Ophir Shalem
@ophirshalem.bsky.social
Scientist, Associate Professor, Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Children’s Hospital of Philadelphia
Functional genomics, Proteostasis, Neurodegeneration
www.shalemlab.org
Functional genomics, Proteostasis, Neurodegeneration
www.shalemlab.org
Pinned
Ophir Shalem
@ophirshalem.bsky.social
· Apr 23
Pooled tagging and hydrophobic targeting of endogenous proteins for unbiased mapping of unfolded protein responses
Sansbury and Serebrenik et al. use pooled gene tagging with in situ sequencing and
high-throughput image analysis to generate a cell pool with endogenous HaloTag fusions.
Hydrophobic targeting is then...
www.cell.com
Check out our paper, now extensively revised and published in @cp-molcell.bsky.social! This has been a real tour de force led by Stephanie Sansbury and @ysereb.bsky.social and we are very excited about the findings and future potential of this approach
www.cell.com/molecular-ce...
www.cell.com/molecular-ce...
Reposted by Ophir Shalem
Happy to announce our paper comparing embryonic gene expression between C. elegans and C. briggsae, work led by Christopher Large with Rupa Khanal and in collaboration with Junhyong Kim and Bob Waterston. www.science.org/doi/10.1126/...
Lineage-resolved analysis of embryonic gene expression evolution in C. elegans and C. briggsae
The constraints that govern the evolution of gene expression patterns across development remain unclear. Single-cell RNA sequencing can detail these constraints by systematically profiling homologous ...
www.science.org
June 20, 2025 at 8:25 PM
Happy to announce our paper comparing embryonic gene expression between C. elegans and C. briggsae, work led by Christopher Large with Rupa Khanal and in collaboration with Junhyong Kim and Bob Waterston. www.science.org/doi/10.1126/...
Congratulation @shiraweingarten.bsky.social! Beautiful work!
If you love #viruses, #ribosomes, and genomic #darkmatter, this thread is for you!! 💫
We're excited to share our new publication developing Massively Parallel Ribosome Profiling (MPRP), which uncovered ~4,000 hidden proteins in ~700 viral genomes. www.science.org/doi/10.1126/...
We're excited to share our new publication developing Massively Parallel Ribosome Profiling (MPRP), which uncovered ~4,000 hidden proteins in ~700 viral genomes. www.science.org/doi/10.1126/...
June 17, 2025 at 6:21 PM
Congratulation @shiraweingarten.bsky.social! Beautiful work!
Excited to to see our collaboration with @gburslem.bsky.social published today! This is part of our ongoing long term goal of achieving scalable non-disruptive and direct imaging and perturbation of the endogenous proteome
Excited to see this out in @science.org today!! www.science.org/doi/10.1126/...
May 1, 2025 at 9:22 PM
Excited to to see our collaboration with @gburslem.bsky.social published today! This is part of our ongoing long term goal of achieving scalable non-disruptive and direct imaging and perturbation of the endogenous proteome
Check out our paper, now extensively revised and published in @cp-molcell.bsky.social! This has been a real tour de force led by Stephanie Sansbury and @ysereb.bsky.social and we are very excited about the findings and future potential of this approach
www.cell.com/molecular-ce...
www.cell.com/molecular-ce...
Pooled tagging and hydrophobic targeting of endogenous proteins for unbiased mapping of unfolded protein responses
Sansbury and Serebrenik et al. use pooled gene tagging with in situ sequencing and
high-throughput image analysis to generate a cell pool with endogenous HaloTag fusions.
Hydrophobic targeting is then...
www.cell.com
April 23, 2025 at 3:41 PM
Check out our paper, now extensively revised and published in @cp-molcell.bsky.social! This has been a real tour de force led by Stephanie Sansbury and @ysereb.bsky.social and we are very excited about the findings and future potential of this approach
www.cell.com/molecular-ce...
www.cell.com/molecular-ce...
Reposted by Ophir Shalem
Super excited to be launching NimbusImage.com! Cloud-based image analysis to democratize machine learning!
Documentation here!
docs.nimbusimage.com
Documentation here!
docs.nimbusimage.com
NimbusImage
NimbusImage.com
March 17, 2025 at 2:46 PM
Super excited to be launching NimbusImage.com! Cloud-based image analysis to democratize machine learning!
Documentation here!
docs.nimbusimage.com
Documentation here!
docs.nimbusimage.com
Reposted by Ophir Shalem
Two new preprints online today!
One with @dremilygoldberg.bsky.social on lysine lactylation
www.biorxiv.org/content/10.1...
Another with @taabaman.bsky.social on new peptide tools to study caspases www.biorxiv.org/content/10.1...
One with @dremilygoldberg.bsky.social on lysine lactylation
www.biorxiv.org/content/10.1...
Another with @taabaman.bsky.social on new peptide tools to study caspases www.biorxiv.org/content/10.1...
Class I histone deacetylases catalyze lysine lactylation
Metabolism and post-translational modifications (PTMs) are intrinsically linked and the number of identified metabolites that can covalently modify proteins continues to increase. This metabolism/PTM ...
www.biorxiv.org
February 28, 2025 at 8:45 PM
Two new preprints online today!
One with @dremilygoldberg.bsky.social on lysine lactylation
www.biorxiv.org/content/10.1...
Another with @taabaman.bsky.social on new peptide tools to study caspases www.biorxiv.org/content/10.1...
One with @dremilygoldberg.bsky.social on lysine lactylation
www.biorxiv.org/content/10.1...
Another with @taabaman.bsky.social on new peptide tools to study caspases www.biorxiv.org/content/10.1...
Reposted by Ophir Shalem
We have a postdoc position available for a very cool collaborative project! Synthetic chemistry expertise is a must!
Unfortunately due to the funding source, this position is only available to US citizens or permanent residents.
chemistryjobs.acs.org/job/postdoct...
Unfortunately due to the funding source, this position is only available to US citizens or permanent residents.
chemistryjobs.acs.org/job/postdoct...
chemistryjobs.acs.org
February 25, 2025 at 9:39 PM
We have a postdoc position available for a very cool collaborative project! Synthetic chemistry expertise is a must!
Unfortunately due to the funding source, this position is only available to US citizens or permanent residents.
chemistryjobs.acs.org/job/postdoct...
Unfortunately due to the funding source, this position is only available to US citizens or permanent residents.
chemistryjobs.acs.org/job/postdoct...
Pooled optical screening bootcamp!
February 5, 2025 at 10:06 PM
Pooled optical screening bootcamp!
Huge congratulations to former lab postdoc @ysereb.bsky.social for starting his own independent lab! Make sure to follow him for exciting future science and check out his lab if you are looking for opportunities in the NJ/NY area!
The Serebrenik Lab is hiring! Join us in unraveling proteostasis with pooled protein tagging and manipulation! Interested postdocs can learn more & meet other excellent labs at the Rutgers Postdoc Peek (Apr 3-4, 2025). Apply by 1/8/25: rutgers.ca1.qualtrics.com/jfe/form/SV_...
December 23, 2024 at 11:05 PM
Huge congratulations to former lab postdoc @ysereb.bsky.social for starting his own independent lab! Make sure to follow him for exciting future science and check out his lab if you are looking for opportunities in the NJ/NY area!
Reposted by Ophir Shalem
Our study with @ericjoyce.bsky.social led by Jailynn Harke is out. We show that allelic configurations at the Shh locus are predominately compact in the mouse forebrain, and that long range E-P interactions rely on transcription dependent and independent mechanisms. www.cell.com/molecular-ce...
Multiple allelic configurations govern long-range Shh enhancer-promoter communication in the embryonic forebrain
Harke et al. use sequential DNA-FISH to achieve single-allele resolution of the Sonic
hedgehog (Shh) regulatory domain in the mouse forebrain. They show that multiple allelic
configurations occur inde...
www.cell.com
November 22, 2024 at 4:36 PM
Our study with @ericjoyce.bsky.social led by Jailynn Harke is out. We show that allelic configurations at the Shh locus are predominately compact in the mouse forebrain, and that long range E-P interactions rely on transcription dependent and independent mechanisms. www.cell.com/molecular-ce...
Reposted by Ophir Shalem
Late-stage graduate students and junior postdoctoral fellows are invited to attend the 2025 Recruitment Summit for CHOP/Penn Postdoctoral Scholars in Cell Biology and Genomics
careers.chop.edu/us/en/event/...
careers.chop.edu/us/en/event/...
Recruitment Summit for Postdoctoral Scholars in Cell Biology and Genomics | Children’s Hospital of Philadelphia
Recruitment Summit for Postdoctoral Scholars in Cell Biology and Genomics in Philadelphia, Pennsylvania, United States. null at Children’s Hospital of Philadelphia
careers.chop.edu
November 25, 2024 at 5:26 PM
Late-stage graduate students and junior postdoctoral fellows are invited to attend the 2025 Recruitment Summit for CHOP/Penn Postdoctoral Scholars in Cell Biology and Genomics
careers.chop.edu/us/en/event/...
careers.chop.edu/us/en/event/...
Reposted by Ophir Shalem
New paper ALERT!! Mara Cowen, PhD discovered and defined how conserved autism-associated genes modify a 'social' behavior in C. elegans!! So proud of her work in the lab!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Conserved autism-associated genes tune social feeding behavior in C. elegans - Nature Communications
C. elegans aggregate in large clumps during feeding. Here, the authors find conserved autism-associated genes mediate distinct molecular and circuit signaling components that tune C. elegans feed...
www.nature.com
November 11, 2024 at 7:49 PM
New paper ALERT!! Mara Cowen, PhD discovered and defined how conserved autism-associated genes modify a 'social' behavior in C. elegans!! So proud of her work in the lab!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Fascinating work from Jongens and @erikaholzbaur.bsky.social labs showing that FMRP granules mark mitochondrial fission sites in axons and dendrites and serve as sites of local translation!
t.co/wXqtte3pqp
t.co/wXqtte3pqp
https://www.nature.com/articles/s41556-024-01544-2
t.co
November 15, 2024 at 9:13 PM
Fascinating work from Jongens and @erikaholzbaur.bsky.social labs showing that FMRP granules mark mitochondrial fission sites in axons and dendrites and serve as sites of local translation!
t.co/wXqtte3pqp
t.co/wXqtte3pqp
Reposted by Ophir Shalem
Happy Friday! New preprint to discuss, led by @ekaplan.bsky.social, entitled "Activity-based selection for enhanced base editor mutational scanning"
www.biorxiv.org/content/10.1...
A thread...
www.biorxiv.org/content/10.1...
A thread...
Activity-based selection for enhanced base editor mutational scanning
Base editing is a CRISPR-based technology that enables high-throughput, nucleotide-level functional interrogation of the genome, which is essential for understanding the genetic basis of human disease...
www.biorxiv.org
November 15, 2024 at 1:18 PM
Happy Friday! New preprint to discuss, led by @ekaplan.bsky.social, entitled "Activity-based selection for enhanced base editor mutational scanning"
www.biorxiv.org/content/10.1...
A thread...
www.biorxiv.org/content/10.1...
A thread...
Reposted by Ophir Shalem
Pathogenic proteotoxicity of cryptic splicing is alleviated by ubiquitination and ER-phagy
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Pathogenic proteotoxicity of cryptic splicing is alleviated by ubiquitination and ER-phagy
RNA splicing enables the functional adaptation of cells to changing contexts. Impaired splicing has been associated with diseases, including retinitis pigmentosa, but the underlying molecular mechanis...
www.science.org
November 15, 2024 at 11:59 AM
Pathogenic proteotoxicity of cryptic splicing is alleviated by ubiquitination and ER-phagy
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Happy to share our new paper where we explore why dCas9-KRAB protein levels drop so drastically after neuronal differentiation in WTC11 and KOL2.1J iPSC lines.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
CRISPR associated enzymes are mislocalized to the cytoplasm in iPSC-derived neurons resulting in KRAB-specific degradation
The use of CRISPR-associated enzymes in iPSC-derived neurons for precise gene targeting and high-throughput gene perturbation screens offers great potential but presents unique challenges compared to ...
www.biorxiv.org
November 10, 2024 at 4:10 PM
Happy to share our new paper where we explore why dCas9-KRAB protein levels drop so drastically after neuronal differentiation in WTC11 and KOL2.1J iPSC lines.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...