@csoulette

~~~ Bioinformatics, amateur photography & marathon runner ~~~

 Daly City, CA
Joined November 2019
  • Tweets79
  • Following58
  • Followers45
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Cameron Soulette retweeted
Liz Tseng@Magdoll16 Aug 2021
What a creative way to use @PacBio Iso-Seq to identify chitin genes in species w/out a genome. They used Cogent+SUPPA so they could see. alt splicing! mdpi.com/1660-3397/19/7/392

Full-Length Transcriptome of Thalassiosira weissflogii as a Reference Resource and Mining of...

β-Chitin produced by diatoms is expected to have significant economic and ecological value due to its structure, which consists of parallel chains of chitin, its properties and the high abundance of...

mdpi.com
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Cameron Soulette retweeted
Heng Li@lh3lh327 May 2021
Minimap2 v2.19 released with better and more contiguous alignment over long INDELs and in highly repetitive regions, improvements backported from unimap. These represent the most significant algorithmic change since v2.1. Use with caution. github.com/lh3/minimap2/rele…

Release Minimap2-2.19 (r1057) · lh3/minimap2

This release includes a few important improvements backported from unimap: Improvement: more contiguous alignment through long INDELs. This is enabled by the minigraph chaining algorithm. All asm...

github.com
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Cameron Soulette retweeted
Maximillian Marin@maxgmarin28 Apr 2021
1/ I am super excited to share our recent work benchmarking short read sequencing performance across the Mtb genome. If you’re using Illumina WGS data to study M. tuberculosis, this work should be extremely useful to you. biorxiv.org/content/10.1101/…

Genomic sequence characteristics and the empiric accuracy of short-read sequencing

Background Short-read whole genome sequencing (WGS) is a vital tool for clinical applications and basic research. Genetic divergence from the reference genome, repetitive sequences, and sequencing...

biorxiv.org
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Cameron Soulette retweeted
Christian Gallardo@MrGalloLA29 Jan 2021
Introducing MrHAMER, our @nanopore-based high accuracy viral sequencing platform that yields single-molecule reads to ≥99.9% accuracy. Truly a team effort at the @BruceTorbett and @AndrewRouth labs. A thread 🧵... biorxiv.org/content/10.1101/…

MrHAMER yields highly accurate single molecule viral sequences enabling analysis of intra-host...

Technical challenges remain in the sequencing of RNA viruses due to their high intra-host diversity. This bottleneck is particularly pronounced when interrogating long-range co-evolution given the...

biorxiv.org
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Congrats Yulianna Ortega for being honored with the 2020 @ucsc Outstanding Staff Award!! Yuli is a passionate @stemdiv student advocate and mentor, working hard to bridge the diversity gap in science, engineering, and technology. sci.ucsc.edu/2P32IVt
Yulianna Ortega, UC Santa Cruz Director of STEM Diversity Programs

ALT Yulianna Ortega, UC Santa Cruz Director of STEM Diversity Programs

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Cameron Soulette retweeted
Graveley Lab@GraveleyLab29 Jul 2020
At long last our RNA binding protein study has been published! Great collaboration with @yeo_lab @daSpliceIsRight Eric Lecuyer and Xiang-Dong Fu! nature.com/articles/s41586-0…

A large-scale binding and functional map of human RNA-binding proteins

Nature - A combination of five assays is used to produce a catalogue of RNA elements to which RNA-binding proteins bind in human cells.

nature.com
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Cameron Soulette retweeted
Eduardo Eyras@EduEyras21 Jul 2020
RNA-Seq Analysis Reveals Localization-Associated Alternative Splicing across 13 Cell Lines biorxiv.org/content/10.1101/…

RNA-Seq Analysis Reveals Localization-Associated Alternative Splicing across 13 Cell Lines

Alternative splicing, a ubiquitous phenomenon in eukaryotes, is a regulatory mechanism for the biological diversity of individual genes. Most studies have focused on the effects of alternative...

biorxiv.org
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Cameron Soulette retweeted
UCSC Xena@UCSCXena13 Jul 2020
Our exploration & visualization tools for public #PCAWG data has been featured in the Genomes and Epigenomes Focus @NatureComms! Collaborative work with @icgc_dcc #ChromothripsisExplorer @ExpressionAtlas (@irenepapatheodo) & #PCAWG-Scout (@mikisvaz) #nciitcr
Nature Communications@NatureComms14 Nov 2018
Looking for exciting research in #genomes and #epigenomes? Explore newly featured research curated by Nature Communications editors. New highlights added monthly. #EditorsHighlights go.nature.com/NCOM-GenomesEp…
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Cameron Soulette retweeted
Manuel Irimia@mirimiam10 Jul 2020
We're releasing the largest batch of annotations of AS event functions in @VastDB so far. We reached ~2200 entries! I honestly never expected there were so many articles experimentally assessing the functions of individual AS events! And we're not done yet! 😃 Please RT!
VastDB@VastDB10 Jul 2020
After the lockdown, here's the largest batch of alternative splicing event annotations released so far (v1.9): 481 new entries from published articles and 114 from another CRISPR screen study. We reach a total of 2197 entries. Please RT to help us! @CRGenomica @mirimiam
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Cameron Soulette retweeted
CarpenterLab@LabCarpenter7 Jul 2020
Excited to share our latest research which is a collaboration with @TheBrooksLab . This work was headed up by our incredible students @elektra_robi and @pratibhajagann_
bioRxiv@biorxivpreprint7 Jul 2020
Inflammation Drives Alternative First Exon usage to Regulate Immune Genes including a Novel Iron Regulated Isoform of Aim2 biorxiv.org/cgi/content/shor… #bioRxiv
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Cameron Soulette retweeted
Brooks Lab@TheBrooksLab6 Jul 2020
Co-chairing a consortium with the amazing @anaconesa and @calizavi! Looking forward to better understanding how long-read @PacBio and @nanopore technologies and analysis methods can contribute to higher quality transcriptomes.
GencodeGenes@GencodeGenes3 Jul 2020
The Long-read RNAseq Genome Annotation Assessment Project Consortium is organizing a systematic evaluation of methods for transcript identification & quantification using long-read data. Those interested in participating can join the mailing list here: gencodegenes.org/pages/lrgas…
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Alright I’m gonna try to explain astigmatism, because this is an extreme example of what you might see at night if you have it.
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Cameron Soulette retweeted
Heng Li@lh3lh34 Jul 2020
SRA plans to drop base quality. This would make resequencing data largely useless for var calling. There are better ways to save space: quality binning and CRAM. If you use reseq data from SRA, please voice yourself in this RFI (deadline in 2 weeks): datascience.nih.gov/sra-rfi-…
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Cameron Soulette retweeted
AnaConesa@anaconesa3 Jul 2020
Excited to be part of this initiative!!! Hope this will be useful for the community using Long Reads to characterize transcriptomes! @PacBio @nanopore @UF_ICBR
GencodeGenes@GencodeGenes3 Jul 2020
The Long-read RNAseq Genome Annotation Assessment Project Consortium is organizing a systematic evaluation of methods for transcript identification & quantification using long-read data. Those interested in participating can join the mailing list here: gencodegenes.org/pages/lrgas…
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Cameron Soulette retweeted
Liz Tseng@Magdoll1 Jul 2020
Want to learn how to use @PacBio Iso-Seq to discover isoforms, annotate genomes, and do differential expression analysis? Sign up for the ISMB tutorial! iscb.org/ismb2020-program/tu… @anaconesa @iscb
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Cameron Soulette retweeted
GencodeGenes@GencodeGenes3 Jul 2020
The Long-read RNAseq Genome Annotation Assessment Project Consortium is organizing a systematic evaluation of methods for transcript identification & quantification using long-read data. Those interested in participating can join the mailing list here: gencodegenes.org/pages/lrgas…
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Baskin Engineering researcher Darrin Schultz at @ucsc contributes to a @nature article on developing a model system for the evolution of marine #bioluminescence , or in other words, finding out why some creatures glow! 💡 nature.com/articles/s41598-0…
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Cameron Soulette retweeted
Jess Davies@jldavies1626 Jun 2020
The first draft human genome at 20!! "This first genetic blueprint of a human being remains one of humanity’s most important scientific endeavours, laying the foundation for revolutions in genomics, biology and medicine". sanger.ac.uk/news_item/the-f… #sangerinstitute
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Cameron Soulette retweeted
CarpenterLab@LabCarpenter23 Jun 2020
If you are tired of spending money on purified murine GM-CSF then look no further!! We are happy to share our new line! Details below Generation and utilization of a HEK-293T murine GM-CSF expressing cell line biorxiv.org/content/10.1101/…

Generation and utilization of a HEK-293T murine GM-CSF expressing cell line

Macrophages and dendritic cells (DCs) are innate immune cells that play a key role in defense against pathogens. In vitro cultures of bone marrow-derived macrophages (BMDMs) and dendritic cells...

biorxiv.org
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Cameron Soulette retweeted
Gordon Simpson@ggsimpsonrna21 Jun 2020
This looks like a nice study: sequencing Arabidopsis nascent RNA with nanopore reveals splicing dynamics nature.com/articles/s41477-0…
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