@KrishnanLab

Laboratory for Biomedical Data Science and Computational Genomics at @CUBiomedInfo and @CUHealthAI | @KrishnanLab@genomic.social

 CU Anschutz Med Campus
thekrishnanlab.org
Joined July 2016
  • Tweets135
  • Following28
  • Followers261
5Media
📢#MLCB2024 Check out our recent review to break into translational biomedicine! We take a deep dive into methods for comparing & transferring data & knowledge across species, and highlight gaps/challenges. Details on implementation, data, & benchmarks: github.com/krishnanlab/cross…
Arjun Krishnan@compbiologist
29 Aug 2024
Preprint 🚨 A review state-of-the-art computational strategies for cross-species knowledge transfer in biomedicine 💻👩‍🦰🐭🐟🪰🪱🧬🫁⚕️ Led by an excellent team at @KrishnanLab: @yhbioinfo, @ChrisAMancuso, & @kaylainbio in collab w/ @FishEvoDevoGeno 🧵 arxiv.org/abs/2408.08503

Computational strategies for cross-species knowledge transfer

Research organisms provide invaluable insights into human biology and diseases, serving as essential tools for functional experiments, disease modeling, and drug testing. However, evolutionary...

arxiv.org
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Preprint 🚨 A review state-of-the-art computational strategies for cross-species knowledge transfer in biomedicine 💻👩‍🦰🐭🐟🪰🪱🧬🫁⚕️ Led by an excellent team at @KrishnanLab: @yhbioinfo, @ChrisAMancuso, & @kaylainbio in collab w/ @FishEvoDevoGeno 🧵 arxiv.org/abs/2408.08503

Computational strategies for cross-species knowledge transfer

Research organisms provide invaluable insights into human biology and diseases, serving as essential tools for functional experiments, disease modeling, and drug testing. However, evolutionary...

arxiv.org
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1/ Excited to share Txt2onto 2.0, an approach combining language models & machine learning to annotate public samples & studies with standardized tissue & disease terms with a focus on interpretability & explainability! 📜 doi.org/10.1101/2024.06.03.5… 💻 github.com/krishnanlab/txt2o… 🧵👇🏼
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Excited to see fruits of a huge community effort! Thanks to @ProfMilenkovic for the leadership and the opportunity to be a part of this 🙌🏽
Dr. Tijana Milenkovic@ProfMilenkovic
18 Sep 2023
Our review+perspective paper on "Current and future directions in network biology" is online (arxiv.org/abs/2309.08478). This has been a Herculean effort by many co-authors, thank you all! Special thanks to @marinkazitnik, @_michellemli, @aydin_wells, and all section coordinators.
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Excited to present new work led by @ChrisAMancuso: GenePlexusZoo, a computational framework to improve discovering new genes linked to pathways, phenotypes, & diseases both within & across species by combining molecular networks from multiple species w/ #machinelearning. [1/n]
bioRxiv@biorxivpreprint
3 May 2023
Joint representation of molecular networks from multiple species improves gene classification biorxiv.org/cgi/content/shor… #bioRxiv
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🎉CONGRATS to the winners of the @FASEBorg DataWorks! Prize🎉 🔁Grand Prize, Data Reuse: BrainChart — "Brain Charts for the Human Lifespan" 🤝Grand Prize, Data Sharing: N3C — "Democratizing Access to Clinical Data" Check out the winning projects: datascience.nih.gov/director… #NIHData
Announcing FASEB DataWorks! Prize Winners

ALT Announcing FASEB DataWorks! Prize Winners

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Congrats to DataWorks! Challenge winners from our department! #N3C, led by @ontowonka, PhD, won the grand prize for #DataSharing, @MonarchInit, won the Distinguished Achievement Award for #Data Reuse, and @KrishnanLab PhD, won the Significant Achievement Award for Data Reuse!
NIH Office of Data Science Strategy@NIHDataScience
21 Feb 2023
🎉CONGRATS to the winners of the @FASEBorg DataWorks! Prize🎉 🔁Grand Prize, Data Reuse: BrainChart — "Brain Charts for the Human Lifespan" 🤝Grand Prize, Data Sharing: N3C — "Democratizing Access to Clinical Data" Check out the winning projects: datascience.nih.gov/director… #NIHData
Announcing FASEB DataWorks! Prize Winners

ALT Announcing FASEB DataWorks! Prize Winners

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The Ramanathan Lab is looking for a Research Tech to join us! We are a young and exciting group interested in how cells of diverse shapes and sizes form functional tissue. Please DM if you are interested in the position or want to know more! unmc.peopleadmin.com/posting… Please RT!
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Three @CUAnschutz teams are DataWorks prize finalists! Learn more about @KrishnanLab, @MonarchInit, and #NationalCovidCohortCollaborative's projects and vote for one here👇
NIH Office of Data Science Strategy@NIHDataScience
30 Nov 2022
Learn about the 20 DataWorks! Prize finalists and how they have used data sharing or reuse to advance human health. Finalists are eligible for $500,000 prize purse and people’s choice recognition awards. #NIHData #DataScience herox.com/dataworks

Teams | DataWorks! Prize 2024 | HeroX

Data is the future of biomedical research, join us and propose an impactful secondary data analysis project today!

herox.com
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A new software created by @compbiologist, PhD, associate professor of biomedical informatics at @CUMedicalSchool, and his team, annotates genomics samples based on unstructured sample text descriptions, making them easier for researchers to find and use.👇 nature.com/articles/s41467-0…
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The @KrishnanLab develops an approach combining natural language processing and machine learning to infer the source tissue of public genomics samples based on their plain text descriptions, making these samples easy to discover and reuse @compbiologist go.nature.com/3UIi9lE

Systematic tissue annotations of genomics samples by modeling unstructured metadata

Nature Communications - The 1+ million publicly-available human –omics samples currently remain acutely underused. Here the authors present an approach combining natural language processing...

nature.com
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This wk, @kaylainbio defended her brilliant PhD work on using #transcriptomes, #networks, & #machinelearning to probe age- & sex-specificity 🎉 Being the first grad student from @KrishnanLab, Kayla has set a v. high bar! Congratulations Dr. Johnson! We're very proud of you!!
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🎇 We're one of 20 finalists for the DataWorks! Prize for our work on: Removing metadata barriers to promote data reuse Methods that address unstructured & missing metadata that are barriers to discovering & reusing public omics data. Learn more & VOTE! herox.com/dataworks/round/24…
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The @KrishnanLab develops an approach combining natural language processing and machine learning to infer the source tissue of public genomics samples based on their plain text descriptions, making these samples easy to discover and reuse @compbiologist go.nature.com/3UIi9lE

Systematic tissue annotations of genomics samples by modeling unstructured metadata

Nature Communications - The 1+ million publicly-available human –omics samples currently remain acutely underused. Here the authors present an approach combining natural language processing...

nature.com
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Krishnan Lab retweeted
Clint Miller@clintomics
8 Nov 2022
Automated NLP and ML approach to annotate samples to their tissue-of-origin by modeling unstructured metadata. Improved performance and scalability compared to MetaSRA ⁦@NatureComms⁩ ⁦@compbiologist⁩ nature.com/articles/s41467-0…
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The Computational Biosciences PhD Program @CUAnschutz is holding an Info Session on Fri, Oct. 21 for interested students to get to know the program! Plus, all registered attendees will receive an application fee waiver!! Please spread the word. graduateschool.cuanschutz.ed…

Graduate School Biomed Expo at the University of Colorado Denver | Anschutz

graduateschool.cuanschutz.edu
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Two posters in @MlcsbC #ISMB2022 @NeutralYh | W-058 Cross-species transcriptome-based regression to discover model equivalents of human samples & genes. w/ @ingo_braasch @filjev46 | W-067 Determining the optimal embedding technique for mapping transcriptomes to ontologies
Arjun Krishnan@compbiologist
12 Jul 2022
We have a bunch of cool projects to share @ #ISMB2022! #TextMining #NetBio @OBF_BOSC @TransMedISMB @MlcsbC #BioVis Interested in working with? Chat with our team! They are great people and you can also learn about how it is to work with us.
Krishnan Lab @ ISMB 2022 Remy Liu NetBio Talk on Tue, Jul 12 at 11:50a Chris Mancuso BOSC Talk on Wed, Jul 13 at 2:50p NetBio Poster L-016 on Mon/Tue Alex McKim NetBio Poster L-017 on Mon/Tue Kayla Johnson TransMed Poster N-023 on Mon/Tue Stephanie Hickey TransMed Poster N-024 on Mon/Tue Kewalin Samart TransMed Poster (Virtual) on Mon/Tue Sarah Percival BioVis Poster R-002 on Wed Hao Yuan MLCSB Poster W-058 on Wed Filip Jevtic MLCSB Poster W-067 on Wed

ALT Krishnan Lab @ ISMB 2022 Remy Liu NetBio Talk on Tue, Jul 12 at 11:50a Chris Mancuso BOSC Talk on Wed, Jul 13 at 2:50p NetBio Poster L-016 on Mon/Tue Alex McKim NetBio Poster L-017 on Mon/Tue Kayla Johnson TransMed Poster N-023 on Mon/Tue Stephanie Hickey TransMed Poster N-024 on Mon/Tue Kewalin Samart TransMed Poster (Virtual) on Mon/Tue Sarah Percival BioVis Poster R-002 on Wed Hao Yuan MLCSB Poster W-058 on Wed Filip Jevtic MLCSB Poster W-067 on Wed

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We have 3 posters at @TransMedISMB #ISMB2022 @kaylainbio | N-023 Age- and sex-specific gene signatures and networks @slepphickey | N-024 Chronic inflammation network signatures in complex diseases @KewalinSamart | Virtual Drug repurposing for infectious diseases w/ @janani137
Arjun Krishnan@compbiologist
12 Jul 2022
We have a bunch of cool projects to share @ #ISMB2022! #TextMining #NetBio @OBF_BOSC @TransMedISMB @MlcsbC #BioVis Interested in working with? Chat with our team! They are great people and you can also learn about how it is to work with us.
Krishnan Lab @ ISMB 2022 Remy Liu NetBio Talk on Tue, Jul 12 at 11:50a Chris Mancuso BOSC Talk on Wed, Jul 13 at 2:50p NetBio Poster L-016 on Mon/Tue Alex McKim NetBio Poster L-017 on Mon/Tue Kayla Johnson TransMed Poster N-023 on Mon/Tue Stephanie Hickey TransMed Poster N-024 on Mon/Tue Kewalin Samart TransMed Poster (Virtual) on Mon/Tue Sarah Percival BioVis Poster R-002 on Wed Hao Yuan MLCSB Poster W-058 on Wed Filip Jevtic MLCSB Poster W-067 on Wed

ALT Krishnan Lab @ ISMB 2022 Remy Liu NetBio Talk on Tue, Jul 12 at 11:50a Chris Mancuso BOSC Talk on Wed, Jul 13 at 2:50p NetBio Poster L-016 on Mon/Tue Alex McKim NetBio Poster L-017 on Mon/Tue Kayla Johnson TransMed Poster N-023 on Mon/Tue Stephanie Hickey TransMed Poster N-024 on Mon/Tue Kewalin Samart TransMed Poster (Virtual) on Mon/Tue Sarah Percival BioVis Poster R-002 on Wed Hao Yuan MLCSB Poster W-058 on Wed Filip Jevtic MLCSB Poster W-067 on Wed

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We have 2 posters at #NetBio #ISMB2022 @ChrisAMancuso | L-016 Jointly modeling networks from multiple species to improve gene classification Alex McKim | L-017 Module-based prediction improves network-based prioritization of genes associated w/ complex traits & diseases
Arjun Krishnan@compbiologist
12 Jul 2022
We have a bunch of cool projects to share @ #ISMB2022! #TextMining #NetBio @OBF_BOSC @TransMedISMB @MlcsbC #BioVis Interested in working with? Chat with our team! They are great people and you can also learn about how it is to work with us.
Krishnan Lab @ ISMB 2022 Remy Liu NetBio Talk on Tue, Jul 12 at 11:50a Chris Mancuso BOSC Talk on Wed, Jul 13 at 2:50p NetBio Poster L-016 on Mon/Tue Alex McKim NetBio Poster L-017 on Mon/Tue Kayla Johnson TransMed Poster N-023 on Mon/Tue Stephanie Hickey TransMed Poster N-024 on Mon/Tue Kewalin Samart TransMed Poster (Virtual) on Mon/Tue Sarah Percival BioVis Poster R-002 on Wed Hao Yuan MLCSB Poster W-058 on Wed Filip Jevtic MLCSB Poster W-067 on Wed

ALT Krishnan Lab @ ISMB 2022 Remy Liu NetBio Talk on Tue, Jul 12 at 11:50a Chris Mancuso BOSC Talk on Wed, Jul 13 at 2:50p NetBio Poster L-016 on Mon/Tue Alex McKim NetBio Poster L-017 on Mon/Tue Kayla Johnson TransMed Poster N-023 on Mon/Tue Stephanie Hickey TransMed Poster N-024 on Mon/Tue Kewalin Samart TransMed Poster (Virtual) on Mon/Tue Sarah Percival BioVis Poster R-002 on Wed Hao Yuan MLCSB Poster W-058 on Wed Filip Jevtic MLCSB Poster W-067 on Wed

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On Wed, July 13, @ChrisAMancuso is giving a talk in @OBF_BOSC #BOSC on "GenePlexus: A web server and Python package for gene discovery using network-based machine learning" Paper: doi.org/10.1093/nar/gkac335 Webserver: geneplexus.net/ Repo: github.com/krishnanlab/genep… #ISMB2022

GenePlexus: a web-server for gene discovery using network-based machine learning

Abstract. Biomedical researchers take advantage of high-throughput, high-coverage technologies to routinely generate sets of genes of interest across a wid

academic.oup.com
Arjun Krishnan@compbiologist
12 Jul 2022
We have a bunch of cool projects to share @ #ISMB2022! #TextMining #NetBio @OBF_BOSC @TransMedISMB @MlcsbC #BioVis Interested in working with? Chat with our team! They are great people and you can also learn about how it is to work with us.
Krishnan Lab @ ISMB 2022 Remy Liu NetBio Talk on Tue, Jul 12 at 11:50a Chris Mancuso BOSC Talk on Wed, Jul 13 at 2:50p NetBio Poster L-016 on Mon/Tue Alex McKim NetBio Poster L-017 on Mon/Tue Kayla Johnson TransMed Poster N-023 on Mon/Tue Stephanie Hickey TransMed Poster N-024 on Mon/Tue Kewalin Samart TransMed Poster (Virtual) on Mon/Tue Sarah Percival BioVis Poster R-002 on Wed Hao Yuan MLCSB Poster W-058 on Wed Filip Jevtic MLCSB Poster W-067 on Wed

ALT Krishnan Lab @ ISMB 2022 Remy Liu NetBio Talk on Tue, Jul 12 at 11:50a Chris Mancuso BOSC Talk on Wed, Jul 13 at 2:50p NetBio Poster L-016 on Mon/Tue Alex McKim NetBio Poster L-017 on Mon/Tue Kayla Johnson TransMed Poster N-023 on Mon/Tue Stephanie Hickey TransMed Poster N-024 on Mon/Tue Kewalin Samart TransMed Poster (Virtual) on Mon/Tue Sarah Percival BioVis Poster R-002 on Wed Hao Yuan MLCSB Poster W-058 on Wed Filip Jevtic MLCSB Poster W-067 on Wed

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