Rodrigo I Castro
@i_rodcast
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Computational Scientist at @jacksonlab working on deep learning for gene regulation with @r_tewhey | Former mathematician, musician, physicist |
Bar Harbor, ME
Joined August 2018
Excited to share our sequence design work published in @Nature. I had the privilege of co-leading this effort alongside my friend and colleague @SagerGosai under the supervision of @r_tewhey, @ReillyLikesIt, and @PardisSabeti 1/7.
nature.com
Nature - A generalizable framework to prospectively engineer cis-regulatory elements from massively parallel reporter assay models can be used to write fit-for-purpose regulatory code.
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RT @SagerGosai: I’m thrilled to share that our paper “Machine-guided design of cell-type-targeting cis-regulatory elements” was published o….
nature.com
Nature - A generalizable framework to prospectively engineer cis-regulatory elements from massively parallel reporter assay models can be used to write fit-for-purpose regulatory code.
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For more insight on where this work fits in the fields of #genomics #bioengineering #genetherapy, check out this great News & Views by @apfenning and prior excellent work from @ibrahimihsan, @deAlmeida_BP and their teams. 7/7.
nature.com
Nature - Engineering cell-type-specific regulatory elements with machine learning.
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A shoutout to the rest of the authors who were instrumental in this paper: @kousuke_mouri, J. Butts, N. Fuentes, S. Kales, @docnitephd, M. Alasoadura, @MaryTeenaJoy1, @thanhthanhphd, and @AryaRao_. #TeamWorkMakesTheDreamWork 6/7.
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We investigated whether these synthetic CREs would drive cell-type-specific expression in whole organisms. We tested some selected sequences in zebrafish and mice, and displayed surprising specificity in tissues analogous to their respective targeted cell lines. 5/7
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We paired Malinois with generative algorithms to design sequences targeting each cell type. The MPRA validation showed that synthetic CREs successfully drive cell-type-specific expression, and generally outperform even the best naturally occurring sequences. 4/7
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Using our massively parallel reporter assay (MPRA) dataset presented in as part of @ENCODE_NIH, we developed Malinois, a deep learning model that accurately predicts CRE activity in three human cell lines. 3/7.
biorxiv.org
Identifying the causal variants and mechanisms that drive complex traits and diseases remains a core problem in human genetics. The majority of these variants have individually weak effects and lie...
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CREs regulate gene expression and play a vital role in determining tissue identity and responses. We aimed to engineer synthetic CREs with programmed, cell-type-specific activity—a task that could have significant implications for therapeutic innovations in the long run. 2/7.
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RT @LaylaSiraj: Could not be more delighted to present our work investigating how over 220,000 complex and molecular trait-associated genet….
biorxiv.org
Identifying the causal variants and mechanisms that drive complex traits and diseases remains a core problem in human genetics. The majority of these variants have individually weak effects and lie...
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RT @anshulkundaje: This is by far the most convincing regulatory DNA synthetic design paper to date. Congrats to the authors 1/.
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RT @SagerGosai: I’m excited to share some work I co-lead with @i_rodcast and spanned the labs of @PardisSabeti, @ReillyLikesIt, and @r_tewh….
biorxiv.org
Cis -regulatory elements (CREs) control gene expression, orchestrating tissue identity, developmental timing, and stimulus responses, which collectively define the thousands of unique cell types in...
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RT @TewheyLab: Starting off our very first #TewheyLabTuesdays with our summer student, Frank Liu! @frankliuyc. Frank has been spending his….
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RT @kousuke_mouri: Excited to share our new work characterizing genome-wide RE1 silencers by using MPRAduo! We modified MPRA to test repres….
biorxiv.org
Both upregulation and downregulation by cis -regulatory elements help establish precise gene expression. Our understanding of how elements repress transcriptional activity is far more limited than...
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RT @jacksonlab: .@UMaine grad @r_tewhey, a genetics researcher at JAX, took his dream job with us back in 2017. Via @PressHerald, read how….
pressherald.com
UMaine grad Ryan Tewhey, a human genetics researcher, took his dream job at The Jackson Laboratory in 2017. Things haven't played out how he imagined so far, but he's OK with that.
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RT @jacksonlab: Happy Hispanic Heritage Month from The Jackson Laboratory! We interviewed some of JAX’s Hispanic and Latinx employees from….
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RT @jacksonlab: .@i_rodcast is a postdoc in @Ry_2E's lab! He is developing generative machine learning models of new cis-regulatory element….
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RT @_julesh_: "A category-theoretic compositional framework of perceptron-based neural networks. ", PhD thesis with an extremely long titl….
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RT @fchollet: Spleeter is an amazing open-source project from Deezer (the French Spotify) that uses Deep Learning to do source separation o….
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