A5022453482- Protein Structure and Dynamics
- Forensic and Genetic Research
- Genetic diversity and population structure
- Enzyme Structure and Function
- DNA and Nucleic Acid Chemistry
- Cancer Genomics and Diagnostics
- Bioinformatics and Genomic Networks
- Nanopore and Nanochannel Transport Studies
- Advanced biosensing and bioanalysis techniques
- Genomics and Phylogenetic Studies
- Influenza Virus Research Studies
- Machine Learning in Bioinformatics
- Spectroscopy and Quantum Chemical Studies
- Glioma Diagnosis and Treatment
- Race, Genetics, and Society
- RNA and protein synthesis mechanisms
- Archaeology and ancient environmental studies
- Microfluidic and Bio-sensing Technologies
- Scientific Computing and Data Management
- Single-cell and spatial transcriptomics
- Gene Regulatory Network Analysis
- Bacteriophages and microbial interactions
- Genetics, Bioinformatics, and Biomedical Research
- Yersinia bacterium, plague, ectoparasites research
- Monoclonal and Polyclonal Antibodies Research
IBM Research - Thomas J. Watson Research Center
2002-2019
IBM (United States)
2006-2017
Columbia University Irving Medical Center
2017
New York Genome Center
2017
Howard Hughes Medical Institute
2017
Memorial Sloan Kettering Cancer Center
2017
Chongqing Institute of Green and Intelligent Technology
2015
Institut Pasteur
2014
Alliance for Safe Kids
2014
All India Institute of Medical Sciences
1986-2009
In December 1999, IBM announced the start of a five-year effort to build massively parallel computer, be applied study biomolecular phenomena such as protein folding. The project has two main goals: advance our understanding mechanisms behind folding via large-scale simulation, and explore novel ideas in machine architecture software. This should enable simulations that are orders magnitude larger than current technology permits. Major areas investigation include: how most effectively...
The search for a method that utilizes biological information to predict humans' place of origin has occupied scientists millennia. Over the past four decades, have employed genetic data in an effort achieve this goal but with limited success. While biogeographical algorithms using next-generation sequencing achieved accuracy 700 km Europe, they were inaccurate elsewhere. Here we describe Geographic Population Structure (GPS) algorithm and demonstrate its three sets 40,000-130,000 SNPs. GPS...
Abstract Background Using next-generation sequencing (NGS) to guide cancer therapy has created challenges in analyzing and reporting large volumes of genomic data patients caregivers. Specifically, providing current, accurate information on newly approved therapies open clinical trials requires considerable manual curation performed mainly by human “molecular tumor boards” (MTBs). The purpose this study was determine the utility cognitive computing as Watson for Genomics (WfG) compared with...
The structural characteristics of a mucin glycopeptide motif derived from the N-terminal fragment STTAV cell surface glycoprotein CD43 have been investigated by NMR. In this study, series molecules prepared total synthesis were examined, consisting peptide itself, three glycopeptides having clustered sites α-O-glycosylation on serine and threonine side chains with Tn, TF, STF carbohydrate antigens, respectively, one β-O-linked TF antigen. Additionally, sequence SSSAVAV, triglycosylated Ley...
Lebanon is an eastern Mediterranean country inhabited by approximately four million people with a wide variety of ethnicities and religions, including Muslim, Christian, Druze. In the present study, 926 Lebanese men were typed Y-chromosomal SNP STR markers, unusually, male genetic variation within was found to be more strongly structured religious affiliation than geography. We therefore tested hypothesis that migrations historical times could have contributed this situation. Y-haplogroup...
Abstract Aboriginal Australians represent one of the oldest continuous cultures outside Africa, with evidence indicating that their ancestors arrived in ancient landmass Sahul (present-day New Guinea and Australia) ~55 thousand years ago. Genetic studies, though limited, have demonstrated both uniqueness antiquity Australian genomes. We further resolved known mitochondrial haplogroups discovered novel indigenous lineages by sequencing mitogenomes 127 contemporary Australians. In particular,...
The single mutation effect on the binding affinity of H3N2 viral protein hemagglutinin (HA) with monoclonical antibody fragment (Fab) is studied in this paper using free energy perturbation (FEP) simulations. An all-atom model explicit solvents used to perform an aggregate several microsecond FEP molecular dynamics A recent experiment shows that a HA, T131I, increases antibody−antigen dissociation constant Kd by factor ∼4000 (equivalent decrease ∼5 kcal/mol), thus introducing escape (Ab)...
We propose a mechanism, based on > or =10-micros molecular dynamics simulation, for the surprising misfolding of hen egg-white lysozyme caused by single mutation (W62G). Our simulations wild-type and mutant lysozymes in 8 M urea solution at biological temperature (with both pH 2 7) reveal that structure is much less stable than wild type, with showing larger fluctuations native-like contacts. Analysis local contacts reveals Trp-62 residue key to cooperative long-range interaction within...
Historically, influenza pandemics have been triggered when an avian virus or a human/avian reassorted acquires the ability to replicate efficiently and become transmissible in human population. Most critically, major surface glycoprotein hemagglutinin (HA) must adapt usage of human-like (alpha-2,6-linked) sialylated glycan receptors. Therefore, identification mutations that can switch currently circulating H5N1 HA receptor binding specificity from might provide leads emergence pandemic...
We present the fabrication of sub-20 nm nanopores and nanopore arrays in membranes with embedded multilayer electrodes using CMOS semiconductor processes.
For decades, the peopling of Americas has been explored through analysis uniparentally inherited genetic systems in Native American populations and comparison these data with current linguistic groupings. In northern North America, two language families predominate: Eskimo-Aleut Na-Dene. Although evidence from nuclear mtDNA loci suggest that speakers share a distinct biological origin, this model not examined using paternally Y chromosomes. To test hypothesis elucidate migration histories...
Biomolecular simulations enabled by massively parallel supercomputers such as BlueGene/L promise to bridge the gap between currently accessible simulation time scale and experimental for many important protein folding processes. In this study, molecular dynamics were carried out both wild-type mutant hen lysozyme (TRP62GLY) study single mutation effect on stability misfolding. Our thermal denaturing at 400-500 K with OPLSAA CHARMM force fields show that structure is indeed much less stable...
Previous studies that pooled Indian populations from a wide variety of geographical locations, have obtained contradictory conclusions about the processes establishment Varna caste system and its genetic impact on origins demographic histories populations. To further investigate these questions we took advantage both Y chromosome designation are paternally inherited, genotyped 1,680 chromosomes representing 12 tribal 19 non-tribal (caste) endogamous predominantly Dravidian-speaking Tamil...
To analyze a glioblastoma tumor specimen with 3 different platforms and compare potentially actionable calls from each.Tumor DNA was analyzed by commercial targeted panel. In addition, tumor-normal whole-genome sequencing (WGS) RNA (RNA-seq). The WGS RNA-seq data were team of bioinformaticians cancer oncologists, separately IBM Watson Genomic Analytics (WGA), an automated system for prioritizing somatic variants identifying drugs.More identified WGS/RNA analysis than panels. WGA completed...
A recent study of 30 soluble globular protein structures revealed a quasi-invariant called the hydrophobic ratio. This invariant, which is ratio distance at second order moment vanished to zero vanished, was found be 0.75 +/- 0.05 for structures. report first describes results profiling 5,387 non-redundant domains Protein Data Bank, yields 0.71 0.08. Then, new score defined based on discriminate native-like proteins from decoy tested three widely used sets, namely Holm and Sander decoys,...
We present an efficient algorithm to systematically and automatically identify patterns in protein sequence families. The procedure is based on the Splash deterministic pattern discovery a framework assess statistical significance of patterns. demonstrate its application fully automated 974 PROSITE families (the complete subset which are defined by contain DR records). generates with better specificity undiminished sensitivity, or vice versa, 28% families; identical statistics were obtained...
We have performed molecular dynamics simulations for a total duration of more than 10 µs (with most trajectories being 1 in duration) to study the effect single mutation on hen lysozyme protein stability and denaturing, using an IBM Blue Gene/L™ supercomputer. One goal this was assess use certain force fields reproduce experimental results unfolding thermal denaturing techniques. A second important gain microscopic insights into mechanism misfolding both chemical found that were robust...
Abstract The mitochondrial DNA hypervariable segment I (HVS-I) is widely used in studies of human evolutionary genetics, and therefore accurate estimates mutation rates among nucleotide sites this region are essential. We have developed a novel maximum-likelihood methodology for estimating site-specific from partial phylogenetic information, such as haplogroup association. resulting estimation problem generalized linear model, with nonstandard link function. develop inference bias correction...
Prompted by the revolution in high-throughput sequencing and its potential impact for treating cancer patients, we initiated a clinical research study to compare ability of different assays analysis methods analyze glioblastoma tumors generate real-time treatment options physicians. A consortium seven institutions New York City enrolled 30 patients with performed tumor whole genome (WGS) RNA (RNA-seq; collectively WGS/RNA-seq); 20 these were also analyzed independent targeted panel...