A5022114369- Protein Structure and Dynamics
- RNA and protein synthesis mechanisms
- Bayesian Modeling and Causal Inference
- Monoclonal and Polyclonal Antibodies Research
- vaccines and immunoinformatics approaches
- Machine Learning in Bioinformatics
- Advanced Causal Inference Techniques
- Health Systems, Economic Evaluations, Quality of Life
- Platelet Disorders and Treatments
- Hemophilia Treatment and Research
- COVID-19 Clinical Research Studies
- Computational Drug Discovery Methods
- Immunotherapy and Immune Responses
- Machine Learning in Healthcare
- Machine Learning and Algorithms
- SARS-CoV-2 and COVID-19 Research
- Inflammatory Bowel Disease
- Enzyme Structure and Function
- Statistical Methods in Clinical Trials
- Colorectal Cancer Screening and Detection
- Biomedical Text Mining and Ontologies
- T-cell and B-cell Immunology
- Genomics and Chromatin Dynamics
- Error Correcting Code Techniques
- Parkinson's Disease Mechanisms and Treatments
IMI TAMI Institute for Research and Development
2020-2025
Kongsberg Innovasjon (Norway)
2023
IBM Research - Haifa
2014-2021
IBM (United States)
2013-2018
Ben-Gurion University of the Negev
2014
Stanford University
2014
Carmel (Israel)
2014
University of Haifa
2014
Fred Hutch Cancer Center
2008-2013
Cape Town HVTN Immunology Laboratory / Hutchinson Centre Research Institute of South Africa
2010-2013
Background: Recent studies of various human microbiome habitats have revealed thousands bacterial species and the existence large variation in communities microorganisms same across individual subjects. Previous efforts to summarize this diversity, notably gut vagina, categorized profiles by clustering them into community state types (CSTs). The functional relevance specific CSTs has not been established. Objective: We investigate whether can be used assess dynamics microbiome. Design:...
Reliably identifying patients at increased risk for coronavirus disease (COVID-19) complications could guide clinical decisions, public health policies, and preparedness efforts. Multiple studies have attempted to characterize at-risk patients, using various data sources methodologies. Most of these studies, however, explored condition-specific patient cohorts (eg, hospitalized patients) or had limited access patients' medical history, thus, investigating related questions and, potentially,...
Abstract Major depressive disorder and exposure to antidepressants during pregnancy have been previously associated with preterm birth (PTB). However, the reported results are inconsistent. In this study, we aimed estimate effects of maternal depression on risk PTB using data from electronic health records (EHRs). This is a population-based retrospective cohort utilizing primary care EHRs. The included 216,070 deliveries 176,866 patients UK between January 1996 February 2019. We analyzed...
A wide range of low level vision problems have been formulated in terms finding the most probable assignment a Markov random field (or equivalently lowest energy configuration). Perhaps successful example is stereo vision. For problem, it has shown that global optimum NP hard but good results obtained using number approximate optimization algorithms. In this paper, we show for standard benchmark pairs, can be found about 30 minutes variant belief propagation (BP) algorithm. We extend...
Side-chain prediction is an important subproblem of the general protein folding problem. Despite much progress in side-chain prediction, performance far from satisfactory. As example, ROSETTA program that uses simulated annealing to select minimum energy conformations, correctly predicts first two angles for approximately 72% buried residues a standard data set. Is further improvement more likely come better search methods, or functions? Given exact minimization NP hard, it difficult get...
Class I major histocompatibility complex proteins play a critical role in the adaptive immune system by binding to peptides derived from cytosolic and presenting them on cell surface for surveillance T cells. The varied peptide specificity of these highly polymorphic molecules has important consequences vaccine design, transplantation, autoimmunity, cancer development. Here, we describe molecular modeling study MHC-peptide interactions that integrates sampling techniques protein–protein...
Mycobacterium tuberculosis (M. tuberculosis) is considered innately resistant to β-lactam antibiotics. However, there evidence that susceptibility antibiotics in combination with β-lactamase inhibitors variable among clinical isolates, and these may present therapeutic options for drug-resistant cases. Here we report our investigation of β-lactam/β-lactamase inhibitor combinations isolates M. tuberculosis, the use comparative genomics understand observed heterogeneity susceptibility....
Abstract Motivation: The development of epitope-based vaccines crucially relies on the ability to classify Human Leukocyte Antigen (HLA) molecules into sets that have similar peptide binding specificities, termed supertypes. In their seminal work, Sette and Sidney defined nine HLA class I supertypes claimed these provide an almost perfect coverage entire repertoire molecules. alleles are highly polymorphic polygenic therefore experimentally classifying each is at present impossible task....
Sequence-specific DNA recognition by gene regulatory proteins is critical for proper cellular functioning. The ability to predict the binding preferences of these from their amino acid sequence would greatly aid in reconstruction interactions. Structural modeling provides one route such predictions: building accurate molecular models complex with candidate sites, and estimating relative affinities sites using a suitable potential function, it should be possible construct profiles. Here, we...
The development of neutralizing anti-drug-antibodies to the Factor VIII protein-therapeutic is currently most significant impediment effective management hemophilia A. Common non-synonymous single nucleotide polymorphisms (ns-SNPs) in F8 gene occur as six haplotypes human population (denoted H1 H6) which H3 and H4 have been associated with an increased risk developing anti-drug antibodies. There evidence that CD4+ T-cell response essential for antibodies such a requires presentation peptides...
Predictive model performance may deteriorate when applied to data sources that were not used for training, thus, external validation is a key step in successful deployment. As access patient-level typically limited, we recently proposed method estimates using only summary statistics. Here, benchmark the on multiple tasks five large heterogeneous US sources, where each, turn, plays role of an internal source and remaining—external. Results showed accurate estimations all metrics: 95th error...
Multistate protein design is the task of predicting amino acid sequence that best suited to selectively and stably fold one state out a set competing structures. Computationally, it entails solving challenging optimization problem. Therefore, notwithstanding increased interest in multistate design, only implementations reported are based on either genetic algorithms or Monte Carlo methods. The dead-end elimination (DEE) theorem cannot be readily transfered problems despite its successful...
Observational medical databases, such as electronic health records and insurance claims, track the healthcare trajectory of millions individuals. These databases provide real-world longitudinal information on large cohorts patients their medication prescription history. We present an easy-to-customize framework that systematically analyzes to identify new indications for on-market drugs.
As the scientific research community along with healthcare professionals and decision makers around world fight tirelessly against coronavirus disease 2019 (COVID-19) pandemic, need for comparative effectiveness (CER) on preventive therapeutic interventions COVID-19 is immense. Randomized controlled trials markedly under-represent frail complex patients seen in routine care, they do not typically have data long-term treatment effects. The increasing availability of electronic health records...