information Resources Report Examines Federal Public Access Plans and Their Implications for the Cultural Heritage Community
      New U.S. government requirements for exposing and managing federally funded research data add urgency to the call for curating data that can be used, reused, and exploited by future generations, according to a new report ...
      Read more
    • Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis.
      Abstract Rheumatoid arthritis (RA) affects millions world-wide. While anti-TNF treatment is widely used to reduce disease progression, treatment fails in ∼one-third of patients. No biomarker currently exists that identifies non-responders before treatment. A rigorous community-based assessment o...
      Read more
    • Long-term outcomes after multidisciplinary management of T3 laryngeal squamous cell carcinomas: Improved functional outcomes and survival with modern therapeutic approaches.
      Abstract BACKGROUND: The purpose of this study was to evaluate the long-term outcomes after initial definitive or adjuvant radiotherapy (RT) for T3 laryngeal cancers. METHODS: We reviewed 412 patients treated for T3 laryngeal squamous cell cancer from 1985 to 2011. RESULTS: The...
      Read more
    • Staying Alive: Measuring Intact Viable Microbes with Electrospray Ionization Mass Spectrometry.
      ...
      Read more
    • Multi-Tissue Decomposition of Diffusion MRI Signals via L0 Sparse-Group Estimation.
      Abstract Sparse estimation techniques are widely utilized in diffusion MRI (DMRI). In this paper, we present an algorithm for solving the `0 sparse-group estimation problem and apply it to the tissue signal separation problem in DMRI. Our algorithm solves the `0 problem directly, unlike existing...
      Read more
    • Metabolomics: beyond biomarkers and towards mechanisms
      Metabolomics, which is the profiling of metabolites in biofluids, cells and tissues, is routinely applied as a tool for biomarker discovery. Owing to innovative developments in informatics and analytical technologies, and the integration of orthogonal biological approaches, it is now possible to ex...
      Read more
    • Endothelial to mesenchymal transition is common in atherosclerotic lesions and is associated with plaque instability
      Endothelial to mesenchymal transition (EndMT) plays a major role during development, and also contributes to several adult cardiovascular diseases. Importantly, mesenchymal cells including fibroblasts are prominent in atherosclerosis, with key functions including regulation of: inflammation, matrix...
      Read more
    • Endothelial to mesenchymal transition is common in atherosclerotic lesions and is associated with plaque instability.
      Abstract Endothelial to mesenchymal transition (EndMT) plays a major role during development, and also contributes to several adult cardiovascular diseases. Importantly, mesenchymal cells including fibroblasts are prominent in atherosclerosis, with key functions including regulation of: inflamma...
      Read more
    • Proteome-wide covalent ligand discovery in native biological systems.
      ...
      Read more
    • Targeting Mitogen-Activated Protein Kinase-Activated Protein Kinase 2 (MAPKAPK2, MK2): Medicinal Chemistry Efforts To Lead Small Molecule Inhibitors to Clinical Trials.
      ...
      Read more
    • NetDecoder: a network biology platform that decodes context-specific biological networks and gene activities.
      Abstract The sequential chain of interactions altering the binary state of a biomolecule represents the 'information flow' within a cellular network that determines phenotypic properties. Given the lack of computational tools to dissect context-dependent networks and gene activities, we develope...
      Read more
    • Interaction of tau with the RNA-Binding Protein TIA1 Regulates tau Pathophysiology and Toxicity.
      Abstract Dendritic mislocalization of microtubule associated protein tau is a hallmark of tauopathies, but the role of dendritic tau is unknown. We now report that tau interacts with the RNA-binding protein (RBP) TIA1 in brain tissue, and we present the brain-protein interactome network for TIA1...
      Read more
    • An R Package for Finlay-Wilkinson Regression that Incorporates Genomic/Pedigree Information and Covariance Structures Between Environments
      The Finlay-Wilkinson regression (FW) is a popular method among plant breeders to describe genotype by environment interaction. The standard implementation is a two-step procedure that uses environment (sample) means as covariates in a within-line ordinary least squares (OLS)regression. This procedu...
      Read more
    • Breast Imaging in the Era of Big Data: Structured Reporting and Data Mining
      OBJECTIVE. The purpose of this article is to describe structured reporting and the development of large databases for use in data mining in breast imaging. CONCLUSION. The results of millions of breast imaging examinations are reported with structured tools based on the BI-RADS lexicon. Much of ...
      Read more
    • Predicting protein function and other biomedical characteristics with heterogeneous ensembles.
      Abstract Prediction problems in biomedical sciences, including protein function prediction (PFP), are generally quite difficult. This is due in part to incomplete knowledge of the cellular phenomenon of interest, the appropriateness and data quality of the variables and measurements used for pre...
      Read more
    • Predicting protein function and other biomedical characteristics with heterogeneous ensembles
      Prediction problems in biomedical sciences, including protein function prediction (PFP), are generally quite difficult. This is due in part to incomplete knowledge of the cellular phenomenon of interest, the appropriateness and data quality of the variables and measurements used for prediction, as ...
      Read more
    • The Quantitative-MFG Test: A Linear Mixed Effect Model to Detect Maternal-Offspring Gene Interactions
      Maternal-offspring gene interactions, aka maternal-fetal genotype (MFG) incompatibilities, are neglected in complex diseases and quantitative trait studies. They are implicated in birth to adult onset diseases but there are limited ways to investigate their influence on quantitative traits. We pres...
      Read more
  • 2015
    • Tabulation as a high-resolution alternative to coarse-graining protein interactions: Initial application to virus capsid subunits
      Traditional coarse-graining based on a reduced number of interaction sites often entails a significant sacrifice of chemical accuracy. As analternative, we present a method for simulating large systems composed of interacting macromolecules using an energy tabulation strategy previously devised for...
      Read more
    • Prediction of Genetic Interactions Using Machine Learning and Network Properties.
      Abstract A genetic interaction (GI) is a type of interaction where the effect of one gene is modified by the effect of one or several other genes. These interactions are important for delineating functional relationships among genes and their corresponding proteins, as well as elucidating comple...
      Read more
    • Charting a Path to Success in Virtual Screening.
      ...
      Read more
    • Computational challenges of structure-based approaches applied to HIV.
      ...
      Read more
    • A virtual screen discovers novel, fragment-sized inhibitors of Mycobacterium tuberculosis InhA.
      ...
      Read more
​​