News

Rachael Bakker left the lab after finishing her postdoctoral project developing a high throughput mutational profiling approach to study protein-RNA interactions. We celebrated her departure with a Vietnamese lunch at BaBar. Goodbye, Rachael!

We went on a lab hike to Lake Ingalls to see the famed larches!

Congratulations to Patrick Nugent on his successful PhD defense! Patrick developed an RNA-linked CRISPR screening approach as part of his thesis research.

Congratulations to Katharine Chen on her successful PhD defense! As part of her thesis work, Katharine discovered several novel sequence motifs that trigger trigger ribosome-associated mRNA decay in S. cerevisiae.

We received the Transformative Research Award from the NIH Director’s Common Fund. This award will support our studies of microproteins’ role in auto- and innate immunity, in collaboration with Anne-Ruxandra Carvunis, Alok Joglekar, and Maninjay Atianand at the University of Pittsburgh. Sabrina Richards at Fred Hutch wrote an article describing the project here. Thank you, U.S. taxpayers!

Ty Bottorff left the lab after finishing his PhD research on uORF-mediated regulation of translation. He will be working as a teaching instructor at University of Washington. We celebrated his departure with yet another vegan Thai lunch 😊. Goodbye, Ty!

Phil Burke left the lab after finishing his PhD research on how coding sequences affect mRNA stability in human cells. He is joining as a scientist at A-Alpha Bio, a local biotech. We celebrated his departure with a vegan Thai lunch. Goodbye and goodluck, Phil!

Congratulations to Phil Burke on his successful PhD defense! Phil’s thesis work was recently published in Nature Communications.

Maria Toro-Moreno was awarded the HHMI Hanna Gray fellowship for postdoctoral and faculty research support. Read more about Maria’s award here. Congratulations, Maria!

Matthew Chan joined the Campbell and our lab as a joint postdoc. Matthew is planning to study ribosome stalling and translational regulation using structural and genomic approaches. Matthew received the Mahan postdoctoral fellowship to pursue this research.

Maria Toro-Moreno was awarded the Jane Coffin Childs postdoc fellowship. Rachael Bakker was awarded the NSF postdoc fellowship. Congratulations, Maria and Rachael!

Yuya Zhao left the lab for graduate school at New York University. We celebrated her departure with her favorite sushi lunch. Goodbye and goodluck, Yuya!

We celebrated 5 years of Subramaniam Lab at the Hutch with a Thai lunch and physical distancing. Thanks Luna Yu for the picture!

Ty Bottorff from the Biophysics, Structure & Design graduate program and Katharine Chen from the Molecular & Cellular Biology graduate program joined our lab for their PhD theses. Welcome Katharine & Ty!

We received the CAREER award from the National Science Foundation, NSF. This award will fund the computational modeling studies of eukaryotic mRNA translation in our lab over the next five years. It will also allow us to further develop our graduate course on Tools for Computational Biology for students in the UW-Fred Hutch MCB Ph.D. program. Thank you, U.S. taxpayers!

Michelle Kriner is joining NanoString Technologies as a Research Scientist. She was highly productive during her time in our lab, finishing a project on bacterial serine metabolism and getting an NRSA postdoc fellowship. We will miss her bacterial and molecular biology expertise. Good luck, Michelle!

Patrick Nugent was awarded a spot in the Molecular Biophysics Training Grant at the University of Washington. Congratulations, Patrick!

We celebrated Michelle and Patrick’s accomplishments with a vegan lab lunch last week.

Yuya Zhao joined our lab as a research technician after finishing her undergrad at UC San Diego. Yuya will be testing kinetic models for translation initiation in budding yeast.

Patrick Nugent joined our lab for his PhD thesis. Patrick will be formulating and testing kinetic models of mRNA translation in mammalian cells.

We just submitted Michelle Kriner’s work for peer review. Michelle found that bacteria produce a spurt of the amino acid serine through glycine catabolism when they run out of glucose. Any excess serine produced during this process needs to be exported by the SdaC transporter to prevent toxic incorporation of serine into bacterial cell wall. To our knowledge, this is the first description of toxicity mediated by endogenously produced serine and its amelioration through export. Read our manuscript on bioRxiv. This work was motivated by our earlier finding of serine depletion during bacterial biofilm formation. Michelle led this project from start to finish, and shepherded it through several unexpected turns and twists. Congratulations, Michelle!

We celebrated Heather’s PhD defense and manuscript submission, all this week. Heather’s thesis was on investigating translation initiation during influenza infection, and she did a fantastic job working jointly with the Bloom lab and our lab. Check out her work on bioRxiv. Heather will continue her MD training over the next three years at UW. Good bye and good luck, Heather!

We just submitted Alicia’s tour de force PhD work on translational control during amino acid limitation in mamamalian cells for peer review. Alicia was jointly mentored by me and my postdoc advisor, Erin O’Shea (a feed-forward loop that was hopefully coherent). Alicia is delving deeper into mammalian metabolism as a postdoc in the Vander Heiden group at MIT. Read our manuscript on bioRxiv. Congratulations, Alicia!

Shea Ransford, who just finished his undergrad in Biophysics at University of Michigan, has joined our lab as a research technician. Shea is planning to measure translation rates in single cells using imaging-based approaches.

Max Ferrin left our lab to join UC Berkeley as an MCB grad student. Max was the first member of our lab; He was instrumental in setting it up and in publishing our first paper. His expertise in ribosome collisions, emacs org-mode, and sludge metal will be sorely missed.

Srividya Chandrasekhar was a talented undergraduate intern who worked in our lab over the past 10 weeks under Michelle’s mentorship. She taught us to use PyMOL and pay attention to the proteins in the ribosome. She is returning to RPI to finish her senior year.

Good luck, Max and Srividya!

Phillip Burke will be co-advised by Jesse Bloom and me for his PhD thesis. Phil is interested in how codon usage regulates translation during influenza infection.

Max’s work on a stimulatory role for ribosome collisions in bacteria just got published. This is the first paper since we started at Fred Hutch. Congrats Max on a terrific job!

Rasi received the Sidney Kimmel Scholarship for early-stage cancer researchers. This award will fund our lab’s studies on the role of synonymous mutations in cancer cells over the next two years. Thank you, Mr. Kimmel for supporting high-risk research!

Michelle Kriner, who just joined our lab as a postdoctoral fellow, was awarded the Chromosome Metabolism and Cancer Training Grant. She is planning to study how amino acid metabolism affects protein expression in bacteria and mammalian cells.

We had two terrific high school interns in our lab this summer, Ayah Idris and Gurleen Bassi. Ayah and Gurleen constructed a genetic reporter for detecting ribosome pauses in E. coli. Max was a fantastic mentor and taught them translation biochemistry, microbiology, and molecular cloning. In addition, both Ayah and Gurleen turned out to be Python wizards: They learned to read data files with Pandas, identify prime numbers, and use Python to send mass spam – all within two days! The jupyterhub setup by Fred Hutch Scientific Computing made all this really easy. Ayah will be starting as a freshman at UW and Gurleen will continue as a high school senior in Federal Way. Good luck, Ayah and Gurleen!

We were awarded the MIRA R35 grant by the National Institute of General Medical Sciences, NIH. This award will support all NIGMS-related research in our lab over the next five years. Thank you, U.S. taxpayers!

Heather Machkovech will be co-advised by Jesse Bloom and me for her PhD thesis. Heather is interested in how codon usage regulates translation during influenza infection.

Heungwon Park has joined our lab as a postdoc. Heungwon plans to develop biochemically-accurate, kinetic models of protein synthesis in eukaryotic cells.

Max Ferrin, who just finished his undergrad at UW, will be starting along with me at the Hutch in July. Max is planning to study bacterial translation using genome-wide and biochemical approaches.

I am moving to Seattle in July – I am excited to become part of the Fred Hutch community!

I am trying to set up the lab as much as possible from Boston. Items on my agenda include recruiting a research assistant, setting up the lab server, shipping strains and plasmids, ordering consumables, and buying used equipment for the lab.

As a first step, I have shamelessly cloned the website of my soon-to-be colleague, Trevor Bedford. I have become a fan of Version Control and Markdown in the last few months, and Trevor’s website is a great showcase for the simplicity and efficiency of these two tools.