Parisa Nejad

ORCID: 0000-0002-3163-0115
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About
Contact & Profiles
Research Areas
  • Genomics and Phylogenetic Studies
  • Genomics and Chromatin Dynamics
  • RNA and protein synthesis mechanisms
  • RNA modifications and cancer
  • Single-cell and spatial transcriptomics
  • Cancer Genomics and Diagnostics
  • Extracellular vesicles in disease
  • Machine Learning in Bioinformatics
  • Cell Image Analysis Techniques

University of California, Santa Cruz
2015-2023

Abstract The UCSC Genome Browser (https://genome.ucsc.edu) is an omics data consolidator, graphical viewer, and general bioinformatics resource that continues to serve the community as it enters its 23rd year. This year has seen emphasis in clinical data, with new tracks expanded Recommended Track Sets feature on hg38 well addition of a single cell track group. SARS-CoV-2 remain focus, regular annotation updates browser continued curation our phylogenetic sequence placing tool, hgPhyloPlace,...

10.1093/nar/gkac1072 article EN cc-by Nucleic Acids Research 2022-10-25

For the past 15 years, UCSC Genome Browser (http://genome.ucsc.edu/) has served international research community by offering an integrated platform for viewing and analyzing information from a large database of genome assemblies their associated annotations. The been under continuous development since its inception with new data sets software features added frequently. Some release highlights this year include updated browsers various assemblies, including bonobo zebrafish; gene annotation...

10.1093/nar/gkv1275 article EN cc-by Nucleic Acids Research 2015-11-20

Since its 2001 debut, the University of California, Santa Cruz (UCSC) Genome Browser (http://genome.ucsc.edu/) team has provided continuous support to international genomics and biomedical communities through a web-based, open source platform designed for fast, scalable display sequence alignments annotations landscaped against vast collection quality reference genome assemblies. The browser's publicly accessible databases are backbone rich, integrated bioinformatics tool suite that includes...

10.1093/nar/gkw1134 article EN cc-by Nucleic Acids Research 2016-01-01

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...

10.1093/nar/gkad987 article EN cc-by Nucleic Acids Research 2023-11-11

ABSTRACT For the past 15 years, UCSC Genome Browser ( http://genome.ucsc.edu/ ) has served international research community by offering an integrated platform for viewing and analyzing information from a large database of genome assemblies their associated annotations. The been under continuous development since its inception with new data sets software features added frequently. Some release highlights this year include updated browsers various assemblies, including bonobo zebrafish; gene...

10.1101/027037 preprint EN cc-by-nc bioRxiv (Cold Spring Harbor Laboratory) 2015-09-17
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