K-mer analysis of long-read alignment pileups for structural variant genotyping
Nature CommunicationsAccurately genotyping structural variant (SV) alleles is crucial to genomics research. We present a novel method (kanpig) for genotyping SVs that leverages variant graphs and k-mer vectors to rapidly generate accurate SV genotypes.
Adam C. English +4 more
doaj +1 more source
FEBS Letters, EarlyView.This perspective highlights emerging insights into how the circadian transcription factor CLOCK:BMAL1 regulates chromatin architecture, cooperates with other transcription factors, and coordinates enhancer dynamics. We propose an updated framework for how circadian transcription factors operate within dynamic and multifactorial chromatin landscapes ...
Xinyu Y. Nie, Jerome S. Menet
wiley +1 more source
Disordered but rhythmic—the role of intrinsic protein disorder in eukaryotic circadian timing
FEBS Letters, EarlyView.Unstructured domains known as intrinsically disordered regions (IDRs) are present in nearly every part of the eukaryotic core circadian oscillator. IDRs enable many diverse inter‐ and intramolecular interactions that support clock function. IDR conformations are highly tunable by post‐translational modifications and environmental conditions, which ...
Emery T. Usher, Jacqueline F. Pelham
wiley +1 more source
Tracking updates in clinical databases increases efficiency for variant reanalysis
Genetics in Medicine OpenPurpose: Variant interpretation, guided by American College of Medical Genetics and Genomics guidelines, can inform clinical decision-making. However, interpretations may change over time for a variety of reasons.
Lele Li +5 more
doaj +1 more source
BMC Biology, 2017 Background The de novo assembly of repeat-rich mammalian genomes using only high-throughput short read sequencing data typically results in highly fragmented genome assemblies that limit downstream applications.
Peter A. Larsen +19 more
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Protein pyrophosphorylation by inositol pyrophosphates — detection, function, and regulation
FEBS Letters, EarlyView.Protein pyrophosphorylation is an unusual signaling mechanism that was discovered two decades ago. It can be driven by inositol pyrophosphate messengers and influences various cellular processes. Herein, we summarize the research progress and challenges of this field, covering pathways found to be regulated by this posttranslational modification as ...
Sarah Lampe +3 more
wiley +1 more source
Study of Thirteen Causal Genes in Turkish Patients with Clinically Suspected Maturity-Onset Diabetes of the Young (MODY) using a Targeted Next-Generation Sequencing Panel [PDF]
, 2021 Mustafa Doğan +6 more
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Sequence ‘minimization’: exploring the sequence landscape with simplified sequences
Current Opinion in Biotechnology, 1995 The challenges of protein engineering arise, in part, from the enormous number of possible sequences and the almost unimaginably small fraction of such sequences that can be studied experimentally or computationally. Fortunately, not all possibilities need to be considered because many different sequences can adopt the same structure.
openaire +2 more sources
Integration of circadian and hypoxia signaling via non‐canonical heterodimerization
FEBS Letters, EarlyView.CLOCK, BMAL1, and HIFs are basic helix‐loop‐helix and Per‐Arnt‐Sim domain (bHLH‐PAS) proteins, which function as transcription factors. bHLH‐PAS proteins are designated in two classes. Many class I proteins are regulated by environmental signals via their PAS domains, but such signals have not been identified for all.
Sicong Wang, Katja A. Lamia
wiley +1 more source
RNA-sequencing and Mathematical Modeling Identify Suite of Light-sensitive Circadian Genes in an Orb-web Weaving Spider [PDF]
, 2021 Natalia Toporikova +7 more
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