@TheBrooksLab

The Brooks Lab @UCSC | Department of Biomolecular Engineering | We study #DNA and #RNA sequencing data to fight #cancer

 UC Santa Cruz
brookslab.soe.ucsc.edu
Joined February 2018
  • Tweets175
  • Following56
  • Followers771
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Thrilled to host former lab mate and long time collaborator @TheBrooksLab as the first Translational Data Science Visiting Scholar @fredhutch! We are working on isoform discovery and functional characterization in lung cancer - it will be great to work face to face this month!
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The Genomics Institute is looking for a new Director for the Genomics Institute Office of Diversity! The role generates and implements DEI initiatives within the Genomics Institute of Baskin Engineering at UC Santa Cruz. Apply Here: tinyurl.com/DirectorGenomics…
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Brooks Lab retweeted
AnaConesa@anaconesa
23 Sep 2023
Replying to @andrei_thomas_t @ForbeckForums @EduEyras @GuccioneLab @yeo_lab @CChengLab
Thank you for the invitation! I am so much enjoying the format of the meeting!!! Also pleased to meet again some of my favorite #LongReadsTranscriptomics people @TheBrooksLab @EduEyras in this beautiful venue
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Interested in an advanced degree in the biomedical sciences and engineering? Check out our virtual open house from 11am-1pm PST on November 9! Register at forms.gle/eNM39Sg3KB6rt7EP8
Flyer advertising the open house. Schedule includes 11-11:30 PBSE overview, 11:30-12pm Track overviews, 12-1 Faculty/Program drop-ins

ALT Flyer advertising the open house. Schedule includes 11-11:30 PBSE overview, 11:30-12pm Track overviews, 12-1 Faculty/Program drop-ins

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Brooks Lab retweeted
AnaConesa@anaconesa
28 Jul 2023
SOO excited to see the final LRGASP preprint out! The largest benchmark of #longreads for transcriptomics. A must-read if you plan on doing lrRNA-seq. Thanks to so many for the huge work @FJPardoPalacios @TheBrooksLab @MarkDiekhans @GSheynkman @calizavi biorxiv.org/content/10.1101/…

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

The Long-read RNA-Seq Genome Annotation Assessment Project (LRGASP) Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. The consortium generated...

biorxiv.org
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Our paper "Full-length transcript alterations in human bronchial epithelial cells with U2AF1 S34F mutations" is now published! Amazing team effort led by @csoulette 1/3 life-science-alliance.org/co…

Full-length transcript alterations in human bronchial epithelial cells with U2AF1 S34F mutations

U2AF1 is one of the most recurrently mutated splicing factors in lung adenocarcinoma and has been shown to cause transcriptome-wide pre-mRNA splicing alterations; however, the full-length altered...

life-science-alliance.org
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Full-length transcript profiling, with our tool FLAIR, helped uncover possible functional impacts of recurrent mutations in the splicing factor U2AF1 in lung cancer 2/3
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We discovered a new lncRNA that is one of the most upregulated transcripts associated with U2AF1 mutation and has been missed by short-read approaches, likely due to overlap with repeat elements. This and many other transcripts to study for further functional follow up! 3/3
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Now published @Nature! We @UWproteindesign @ChristofferNorn designed a prototype luciferase from scratch with brightness similar to native luciferases. Also, I am thrilled to announce that my lab will open this summer @ucscbme. Join us to push boundaries in protein engineering!
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Calling all postdocs! 📣 We are hosting the Next Wave of Faculty in Genomics Symposium to showcase rising talent in genomics research. *Money for travel to the beautiful Santa Cruz coast and an honorarium are available!* Learn more and apply by Feb 28: genomics.ucsc.edu/calendar_e…
Text reads: UC Santa Cruz Genomics Institute Next Wave of Faculty in Genomics Symposium. Photo of a wave breaking on the beach on a clear day as birds circle.

ALT Text reads: UC Santa Cruz Genomics Institute Next Wave of Faculty in Genomics Symposium. Photo of a wave breaking on the beach on a clear day as birds circle.

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Check out this #bioinformatics #protocol from Dr. Angela Brooks' lab @TheBrooksLab @AlexisThornton_ @ucscbme @UCSC for expression-based variant impact phenotyping to predict the impact of gene variants in cell lines: star-protocols.cell.com/prot…
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Alexis Thornton, PhD (@AlexisThornton_) is from USA 🇺🇸. She completed her PhD with Dr. @theBrooksLab in the Department of Biomolecular Engineering (BME) in the Baskin School of Engineering at UC Santa Cruz (@UCSCBME ) and has started new position at GRAIL (@GRAILbio)
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I hope the University of California is throwing its substantial lobbying power at the NIH to raise the R01 modular budget cap, which has been set at $250,000 per year since 2000. Twenty-two years. The entire lifetime of many grad students.
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Congratulations to Vid and the rest of the iGEM team!
Alexander Wolf@BaskinEng_Dean
28 Oct 2022
BREAKING! #BaskinEngineering’s #iGEM team won gold & earned a nomination for Best Therapeutics Project at the 2022 @iGEM Jamboree. Through #SyntheticBio, Team @UCSC engineered a yeast-based treatment to address the high costs & limited availability of Type 2 #diabetes medication.
Team UCSC at the 2022 iGEM Grand Jamboree in Paris, France.

ALT Team UCSC at the 2022 iGEM Grand Jamboree in Paris, France.

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🧵 HOT OFF THE PRESS: BWCB is pleased to announce the publication of our editorial in @PLOSCompBiol titled "Ten simple rules for creating a global network in computational biology." doi.org/jjhn
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🚨Headed to #ASHG22 next week? 🧬Be sure to support BWCB members contributing posters, panels, and booths at the @GeneticsSociety Annual Meeting in sunny LA. 🤝Follow for the latest info on opps. to learn more about us during the meeting. See you there Oct 24- 29th!
The Black women in Computational Biology Network BWCB at ASHG Annual Meeting 2022. Los Angeles, CA. October 25-29. Connect with and support our members at #ASHG22 Headshots of 5 women. All smiling. Their names and poster/booth/presentation numbers are the following: Angela Brooks, PhD (UC Santa Cruz) - S55. Markia Smith, PhD (Novartis) - S59. Asia Mitchell, PhD (Invitae) - Booth #1543. Jenea Adams (Uni. of Pennsylvania) - PB3122. Kaylyn Clark (Uni. of Pennsylvania) - PB3474. @blkwomencompbio blackwomencompbio.org

ALT The Black women in Computational Biology Network BWCB at ASHG Annual Meeting 2022. Los Angeles, CA. October 25-29. Connect with and support our members at #ASHG22 Headshots of 5 women. All smiling. Their names and poster/booth/presentation numbers are the following: Angela Brooks, PhD (UC Santa Cruz) - S55. Markia Smith, PhD (Novartis) - S59. Asia Mitchell, PhD (Invitae) - Booth #1543. Jenea Adams (Uni. of Pennsylvania) - PB3122. Kaylyn Clark (Uni. of Pennsylvania) - PB3474. @blkwomencompbio blackwomencompbio.org

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One of our stellar undergrads, Rakshya Sharma, was featured for Baskin Engineering's celebration of National Transfer Week!
Baskin Engineering at UCSC@BaskinEng
20 Oct 2022
Through joining several campus organizations, including AAPIRC's Bridge to Success Program & MEP, Rakshya Sharma's #BaskinEngineering transfer student journey has been filled with endless opportunities & meaningful connections. engineering.ucsc.edu/people/… #NationalTransferStudentWeek
Rakshy Sharma

ALT Rakshy Sharma

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#BaskinEngineering faculty and students tackle big ideas through bold innovation. @UCSCBME's @KHMiga led the extraordinary effort to complete the 1st gapless human #genome sequence, providing new insights into #genetic disease, evolution, and more. magazine.ucsc.edu/2022/08/op…

Opening the black box

One scientist’s vision to reveal the secrets of our ‘junk’ DNA launches a worldwide effort to complete a human genome

magazine.ucsc.edu
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Our paper showing putative IRESes from #HOXA9 and other genes are false-positives is now published at #PNAS. Great #RNA and #RNAtranslation work by Christina Akirtava @bio2data and Gemma May @gemmaemay! pnas.org/doi/10.1073/pnas.21…

False-positive IRESes from Hoxa9 and other genes resulting from errors in mammalian 5′ UTR annota...

Hyperconserved genomic sequences have great promise for understanding core biological processes. It has been recently proposed that scores of hyper...

pnas.org
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Our new webinar series kicks off on September 8, at 6 pm ET - tune in to hear 2019 Nobel Laureate William G. Kaelin, Jr., MD, reflect on his early days as a scientist, his passion for mentoring, and how he just happened to win a Nobel Prize. Register here: bit.ly/3KbpJBh
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