User profiles for Adam Godzik
 | Adam GodzikProfessor, University of California Riverside School of Medicine Verified email at medsch.ucr.edu Cited by 54282 |
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
Motivation: In 2001 and 2002, we published two papers (Bioinformatics, 17, 282–283,
Bioinformatics, 18, 77–82) describing an ultrafast protein sequence clustering program called cd-…
Bioinformatics, 18, 77–82) describing an ultrafast protein sequence clustering program called cd-…
[HTML][HTML] Detection of a SARS-CoV-2 variant of concern in South Africa
…, O Laguda-Akingba, A Alisoltani-Dehkordi, A Godzik… - Nature, 2021 - nature.com
Continued uncontrolled transmission of SARS-CoV-2 in many parts of the world is creating
conditions for substantial evolutionary changes to the virus 1 , 2 . Here we describe a newly …
conditions for substantial evolutionary changes to the virus 1 , 2 . Here we describe a newly …
Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa
…, O Laguda-Akingba, A Alisoltani-Dehkordi, A Godzik… - medrxiv, 2020 - medrxiv.org
Continued uncontrolled transmission of the severe acute respiratory syndrome-related
coronavirus 2 (SARS-CoV-2) in many parts of the world is creating the conditions for significant …
coronavirus 2 (SARS-CoV-2) in many parts of the world is creating the conditions for significant …
[HTML][HTML] Protein tyrosine phosphatases in the human genome
Tyrosine phosphorylation is catalyzed by protein tyrosine kinases, which are represented by
90 genes in the human genome. Here, we present the set of 107 genes in the human …
90 genes in the human genome. Here, we present the set of 107 genes in the human …
S-nitrosylation of Drp1 mediates β-amyloid-related mitochondrial fission and neuronal injury
Mitochondria continuously undergo two opposing processes, fission and fusion. The
disruption of this dynamic equilibrium may herald cell injury or death and may contribute to …
disruption of this dynamic equilibrium may herald cell injury or death and may contribute to …
Clustering of highly homologous sequences to reduce the size of large protein databases
We present a fast and flexible program for clustering large protein databases at different
sequence identity levels. It takes less than 2 h for the all-against-all sequence comparison and …
sequence identity levels. It takes less than 2 h for the all-against-all sequence comparison and …
[PDF][PDF] The NLR gene family: a standard nomenclature
Immune regulatory proteins such as CIITA, NAIP, IPAF, NOD1, NOD2, NALP1, and cryopyrin
(also known as NALP3) are members of a family characterized by the presence of a NACHT …
(also known as NALP3) are members of a family characterized by the presence of a NACHT …
[HTML][HTML] The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families
Metagenomics projects based on shotgun sequencing of populations of micro-organisms
yield insight into protein families. We used sequence similarity clustering to explore proteins …
yield insight into protein families. We used sequence similarity clustering to explore proteins …
[HTML][HTML] A primer on metagenomics
JC Wooley, A Godzik, I Friedberg - PLoS computational biology, 2010 - journals.plos.org
Metagenomics is a discipline that enables the genomic study of uncultured microorganisms.
Faster, cheaper sequencing technologies and the ability to sequence uncultured microbes …
Faster, cheaper sequencing technologies and the ability to sequence uncultured microbes …
[PDF][PDF] Flexible structure alignment by chaining aligned fragment pairs allowing twists
Motivation: Protein structures are flexible and undergo structural rearrangements as part of
their function, and yet most existing protein structure comparison methods treat them as rigid …
their function, and yet most existing protein structure comparison methods treat them as rigid …