Applying to Graduate School and PhD programs?

We will be accepting rotation students for the 2021 and 2022 years!

For PhD-programs in the biosciences, please apply through the Graduate Program in Biosciences (GPB) https://bioscience.ucla.edu/; Valerie Arboleda is a member of the Home Areas of : Genetics and Genomics, Gene Regulation Epigenomics and Transcriptomics (GREaT), and Bioinformatics!

Interested in an MD-PhD dual degree program? Consider https://mstp.healthsciences.ucla.edu/ . Its an amazing program that continues to evolve and consistently improve!

Swab-Seq: Development of a high-throughput platform for massively scaled up SARS-CoV-2 testing and Sequencing

Our work on a novel, sequencing-based diagnostic platform for COVID-19 is out in Nature Biomedical Engineering, click here for full paper!

Here we describe SwabSeq— our efforts to circumvent the supply chain disruptions with nasal swabs and use untapped sequencing capacity for widespread screening of individuals for COVID19. Together with a team from the Departments of Human Genetics and Computational Medicine , we have developed and deployed scalable testing that was used throughout the winter surge in Southern California and has performed over 150,000 tests since starting testing 7 months ago.

Today, our test is used for widespread asymptomatic screening across the UCLA campus and other southern California sites.

I’m incredibly proud of our team for developing and deploying the assay! It was a lot of work, but 100% worth it. Stay safe out there— from what we are seeing— the delta variant is definitely spreading.

Chemoproteomics integration paper is out in Molecular Systems Biology!

Congrats to @mariafpalafox on her first, first-author publication! Maria is the first graduate student in my lab and is jointly mentored by @Keribackus. In this manuscript, we map chemoproteomics data to genomic annotations. For genetics folks- chemoproteomics detected (CpD) means that one used chemical probes to label specific amino acids that are reactive. These labeled residues are associated with residue function and, we think, represent a way to prioritize functional variants in disease. We use some Cp-detected (CpD) data generated by @Keribackus and others to explore mapping of CpD with the growing list of genomic functional annotations.

https://twitter.com/MolSystBiol/status/1362381432954499073

Have a favorite protein? Or a curious VUS? check out and see if your favorite gene has some labeled residues! https://multiomics-ucla.shinyapps.io/CpDAA/

So proud of @mariafpalafox and her hard work :) and hopefully the first of many exciting collaborations with @Keribackus!

Joint Post-doctoral Positions

Two postdoctoral positions are available jointly in the Zaitlen and Arboleda Labs at UCLA. The fellows will work closely with Drs. Zaitlen and Arboleda, with other quantitative Ph.D’s in their groups, and with clinical and scientific collaborators at UCLA, the Mt. Sinai School of Medicine, and the University of Colorado. We are an integrated team within the Departments of Neurology, Human Genetics, Pathology & Laboratory Medicine and the UCLA Institute of Precision Health. Together we will take part in innovative research that explores the role of genomic medicine within fine-scale populations. Therefore, we are looking for highly motivated individuals with a background in computational genetics and genomics, statistical genetics and/or population genetics. Our projects will leverage genomic data linked to de-identified electronic medical records across multiple institutions, representing a rich compilation of clinical phenotypes. More details are linked here .

Our adventure into covalent proteogenomics has its first Preprint

I’m a little late to publishing this— but these went around on twitter a month ago— and pandemic life is just crazy.

But I can’t miss actually writing a post to what is a huge milestone for a new laboratory: the first paper to come out of the lab on the work done one of the amazing graduate student trainees that I’m privileged to mentor: Maria Palafox. Maria is co-mentored by myself and my colleague, Keriann Backus, and she’s been working at the intersection of our labs:

As a geneticist, I had never given much thought to proteins until the end of a project when we aim to functionally validate a genetic variant. But learning more about the exciting world of chemoproteomics— we have started to work on how integration of genomic annotations and chemoproteomics data sets presents a powerful tool to identify novel biology, particularly when it comes to functionally validating missense variation.

Our study provides a roadmap for more precise inter-database comparisons and points to untapped opportunities to improve the predictive power of pathogenicity scores and to advance prioritization of putative druggable sites through integration of predictions of pathogenicity with chemoproteomic datasets.

See the full study here and let us know what you think!

The lab’s work on COVID19 testing is out!

In collaboration with a team in the UCLA Departments of Human Genetics, Computational Medicine and a startup Octant, we have developed and validated a novel platform for COVID-19 testing.

SwabSeq is a high-throughput testing platform for SARS-CoV-2 that uses next-generation sequencing as a readout. SwabSeq employs sample-specific molecular barcodes to enable thousands of samples to be combined and simultaneously analyzed for the presence or absence of SARS-CoV-2 in a single run. Importantly, SwabSeq incorporates an in vitro RNA standard that mimics the viral amplicon, but can be distinguished by sequencing.

This standard allows for end-point rather than quantitative PCR, improves quantitation, reduces requirements for automation and sample-to-sample normalization, enables purification-free detection, and gives better ability to call true negatives. We show that SwabSeq can test nasal and oral specimens for SARS-CoV-2 with or without RNA extraction while maintaining analytical sensitivity better than or comparable to that of fluorescence-based RT-qPCR tests. SwabSeq is simple, sensitive, flexible, rapidly scalable, inexpensive enough to test widely and frequently, and can provide a turn around time of 12 to 24 hours.

We are working hard to see this deployed and bring up more testing where it is needed most. We released are preprint here and if you are interested in working on SwabSeq here or elsewhere let me know! There are tons of opportunities!

Link to the preprint

Welcome to New PhD Students: Aileen and Issy!

I’m so excited to welcome two new members to our growing laboratory: Aileen Nava and Isabella Lin. They are both engaged, creative and brilliant women Aileen is going to be working on organoid-based models of rare genetic disorders such as KAT6A syndrome. Issy will be working on exploring the functional mechanisms underlying the intersection between rare diseases and complex traits. I’m excited to have them join our group!

Summer Time!

Its Summertime and a time of transition in the Arboleda Lab and reflecting on all our growth in the past 1.5 years.

We said good bye to my first technician, Albert who is off to graduate school! And we welcome to the lab some new people in new positions:: Laila Sathe as an SRA, Angela Wei as an SRA, and a rotation student from UCLA MSTP, Isabella Lin.

We are excited to have them working in the team!

Contact us: 

David Geffen School of  Medicine, UCLA
Department of Pathology and Laboratory Medicine
615 Charles E. Young Drive South
lab: BSRB 346
Los Angeles, CA 90095
Map

 

Join Us

We are looking for highly motivated and enthusiastic postdocs, graduate students, and undergraduates. Please see our Opportunities page or contact Valerie by email if you are interested in joining the lab.