Mandi Ma wins the prestigious Porter Prize from the ASCB.
Congratulations to Mandi Ma from the Rohatgi Lab for being awarded the Porter Prize in Research Excellence from the ASCB!
Maria Nguyen from FUNR Lab is awarded an HHMI Gilliam Fellowship
Congratulations to Maria from FUNR Lab on becoming an HHMI Gilliam Fellow!
https://www.hhmi.org/news/hhmi-names-50-gilliam-fellows-milestone-year
Kim Lab published in Science magazine for their approach combining the 3D structure of the protein backbone with large language models based on amino acid sequence.
Biochemistry Professor Peter S. Kim, Assistant Professor of Chemical Engineering and Stanford Data Science faculty Brian Hie, and members from Kim Lab co-led research on a new machine learning-based method for designing antibody drugs.
Biochemistry Conference October 21-23, 2024
Please save-the-date for the annual Biochemistry Department Conference at Stanford Sierra Camp at Fallen Leaf Lake
Monday, October 21st to Wednesday,
Ph.D. Thesis Defense: “Obelisks”
- Tuesday, July 9, 2024
- 10 am –
Biochemistry Special Seminar
Presented by Prof. Suzanne Pfeffer
Biochemistry Special Seminar: “Unravelling the inner secrets of cells with live-cell super-resolution microscopy”
Ph.D. Thesis Defense: R. Lorenzo D. Labitigan
“Mapping variation in the morphological landscape of human cells with optical pooled CRISPRi screening.”
📅 Friday,
Suzanne Pfeffer is elected to the National Academy of Sciences
We are thrilled to announce the election of 120 members and 24 international members to the National Academy of Sciences in recognition of their distinguished and continued achievements in original research.
Krasnow Lab members’ study has important implications for prevent severe COVID
Krasnow Lab and collaborators help identify source of severe COVID:
http://med.stanford.edu/news/all-news/2024/04/covid-lung-cells.html
Flora Rutaganira is awarded the Hypothesis Fund!
Congratulations to Flora Rutaganira!
Reconstructing the Emergence of Cancer at the Dawn of Multicellularity
What does early multicellular life teach us about the origins of cancer?
Maia Kinnebrew wins NIH DP5 award
Stanford Distinguished Fellow and Hanna Gray Fellow Maia Kinnebrew wins NIH DP5 Award
https://commonfund.nih.gov/earlyindependence/AwardRecipients
Q&A with Julia Salzman, a faculty member with an unconventional path
Julia Salzman, PhD, started out as a statistician but couldn’t ignore the call of the natural world. She is now an associate professor of Biomedical Data Science and Biochemistry,
Li lab identifies ENPP1 as innate immune checkpoint and on/off switch for breast cancer metastasis in patients
Konermann Lab/ARC Institute’s article on optimized RNA targeting
https://www.sciencedirect.com/science/article/abs/pii/S2405471223003290?dgcid=coauthor
Dan Herschlag is inducted into the Academy of Arts and Sciences
On Saturday, September 30th, Dan Herschlag was inducted into the American Academy of Arts and Sciences in a ceremony in Cambridge,
Pragya Sidhwani publishes review in Science Direct on Epigenetic inheritance and boundary maintenance
Pragya Sidhwani and Aaron Straight
https://www.sciencedirect.com/science/article/pii/S0959440X23001689
Global mapping of RNA findings published in Nature
Charles Limouse, Owen K. Smith, David Jukam,
Repression of CENP-A assembly in metaphase requires HJURP phosphorylation and inhibition by M18BP1
Julio Flores Servin and Rachel Brown from Straight Lab publish a paper on their findings on the “Repression of CENP”
Memorial Service for Dr. Paul Berg-May 22, 2023
Please join us for a celebration of life in honor of Stanford Biochemistry Co-Founder Dr. Paul Berg
Monday,
Frontiers Seminar, April 19, 2023-Dr. Jim Hurley
Please see the pre-recorded Frontiers video by Dr. Jim Hurley here: https://drive.google.com/file/d/1topY29OS8LYD_J4lycax5FB2XKwlIApS/view?usp=sharing
Kim Lab Publication on ferritin-based COVID-19 nanoparticle vaccine
A ferritin-based COVID-19 nanoparticle vaccine that elicits robust, durable, broad-spectrum neutralizing antisera in non-human primates. Payton A.-B. Weidenbacher,
Stanford collaboration with Arc Institute aims to expand academic, research and funding opportunities.
2021 Arthur Kornberg and Paul Berg Lifetime Achievement Award in Biomedical Sciences
Maia Kinnebrew, from the Rohatgi lab, describes a new mechanism for how cholesterol levels in the plasma membrane regulate signal transduction.
Read the article here.
Mildred Berg, wife of Paul Berg. 1927 – 2021.
Mildred Berg has passed away. See article here.
Chan Zuckerberg Biohub reported on new technology developed by Dan Herschlag group and Polly Fordyce.
Read the publication here.
Dan Herschlag quoted in article on PRISM postdoc program.
Dan Herschlag quoted in article on PRISM postdoc program, which was launched under his leadership when he served as Senior Associate Dean of Graduate Education and Postdoctoral Affairs.
Congratulations to Lingyin Li who has been promoted to Associate Professor with tenure effective Dec 1st.
This reflects the extraordinary work of her lab and her vision for understanding the signaling mechanisms that control the innate immune response.
Congratulations to Lauren Hagler, of the Herschlag lab, for being selected as a Stanford Propel Postdoctoral Scholar.
Rhiju Das and Biochemistry Alumnus Kristy Red-Horse named HHMI Investigators.
Read the announcement here.
Herschlag lab develops tool to drastically speed up the study of enzymes.
Read the pre-print article, in BioRxiv, here. The article was also referenced in Nature,
Margaux Pinney, who graduated this year and was with the Herschlag lab, received a UCSF Sandler Fellowship.
SSRL highlights Herschlag Lab publication
Read the article on the SLAC website here.
Dan Herschlag publishes paper on RNA tertiary contact motifs.
Read the article in PNAS here.
Magda Gebala and Kousik Sundararajan, of the Straight lab, published a preprint of their recent work with Karolin Luger’s lab on the centromere.
Read the full article in bioRxiv here.
Steven Tang, from the Kim lab, awarded K99 Grant NIH Pathway to Independence Award.
The program provides independent NIH research support in order to help awardees to launch competitive, independent research careers.
Mark Krasnow was interviewed by RadioLab as an expert on lung function.
Listen to the podcast here. On the second segment of the Breath episode (~13 mins into the podcast).
Broder Schmidt and the Rohatgi and Brandman labs reveal that a major anti-cancer drug acts via disruption of nucleolar phase separation.
Read the full article in bioRxiv here.
Julia Salzman recommends article regarding Master-Slave terminology in biology.
Read the article in Nature here.
Julia Salzman and Mark Krasnow define tissue compartments and cell types using RNA splicing
Read the publication on bioRxiv.
Owen Smith from the Straight Lab uncovers the mysteries of the frog centromere in his latest paper in Genome Research
Read the publication in Genome Research.
Ron Davis featured in People magazine for his fight against Chronic Fatigue Syndrome
Read the March 31 People article and the April 2 article.
Das lab, in collaboration with Maria Barna’s lab in Genetics and Eterna, report new principles and methods for designing stabilized mRNA therapeutics
Read the publication on bioRxiv.
Broder Schmidt and Rajat Rohatgi share a detailed protocol for their reporter-based TDP43 splicing assay.
Read the publication on Bio-Protocol.
Ben Bell and Peter Kim identify three neutralizing antibodies targeting the receptor-binding domain of SARS-CoV-2 with high similarity to germline antibody precursors.
Read the publication on Wiley Online Library.
Ramya Rangan and Andrew Watkins, of the Das lab, report on de novo 3D models for conserved RNA regions of SARS-CoV-2.
Read the publication on Oxford Academic.
Zoe Davis, of the Brandman lab, reports that defective mRNAs lacking stop codon create proteins that localize to and disrupt the nucleolus. The most common type of defective mRNA.
Read the publication on Springer.
Herschel Dhekne and Pfeffer lab collaborators show that Parkinson’s disease-associated LRRK2 kinase sequesters the MyoVa motor at the mother centriole by phosphoRab10 binding
Read the publication in Life Science Alliance.
Yuriko Sobu and Pfeffer lab collaborators show that Parkinson’s disease-associated LRRK2 kinase regulates early steps in primary cilia formation, upstream of TTBK2 kinase
Read the publication in PNAS.
Lingyin Li selected as one of C&EN’s annual Talented 12 of 2020
Read the announcement in the journal Chemical and Engineering News. Lingyin will speak on August 25 at C&EN’S Futures Festival,
Chaitan Khosla reports antibody probes of Module 1 of the 6-Deoxyerythronolide B Synthase reveal an extended conformation during ketoreduction
Read the publication in The Journal of the American Chemical Society.
Inga Jarmoskaite and Dan Herschlag report how to measure and evaluate binding affinities
Read the publication in the journal eLife.
Jackie Carozza reports structure-aided development of small-molecule inhibitors of ENPP1, the extracellular phosphodiesterase of the immunotransmitter cGAMP
Read the publication in the journal Cell Chemical Biology.
Dan Herschlag discusses the individual and the team in collaborative science
Read the letter in the journal Proceedings of the National Academy of Sciences.
Jim Ferrell reports the apparent requirement for protein synthesis during G2 phase is due to checkpoint activation
Read the publication in the journal Cell Reports.
Mark Krasnow reports brain circuit of claustrophobia-like behavior in mice identified by upstream tracing of sighing
Read the publication in the journal Cell Reports.
Maia Kinnebrew receives 2019-20 Stanford Biosciences Excellence in Service to Graduate Students award
As stated about the award “This award recognizes students who devote a large amount of time trying to improve the quality of the Stanford graduate student experience.” Congratulations,
Cole Sitron and Onn Brandman review the detection and degradation of stalled nascent chains via ribosome-associated quality control
Read the publication in the journal Annual Review of Biochemistry.
Chaitan Khosla reports enhancing the antiviral efficacy of RNA-dependent RNA polymerase inhibition by combination with modulators of pyrimidine metabolism
Read the publication in the journal Cell Chemical Biology.
Ramin Dubey of Rohatgi Lab reports R-spondins engage heparan sulfate proteoglycans to potentiate WNT signaling
Read the publication in the journal eLife.
Suzanne Pfeffer reports inter-domain dynamics drive cholesterol transport by NPC1 and NPC1L1 proteins
Read the publication in the journal eLife.
Ann Kladwang of Das Lab reports anomalous reverse transcription through chemical modifications in polyadenosine stretches
Read the publication in the journal Biochemistry.
Ramya Rangan
Check out the PBS NOVA program “Decoding COVID-19: Scientists race to understand and defeat the coronavirus behind the COVID-19 pandemic.” The show premiered on May 13 at 9 PM.
Ramya Rangan of Das Lab reports on RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses
Ramya Rangan of the Das Lab provides a first look at RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses.
Sabrina Ergun awarded Gerald J. Lieberman Fellowship
The Lieberman Fellowships were established in 1993 to honor Stanford Professor and Provost Emeritus Jerry Lieberman for his many years of distinguished service to the University.
Chaitan Khosla, John Rubenstein, and Sandy Schmid elected to NAS
Chaitan Khosla, Professor of Chemical Engineering and Chemistry and, by courtesy, Biochemistry has been elected to the National Academy of Sciences.
Kalli Kappel, Das Lab alum, named 2020 Schmidt Science Fellow
The program supports 22 early-career scientists who aim to harness interdisciplinary approaches to tackle long-term societal challenges, including infectious disease,
Saswata Sarkar, Darshan Trivedi, and Makenna Morck of Spudich Lab report Report hypertrophic cardiomyopathy mutations R403Q and R663H increase number of myosin heads available to interact with actin
Read the publication in the journal ScienceAdvances.
Darshan Trivedi of Spudich Lab reviews mechanisms and therapeutic approaches of myosin family of mechanoenzymes
Read the publication in the journal Annual Review of Biochemistry.
Rachel Mardjuki of Li Lab reports development of cGAMP-Luc, a sensitive and precise coupled enzyme assay to measure cGAMP in complex biological samples
Read the publication in the Journal of Biological Chemistry.
The Li Lab reports extracellular cGAMP is a cancer-cell-produced immunotransmitter involved in radiation-induced anticancer immunity
Read the publication in the journal Nature Cancer. The article is highlighted in a story by ChEM-H.
Steve Artandi reports loss of human TGS1 hypermethylase promotes increased telomerase RNA and telomere elongation
Read the publication in the journal Cell Reports.
Cole Sitron of Brandman Lab reports aggregation of CAT tails blocks their degradation and causes proteotoxicity in S. cerevisiae
Read the publication in the journal PLoS One.
Ramin Dubey of Rohatgi Lab reports lipid droplets can promote drug accumulation and activation
Read the publication in the journal Nature Chemical Biology. The article is highlighted in this accompanying News and Views.
Caroline Horn of Salzman Lab introduces molecular sampling at logarithmic rates for next-generation sequencing
Read the publication in the journal PLoS Computational Biology.
Kalli Kappel of Das Lab reports cryo-EM structure of a 40 kDa SAM-IV riboswitch RNA at 3.7 Å resolution
Read the publication in the journal Nature Communications.
Jim Ferrell reports spontaneous emergence of cell-like organization in Xenopus egg extracts
Read the publication in the journal Science.
Maia Kinnebrew of Rohatgi Lab reports cholesterol accessibility at the ciliary membrane controls hedgehog signaling
Read the publication in the journal eLife.
Broder Schmidt from Rohatgi Lab reports phase separation-deficient TDP43 remains functional in splicing
Read the publication in the journal Nature Communications.
Rachel Gomez of Pfeffer Lab reports membrane association but not identity is required for LRRK2 activation and phosphorylation of Rab GTPases
Read the publication in the Journal of Cell Biology.
Joe Ouadah of Krasnow Lab reports rare pulmonary neuroendocrine cells are stem cells regulated by Rb, p53, and Notch
Read the publication in the journal Cell.
Silvana Konermann joins Stanford Biochemistry as Assistant Professor
Welcome, Silvana!
Ellen Yeh named PATH Investigator by Burroughs Wellcome Fund
Ellen Yeh has been named an Investigator in the Pathogenesis of Infectious Disease by the Burroughs Wellcome Fund.
Maia Kinnebrew of the Rohatgi Lab helps to reveal how the cholesterol molecule attached to Sonic Hedgehog inactivates Patched
Congratulations to Maia Kinnebrew from the Rohatgi Lab for her contributions to a new paper describing how the cholesterol molecule attached to the ligand Sonic Hedgehog inactivates its receptor Patched.
The New Yorker profiles Emeritus Professor Pat Brown and his company Impossible Foods
Pat Brown, Emeritus Professor of Biochemistry and Impossible’s founder, argues that we can’t fight climate change unless we get rid of cows.
Magda Gebala and Dan Herschlag report quantitative studies of an RNA duplex electrostatics by ion counting
Read the publication in Biophysical Journal.
Dan Herschlag to receive Biophysical Society’s 2020 Founders Award
The Biophysical Society has announced that Dan Herschlag will receive the Society’s Founders Award in 2020.
Ron Davis to host 3rd Annual Community Symposium on the Molecular Basis of ME/CFS on 9/7
The 3rd Annual Community Symposium on the Molecular Basis of ME/CFS will be held on Saturday, September 7,
Sharon Long creates new way to find potential treatments for citrus greening
Finding a treatment for a devastating, incurable citrus disease was personal for Sharon Long and Melanie Barnett. Now, a system they developed could provide clues to a cure.
Joe Yesselman of Das Lab reports computational design of 3D RNA structure and function
Read the publication in the journal Nature Nanotechnology.
Jackie Carozza of Li Lab receives 3rd Annual WCC/Merck Research Award from ACS Women Chemists Committee
The WCC/Merck Research Award is given to 3rd and 4th year graduate students with a research focus in organic,
Joseph Yesselman of Das Lab reports that sequence-dependent RNA helix conformational preferences predictably impact tertiary structure formation
Read the publication in the journal Proceedings of the National Academy of Sciences.
Robert Bierman of Salzman Lab receives F31 from NCI
Robert Bierman of the Salzman Lab has received the F31 Ruth Kirschstein National Research Service Award (NRSA) from the NCI.
Rhiju Das writes about scientific discovery games for biomedical research
Read the publication in the journal Annual Review of Biomedical Data Science.
Roozbeh Dehghannasiri of Salzman Lab reports improved detection of gene fusions to reveal oncogenic RNA cancer drivers
Read the publication in the journal Proceedings of the National Academy of Sciences.
Michelle Wu of Das Lab reports automated design of diverse stand-alone riboswitches
Read the publication in the journal ACS Synthetic Biology.
Sabrina Ergun of Li Lab reports mechanisms for activation, hyperactivation, and inhibition of STING from polymer structure
Read the publication in the journal Cell.
Suzanne Pfeffer promoted to Senior Editor at eLife
Suzanne Pfeffer has been promoted to Senior Editor at eLife. eLife is a non-profit organization that publishes work in all areas of the life and biomedical sciences.
A new AI tool captures strategies used by top players of Eterna to design new RNA molecules
A new artificial-intelligence tool captures strategies used by top players of an internet-based videogame to design new RNA molecules.
Hannah Wayment-Steele of Das Lab reports how to evaluate riboswitch optimality
Read the publication in the journal Methods in Enzymology.
Arjun Adhikari of Spudich Lab reports β-Cardiac myosin hypertrophic cardiomyopathy mutations release sequestered heads and increase enzymatic activity
Read the publication in the journal Nature Communications by this former member of the Spudich lab.
Makenna Morck selected for Excellence in Service to Graduate Students Award
Makenna Morck has been selected for a 2018-19 Stanford Biosciences Excellence in Service to Graduate Students Award. This award recognizes students who devote a large amount of time trying to improve the quality of the Stanford graduate student experience.
Dan Herschlag receives Stanford Biosciences Excellence in Mentoring and Service Award
Dan Herschlag has been selected for the 2018-19 Stanford Biosciences “Excellence in Mentoring and Service Award.” This honor is given to faculty who make distinguished contributions towards enhancing the quality of training and the mentoring experiences for Stanford Biosciences graduate students.
Andy Watkins of Das Lab reports how to use Rosetta for RNA homology modeling
Read the publication in the journal Methods in Enzymology.
Magda Gebala and Dan Herschlag report that ion counting demonstrates high electrostatic field generated by nucleosome
Read the publication in the journal eLife.
Siggy Nachtergaele to join faculty of Molecular, Cellular and Developmental Biology at Yale
Siggy Nachtergaele, a former member of the Rohatgi Lab, will join the Department of Molecular, Cellular and Developmental Biology at Yale University as an assistant professor.
Citron Sitron of Brandman Lab reports that CAT tails drive degradation of stalled polypeptides on and off the ribosome
Read the publication in the journal Nature Structural & Molecular Biology.
Chris Ritchie of Li Lab reports that SLC19A1 is importer of immunotransmitter cGAMP
Read the publication in the journal Molecular Cell.
Four students receive graduate fellowships
Jackie Carozza of the Li Lab has received the F31 Ruth Kirschstein National Research Service Award (NRSA) from the NCI.
Jennifer Kong of Rohatgi Lab writes review about biochemical mechanisms of vertebrate hedgehog signaling
Read the publication in the journal Development.
Margaux Pinney receives Stanford’s Gerald J. Lieberman Fellowship
Margaux Pinney of the Herschlag Lab has received a Gerald J. Lieberman Fellowship from Stanford University. In announcing the creation of the Lieberman Fellowships in 1993,
Inga Jarmoskaite of Herschlag Lab reports quantitative and predictive model for RNA Binding by human pumilio proteins
Read the publication in the journal Molecular Cell.
Mark Krasnow elected to the National Academy of Sciences
Four Stanford researchers are among the 100 newly elected members of the National Academy of Sciences. Congratulations,
Biomarker for chronic fatigue syndrome identified
Ron Davis and colleagues have devised a blood-based test that accurately identified people with chronic fatigue syndrome. Read the News Center of the School of Medicine and the San Francisco Chronicle.
Payton Weidenbacher of Kim Lab reports new research that could lead to lifetime flu vaccine
Read the news announcement. Read the publication in the journal the Proceeding of the National Academy of Science.
Andy Renteria receives 2018 NSF Graduate Research Fellowship
Andy Renteria, a first-year biochemistry student, has received a 2018 NSF Graduate Research Fellowship. Martha Kahlson, a first-year biochemistry student,
Gilbert Chu and Julia Salzman report hyperammonemia after capecitabine is associated with occult impairment of the urea cycle
Read the publication in the journal Cancer Medicine.
Kalli Kappel of Das Lab reports blind tests of RNA–protein binding affinity prediction
Read the publication in the journal Proceedings of the National Academy of Sciences.
Jennifer Kong of Rohatgi Lab receives NIH K99/R00 Pathway to Independence Award
The NIH has awarded Jennifer Kong of the Rohatgi Lab the K99/R00 Pathway to Independence Award. This award aims to help outstanding postdoctoral researchers complete training and transition to independent,
Mystery novel and dream spur key scientific insight into heart defect
On Dec. 14, 2014, after many months of not getting expected results, Jim Spudich got into bed, read a chunk of a novel,
Scientists probe STING structure and activity
Drug companies want to use STING to fight cancer. Now insights into the structure and activity could help that quest.
Jim Spudich provides three perspectives on the molecular basis of hypercontractility caused by hypertrophic cardiomyopathy mutations
Read the publication in the European Journal of Physiology.
Yong Tang of the Yeh Lab reports a mutagenesis screen for essential plastid biogenesis genes in human malaria parasites
Read the publication in the Journal of Biological Chemistry.
Suzanne Pfeffer writes about NPC intracellular cholesterol transporter 1 (NPC1)-mediated cholesterol export from lysosomes
Read the publication in the Journal of Biological Chemistry.
Bhaven Patel and Andres Lebensohn of the Rohatgi Lab report discovery of gene regulatory elements through new bioinformatics analysis of haploid genetic screens
Read the publication in the journal PLOS One by these former members of the Rohatgi Lab.
Sharon Long will receive the 2019 NAS Selman A. Waksman Award in Microbiology
The National Academy of Sciences will honor Sharon Long with the 2019 Selman A. Waksman Award in Microbiology. The award will be presented on April 28 during the Academy’s 156th annual meeting.
Michael Boucher of Yeh Lab reports that disruption of apicoplast biogenesis by chemical stabilization of an imported protein evades the delayed-death phenotype in malaria parasites
Read the publication in the journal mSphere.
Bradley French of Straight Lab reports that CDK phosphorylation of Xenopus laevis M18BP1 promotes its metaphase centromere localization
Read the publication in the EMBO Journal by this former member of the Straight Lab.
The puzzle of a mutated gene lurking behind many Parkinson’s cases
Why a defective gene is tied so strongly to Parkinson’s disease has baffled researchers. Now, a study led by Stanford scientists appears to have pieced together a major part of the puzzle.
An improbable journey: Creativity helped Elizabeth Winzeler make the transition from art to curing malaria
Elizabeth Winzeler, a former postdoctoral fellow of the Davis Lab, was awarded the Alice and C. C. Wang Award in Molecular Parasitology for her contributions to antimalarial drug development.
Peter Kim receives Stanford Medicine Alumni Association Award
Peter Kim is one of three recipients of the 2019 Stanford Medicine Alumni Association Award, presented to distinguished alumni for exceptional service to Stanford Medicine and outstanding lifetime contributions to medicine and the biomedical sciences.
Steven Artandi tapped to lead Stanford Cancer Institute
Steve Artandi has been named the next director of the Stanford Cancer Institute (SCI). A strategic thinker and collaborative physician-scientist,
Gil Chu elected Fellow of the American Physical Society
Gilbert Chu was elected to the American Physical Society for contributions at the intersection of physics and the life sciences.
Inga Jarmoskaite wins poster prize at Gordon Research Conference
Inga Jarmoskaite of the Herschlag Lab has won a poster prize at the 2018 Gordon Research Conference on Post-Transcriptional Gene Regulation.
Stanford researchers map intricacies of lung cancer in one of their own
When James Spudich was diagnosed with lung cancer, researchers had a rare, and unexpected, opportunity to study healthy and diseased human tissue at an unprecedented level of detail.
