James Knight
A5082730880- Genomics and Phylogenetic Studies
- Genomics and Rare Diseases
- Genetic diversity and population structure
- Chromosomal and Genetic Variations
- Identification and Quantification in Food
- Algorithms and Data Compression
- Fetal and Pediatric Neurological Disorders
- Respiratory viral infections research
- Genetic and Kidney Cyst Diseases
- Cutaneous Melanoma Detection and Management
- Cerebral Palsy and Movement Disorders
- Congenital heart defects research
- Congenital Heart Disease Studies
- Epigenetics and DNA Methylation
- Bacteriophages and microbial interactions
- Endoplasmic Reticulum Stress and Disease
- Melanoma and MAPK Pathways
- Neurological Disease Mechanisms and Treatments
- Machine Learning and Algorithms
- Gynecological conditions and treatments
- Microbial infections and disease research
- Neurofibromatosis and Schwannoma Cases
- Genetic Associations and Epidemiology
- Network Packet Processing and Optimization
- Mobile Health and mHealth Applications
Yale University
2016-2025
Kyungpook National University
2024
Osong Medical Innovation Foundation
2024
Yale Cancer Center
2018-2023
Baylor College of Medicine
2022
Baylor Genetics
2022
The Ohio State University
2014-2022
University of California System
2019
St. Jude Children's Research Hospital
2014
Enzo Life Sciences (United States)
2007-2013
Drosophila melanogaster is a proven model system for many aspects of human biology. Here we present two-hybrid-based protein-interaction map the fly proteome. A total 10,623 predicted transcripts were isolated and screened against standard normalized complementary DNA libraries to produce draft 7048 proteins 20,405 interactions. computational method rating two-hybrid interaction confidence was developed refine this higher 4679 4780 Statistical modeling network showed two levels organization:...
Atlantic cod (Gadus morhua) is a large, cold-adapted teleost that sustains long-standing commercial fisheries and incipient aquaculture. Here we present the genome sequence of cod, showing evidence for complex thermal adaptations in its haemoglobin gene cluster an unusual immune architecture compared to other sequenced vertebrates. The assembly was obtained exclusively by 454 sequencing shotgun paired-end libraries, automated annotation identified 22,154 genes. major histocompatibility (MHC)...
Bacterial involvement in autoimmunity The composition of the commensal microbiota is known to influence autoimmune disease development and persistence. Manfredo Vieira et al. identified a gut microbe, Enterococcus gallinarum , that translocates from into organs mice with genetic predisposition lupus-like (see Perspective by Citi). Molecular signatures barrier disintegration pathogenic T helper cells were evident gut, liver, lymphoid during colonization pathobiont. ensuing pathology could be...
The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly such into high-quality, finished sequences remains challenging. Many tools are available, but they differ greatly in terms their performance (speed, scalability, hardware requirements, acceptance newer read technologies) final output (composition assembled sequence). More importantly, it largely unclear how best assess the quality sequences. Assemblathon competitions...
Sequencing of the bonobo genome shows that more than three per cent human is closely related to either or chimpanzee those genomes are each other. The and our species' two closest living relatives. This paper reports sequence bonobo, last ape be sequenced. Comparative genomic analyses reveal 3% these results shed light on ancestry species might eventually help us understand genetic basis phenotypes humans share with one other species. Two African apes relatives humans: (Pan troglodytes)...
Between July 18(th) and 24(th) 2010, 26 leading microbial ecology, computation, bioinformatics statistics researchers came together in Snowbird, Utah (USA) to discuss the challenge of how best characterize world using next-generation sequencing technologies. The meeting was entitled "Terabase Metagenomics" sponsored by Institute for Computing Science (ICiS) summer 2010 workshop program. aim explore fundamental questions relating ecology that could be addressed advances potential....
Although the application of sequencing-by-synthesis techniques to DNA extracted from bones has revolutionized study ancient DNA, it been plagued by large fractions contaminating environmental DNA. The genetic analyses hair shafts could be a solution: We present 10 previously unexamined Siberian mammoth (Mammuthus primigenius) mitochondrial genomes, sequenced with up 48-fold coverage. observed levels damage-derived sequencing errors were lower than those in published frozen bone samples, even...
OBJECTIVE—To evaluate the efficacy and safety of tadalafil taken as needed before sexual activity by men with diabetes erectile dysfunction (ED). RESEARCH DESIGN AND METHODS—Men type 1 or 2 a minimum 3-month history ED were randomly allocated to one three groups: placebo (n = 71), 10 mg 73), 20 72) up once daily for 12 weeks. Changes from baseline in mean scores on function domain International Index Erectile Function (IIEF) changes proportion “yes” responses question 2, “Were you able...
The Tasmanian devil ( Sarcophilus harrisii ) is threatened with extinction because of a contagious cancer known as Devil Facial Tumor Disease. inability to mount an immune response and reject these tumors might be caused by lack genetic diversity within dwindling population. Here we report whole-genome analysis two animals originating from extreme northwest southeast Tasmania, the maximal geographic spread, together genome tumor taken one them. A 3.3-Gb de novo assembly sequence data...
We report five new complete mitochondrial DNA (mtDNA) genomes of Siberian woolly mammoth ( Mammuthus primigenius ), sequenced with up to 73-fold coverage from extracted hair shaft material. Three the sequences present first mtDNA clade II. Analysis these and 13 recently published demonstrates existence two apparently sympatric clades that exhibit high interclade divergence. The analytical power afforded by analysis reveals a surprisingly ancient coalescence age clades, ≈1–2 million years,...
Dominantly inherited isolated polycystic liver disease (PCLD) consists of cysts that are radiologically and pathologically identical to those seen in autosomal dominant kidney disease, but without clinically relevant cysts. The causative genes known for fewer than 40% PCLD index cases. Here, we have used whole exome sequencing a discovery cohort 102 unrelated patients who were excluded mutations the 2 most common genes, PRKCSH SEC63, identify heterozygous loss-of-function 3 additional ALG8,...
The first Atlantic cod (Gadus morhua) genome assembly published in 2011 was one of the early assemblies exclusively based on high-throughput 454 pyrosequencing. Since then, rapid advances sequencing technologies have led to a multitude generated for complex genomes, although many these are fragmented nature with significant fraction bases gaps. development long-read and improved software now enable generation more contiguous assemblies. By combining data from Illumina, longer PacBio...
OBJECTIVE Recent large-cohort sequencing studies have investigated the genomic landscape of meningiomas, identifying somatic coding alterations in NF2 , SMARCB1 SMARCE1 TRAF7, KLF4, POLR2A BAP1 and members PI3K Hedgehog signaling pathways. Initial associations between clinical features subgroups been described, including location, grade, histology. However, further investigation using an expanded collection samples is needed to confirm previous findings, as well elucidate relationships not...
Significance Craniosynostosis is a common congenital malformation resulting from premature fusion of the bones that comprise cranial vault, requiring surgery in infancy to prevent adverse neurologic outcomes. Eighty-five percent cases are non-syndromic and unknown cause. By exome sequencing families with midline craniosynostosis, we show 5% have de novo damaging mutations negative regulators Wnt, bone morphogenetic protein (BMP), Ras/ERK signaling pathways, developmental cascades converge on...
If the genome contains outlier sequences extraordinarily sensitive to environmental agents, these would be sentinels for monitoring personal carcinogen exposure and might drive direct changes in cell physiology rather than acting through rare mutations. New methods, adductSeq freqSeq, provided statistical resolution quantify lesions at single-base across genome. Primary human melanocytes, but not fibroblasts, carried spontaneous apurinic sites TG sequence more frequent ultraviolet...
Acral melanoma, the most common melanoma subtype among non-White individuals, is associated with poor prognosis. However, its key molecular drivers remain obscure. Here, we perform integrative genomic and clinical profiling of acral melanomas from 104 patients treated in North America (n = 37) or China 67). We find that recurrent, late-arising focal amplifications cytoband 22q11.21 are a leading determinant inferior survival, strongly metastasis, linked to downregulation immunomodulatory...
Graphical abstractAbstractBackgroundMUPPITS-2 was a randomized, placebo-controlled clinical trial that demonstrated mepolizumab (anti-IL-5) reduced exacerbations and blood airway eosinophils in urban children with severe eosinophilic asthma. Despite this reduction eosinophilia, exacerbation risk persisted certain patients treated mepolizumab. This raises the possibility subpopulations of exist contribute to breakthrough exacerbations.ObjectiveWe aimed determine effect on childhood...