Melissa Cline
A5053719847- Genomics and Rare Diseases
- RNA and protein synthesis mechanisms
- Cancer Genomics and Diagnostics
- Genomics and Phylogenetic Studies
- Machine Learning in Bioinformatics
- RNA Research and Splicing
- Gene expression and cancer classification
- Bioinformatics and Genomic Networks
- BRCA gene mutations in cancer
- RNA modifications and cancer
- Molecular Biology Techniques and Applications
- Protein Structure and Dynamics
- Genetic Associations and Epidemiology
- Biomedical Text Mining and Ontologies
- Genetics, Bioinformatics, and Biomedical Research
- Genomics and Chromatin Dynamics
- Genomic variations and chromosomal abnormalities
- Ethics in Clinical Research
- Muscle Physiology and Disorders
- Gene Regulatory Network Analysis
- Genetic factors in colorectal cancer
- Epigenetics and DNA Methylation
- Genetic Neurodegenerative Diseases
- Nutrition, Genetics, and Disease
- Prenatal Screening and Diagnostics
University of California, Santa Cruz
2014-2024
Northwell Health
2024
Corewell Health
2024
University of California, San Francisco
2017
Santa Cruz County Office of Education
2016
Howard Hughes Medical Institute
2011-2013
Stanford University
2013
University of California, Berkeley
2013
Centre for Genomic Regulation
2011-2012
Pennsylvania State University
2011-2012
The University of California, Santa Cruz Genome Browser ( http://genome.ucsc.edu ) offers online access to a database genomic sequence and annotation data for wide variety organisms. also has many tools visualizing, comparing analyzing both publicly available user-generated sets, aligning sequences uploading user data. Among the features released this year are gene search tool track drag-reorder functionality as well support BAM BigWig/BigBed file formats. New display enhancements include...
The laboratory mouse shares the majority of its protein-coding genes with humans, making it premier model organism in biomedical research, yet two mammals differ significant ways. To gain greater insights into both shared and species-specific transcriptional cellular regulatory programs mouse, Mouse ENCODE Consortium has mapped transcription, DNase I hypersensitivity, transcription factor binding, chromatin modifications replication domains throughout genome diverse cell tissue types. By...
The University of California Santa Cruz (UCSC) Genome Browser (http://genome.ucsc.edu) offers online public access to a growing database genomic sequence and annotations for wide variety organisms. is an integrated tool set visualizing, comparing, analysing sharing both publicly available user-generated datasets. As September 2012, basic annotation 'tracks' are provided 63 organisms, including 26 mammals, 13 non-mammal vertebrates, 3 invertebrate deuterostomes, insects, 6 worms, yeast sea...
The University of California Santa Cruz (UCSC) Genome Browser (http://genome.ucsc.edu) offers online public access to a growing database genomic sequence and annotations for large collection organisms, primarily vertebrates, with an emphasis on the human mouse genomes. Browser's web-based tools provide integrated environment visualizing, comparing, analysing sharing both publicly available user-generated data sets. As September 2013, contained basic set annotation 'tracks' ∼90 organisms....
Regulation of gene expression is executed in many cases by RNA-binding proteins (RBPs) that bind to mRNAs as well non-coding RNAs. RBPs recognize their RNA target via specific binding sites on the RNA. Predicting known be a major challenge. We present new webserver, RBPmap, freely accessible through website http://rbpmap.technion.ac.il/ for accurate prediction and mapping RBP sites. RBPmap has been developed specifically human, mouse Drosophila melanogaster genomes, though it supports other...
The University of California Santa Cruz Genome Browser (http://genome.ucsc.edu) offers online public access to a growing database genomic sequence and annotations for wide variety organisms. is an integrated tool set visualizing, comparing, analyzing sharing both publicly available user-generated data sets. In the past year, local has been updated with four new species assemblies, we anticipate another will be released by end 2011. Further, large number annotation tracks have either added,...
The UCSC Cancer Genomics Browser (https://genome-cancer.ucsc.edu/) is a web-based application that integrates relevant data, analysis and visualization, allowing users to easily discover share their research observations. Users can explore the relationship between genomic alterations phenotypes by visualizing various -omic data alongside clinical phenotypic features, such as age, subtype classifications biomarkers. currently hosts 575 public datasets from genome-wide analyses of over 227 000...
The UCSC Cancer Genomics Browser (https://genome-cancer.ucsc.edu) offers interactive visualization and exploration of TCGA genomic, phenotypic, clinical data, as produced by the Genome Atlas Research Network. Researchers can explore impact genomic alterations on phenotypes visualizing gene protein expression, copy number, DNA methylation, somatic mutation pathway inference data alongside features, Pan-Cancer subtype classifications biomarkers. Integrated Kaplan-Meier survival analysis helps...
The Encyclopedia of DNA Elements (ENCODE) Consortium is entering its 5th year production-level effort generating high-quality whole-genome functional annotations the human genome. past has brought ENCODE compendium elements to critical mass, with a diverse set 27 biochemical assays now covering 200 distinct cell types. Within mouse genome, which been under study by groups for 2 years, 37 types have assayed. Over 2000 individual experiments completed and submitted Data Coordination Center...
The UCSC Genome Browser (https://genome.ucsc.edu) is a web-based genomic visualization and analysis tool that serves data to over 7,000 distinct users per day worldwide. It provides annotation on thousands of genome assemblies, ranging from human SARS-CoV2. This year, we have introduced new the Human Pangenome Reference Consortium viral genomes including We added 1,200 our GenArk system, increasing overall diversity representation. support for nine user-contributed track hubs public hub...
To develop RNA splicing biomarkers of disease severity and therapeutic response in myotonic dystrophy type 1 (DM1) 2 (DM2).
The BRCA Challenge is a long-term data-sharing project initiated within the Global Alliance for Genomics and Health (GA4GH) to aggregate BRCA1 BRCA2 data support highly collaborative research activities. Its goal generate an informed current understanding of impact genetic variation on cancer risk across iconic predisposition genes, BRCA2. Initially, reported variants in available from public databases were integrated into single, newly created site, www.brcaexchange.org. purpose Exchange...
The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical genomic data through both harmonized aggregation federated approaches. decreasing cost sequencing (along with other genome-wide molecular assays) increasing evidence its utility will soon drive generation sequence from tens millions humans, levels diversity. In this perspective, we present GA4GH strategies addressing major challenges revolution. We...
Two major goals of regenerative medicine are to reproducibly transform adult somatic cells into a pluripotent state and control their differentiation specific cell fates. Progress toward these would be greatly helped by obtaining complete picture the RNA isoforms produced due alternative splicing (AS) promoter selection (APS). To investigate roles AS APS, reciprocal exon–exon junctions were interrogated on genome-wide scale in differentiating mouse embryonic stem (ES) with prototype...
An important problem in computational biology is predicting the structure of large number putative proteins discovered by genome sequencing projects. Fold-recognition methods attempt to solve relating target known structures, searching for template homologous target. Remote homologs that may have significant structural similarity are often not detectable sequence similarities alone. To address this, we incorporated predicted local structure, a generalization secondary into two-track profile...
Alternative splicing contributes to both gene regulation and protein diversity. To discover broad relationships between of alternative sequence conservation, we applied a systems approach, using oligonucleotide microarrays designed capture information across the mouse genome. In set 22 adult tissues, observe differential expression RNA containing at least two splice junctions for about 40% 6,216 events could detect. Statistical comparisons identify 171 cassette exons whose inclusion or...
The ENCODE project is an international consortium with a goal of cataloguing all the functional elements in human genome. Data Coordination Center (DCC) at University California, Santa Cruz serves as central repository for data. In this role, DCC offers collection high-throughput, genome-wide data generated technologies such ChIP-Seq, RNA-Seq, DNA digestion and others. This helps illuminate transcription factor-binding sites, histone marks, chromatin accessibility, methylation, RNA...