Kaden Southard, PhD

Postdoc @MSKCC
Previously @ucberkeley
@UCSF PhD

[Kaden Southard, PhD @kmsouthard]

@jmfunt Congrats! Love this

[Thomas Norman @thenormanlab]

1/ Most genes and variants matter somewhere but look silent in any one cell model. Can we build conditions that reveal phenotypes? With @kanishkadey, we engineer cell states to expose hidden disease biology and trace how genetic risk reaches disease genes. https://t.co/pUHPPjxTkX

[Kaden Southard, PhD @kmsouthard]

@CalebLareau @MSKCancerCenter @natBME Awesome! Congrats!

[Thomas Norman @thenormanlab]

In my excitement I forgot to actually link the preprint!

https://t.co/BCSkTy9242

[Thomas Norman @thenormanlab]

New preprint on technologies to scale up CRISPR screens.

We use them to map 665,856 pairwise genetic perturbations and outline a path to comprehensive interaction mapping in human cells.

We also introduce an approach for cloning lentiviral libraries with billions of elements.

[Thomas Norman @thenormanlab]

Our paper is now out in final form at Nature Genetics! For those who missed the preprint, we used large-scale Perturb-seq targeting transcription factors to push primary fibroblasts into diverse transcriptional states, including those observed in cell atlas studies.

[Kaden Southard, PhD @kmsouthard]

check out our vectors published with our Mutliome Perturb-seq paper (https://t.co/s0SfOAxWNG). Not only for Multiome experiments! A drop in replacement for any CROP-seq style experiment and the +SIRLION vector is especially useful for single-nuclei RNA-seq.

[Thomas Norman @thenormanlab]

Our vectors are available on Addgene. All you need is this and 10x Multiome reagents to get started with Multiome Perturb-seq experiments! https://t.co/SM86nWUrC4

[Kaden Southard, PhD @kmsouthard]

So excited that this is officially published! Big thank you to co-author and truly amazing grad student @elimetzner

[Thomas Norman @thenormanlab]

Our Multiome Perturb-seq paper is now out in @CellSystemsCP! As discussed in my thread on the preprint, this is an approach for linking CRISPR-mediated genetic perturbations to their effects on cellular chromatin state and gene expression. https://t.co/SeqTCGM6vH

[Alireza Karbalayghareh @karbalayghareh]

Hi all,

I am currently on the academic job market. I am a postdoctoral researcher in Dr. Christina Leslie's lab at the Computational and Systems Biology Program at Memorial Sloan Kettering Cancer Center.

My research focuses on deciphering causal and dynamic gene regulation mechanisms by integrating observational data—genomics, epigenomics, transcriptomics, and 3D chromatin conformation like Hi-C—with perturbational data from CRISPRi/a screens and Perturb-seq in single-cell multiomics. I employ techniques from statistical machine learning, causal inference, dynamical modeling, and artificial intelligence (AI) to achieve this goal. The models that I have developed include GraphReg, ENCODE-rE2G, and DynaVelo (to be submitted soon).

Why is this important? Designing any effective and off-target-free therapeutic intervention for diseases, including cancer, first requires a complete understanding of the underlying wildtype system and then identifying the components that malfunction in disease states. With the ever-growing role of AI in synthetic biology and drug design, it is crucial to ensure that the models are causal and comprehend the basic biology of all cells. This is a challenging problem, but I am very hopeful that with the increasing scale of perturbational and multiomic data across cell types, we will achieve significant outcomes.

If you believe I could be a good fit for your department, please reach out to me.

Sincerely,
Alireza

[Kaden Southard, PhD @kmsouthard]

@RawiDuaa @ricocardy @thenormanlab So thankful for all your support! ❤️❤️❤️

[Kaden Southard, PhD @kmsouthard]

@melodyDiBona @RawiDuaa @ricocardy @thenormanlab Thank you Melody!

[Kaden Southard, PhD @kmsouthard]

So excited to share this work! It has been incredible to work with Tom @thenormanlab and the Norman Lab members to put this together. We made several key advances, did truly massive experiments, and learned about fibroblast biology. Big shout out co-author @ricocardy!

[Thomas Norman @thenormanlab]

Can we recreate the transcriptional states seen in single-cell atlas projects? In our new preprint we try to do this using large-scale Perturb-seq experiments. Along the way we discuss off-target effects of CRISPR epigenetic editors and identify drivers of key fibroblast states.

[Thomas Norman @thenormanlab]

Excited to share our preprint "Multiome Perturb-seq unlocks scalable discovery of integrated perturbation effects on the transcriptome & epigenome". This work extends single-cell CRISPR screens to simultaneously profile gene expression & chromatin accessibility.

[Kaden Southard, PhD @kmsouthard]

@FitzsimmonsCM Woot woot!

[Duaa Al-Rawi, MD PhD @RawiDuaa]

Thrilled and humbled to be a recipient of a ASCO Conquer Cancer Foundation YIA award. Grateful for the opportunity to investigate the nearly events in #ovariancancer. Thankful for my mentors @SohrabShah @Samuel_Bakhoum @KaraLongRoche Carol Aghajanian. @TeamOvary_MSK

[IGVF @IGVFConsortium]

NHGRI, NIEHS, and NCI are co-collaborating on a new initiative – Multi-Omics for Health and Disease. The goal is to advance the application of multi-omic technologies to study health and disease in ancestrally diverse populations. https://t.co/y6kezIj4d7

[seemay chou @seemaychou]

Love this term - “productive stupidity”

[Duaa Al-Rawi, MD PhD @RawiDuaa]

Eid Mubarak to all those celebrating!! #EidMubarak #eiduladha2022

[Duaa Al-Rawi, MD PhD @RawiDuaa]

Shameless plug! @Samuel_Bakhoum @TeamOvary_MSK Featured today by @MSKLibrary: Chromosomal instability as a source of genomic plasticity https://t.co/IeBDZ8DH6q

[Duaa Al-Rawi, MD PhD @RawiDuaa]

Please retweet! We are hiring a technician to join us in our work dissecting the role of #chromosomal #instability in #ovariancancer. We do great science in an inclusive environment! @TeamOvary_MSK @MSKCancerCenter