Sue Rhee

Senior Staff Scientist

Plant Biology

Carnegie Institution for Science

srhee@carnegiescience.edu
650-739-4251
Office:
260 Panama Street
Stanford, CA 94305, US

Profile

Bio

Where do you come from?

I find two things magical: plants and movies. My love of plants started when I wrote a little story about a tree that grew next to the apartment building we lived in Seoul when I was 12. We lived on the sixth floor and my room had a window next to the tree whose canopy was the same height. I was amazed that a tree could grow so tall amidst the concrete towers in the high-rise jungle and wrote an imaginary biography of the tree and its thousands of dancing leaves. My story got a national award and I thought I was destined to become a writer. Little did I know that my little world would be uprooted and transplanted across the globe within a year. A new life in the US where I no longer had control over the language dissolved my dream of becoming a writer. Little did I know that I would eventually end up studying and writing about the mysteries of plants for a living!

What was your first experience with research?

The smell of ether singularly captures my memory of science and research in high school and college. We had a little room behind the biology classroom of Dr. Kowalski’s at Yorktown High, where we conducted genetics experiments with the fruit fly. We would knock them out with ether so that we could count their eye colors and learn about the magical ratio of Mendelian segregation. At Swarthmore college, in the fancy Howard Hughes laboratory of Dr. Mark Jacobs, we wanted to identify protein kinase C from plants and purified the protein from rat brains (one of the most abundant sources of PKC) to establish the biochemical assays. Trips to the Psychology department for the source of PKC were angst-ridden as we ‘took care’ of the rats by knocking them out with ether in a large aluminum garbage can on the roof and surgically removed their brains with rusted guillotine and scissors. These were ‘exciting’ times but also solidified my distaste for doing experiments with animals.

How did you choose graduate school?

A new life in the beautiful San Francisco bay area got started when I came for an interview to do graduate work at Stanford. Learning about the cutting-edge research at Stanford was thrilling, but what really made me decide to settle here were the lovely dinners hosted by plant biologists Drs. Ginny Walbot and Sharon Long. Ginny grilled a whole salmon on her deck and we sat around a picnic table overlooking her gorgeous garden of native plants in full bloom. Sharon and Hal McGee (a science food writer with a cult following) made a wonderful meal and we talked about science and food around the table for hours. In my eyes, they were the Meryl Streeps and Katharine Hepburns of science.

How did you choose a graduate project and lab?

A lot of soul searching goes on during a graduate program. I probably hold a record in not settling into a laboratory to perform graduate work. After doing 4 rotations in various labs, I was still uncertain about where to do my Ph.D. work, and I was gearing up to do yet another rotation when Ginny interjected and encouraged me to talk with a plant biologist, Dr. Chris Somerville, who was coming to Carnegie (a non-profit research institute whose plant biology department was located on campus) as the new director. He was gracious enough to meet me during one of his visits to Stanford and we sat in the white plastic picnic chairs outside the seminar room. Before I realized, we had talked for over two hours, sharing our ideas, perspectives, and science, and I was certain that he was the ideal mentor I was looking for. Although I had to wait another year until his lab moved to Carnegie and didn’t get started with my Ph.D. research until my third year into graduate school, it was a wonderful experience and Chris remains as one of my favorite scientists and friends of all time.

What was your path after getting a Ph.D.?

A lot of soul searching goes on after getting a Ph.D. While I enjoyed the intense period of digging deep into the mysteries of how pollen cell wall formed and unformed into the wee hours of the night, I wasn’t sure whether this was the life I wanted to pursue for the rest of my life. My curiosity knew no bounds, yet what I could do to attack these bouts of curiosities remained frustratingly limiting. So I decided to leave science and turned my attention to the other magical medium, filmmaking. I developed a project with a dear friend from college, Nan Bress, who had just finished a masters program in documentary filmmaking at Stanford. We wanted to make a series of short documentaries about career paths and choices with a degree in science. We pursued our project for two years with a lot of zeal and heart but couldn’t raise enough funds to realize our goals. While I was pursuing this path, I took on a part-time job as a database curator at the Genetics department at Stanford. The database, AtDB, held genetic information about Arabidopsis, the plant I studied as a graduate student. I shared the office with postdocs from Dr. David Botstein’s lab where new genomics technologies were being developed. With the human and Arabidopsis genome sequencing projects well underway and the Internet becoming a household name, I could almost taste the beginning of a new era in biology and I wanted to be a part of it!

I was in the right place at the right time. The Arabidopsis community, which amassed its critical mass, thanks to dynamic leaders like Chris Somerville and Elliot Meyerowitz, wanted a brand new database to hold all of Arabidopsis data that was about to explode. I was part of one of the teams that submitted a proposal to this call and we were successful in getting it. We got the news on my 30^th birthday and because I was second in charge (the person who was going to run the project had just taken a job at industry a month before), this project essentially landed on my lap. With a team of about 10 people I put together back at Carnegie, we created the next generation Arabidopsis database called The Arabidopsis Information Resource (TAIR).

This is my 20^th year at Stanford 18^th year at Carnegie. Since I (re)-started at Carnegie as a staff associate building TAIR and other biological databases in 1999, I was promoted to a staff scientist in 2005 at which time I passed on the baton of running TAIR to Dr. Eva Huala. Since 2005, I have been revamping my scientific program to understand how plants exhibit complex traits like drought and salt tolerance by elucidating the underlying genome-wide networks of proteins and metabolites. We want to identify all of the unknown processes and functions in plants using methods and concepts from computer science, evolution, and genetics and connect the dots in a way that we can explain the complex behavior of plants mechanistically, quantitatively, and predictably.

Affiliation

Carnegie Affiliation:

DPB Employees

DPB Affiliation:

DPB Faculty

Labs:

Rhee Lab

Research Programs:

Pathway Metabolic Network

Download:

Rhee_CV.pdf

Teaching

2020

Fundamentals and Frontiers in Plant Biology

Stanford University

Winter 2020: BIO229/BIO129

BIO129/229: Fundamentals and Frontiers in Plant Biology

Quarter/Year: Winter 2020 Tues/Thurs 12-1:20 pm Grading: Satisfactory/No Credit

This course can serve as an elective course for Biology PhD candidates in the CMOB track for the following areas: Cell Biology, Genetic and Genomics, or the Biology of Molecules. This course can also serve as an upper division biology elective for undergraduates.

Location: STLC room 105 Number of Units: 3

Audience: Graduate students at any level, co-term and upper-level undergraduate students with permission of instructor.

Enrollment Cap: 20

Prerequisites: For graduate students, no prerequisites. For undergraduates, at least two of the following Bio82 (Genetics), Bio86 (Cell Biology), Bio84 (Physiology), and ongoing research in a Stanford or Carnegie plant biology laboratory.

Auditing: TGA graduate students can audit lecture classes on Tuesdays

Description and learning outcomes: This course will serve as a primer for all levels of graduate, co-term, and upper-level undergraduates interested in learning about the fundamental aspects of plant biology as well as the latest advances in tools, techniques, and theories that link basic science with translational science and applications for solving major societal challenges of today and tomorrow. Topics include plant evolution, genomics, genetics, biotic and abiotic interactions, cell and development, and systems and synthetic biology.

Overall learning goals: Students will learn major concepts and methods in plant biology and gain the tools and resources to research the literature more independently and deeply. In addition, students will learn fundamental ways that plants are different from animals and microbes. In each module, students will learn major concepts and skills from lectures and primary literature discussions. Students will also learn how to write a succinct critique of research papers.

Class activities: Each week will compose of one lecture and one paper discussion class. The discussion class is structured like a journal club, where teams of students will lead discussions on various sections of the paper. Students will write a 1 page critique of the paper and submit before class. Carnegie Winter Quarter Seminar Series will include speakers from the papers or topics of discussion and students will have an opportunity to meet with the speakers. There may be 1-2 field trips.

Grading: Based on attendance (required at all sessions for credit), participation in discussion, and turning in an acceptable critique for all 9 weekly assignments.

Topics (*Module Coordinator):

Module 1 (Weeks 1-3): Plant Genetics, Genomics, and Evolution (Walbot*, Evans, Exposito-Alonso)

Module 2 (Weeks 4-5): Plant Cell and Developmental Biology (Bergmann*, Ehrhardt)

Module 3 (Weeks 6-8): Biotic and Abiotic Interactions (Long*, Grossman, Wang)

Module 4 (Weeks 9-10): Plant Systems and Synthetic Biology (Rhee*, Bhaya)

Date	Module	Instructors (Teaching)	Topic/Papers/Learning Goals
Jan 7 12-1:20pm	Mod 1	Exposito-Alonso, Walbot, Evans	Introduction of plant macro- and micro- evolution from geological times to the anthropocene. The complexity of plant genomes and its relationship to speciation, environmental adaptation, and contemporary rapid evolutionary processes.
Jan 9 12-1:20pm	Mod 1	Exposito-Alonso, Walbot, Evans	Classic paper that contributed to the modern synthesis of evolution: Clausen J, Keck DD, Hiesey WM. Regional Differentiation in Plant Species. Am Nat. 1941;75: 231–250. Available: http://www.jstor.org/stable/2457513 Frontier paper addressing global change problems using fundamental plant biological principles: Monroe JG, Powell T, Price N, Mullen JL, Howard A, Evans K, et al. Drought adaptation in Arabidopsis thaliana by extensive genetic loss-of-function. Elife. 2018;7: e41038. https://doi.org/10.7554/eLife.41038
Jan 10 4-5 pm	Carnegie Seminar		Host: Moises Exposito-Alonso Speaker: Dan Jacobson
Jan 14 12-1:20pm	Mod 1	Exposito-Alonso, Walbot, Evans	Alternation of generations and practical applications of controlling reproduction: [1] genetics of sporophytic and gametophytic self-incompatibility, [2] gametophyte advantage genetics and the popcorn industry, [3] haploid induction and CRISPR editing via pollen in plant breeding.
Jan 16 12-1:20pm	Mod 1	Exposito-Alonso, Walbot, Evans	Genetics of self-incompatibility: Background paper: Specificity determinants and diversification of the Brassica self-incompatibility pollen ligand (2004) Thanat Chookajorn, Aardra Kachroo, Daniel R. Ripoll, Andrew G. Clark, and June B.Nasrallah. PNAS 101: 911-917. https://doi.org/10.1073/pnas.2637116100 Discussion paper: S-Locus F-Box proteins are solely responsible for S-RNase-based self-incompatibility of Petunia Pollen (2018) Linhan Sun, Justin S. Williams, Shu Li, Lihua Wu, Wasi A. Khatri, Patrick G. Stone, Matthew D. Keebaugh, and Teh-hui Kao. The Plant Cell 30: 2959-2972. DOI: https://doi.org/10.1105/tpc.18.00615
Jan 17 4-5 pm	Carnegie Seminar
Jan 21 12-1:20pm	Mod 1	Exposito-Alonso, Walbot, Evans	Epigenetic regulation of gene expression in the context of plant development and heritable gene silencing
Jan 23 12-1:20pm	Mod 1	Exposito-Alonso, Walbot, Evans	One classic paper to read and one recent paper for discussion Classic Paper: First demonstration of imprinting of an individual gene in any organism, showing that parent-of-origin, rather than gene dosage, is responsible for expression differences of R-r in maize endosperm. J.L. Kermicle (1970) DEPENDENCE OF THE R-MOTTLED ALEURONE PHENOTYPE IN MAIZE ON MODE OF SEXUAL TRANSMISSION. Genetics 66:69-85. https://www.genetics.org/content/66/1/69.long Recent Papers: Movement of small RNAs from the vegetative cell to sperm cells in pollen for transposon silencing. G. Martinez, K. Panda, C. Kohler, and R.K. Slotkin (2016) Silencing in sperm cells is directed by RNA movement from the surrounding nurse cell. Nature Plants 2:1-8. https://www.nature.com/articles/nplants201630 Demethylation in the endosperm is correlated with demethylation in the central cell. Park et al. (2016) DNA demethylation is initiated in the central cells of Arabidopsis and rice. PNAS 113:15138-15143 https://www.pnas.org/content/113/52/15138
Jan 24 4-5 pm			Host: Ginny Walbot Speaker: Tim Kelliher
Jan 28 12-1:20pm	Mod 2	Bergmann, Ehrhardt	The creation of plant bodies with an emphasis on defining features of plant development such as modularity, meristematic growth, and morphogenesis without cellular movement.
Jan 30 12-1:20pm	Mod 2	Bergmann, Ehrhardt	Several classic (short!) papers using microsurgery to define organ positions, https://www-nature-com.laneproxy.stanford.edu/articles/167651a0 https://www-nature-com.stanford.idm.oclc.org/articles/171224b0.pdf A decades-later revisit of these surgeries https://dev-biologists-org.stanford.idm.oclc.org/content/develop/132/1/15.full.pdf and a recent paper identifying the molecules and mechanisms that are responsible for the positional information. https://elifesciences.org/articles/27421
Jan 31 4-5 pm	Carnegie seminar		Host: Dominique Bergmann Speaker: Courtney Hollender
Feb 4 12-1:20pm	Mod 2	Bergmann, Ehrhardt	Principles of growth and morphogenesis in cells constrained by cell walls. Topics include biophysics of cells under high turgor pressure, organization of cell wall biosynthesis and yielding, establishment of asymmetries in cell growth.
Feb 6 12-1:20pm	Mod 2	Bergmann, Ehrhardt	Classic paper: Green P.B. (1962) Mechanism for plant cellular morphogenesis. Science 138: 1404-1405. Recent Paper: Oda Y. Fukuda H. (2012) Initiation of cell wall pattern by a Rho- and microtubule-driven symmetry breaking. Science 337: 1333-1336.
Feb 7 4-5 pm
Feb 11 12-1:20pm	Mod 3	Long, Grossman, Wang	Overview of plant-microbe interactions. Major topics: recognition, bacterial signals and plant responses; genes for symbiosis with bacteria and fungi; different levels of plant defense against pathogens.
Feb 13 12-1:20pm	Mod 3	Long, Grossman, Wang	Classic paper: Lerouge, P. et al (1990) Symbiotic host-specificity of Rhizobium meliloti is determined by a sulphated and acylated glucosamine oligosaccharide signal. Nature 344: 781-784. https://www.nature.com/articles/344781a0.pdf Recent paper: Teulet, A. et al (2019) The rhizobial type III effector ErnA confers the ability to form nodules in legumes. Proc. Nat. Acad. Sci. 116: 21758-21768. https://www.pnas.org/content/pnas/116/43/21758.full.pdf
Feb 14 4-5 pm	Carnegie seminar		Host suggestion: Sharon Long Speaker suggestion: Ksenia Krasileva
Feb 18 12-1:20pm	Mod 3	Long, Grossman, Wang	Basic aspects of photosynthetic metabolism; from the fixation of inorganic carbon to the generation of reactive oxygen species.
Feb 20 12-1:20pm	Mod 3	Long, Grossman, Wang	Classic Papers: Photosynthesis. (2016) Johnson MP. Essays Biochem. Oct 31;60(3):255-273. Review. PubMed PMID: 27784776; PubMed Central PMCID: PMC5264509. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5264509/pdf/bse0600255.pdf Efficient photosynthesis in dynamic light environments: a chloroplast's perspective. (2019) Kaiser E, Correa Galvis V, Armbruster U. Biochem J. 2019 Oct 15;476(19):2725-2741. doi: 10.1042/BCJ20190134. PubMed PMID: 31654058. https://portlandpress.com/biochemj/article-lookup/doi/10.1042/BCJ20190134 Recent paper: Improving photosynthesis and crop productivity by accelerating recovery from photoprotection. (2016) Kromdijk J, Głowacka K, Leonelli L, Gabilly ST, Iwai M, Niyogi KK, Long SP. Science Nov 18;354(6314):857-861. PubMed PMID: 27856901. https://science.sciencemag.org/content/354/6314/857/tab-pdf
Feb 21 4-5 pm	Carnegie Seminar		Host suggestion: Arthur Grossman Speaker suggestion: Kris Niyogi
Feb 25 12-1:20pm	Mod 3	Long, Grossman, Wang	Developmental plasticity and acclimation to the environment, the underlying cell signaling and regulatory systems, protein networks and proteomics.
Feb 27 12-1:20pm	Mod 3	Long, Grossman, Wang	Classic paper: (1) Park et al., Abscisic acid inhibits type 2C protein phosphatases via the PYR/PYL family of START proteins. Science. 2009 May 22;324(5930):1068-71. PMID: 19407142 https://science.sciencemag.org/content/324/5930/1068/tab-pdf (2) Pandey et al., Two novel GPCR-type G proteins are abscisic acid receptors in Arabidopsis. Cell. 2009 Jan 9;136(1):136-48. PMID: 19135895 https://www.ncbi.nlm.nih.gov/pubmed/19135895 Recent paper: Vaidya et al., Dynamic control of plant water use using designed ABA receptor agonists Science 366, eaaw8848 (2019) 25 October 2019. PMID: 31649167
Feb 28 4-5 pm	Carnegie Seminar
Mar 3 12-1:20pm	Mod 4	Rhee, Bhaya	Overview of plant systems biology with topics including biological networks, cell and tissue modeling, and comparison of traditional plant physiology with systems biology
Mar 5 12-1:20pm	Mod 4	Rhee, Bhaya	Classic papers: Milo, R. et al. Network motifs: simple building blocks of complex networks. Science 298, 824–827 (2002).https://science.sciencemag.org/content/298/5594/824 Just-in-time transcription program in metabolic pathways. (2004) Zaslaver A, Mayo AE, Rosenberg R, Bashkin P, Sberro H, Tsalyuk M, Surette MG, Alon U. Nat Genet.May;36(5):486-91. Epub 2004 Apr 25. PubMed PMID: 15107854. https://www.nature.com/articles/ng1348.pdf Recent paper: Temporal transcriptional logic of dynamic regulatory networks underlying nitrogen signaling and use in plants. (2018) Varala K, Marshall-Colón A, Cirrone J, Brooks MD, Pasquino AV, Léran S, Mittal S, Rock TM, Edwards MB, Kim GJ, Ruffel S, McCombie WR, Shasha D, Coruzzi GM. Proc Natl Acad Sci U S A. 2018 Jun 19;115(25):6494-6499. doi: 10.1073/pnas.1721487115. Epub 2018 May 16. PubMed PMID: 29769331; PubMed Central PMCID: PMC6016767. https://www.pnas.org/content/pnas/115/25/6494.full.pdf
Mar 6 4-5 pm	Carnegie Seminar
Mar 10 12-1:20pm	Mod 4	Rhee, Bhaya	Principles of synthetic biology; a discussion of successes and challenges. How has synthetic biology been used in plant engineering?
Mar 12 12-1:20pm	Mod 4	Rhee, Bhaya	Classic paper: Refactoring the nitrogen fixation gene cluster from Klebsiella oxytoca. Temme K, Zhao D, Voigt CA. Proc Natl Acad Sci U S A. 2012 May 1;109(18):7085-90. doi: 10.1073/pnas.1120788109. Epub 2012 Apr 16. PMID: 22509035 Recent paper: Polyprotein strategy for stoichiometric assembly of nitrogen fixation components for synthetic biology. Proc Natl Acad Sci U S A. 2018 Sep 4E8509-E8517. doi: 10.1073/pnas.1804992115. Epub 2018 Jul 30.
Mar 13 4-5 pm	Carnegie Seminar

Career Exploration and Planning

Stanford University

Spring 2020: BIO380

BIO 380: Career Exploration and Planning

Dr. Sue Rhee (srhee@carnegiescience.edu)

Senior Staff Scientist, Carnegie Institution for Science

Associate Professor by Courtesy, Biology Department, Stanford University

Format: Discussion

Enrollment Cap: 20

Quarter/Year: Spring 2020

Prerequisite: Grad students in Life Sciences PhD programs

Grading: Satisfactory/No Credit

Number of Units: 1

Meeting Time: Thursdays 4:30-6:20 pm Location: Carnegie Seminar Room

Course Assistants:

Benjamin Jin (bjin@carnegiescience.edu)
Emily Fryer (efryer@carnegiescience.edu)

Description

Thinking about and planning for life beyond graduate school is one of the most anxiety-provoking activities students face. In this course, students will share their personal stories and dilemmas about career decisions; have the opportunity to take various self-assessments for characterizing their personalities and identify fitting professions; discuss various career options with a life sciences PhD; and ultimately learn to design their own path. There will be three career panels with invited guests from various career tracks, including research, teaching, administration, business, law, journalism, policy, and more. Open to life sciences PhD students in year 3 or beyond. The class will meet at Carnegie Institution for Science's seminar room building 600, located at 260 Panama St, Stanford, CA 94305 (https://dpb.carnegiescience.edu/about/contact).

Requirements

Students are expected to attend all class meetings, actively contribute to group discussions, and give a short group presentation on the final class meeting.

Schedule

April 02 — Introductions and Class Logistics, myIDP Assessment

Introduction to the structure and context of the course: we will go over requirements and expectations, complete a preliminary survey, and engage in small groups to get to know each other and discuss career opportunities in the life sciences. What are our personal and professional dreams, how do we find an overlap between the two? We will conduct the myIDP assessment in class.

Homework: Take the Myers-Briggs Type Indicator Test, to be independently completed by Tuesday, April 7th, 5 pm PST.

April 09 — Discussion of Myers-Briggs Type Indicator Test Results (guest lecture by MJ Mangiarelli of Stanford BioSci Careers)

The Myers-Briggs Type Indicator (MBTI) personality inventory is widely acknowledged as one of the most accurate and respected personality tests in psychology. It can be utilized in considering future career decisions as a practical tool for investigating work styles and work settings that are most conducive to one’s personality. We will be discovering our personality types, and how to maximize our "gifts" (our personality preferences) in order to contribute to team success--while understanding how the many facets of our complex identities affect overall career satisfaction. Stanford’s BioSci Careers (https://med.stanford.edu/bioscicareers.html) will help with evaluating the results.

Homework: Take the CliftonStrengths test by Gallup, to be independently completed by Tuesday, April 14th, 5 pm PST.

April 16 — Discussion of CliftonStrengths Test Results (guest lecture by Marlene Scherer Stern of Stanford BioSci Careers)

The CliftonStrengths test is designed to highlight the user’s character strengths, which can be used to assess what roles would be best in both utilizing and developing such strengths. We will be discovering our individual strengths and how these can contribute to success in our future careers, while understanding how they are only a part of our unique personalities. Stanford’s BioSci Careers will help with evaluating the results.

April 23 — Self-Assessment Decompression and Career Planning Lecture

Post-MBTI/CliftonStrengths test discussion in small groups to put the results in the context of career choices. There will also be a lecture on career planning, regarding key concepts and tools that are useful in professional development, with small group discussions to follow. Final Presentation projects will be assigned and expectations will be discussed.

April 30 — Career Panel I: “Business”

Panelists will be briefly introduced, then the floor will be opened up for student questions. This panel, along with the panels to follow, will serve as the perfect opportunity for lively discussion, and give students unique insight regarding career options and expectations. Carnegie will provide a reception after the panel to continue discussions and networking.

Kirk Clark	Executive Director, Novartis Institutes for BioMedical Research
Pamela Marrone	CEO and Founder, Marrone Bio Innovations
Jayaranjan Anthonypillai	Founder/CEO, Berkeley BioLabs; Co-Founder/Managing Partner, Focus Academy LLC
Mowgli Holms	Co-founder and CEO, Phylos Biosciences

May 7 — Career Panel II: “Academic Research”

Pleuni Pennings	Assistant Professor, San Francisco State University
Miriam Goodman	Professor, Molecular and Cellular Physiology, Stanford University
Jennifer Mortimer	Staff Scientist, Berkeley Lab; Director of Plant Systems Biology, JBEI
Rebecca Albright	Assistant Curator, California Academy of Sciences

May 14 — Career Panel III: “Scientific Journalism, Administration, Law, Philanthropy”

Amy Adams	Director of Long Range Vision Communications, Stanford University
James Keddie	Senior Patent Agent, Bozicevic, Field & Francis LLP
Rieko Yajima	Director for Drug Discovery Innovation, SPARK Translational Research Program, Stanford University
Milan Karol	Senior Development Officer, Carnegie Institution for Science

May 21 — Career Panels Decompression and Preparation for Final Presentations

Group discussions to follow the career panels. Students will be encouraged to share their responses to the panel, their ideas about what careers in these fields may look like, as well as their likes and dislikes about panelist responses. We will also do some brainstorming exercises called 30 circles and mind-maps, and draft a personal mission statement. Small group discussions on the draft mission statements.

May 28 — Student Final Presentations

Students will give their final presentations, followed by extensive group discussions to wrap up all that we have discovered together about ourselves, and about the career options that are available to us. We will also discuss ways to follow up from this course and additional resources that are available on and off campus. Staff from BioSci Careers will be present to provide feedback.

Notices

Disability Access

Students with disabilities necessitating accommodation and/or services in class should notify the teaching assistants and initiate a request with the Office of Accessible Education (OAE). The OAE will evaluate the request with required documentation, recommend appropriate accommodations, and prepare a verification letter dated in the current academic term in which the request is being made. Please contact the OAE as soon as possible; timely notice is needed to arrange for appropriate accommodations. The OAE is located on the first floor of the Student Services Building, between the Munger Graduate Residences and the Haas Center for Public Service, at 563 Salvatierra Walk, Stanford, CA 94305 (office hours Monday - Friday, 9 am - 5 pm). You may contact them through their website (oae.stanford.edu), email (oae-contactus@stanford.edu), or phone (650-723-1066).

Honor Code

Please visit and read the honor code from Stanford’s community standards website: https://communitystandards.stanford.edu/policies-and-guidance/honor-code. The difference between utilizing information from or taking quotes and giving proper citation to external information sources versus plagiarism should be apparent by now. These standards will be strictly upheld throughout this class.

Career Panel Participants

Career Panel I (April 30th, 2020): Business

Kirk Clark

Executive Director, Novartis Institutes for BioMedical Research

Dr. Clark received his PhD in Biochemistry at Kansas State University. After training in protein crystallography as a postdoc at The Rockefeller University, he joined the Swiss pharmaceutical company Ciba-Geigy to establish in-house protein crystallography capabilities in New Jersey. Upon the Ciba-Giegy/Sandoz merger to form the Novartis Institutes for Biomedical Research, Dr. Clark has taken on increasing responsibilities locally and globally within the company, including heading their Protein Structure “home” in Cambridge, co-chairing the Drug Prototype project sub-portfolio, and participating in both the global Chemical Biology & Therapeutics and Protein Sciences global leadership teams. He currently serves as the Director of Novartis’ Protein Sciences group.

Pamela Marrone

CEO and Founder, Marrone Bio Innovations

Dr. Marrone received her PhD in Entomology from North Carolina State University. She has built her career towards the discovery and development of environmentally-responsible bio-based products for pest management and plant health. Originally working as the group leader of Monsanto’s Insect Biology group, she branched out and started her first company, Entotech, Inc., where she screened over 50,000 microorganisms for naturally-produced insecticidal products. Dr. Marrone subsequently started another company, AgraQuest, which developed a line of naturally-derived pest management products from similarly-robust screens of microorganisms. In 2006, she left AgraQuest to found her current company, Marrone Bio Innovations (MBI). MBI has produced award-winning bio-based products for use in many agricultural markets and is additionally marketing products for invasive zebra and quagga mussel control. Dr. Marrone also serves as a board member of a number of associations and companies, such as the Association for Women in Science, the Foundation for Food and Ag Research, and the startups Pheronym and AgShift. In addition, she is a Trustee of Cornell University.

Jayaranjan (J) Anthonypillai

Founder and CEO, Berkeley BioLabs; Co-Founder and Managing Partner, Focus Academy LLC

J is a scientist and entrepreneur devoted to facilitating healthy and productive biotech startup cultures. He has a background in developing, validating, and scaling technologies, and has worked in clinical, clean-tech, biotech, and agri-tech sectors. Leveraging his experience and background in biology and lipid chemistry, he has developed novel technologies for overcoming product development, process development, and engineering challenges. Through his creations, Berkeley Biolabs and Focus Academy, he has helped seed and grow over 50 companies in the biotech sector. Berkeley Biolabs is an incubator lab while Focus Academy serves as a ‘Soft Landing’ for international biotech startups in the Bay Area. As an entrepreneur and mentor for several startups, J’s emphasis is often on product/market fit as the main driver of R&D effort and strategy.

Mowgli Holmes

Co-founder and CEO, Phylos Biosciences

Dr. Holmes earned his PhD in Microbiology and Immunology from Columbia University, and works on applying biotechnological skills towards the development of the contemporary cannabis industry. His company, Phylos Biosciences, provides genetic and sex testing services for marijuana growers, and additionally maintains an evolutionary database of different cannabis strains from thousands of varieties from over eighty countries. They also work to provide discounted services to support small-scale local growers. Holmes is the founding board member of the Cannabis Safety Institute and the Open Cannabis Project, and serves as Chair of the Oregon State Cannabis Research Task Force.

Career Panel II (May 7th, 2020): Academia

Pleuni Pennings

Assistant Professor, San Francisco State University

Dr. Pennings received her PhD in Evolutionary Biology at the University of Munich in Germany. Throughout her time in academia, she has engaged in a plethora of projects across the scales of life, from work on ant population genetics, to her current work as an Assistant Professor at SFSU studying the evolution of Human Immunodeficiency Virus drug resistance. In addition to research, she has devoted herself to science education, starting her own consulting agency to promote science communication and education in Amsterdam, and coordinating the Munich Graduate Program for Evolution, Ecology, and Systematics.

Miriam Goodman

Professor, Molecular and Cellular Physiology, Stanford University

Dr. Goodman earned a PhD from the University of Chicago in Neurobiology. Her academic career has revolved around elucidating the biological mechanisms of sensation, from her dissertation research on the ion channels necessary for hearing, to the analysis of ion channel biophysics and touch sensing as a postdoctoral fellow at Columbia University. Currently, her work at the Stanford University School of Medicine includes using C. elegans as a model to better understand touch and pain sensation, and the mechanisms in which sensory neurons are protected from damage.

Jennifer Mortimer

Staff Scientist, Berkeley Lab and Director of Plant Systems Biology, JBEI

Dr. Mortimer received her PhD in Plant Science from the University of Cambridge, as well as a Masters of Research in Bioinformatics from the University of Exeter. After attaining her degrees, she worked as a Research Associate for several years, studying a number of topics regarding Arabidopsis physiology. Her research has focused on the synthesis, transport, and use of polysaccharides for plant cell wall formation and engineering. Currently she heads a lab that utilizes numerous different model plants to investigate these questions, and serves as Director of Plant Systems Biology at the Joint BioEnergy Institute (JBEI) at the Lawrence Berkeley National Lab, where she investigates how to make biofuels and biochemicals from plant biomass.

Rebecca Albright

Assistant Curator, California Academy of Sciences

Dr. Albright got her PhD from the University of Miami in Marine Biology and Fisheries. Her work has been devoted to in-depth research on the impacts of environmental changes upon coral reef ecosystem health. She has worked as a postdoc at both the Australian Institute of Marine Science and the Carnegie Institution for Science’s Global Ecology Department, studying coral reef biogeochemistry and carbonate chemistry, as well as the effects of ocean acidification upon these processes. Currently as a curator at the California Academy of Sciences in San Francisco, Dr. Albright works on creating a coral culturing facility.

Career Panel III (May 14th, 2020): Scientific Journalism, Administration, Law, Philanthropy

Amy Adams

Director of Long Range Vision Communications, Stanford University

Adams received her MS from Cornell University in genetics and development, as well as a certification from UC Santa Cruz in science communications. Her experiences with news and feature writing regarding a range of scientific topics include freelance writing and editing for a number of notable publications and websites, such as Science, Natural History, and CBSHealthWatch.com; science writing for the Stanford University School of Medicine; communications manager for the California Institute for Regenerative Medicine; and finally back to Stanford, where she has worked as the Director of Science Communications and currently serves as Director of Long Range Vision Communications.

James Keddie

Senior Patent Agent, Bozicevic, Field & Francis LLP

Dr. Keddie received his PhD in Plant Molecular Biology from the John Innes Institute in Norwich, UK. Though he began his post-doctoral career as a fellow in several plant biology labs, including the Carnegie Institution for Science’s Plant Biology Department, studying a range of topics from plant disease resistance to development to gene expression, he began work with intellectual property as a Senior Scientist and IP Manager at Mendel Biotechnology, Inc. Dr. Keddie currently serves as a Senior Patent Agent at Bozicevic, Field & Francis LLP, where his expertise in all aspects of patent prosecution are used to provide biotech-focused clients with patent drafting and prosecution services.

Rieko Yajima

Director for Drug Discovery Innovation, SPARK Translational Research Program, Stanford University

Dr. Yajima received her PhD in Chemical Biology from Penn State University. Her interests lie at the intersections of science, policy, and design. Dr. Yajima’s postdoctoral work as a Science & Design Research Scholar at Stanford University’s Center for Design Research investigated how design practices can catalyze scientific research and innovation; additionally, she has been an Associate Program Director at the American Association for the Advancement of Science in Washington, DC, and served as a science policy fellow at the National Academy of Sciences. She currently works on human-centered drug discovery research and translational medicine as a Director at Stanford’s SPARK Translational Research Program while also serving as a member of the Global Young Academy, an organization for young scientists to lead intersectional dialogue to diversify global decision-making.

Milan Karol

Senior Development Officer, Carnegie Institution for Science

Mr. Karol received an MS in Library and Information Science from the University of Illinois at Urbana-Champaign. Throughout his career, he has become an experienced development officer and fundraiser in various environments, from working as a Sales Representative for a company in the software industry, to working as a Development Officer at two liberal arts colleges, to raising philanthropic dollars for medical research at Johns Hopkins Medicine. Currently, he is the Senior Development Officer for the Carnegie Institution for Science, building relationships and working with donors and philanthropists to achieve institutional goals.

2019

Career Exploration and Planning

Stanford University

Spring 2019: BIO380

Description: Thinking about and planning for life beyond graduate school is one of the most anxiety-provoking activities students face. In this course, students will share their personal stories and dilemmas about career decisions, discuss various career options with a PhD in life sciences, and learn to design their own path. There will be three career panels with invited guests from various career tracks, including research, teaching, administration, business, law, journalism, policy, and more. Open to PhD students in Biosciences programs. The class will meet at Carnegie Institution for Science's seminar room building 600, located at 260 Panama St, Stanford, CA 94305.

Requirements: Students are expected to attend all class meetings, actively contribute to group discussions, and to give a short group presentation on the final class meeting.

Schedule

April 4 — Introductions

Introduction to the structure and context of the course, as well as an excellent opportunity for participants to get to know one another. We will go over requirements and expectations of the course, complete a preliminary survey, and engage in small group activities discussing career opportunities in the life sciences, personal/professional dreams, and how to find an overlap between the two.

April 11 — Myers-Briggs Type Indicator Test

The Myers-Briggs Type Indicator (MBTI) personality inventory is widely acknowledged as one of the most accurate and respected personality tests in psychology. It can be utilized in considering future career decisions as a practical tool for investigating work styles and work settings that are most conducive to one’s personality. We will be discovering our personality types, and how to maximize our "gifts" (our personality preferences) in order to contribute to team success--while understanding how the many facets of our complex identities affect overall career satisfaction. Staff from Stanford’s BioSci Careers (https://med.stanford.edu/bioscicareers.html) will help with evaluating the results.

April 18 — Career Panel I: “Policy, Administration, and Scientific Journalism”

Policy: Mary Maxon, Ph.D. Associate Laboratory Director, Biosciences Labs at UC Berkeley
Govt Program Management: Devaki Bhaya, Ph.D. Adjunct Staff Scientist, Carnegie Institute for Science, Department of Plant Biology
Science Writing: Amy Adams, M.S. Director of Science Communications, Stanford University
Academic Administration: Rieko Yajima, Ph.D. Director for Drug Discovery Innovation, SPARK Translational Research Program, Stanford University

April 25 — Career Panel I Decompression

Group discussions to follow the “Policy, Administration, and Scientific Journalism” panel. Students will be encouraged to share their responses to the panel, their ideas about what careers in these fields may look like, as well as their likes and dislikes about panelist responses.

May 2 — Introduction to Final Presentations/Career Planning Lecture

Final Presentation projects will be assigned and expectations will be discussed. In addition, there will be a lecture on career planning to introduce students to key concepts and tools that are useful in professional development, with group discussions to follow.

May 9 — Career Panel II: “Business”

Venture Capital: James Zhang, Ph.D. Chief Strategy Officer, Centrillion Technologies Inc., and Partner, GRC Fund
Patent Law: James Keddie, Ph.D. Senior Patent Agent, Bozicevic, Field & Francis LLP
Industry: Lee Chae, Ph.D. Co-Founder and CTO, Brightseed
Entrepreneurship: Fred Hempel, Ph.D. Co-Owner of Baia Nicchia Farm and Artisan Seeds
Industry administration: Malavika Kannuswamy, M.S. Associate Director, Portfolio Planning and Program Management, Denali Therapeutics

May 16 — Career Panel III: “Research”

Academic Research: Ashby Morisson, Ph.D. Associate Professor of Biology, Stanford University
NGO Research: Rebecca Shaw, Ph.D. Senior Vice President and Chief Scientist, World Wildlife Fund
Government Research: John Vogel, Ph.D. Staff Scientist, Joint Genome Institute, and Adjunct Professor, UC Berkeley Department of Plant and Microbial Biology
Teaching: Jesse Miller, Ph.D. Lecturer, Stanford University

May 23 — Career Panels II & III Decompression

Group discussions to follow the “Business” and “Research” panels. Students will be encouraged to share their responses to the panel, their ideas about what careers in these fields may look like, as well as their likes and dislikes about panelist responses.

May 30 — Student Final Presentations

Notices

Disability Access: Students with disabilities necessitating accommodation and/or services in class should notify the teaching assistants and initiate a request with the Office of Accessible Education (OAE). The OAE will evaluate the request with required documentation, recommend appropriate accommodations, and prepare a verification letter dated in the current academic term in which the request is being made. Please contact the OAE as soon as possible; timely notice is needed to arrange for appropriate accommodations. The OAE is located on the first floor of the Student Services Building, between the Munger Graduate Residences and the Haas Center for Public Service, at 563 Salvatierra Walk, Stanford, CA 94305 (office hours Monday - Friday, 9 am - 5 pm). You may contact them through their website (oae.stanford.edu), email (oae-contactus@stanford.edu), or phone (650-723-1066).

Honor Code: Please visit and read the honor code from Stanford’s community standards website: https://communitystandards.stanford.edu/policies-and-guidance/honor-code. The difference between utilizing information from or taking quotes and giving proper citation to external information sources versus plagiarism should be apparent by now. These standards will be strictly upheld throughout this class.

Scientific Writing Workshop

Carnegie Institution for Science, Department of Plant Biology

Summer 2019

Carnegie Scientific Writing Workshop Syllabus

Overview: To become a successful scientist, we must write well and effectively communicate our work to a broad audience. Nevertheless, many of us do not receive official training on the fundamentals of scientific writing, and as a result struggle to highlight the significance of our work. This summer, we are offering an intensive scientific writing workshop to help you set up a writing routine, improve your writing, and gain the tools and confidence you need to become a leader in your field. * In-class exercises and lessons will be adapted from Anne E.Greene’s book titled Writing Science in Plain English.

Schedule and Location: The Carnegie scientific writing workshop is a 10-week series starting June 28th, 2019. Meetings will be held in the Carnegie Institution for Science’s Plant Biology Department Seminar Room (260 Panama Street, Stanford, CA, Building 600) on Fridays from 3-5pm.

Topics:

Week 1 (6/28): Introduction to creating a compelling narrative

Discuss the overview, goals and expectations of the writing workshop
Form scientific writing groups based off of writing experience and document type
Setup electronic folders for submitting writing material
Discuss how to tell your scientific story
- Identifying your audience
- Informal vs. formal register
- Determining your tone
- Defining subjects and action verbs
- Using active vs. passive voice
- Benefits of short vs. long words
- Simplifying noun strings
- Defining technical terms
- Concise writing
- Using transition statements
- Affirmative vs. negative statements
In-class writing exercises

Homework for next class: Create a scientific storyboard

Week 2 (7/12): Workshop Scientific Storyboard

Present scientific storyboards in writing groups
Discuss Background and Significance
- Identifying the scope and structure
- Incorporating new vs. old information
- Highlighting deficiencies in current knowledge and understanding
- Justifying your project
- Using parallel writing structures
In-class exercises

Homework for next class: write up a draft of your background and significance section

Week 3 (7/19): Workshop Background and Significance Sections

Review the Background and Significance section for two people in each writing group
Discuss designing paragraphs
- Identifying the issue
- Development phase
- Conclusion sentences
- Coming to the point
In-class exercises

Week 4 (7/26): Workshop remaining Background and Significance Sections

Review the Background and Significance section for remaining people in each writing group
Discuss different ways to arrange paragraphs
- Chronological order
- Broad ideas to narrow ideas
- Least important to integral information
- Problem to solution
- Compare and contrast
- Transition statements associated with different paragraph styles
In-class exercises

Homework for next class: write up a draft of your Results and Approach

Week 5 (8/9) Workshop Results and Approach

Review the results and approach section for two people in each writing group
Discuss useful tips for making figures and figure legends
- Identify your message
- Writing strong captions
- Writing stand alone text
- Data visualization
In-class exercise

Week 6 (8/16): Discuss Authorship, Publishing, and Reviewing/ Wine tasting

Using a few case scenarios, we will discuss topics relevant for publication

Discuss available authorship guidelines from journals and scientific societies
Discuss the process of publishing and reviewing

Week 7 (8/23): Workshop remaining Results and Approach

Review the results and approach section for remaining people in each writing group
Discuss how to organize a discussion and impact

Homework for next class: write up a draft of your discussion and impact

Week 8 (8/30): Workshop Discussion and Impact sections

Review the discussion and impact section for all people in each writing group
Discuss how to write an abstract

Homework for next class: write an abstract

Week 9 (9/6): Workshop Abstract sections

Review the abstract sections of all writing group members.
Introduce how to write a cover letter

Homework for next class: write a cover letter

Week 10 (9/13): Workshop three Cover letter sections/ Review a manuscript

Review the cover letters for all members in the writing group
Discuss how to review a manuscript

Calendar

Websites

Search form

Senior Staff Scientist

Profile

2020

Fundamentals and Frontiers in Plant Biology

Career Exploration and Planning

2019

Career Exploration and Planning

Scientific Writing Workshop

Carnegie Scientific Writing Workshop Syllabus

Week 1 (6/28): Introduction to creating a compelling narrative

Week 2 (7/12): Workshop Scientific Storyboard

Week 3 (7/19): Workshop Background and Significance Sections

Week 4 (7/26): Workshop remaining Background and Significance Sections

Week 5 (8/9) Workshop Results and Approach

Week 6 (8/16): Discuss Authorship, Publishing, and Reviewing/ Wine tasting

Week 7 (8/23): Workshop remaining Results and Approach

Week 8 (8/30): Workshop Discussion and Impact sections

Week 9 (9/6): Workshop Abstract sections

Week 10 (9/13): Workshop three Cover letter sections/ Review a manuscript