@alerasool
Joined August 2009
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  • Following3.6K
  • Followers302
1/7 First of all, big shoutout to co-authors on modeling (@MKarimzade, @neal_ravindra, @RexMa9, @HAOTIANCUI1, @LeeTaliq), huge appreciation to data generation (Lexi, @alerasool, Adam) and bioinformatics team (@_annhuang), and leadership for vision and direction (@BoWang87, @inCiChu)! Preprint is now live on bioRxiv: biorxiv.org/content/10.64898… All models start from high-quality data.

X-Cell: Scaling Causal Perturbation Prediction Across Diverse Cellular Contexts via Diffusion...

Causal models of cellular systems hold the promise to empower broad biological discovery, including the systematic identification of novel targets for drug discovery. Predicting how genetic and...

biorxiv.org
Bo Wang
@BoWang87Mar 20
Our X-cell is up at @biorxiv_bioinfo ! Read our full paper at biorxiv.org/content/10.64898… Part of the data and the model weights will be shared soon. stay tuned!
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Our latest paper is out! In collaboration with @DrAnneCarpenter, we conducted a systematic high-content screen to understand the role of protein mislocalization in diverse human disorders. 1/ cell.com/cell/fulltext/S0092…

Pervasive mislocalization of pathogenic coding variants underlying human disorders

Pathogenic missense variation can affect protein function in many ways, but the role of protein mislocalization has not been systematically assessed. By characterizing the localization of 3,400...

cell.com
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Our latest work on developing a potent and specific tool for activating or repressing endogenous splicing events is out! authors.elsevier.com/c/1jJci…
The Blencowe Lab @ U of T@Blencowe_Lab24 Jun 2024
Graduate student Jack Li's work out in Molecular Cell now: By conducting a screen of 341 splicing factors, Jack identified RBM25 coupled to dCasRx as a superior tool to boost inclusion of endogenous exons /1
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Graduate student Jack Li's work out in Molecular Cell now: By conducting a screen of 341 splicing factors, Jack identified RBM25 coupled to dCasRx as a superior tool to boost inclusion of endogenous exons /1
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Check out our CRISPR genome-scale exon perturbation study @MolecularCell. We identified exons influencing cell fitness and uncovered a novel mechanism by which #splicing affects #transcription. @Michael_Aregger @dlarun88 @meisheng_xiao @NCIResearchCtr @NIH doi.org/10.1016/j.molcel.202…
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Our paper on functional discovery of protein degradation and stabilization effectors with proteome-scale induced proximity screens is out in its final version! 1/ nature.com/articles/s41586-0… rdcu.be/dBUju

Proteome-scale discovery of protein degradation and stabilization effectors

Nature - A synthetic proteome-scale strategy enables the identification of a diverse range of human proteins that can induce the degradation or stabilization of a target protein in a...

nature.com
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early winter @newlimit: - >10X more reprogramming factor sets tested than ever before - >2M cells profiled, 10TB+ of raw seq data - +3 team members - 2X speed up in reprogramming library build times - +1 cell types on our Engine - 1st rejuvenating hits
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📜 Happy to share our recent preprint featuring ORFtag - a versatile, easy and cost-effective method for probing protein function at a proteome scale. This work is the result of a collaborative effort by the @stark_lab, @AmeresSL, @EllingUlrich and @juliusbrennecke labs. 1/2
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2023 @newlimit: - 50X more reprogramming factor sets tested than the field before us - 20X factor demultiplexing performance (reading), 7X factor delivery (writing) - 2X team size - +3 functional assays for immunology program - +2 in silico model metrics > SOTA blog ⬇️
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Induxion is looking for a Research Associate/Technician to support its platform activities - Located in Toronto. jobrxiv.org/job/induxion-the…

Research Associate

Post a job in 3min, or find thousands of job offers like this one at jobRxiv!

jobrxiv.org
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early autumn @newlimit: - 6X'd the # of reprogramming factors we've tested - >4X'd signal-to-noise for our core pooled screening assay - shortened feedback cycles by 40% - improved in silico reprog models >30% all covered in our latest blog
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Help me find my stolen bike! bikeindex.org/bikes/1692267
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Our latest preprint is out! In a fun collaboration with @DrAnneCarpenter, we conducted a systematic high-content screen to understand the role of protein mislocalization in diverse human disorders. 1/8 biorxiv.org/content/10.1101/…

Pervasive mislocalization of pathogenic coding variants underlying human disorders

Widespread sequencing has yielded thousands of missense variants predicted or confirmed as disease-causing. This creates a new bottleneck: determining the functional impact of each variant – largely...

biorxiv.org
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Ever wondered if you could read 100s of metabolites and drugs in parallel using a @illumina or a @10X platform? But metabolites aren’t nucleic acids — how can that work? Check out our new preprint and read on for a thread: biorxiv.org/content/10.1101/….

A novel platform for metabolomics using barcoded structure-switching aptamers

Small organic molecules like metabolites and drugs are critical for diagnostics, treatment, and synthetic biology. Measuring them presents two key challenges however: they are biochemically highly...

biorxiv.org
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We're excited to announce that we've raised our Series A from @_DimensionCap, @foundersfund, & @kleinerperkins blog.newlimit.com/p/newlimit…

NewLimit secures $40 million in venture funding from Dimension Capital, Founders Fund, Kleiner...

NewLimit works across cell biology, genomics, machine learning, and cellular reprogramming to treat diseases and reverse aging

blog.newlimit.com
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New preprint! 🗞️ We used pooled protein screens to develop compact human transcriptional effectors that work across diverse biological contexts to activate or silence gene expression biorxiv.org/content/10.1101/…

Development of compact transcriptional effectors using high-throughput measurements in diverse...

Human nuclear proteins contain >1000 transcriptional effector domains that can activate or repress transcription of target genes. We lack a systematic understanding of which effector domains regulate...

biorxiv.org
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last month @newlimit: - 1st reprogramming screens in primary cells - Immunology team 3X'd - 1st model-driven hypotheses this month: - improving screen efficiency: more exps/{$, time} - multi-modal in silico reprogramming models all this & more in our April update ⬇️
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Our paper on 14-3-3 proteins and their role in protein aggregation and phase separation is out! This paper represents the main PhD thesis work by my student Dmitri Segal. 1/ cell.com/molecular-cell/full…

A central chaperone-like role for 14-3-3 proteins in human cells

Segal and colleagues used quantitative proteomics to generate the most comprehensive and directly comparable interaction networks for all human 14-3-3 paralogs. They also uncovered a major role for...

cell.com
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last month @newlimit: - largest partial reprogramming screen yet - 50% more TFs to test - first in silico reprogramming models this month: - screens in old donor cells - library rebuild -- 10X manufacturing efficiency - automating screen analysis to shorten DBTL loops
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A universal deep-learning model for zinc finger design enables transcription factor reprogramming go.nature.com/3HBtUH5
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