PEOPLE:
James Ferrell. James Ferrell was born in Gary Indiana and raised in Chicago and Pittsburgh. He was an undergraduate at Williams College, where he majored in Physics, Chemistry, and Mathematics, and graduated in 1976. For his undergraduate thesis he worked with David A. Park on nonlinear dynamics and chaos in the Hénon-Heiles model of stars in an axisymmetrical galactic potential. After graduating he came west to Stanford for medical school and graduate school. His did his Ph.D. thesis in Chemistry with Wray H. Huestis, working on cell shape control and phosphoinositide metabolism in human erythrocytes. He received his Ph.D. in 1984 and his M.D. in 1986. He then moved to UC Berkeley for postdoctoral studies with G. Steven Martin on tyrosine-specific protein phosphorylation in human platelets, mammalian cell lines, and Xenopus laevis oocytes, eggs, and embryos.
He began his independent career in the Dept. of Zoology at the University of Wisconsin–Madison in 1990. He moved to the Dept. of Pharmacology at Stanford University School of Medicine in 1992. The Department later became the Dept. of Chemical and Systems Biology, which he chaired from its inception in 2006 until 2011. Currently he is Professor of Chemical and Systems Biology and Professor of Biochemistry.
For James Ferrell the rock musician, click here.
Yuping Chen. Yuping grew up in Ningde, a coastal city in Fujian, China. Since his childhood, he was curious about the universe and the lives in the sea, and he dreamed about having his own lab in the small storage space next to his parent's house when he grew up. As an undergraduate, he attended China Agricultural University, where he was trained in the laboratories of Drs. Zhongzhou Chen and Bin Wang. In 2010, he became interested in and read extensively about an adaptive immune system found in bacteria and archaea, termed CRISPR, and later joined Dr. Jennifer Doudna's group at the University of California, Berkeley to study the spacer acquisition process in the CRISPR system. After graduating from college, he attended Stony Brook University as a Genetics Ph.D. student in Dr. Bruce Futcher's lab, where he focused on 1) how the central cell cycle regulator, CDK (Cyclin-Dependent Kinase) directly regulates carbohydrate storage, and 2) how cell size is controlled through differential expression of cell cycle activators and cell cycle inhibitors in budding yeast. He joined the Ferrell lab in 2019, where he is studying the effects of density in biological systems, from how organismic density drives the formation of organismic assemblies to how cytoplasmic density affects protein translation and degradation. In his spare time, Yuping enjoys playing the guitar, reading books, fixing household items, playing soccer, and doing outdoor activities.
Jo-Hsi Huang. Jo-Hsi was born and raised in the vibrant city of Taipei, Taiwan. He went to National Taiwan University for his B.S. in general biology and M.S. in molecular genetics, during which he studied the transport and function of a DEAD-box helicase. After graduation, he worked with Dr. Sheng-hong Chen in Academia Sinica to investigate redox metabolism in human cells and how it collapses under starvation. Jo-Hsi became interested in systems biology thanks to the studies in cell fate decisions and ecological population dynamics that founded themselves on the theory of nonlinear dynamics. He wants to understand how parts interact to constitute the system and how environmental/global parameters can influence the way the system works. Now in the Ferrell lab, Jo-Hsi is conducting his Ph.D. research on how the physical properties of the cytoplasm govern the speed of complex cellular processes. Outside lab, Jo-Hsi enjoys biking around the Bay Area and street food. His favorite animals are the sea otters that reside near the Monterey Bay.
William Huang. William was born and raised in Taipei, Taiwan. He received a B.S. degree in Chemistry from National Taiwan University in 2010. He then moved across the Pacific Ocean to pursue his Ph.D. in Chemistry at UC Berkeley, with an emphasis on biophysics and physical chemistry. Under the guidance of Jay Groves, William investigated the activation mechanism of membrane-associated proteins by analyzing the molecular timing of membrane signaling reactions. For this, he has developed extensive imaging-based membrane assays that map complex signaling reactions into quantifiable reconstituted systems. He received his Ph.D. in 2016. In 2018, his interest in dissecting the complexity of signal transduction led him to the Ferrell lab, where he continues to advance the reconstitution approach integrating cell-extract methods. The cell-extract approach further enables him to expand his study to the physical organization of the cytoplasm. Additional information about William’s work can be found here. In his little spare time, he enjoys analyzing the complexity of underground music, recreating the authentic sound of records, and finding the right stimulus for his palate.
Zhengda Li. Zhengda was born in Henan, a central province in China. He attended Peking University to study Biological Science, and got interested in using theoretical and computational tools to solve biological problems. He joined Qiong Yang’s lab at the University of Michigan to study design principles of biological oscillators and used Xenopus extract droplets to test theoretical predictions. He got his Ph.D. in 2019 and moved to the Ferrell lab to study trigger wave propagation in two dimensional space. His current project is to investigate the spatial constrictions in neuronal pruning. In his free time, Zhengda enjoys hiking, table tennis and cooking.
Shixuan Liu. Shixuan Liu is a postdoctoral fellow jointly advised by Jim Ferrell and Mark Krasnow. Shixuan was trained as a systems biologist. She obtained her B.S. degree at Peking University in Beijing where she was first introduced to the beauty of systems biology by Chao Tang. She then moved to Toronto, Canada and studied in Ran Kafri’s lab at the University of Toronto. In her Ph.D., Shixuan worked on cell size and cell cycle control through high-content screening.
Shixuan is now applying systematic screening approaches to studies of the molecular clock that controls the animal seasonal rhythms, such as hibernation and seasonal reproduction cycles. As is the case with circadian rhythms, seasonal rhythms can be entrained by environmental signals (e.g., photoperiod) but can also be maintained as free-running cycles in the absence of external cues.
DOG:
Scout. At about 4 months of age Scout was found wandering on Page Mill Road in Los Altos Hills and was taken in by Palo Alto Animal Services. JF saw her profile online while lecturing in Buenos Aires, and adopted her on the way home from SFO.
Scout's lab responsibilities include psychological counseling and shedding. She enjoys snoozing on the couch in Jim's office, and likes nothing more than visiting with all her Stanford friends every day.
Scout is a good doggie. She is a friend to all and a sister to every other dog.
ALUMNI:
| Name | Position and Approx. Vintage | Current Position |
|---|---|---|
| Oshri Afanzar |
Postdoc, 2018-2021 | Scientist, Priscilla Yang Lab, Stanford University School of Medicine |
| Graham Anderson |
Grad student and postdoc, 2007-2017 | Strain Build Lead, Zymergen, Emeryville CA |
| Christoph Bagowski | Postdoc, 1999-2002 |
Head of Molecular Genetics, Pränatal-Medizin München, Germany |
| Alex Bazarov | Postdoc, 1999-2002 |
Director of Cell Engineering, CHO Plus |
| Ramesh Bhatt | Grad student, 1993-2000 |
Vice President: Discovery Biology and Translational Research at Protagonist Therapeutics |
| Salvador Buse | Undergrad, 2018 |
Bioengineering PhD Student, Caltech |
| David Byron | Tech, 1999-2001 |
Family Practice Physician, Tuscon AZ |
| Annie Carilli | Undergrad, 2017 and 2018 |
Senior Financial Analyst at Providence Saint Joseph Medical Center |
| Jeremy Chang | Grad student, 2007-2013 |
Senior Associate, Asset Acquisition at BridgeBio |
| Yuxin Chen | Postdoc, 2018-2022 |
Scientist, Synlico Inc. |
| Tzu-Chi Chen | Visiting grad student, 2013-2014 | Postdoc, Huang lab, National Yang-Ming University |
| Xianrui Cheng | Postdoc, 2013-2020 | Asst. Professor, University of Southern California |
| Yoon Sup Choi | Visiting grad student, 2007-2008 | Res. Asst. Professor, Seoul National University Hospital |
| Szu-yi (Sam) Chou | Grad student, 1991-1997 |
President and CEO, Viogene-Biotek |
| Delquin Gong | Grad student, 2002-2008 |
Senior Scientist, Bio-Rad |
| Lendert Gelens | Postdoc, 2013-2016 |
Asst. Professor, University of Leuven, Belgium |
| Sherril Green | Fellow, 1997-2002 |
Professor and Chair of Comparative Medicine, Stanford University School of Medicine |
| Tom Guadagno | Postdoc, 1995-1999 |
Science Teacher, Newton County Day School |
| Sang Hoon Ha | Postdoc, 2010-2017 |
Deceased 2021 |
| Dave Hendrickson | Grad student, 2002-2009 |
Associate Director, Calico |
| Kuang-Ming Hsiao | Grad student, 1991-1992 |
Professor, Life Science, National Chung Cheng University |
| Chi-Ying Frederick Huang | Postdoc, 1994-1998 |
Professor and Chair, Inst. of Biopharmaceutical Sciences, National Yang-Ming University |
| Narae Hwang | Visiting grad student, 2003 | Medical Intern, Seoul Korea |
| Julia Kamenz | Postdoc, 2015-2020 |
Asst. Professor, U Groningen |
| Minjung Kang | Postdoc, 2016-2017 |
Principal Scientist, Samsung Bioepis, Inchong Korea |
| Sun Young Kim | Postdoc, 2002-2010 |
Scientific Ambassador, ILDONG Pharmaceutical Company, Seoul Korea |
| Chung Han Lee | Undergrad, 1998-2001 |
Postdoc, Hsieh lab, MSKCC |
| Tek Hyung Lee | Postdoc, 2014-2017 |
Yung lab, Lawrence Livermore National Laboratory |
| Thomas Leung | Undergrad, 1997-1998 |
Asst. Professor of Dermatology, University of Pennsylvania |
| Xuedong Liu | Sabbatical visitor, 2009-2010 | Professor of Chemistry and Biochemistry, University of Colorado, Boulder |
| Sarah Lockhead | Grad student, 2008-2016 |
Senior Manager, Oncology Resource Group |
| Eric Machleder | Grad student, 1996-1998 |
Software Architect, Walmart Global eCommerce |
| Alisa Moskaleva | Grad student, 2010-2015 |
Scientist II, Pacific Biosciences |
| Jason Myers | Grad student, 1999-2005 |
CEO, GenapSys, Golden CO |
| Michele Nelson | Grad student, 1996-1998 |
Research Program Officer Associate, University of Michigan, Grand Rapids |
| Sam Pearlman | Grad student, 2005-2012 |
Senior Software Engineer, Myriad Genetics, South San Francisco |
| Eva Petschnigg | Undergrad and visiting medical student | Physician, Newton-Wellesley Hospital, MA |
| Connie Phong | Postdoc, 2016-2022 |
|
| Joe Pomerening | Postdoc, 2000-2006 |
Chief Scientist, Aveshka Inc. |
| Andy Poon | Grad student, 2004-2012 |
Head of Analytics, Flow Commerce Inc. |
| Diana Ríos-Cardona | Grad student, 2003-2009 |
Agriculture Specialist, U.S. Customs and Border Protection |
| Michal Ronen | Postdoc, 2003-2005 |
Algorithms Team Leader, Oridion, Jerusalem, Israel |
| Marsha Rosner | Sabbatical visitor, 2009-2010 | Charles B. Huggins Professor and Chair, Ben May Dept. for Cancer Research, University of Chicago |
| Mauro Ruffy | Undergrad, 1995-1996 |
ENT Physician, San Jose Medical Group |
| Silvia Santos | Postdoc, 2008-2013 |
Asst. Professor, Imperial College London |
| Zach Serber | Postdoc, 2003-2007 |
Founder and Chief Scientific Officer, Zymergen, Inc. |
| Shian-Jiun Shih | Postdoc, 1991-1993 |
Section Head, Translational Medicine Research Center, Merck Sharp & Dohme |
| Mike Sohaskey | Grad student, 1993-2000 |
Co-Founder, Chief Racing Officer, RaceRaves LLC |
| Nikki Trunnell | Grad student, 2003-2010 |
Director of Operations, Oncology Resource Group |
| Tony Tsai | Grad student, 2007-2013 |
Asst. Professor, Washington University |
| Jeff Ubersax | Postdoc, 2004-2008 |
CEO, Demetrix, Berkeley CA |
| Alexandra Vanderwelde | Visiting postdoc, 2018 |
Research Policy Officer at Research Foundation Flanders - FWO |
| Sarah Walter | Grad student, 1993-2000 |
VP Nonclinical Development at Antiva Biosciences, Inc., South San Francisco |
| Joanne Westendorf | Postdoc, 1997-2001 |
CPA, Patent Agent |
| Xiao Min Wang (Schebye) | Postdoc, 1997-2001 |
Senior Research Investigator, Cancer Immunotherapy Discovery, Bristol-Myers Squibb |
| Polly Wong | Grad student, 1993-1999 |
Senior Group Director, Regulatory Affairs, Genentech Inc., South San Francisco CA |
| Jinger Xie | Tech, 1993-1994 |
Senior Staff Research Scientist, Bayer Health Care |
| Wen Xiong | Postdoc, 1999-2003 |
General Manager/Head of Biolog, Allorion Therapeutics, Shanghai |
| Qiong Yang | Postdoc, 2008-2013 |
Assoc. Professor of Biophysics, University of Michigan |
| John Yoon | Undergrad and tech, 1997-2001 | Neuroradiologist, Cottage Center for Advanced Imaging, Santa Barbara CA |
| Jianbo Yue | Postdoc, 2000-2006 | Assoc. Prof. of Biomedical Sciences, City University of Hong Kong |
