Whitehead lab personnel
Andrew Whitehead is the lab PI, and a Professor in the Department of Environmental Toxicology. Dr. Whitehead earned his B.Sc. from the University of Guelph in Ontario, Canada, and his Ph.D. from the University of California at Davis (with Dr. Susan Anderson at Bodega Marine Lab). He then went on to do post-doctoral research at the University of Miami Rosenstiel School of Marine and Atmospheric Science (with Dr. Douglas Crawford) , and was an Assistant then Associate Professor in the Department of Biological Sciences at LSU before moving to UC Davis in summer 2012. Research interests include evolutionary and ecological functional genomics, population genomics, conservation genetics, stress physiology, and ecotoxicology. He is a member of the Population Biology Graduate Group, the Graduate Group in Ecology (Chair of the Ecological Genomics and Genetics AOE), the Integrative Genetics and Genomics Graduate Group, and the Pharmacology and Toxicology Graduate Group. He is a member of the UC Davis Center for Population Biology, and the Coastal and Marine Sciences Institute. Email: firstname.lastname@example.org
Jen Roach is a Research Associate and Lab Manager of the Whitehead lab. Jen earned her B. Sc. from University of California Davis and her M.Sc. from Colorado State University where she studied the genetic structure of black-tailed prairie dog metapopulations (with Dr. Mike Antolin and Dr. Bea Van Horne). She went on to work as a research associate and lab manager with Dr. Bernie May at UC Davis and then with Dr. Douglas Crawford at the University of Miami’s Rosenstiel School of Marine and Atmospheric Science. She has been working for Dr. Whitehead since August 2005. Her research interests include conservation genetics, population genetics, and evolutionary and ecological functional genomics. Email: email@example.com.
Joanna Griffiths (personal website) is a postdoctoral researcher (co-advised by Dr. Nann Fangue). Before joining the lab, she received her PhD at Louisiana State University with Dr. Morgan Kelly. During her PhD, Joanna worked on three species of marine invertebrates (corals, oysters, and copepods) to determine their evolutionary responses to climate change. At UC Davis, she is using quantitative genetics and physiology to explore the mechanistic basis of variation in thermal tolerance of hatchery-reared and wild Delta smelt, a critically endangered fish. Email: firstname.lastname@example.org.
Kaho Tisthammer (personal website) is a post-doctoral researcher, investigating population genomics of Pacific herring at the Whitehead Lab. She earned her Ph.D. in Marine Biology from the University of Hawaii at Manoa with Dr. Robert Richmond, researching local adaptation of reef-building corals using genomics and proteomics. She joined the CoDE Lab of Dr. Pleuni Pennings at San Francisco State University (SFSU) as a postdoc, working on evolutionary and computational genomics of disease viruses. She has taught marine ecology and bioinformatics classes and has been involved in promoting diversity, equity and inclusion in coding and STEM education at SFSU. Her passion is coral reefs and marine conservation and she loves marine organisms! Email: email@example.com.
Tony Gill (personal website) is a Ph.D. student in Integrative Genetics and Genomics Graduate Group. He received his B.A. from Purdue University and an M.S. in Science-Medical Writing from Johns Hopkins University, Krieger School of Arts and Sciences. He spent seven years as a molecular biologist generating transgenic zebrafish models to study mutations in leukemia in Dr. Peter Aplan’s laboratory at the National Cancer Institute in Bethesda Maryland. He went on to work as a laboratory manager for Dr. Adam Leaché at the University of Washington in the development of sequencing technologies for comparative genomics. Before joining the Whitehead lab in 2017, Tony came from the Northwest Fisheries Science Center in Seattle where he was introduced to environmental toxicology under the mentorship of Dr. John Incardona and Dr. Nathanial Sholtz. He is broadly interested in applying evolutionary functional genomics to questions in ecotoxicology. For his dissertation work Tony is integrating comparative genomics and physiology to determine the genetic mechanisms underlying the collapse and lack of recovery of Prince William Sound herring. Email: firstname.lastname@example.org Twitter: @tonygill3.
Nicole McNabb (personal website) is a Ph.D. student in the Pharmacology and Toxicology Graduate Group. She earned her B.Sc. in Biology from Maryville College and M.Sc. in Marine Biology from the College of Charleston, where she investigated the potential estrogenic activity and effects of the oil dispersant Corexit 9500 on sex determination in the American alligator and diamondback terrapin (with Dr. Satomi Kohno and Dr. Louis J. Guillette, Jr.). Nicole then went on to work as a contract research associate with Dr. Shaun McCullough at the U.S. EPA Clinical Research Branch in Chapel Hill, NC, where she was involved in the development of an organotypic model to assess response to inhaled toxicants in the airway. Broadly, she is interested in using genomics tools and approaches to answer questions about how populations will respond to anthropogenic environmental contaminants, as well as the interconnection between human and environmental health. Nicole’s current research focuses on the multigenerational impacts of dietary exposure to the flame retardant, BDE-99, in Atlantic killifish (Fundulus heteroclitus). Email: email@example.com.
Anthony (Tony) Tercero (personal website) is a PhD student in the Integrative Genetics and Genomics Graduate Group and co-advised by Dr. Anne Todgham. He earned his B.S and M.S from Sonoma State University where he studied the genetic underpinnings of the altered heat shock response in Antarctic fish. Anthony’s broad research interests seek to understand mechanisms that facilitate phenotypic variation and adaptation of marine taxa in response to natural and anthropogenic stress. More specifically, Anthony wants to understand the capacity marine organisms have for epigenetic and genetic alterations and the interplay between those mechanisms under current and future environmental conditions. These insights can be applied to aquaculture, biomonitoring, biological invasions, and conservation, and hopefully improve our ability to detect, explain, and predict responses of marine taxa to global change. Email: firstname.lastname@example.org.
Ashley De La Torre is an undergraduate student majoring in Environmental Toxicology (emphasis in Aquatic Toxicology) with a minor in Oceanography. She grew up in the San Francisco Bay area and transferred from Los Medanos Community College in spring of 2020. Her interests are related to aquatic organisms and their response to environmental stressors induced by anthropogenic activities. Ashley’s interests stemmed from her fascination with coral bleaching from climate change. Additionally, she is interested in the developmental effects in aquatic organisms when they are exposed to pollution. Ashley is interested in understanding how adaptations can evolve in response to pollution and climate change, and seeks to have as much exposure to research involving these topics. In her free time she enjoys collecting and caring for her plants, hiking, and camping. Email: email@example.com.
- Dr. Joe McGirr (personal website) was a Postdoctoral Researcher in the Whitehead lab from 2020 to 2021.
- Dr. Matt Osmond (personal website) was a Postdoctoral Fellow (Co-advised with Dr. Graham Coop and Dr. Sebastian Schreiber) at the UC Davis Center for Population Biology. Matt moved from UC Davis in 2021 to start a faculty position at the University of Toronto.
- Dr. Jane Park (Linkedin site) was a PhD student in the Integrative Genetics and Genomics Graduate Group. Jane graduated in September 2020.
- Dr. Sara Boles (personal website) was a Ph.D. student in the Pharmacology and Toxicology Graduate Group. Sara graduated in September 2020.
- Haley Hudson (Undergraduate researcher, UC Davis, graduated 2020). Linkedin.
- Picasso Vasquez (Undergraduate researcher, UC Davis, graduated 2020). Linkedin.
- Dr. Lisa Johnson (personal website) was a Ph.D. student in the Molecular, Cellular, and Integrative Physiology graduate group and was co-advised by Dr. C. Titus Brown in the Lab for Data Intensive Biology. Lisa graduated in October 2019.
- Natasha Mariano (Undergraduate researcher, UC Davis, graduated 2019). Linkedin.
- Dr. Elias Oziolor (Personal Website) was a Postdoctoral Research Associate in the Whitehead lab from 2017 to 2019.
- Dr. Jeffrey Miller (personal website) was a Ph.D. student in the Pharmacology and Toxicology Graduate Group, and graduated in December 2018.
- Dr. Marisa Trego (personal website) was a Ph.D. student in the Joint Doctoral Program in Ecology (Rebecca Lewison primary advisor), and graduated in 2018.
- Dr. Reid Brennan (personal website) was a Ph.D. student in the Graduate Group in Ecology. and completed his Ph.D. in August 2017.
- Van La (Undergraduate researcher, UC Davis, graduated 2017). Linkedin.
- Dr. Yun-wei Dong (personal website) was a Visiting Researcher in the Whitehead lab from 2016 to 2017.
- Dr. Noah Reid (personal website) was a Postdoctoral Research Associate in the Whitehead lab from 2014 to 2016.
- Michelle Tse (Undergraduate researcher, UC Davis, graduated 2016). Linkedin.
- Ruth Hwang (Undergraduate researcher, UC Davis, graduated 2015). Linkedin.
- Dr. Eve McCulloch (Ph.D., LSU, 2012). Eve is currently faculty at Kansas State University.
- Whitney Pilcher (M.Sc., LSU, 2012). Linkedin.
Letter to Prospective Students
Dear Prospective Student,
Thank you for your interest in our lab. I would like to discuss our mutual interests more personally, but first I thought I’d show my hand a bit so you could see whether this particular game is for you. I am excited about integrating functional genomics and physiology to understand the evolution and ecological distributions of organisms in nature. I am interested in basic science questions, such as “how does genome regulation enable physiological resilience/plasticity in stressful environment, and how do genomes and genome regulation evolve in different species and habitats?” At the applied science end of things I am interested in using genomics tools to diagnose environmental problems. If these topics spin your propeller as well, then we’re off to a great start!
What are you interested in? Are you genuinely interested in evolutionary and ecological physiology and genomics? Genome-scale tools are revolutionizing the biological sciences, and it is a very exciting time to be training as a biologist. However, application of these tools is demanding of practitioners, requiring sophisticated statistics and computational skills, mastery of a diverse and specialized literature, as well as the creativity and drive to come up with cool ideas, clever experiments, and in-depth data analyses. If this excites you, then we are making progress here.
Why do you want a graduate degree? Employment in the basic sciences, particularly at research universities, is highly competitive. Fewer than half of new Ph.D.’s obtain academic positions of the sort for which universities have traditionally trained graduate students. On the other hand, opportunities for biologists outside of traditional academia (in government, industry, NGOs, and the like) are growing. So you have to ask yourself: What sort of position, specifically, do I ultimately want, and what skills must I acquire to excel at that position? Your thoughts about this are likely to evolve while in grad school, as mine did, and I can help you with this, but it is good to have formulated a long vision before making a commitment to grad school.
Now I’ll answer a few questions for you.
What would I expect of you? Graduate education is fundamentally about becoming an independent scientist. This means knowing the background in your field (and as much as possible in related fields), being aware of emerging ideas and approaches, generating interesting yet answerable questions about how life works, and sharing your findings with the larger scientific community. You also must know how to make convincing arguments to funding agencies to provide the financial support for these activities. Similarly, you must also be able to convince your Aunt Ruth at the Thanksgiving dinner table that what you are doing is worthwhile – science in this country is, after all, a socialized endeavor, so we are ultimately answerable to the taxpayer, the general public. All of these things require self-motivation and organization.
To succeed, then, I would expect you to read broadly in the current literature, attend (and present at) scientific meetings and departmental seminars, and devote yourself to learning the analyses and laboratory techniques that are the tools of this trade. You should also develop a broad knowledge of the ecology, physiology, and evolutionary history of the organisms that you would be working on. Most importantly, I will expect you to hone your oral and written communications skills. You get professional credit for having mastered these skills by writing successful proposals and publishing papers in high-quality journals, so I would expect you to pursue these ends soon and often. Finally, the operative unit of selection here is neither just you nor just me, but the lab as a whole, so I will expect you to contribute to cultivating positive lab mojo.
I am flexible in my mentoring style, but beginning students are usually assigned to an existing project for the first year or two. This for two reasons: 1) to serve as a training device for new students, and 2) to aid in fulfilling ongoing grant obligations. But from Day 1 I expect new students to be forming their own research ideas, so that in later years, they can contribute in unique ways to research in the lab, and to the science in general. Students may choose to stay working on the project to which they were assigned. If so, then I expect them to contribute new and novel ideas and approaches. Alternatively, students may create and choose projects that are outside of the specific objectives of a grant, but still within the spirit and scientific scope of that funded project. Alternatively, students may design and choose a project that is outside the scope of funded projects, in which case they are expected to have secured their own funding.
What can I offer you? I have broad interests and experiences in applying genetic and genomic techniques to examine how closely related organisms evolve in different environments, and how they respond differently to variable stressors in those environments. Complementary interests include ecotoxicology and conservation genetics. I wear many hats, and I strongly encourage truly interdisciplinary training of my students. It is important to me to train outstanding biologists, and I will make the time needed to offer you all I can to make you the best independent scientist you can be. Finally, the biggest thing I can offer you is freedom. If we have common interests, then you will be able to formulate your own questions and approaches. I impose few limitations on projects though I strongly emphasize the integration of ecological, evolutionary, physiological, and genomic approaches and perspectives to the questions you address.
What can UC Davis offer you? The UC Davis graduate programs in Ecology and Environmental Sciences consistently rank among the top in the world, and the University regularly attracts top scientists from around the world to present seminars. Your exposure to cutting-edge science here would be hard to beat. I am a member of the Population Biology Graduate Group, the Graduate Group in Ecology which has many areas of emphasis including Ecological Genomics, Physiological Ecology, Marine Ecology, and Ecotoxicology, and a member of the Pharmacology and Toxicology Graduate Group, the Integrative Genetics and Genomics Graduate Group, the Center for Population Biology, and the Coastal and Marine Sciences Institute. I have students from different groups, and all groups offer outstanding training where you have access to a diverse group of world-class biology faculty. The department-independent structure of the UC Davis graduate programs facilitates cross-disciplinary interactions. This is good for students since you can organize a very diverse and robust dissertation committee, and you can choose from a wide variety of excellent courses to firm up your training in a diversity of specialties. We have excellent infrastructure for genetics and genomics research, which in addition to equipment in our lab includes access to the world-class UC Davis Genome Center.
Are we a good fit? Between this letter and the rest of the webpage, you probably have some idea of what working here would be like. But impressions in written words are never the same as back-and-forth interactions. So if you’re still interested, and believe you would be a strong candidate, please contact me. When you do, please include your CV and information about your experiences and interests (questions, animals, techniques). Furthermore, you should feel free to contact current students and staff to ask questions about life in the lab
Once again, thanks for your interest and all the best in your future endeavors!
Whitehead Mentorship Philosophy
Updated: May 2022
[NOTE: please feel free to use/modify these materials for your own purposes, with attribution]
My job as a research group leader requires accountability to two primary groups: 1) the individual trainees, staff, and collaborators that constitute our research group, and 2) the agencies that fund our research programs which often includes the broader general public because they ultimately fund our research through their tax dollars. Accordingly, the research and training activities that we pursue, and how we go about pursuing them, should be aligned toward fulfilling our twin goals of A) producing relevant, valuable, rigorous, reproducible, and cutting-edge research, and B) uplifting our laboratory personnel to support our research visions and career goals, to enrich our lives and the lives of those around us, and to build, refine, and live our values.
I recognize that every individual is different – we come from diverse backgrounds and have been shaped by different experiences, and desire different career paths. Also, those envisioned career paths are likely to change during your tenure in our group. As such, I seek to be flexible and nimble in my approach to mentorship, but my approach to each mentee will be grounded by some broader guiding principles and fundamental goals. My goals as a mentor are to support the development of mentees toward being scientific leaders who are positioned to pursue research careers of their choice in academia, government, or the private sector. Graduate training has multiple dimensions, which include 1) development as an independent research science leader, 2) development as a communicator of science, 3) development as an educator, and 4) relationship and network building. My mentoring philosophy is organized around supporting these four dimensions.
- Development as an independent research scientist. My role is to provide research opportunities, and to transfer knowledge and skills to the mentee. I am therefore responsible for securing research funding and related resources, working with the mentee to formulate compelling and testable hypotheses, working with the mentee toward building strategic, meaningful, fruitful, and durable partnerships and collaborations, to help design contrasts and experiments, to act as a guide through data analysis, to act as a partner in data interpretation, and to guide the construction and editing of conference posters, conference talks, and publishable peer-reviewed manuscripts. I also work with mentees to construct strategies for building the foundation of knowledge that supports cutting-edge research, such as designing a curriculum of study including courses, reading lists, workshops, and conference attendance.
- Development as a communicator of science. Our research findings have no value unless they are converted into forms that are accessible and understandable to diverse interest groups. These interest groups could include fellow research specialists, the local Girl Scout Troop, and your Aunt Dorothy. Communication of scientific ideas and discoveries requires writing skills and presentation skills at both the front end of the scientific enterprise (securing research funding for your ideas) and at the back end (reporting your research findings). Core writing and presentation skills are crucial for Ph.D. scientists no matter their future career – whether in academia, industry, or the private sector – such that these skills are a crucial component of every mentee’s training. I therefore strongly encourage mentees to apply for research funding throughout their tenure in my group, and guide them through these activities. Repeated exercises build crucial skills, and results in text that can be recycled and modified for other funding applications, thesis proposals, and manuscripts. When funding is awarded this enhances a growing CV, and it provides the research group with extra resources that expand the scientific enterprise. Everyone wins. I also work with mentees to build opportunities for outreach to non-specialist communities, and build communication skills that are appropriate for those audiences. These might include environmental managers and regulators, school groups, and the general public. This outreach is important for building a more scientifically literate society, which is a core mission of the academic enterprise.
- Development as an educator. Ph.D. scientists should be skilled educators. Most of us think of education in the traditional classroom setting. But no matter their career choice, Ph.D. scientists are responsible for transferring knowledge and skills to their students and trainees. Training and experience in the classroom and in small-group or one-on-one mentorship contexts are therefore important components of Ph.D. training. I help mentees to find TA-ships to support classroom training and to periodically supplement their income. I also seek to provide mentorship opportunities where Ph.D. students, postdocs, and visiting scholars can mentor each other and more junior trainees (e.g., undergraduate or high school students).
- Relationship and network building. The scientific enterprise requires teamwork and collaboration. Building effective teams and durable and fruitful collaborations requires skill and effort. It requires that all parties respect each other, it requires strong communication skills and effective behaviors, and it requires bravery, transparency, and accountability. Mindful of these multiple dimensions, we start by building a strong professional relationship with each other, and extend that out to our research group and collaborators. As the career objectives of the mentee start to mature and take shape, I will help to provide opportunities for expanding the mentee’s professional network beyond our immediate group, and thereby help to lay the foundation for the next steps in their career.
I aspire towards excellence in mentoring, while acknowledging to myself that this is a learning process for me and for those in my group. I seek to guide trainees toward a meaningful understanding of their own strengths and challenges, and to recommend activities that serve to amplify strengths, and transform challenges to mastery. Sometimes it will feel to trainees that everything is a challenge, and it is often difficult to receive feedback (especially critical feedback) in a positive way and then to pivot toward actions that enable positive progress, while avoiding slipping into bitterness or harmful self-criticism. Trainees should expect to be on the receiving end of a lot of critical feedback during their academic training. They should also expect to fail – at experiments, at winning fellowships, at mastering concepts and skills. But the biggest strides toward personal and scientific growth are achieved through how we respond to challenges and failures. For this to work as it must, effective communication between mentor and mentee is essential. For both of us, this requires honesty, kindness, mindfulness, bravery, integrity, maturity, and emotional resilience. By the time that mentees move on from our research group, my goal is for them to have achieved a mature scientific vision, constructed a sophisticated intellectual and technical toolkit, and formed a foundation of relationships and networks that enable the next desired step in their career.
Expectations for Trainees/Mentees and for Myself (Whitehead) as Mentor
Updated: May 2022
[NOTE: please feel free to use/modify these materials for your own purposes, with attribution]
Academic success requires a fulfilling, effective, and productive relationship between mentor and mentee. An effective mentor-mentee relationship contributes to building experience, skills, and accomplishments in research, teaching, and communication (writing and oral), and to building relationships and professional networks, and to building professional development skills (writing, speaking, interviewing, job applications, negotiation, media relations, work-life balance, etc.). The quality of this relationship can be tightly correlated with the quality of your academic experience. For this relationship to work as it should requires alignment of expectations, which itself requires effective communication. Expectations should be discussed and aligned at the beginning of your tenure. And since expectations will change through time, they should be regularly discussed and updated throughout your tenure.
Expectations for myself (PI Whitehead) as a mentor:
- I take the training and professional development of mentees (undergraduate students, graduate students, postdoctoral scholars, and staff scientists) very seriously, and try my best to equip trainees with the experience, skills, and relationships that are important for the next steps in their careers, and to guide them into and through research projects that are of mutual interest and that contribute in meaningful ways to the broader scientific enterprise.
- In administering our research program, I have an obligation to ensure that the science that emerges from our group is relevant, rigorous, well-communicated, and transparent, and that research resources and dollars are well spent.
- I am ultimately responsible for securing research funding, accounting, scientific oversight, oversight of research animal welfare, and training and oversight of personnel.
- I try to be available to discuss personnel and scientific issues at most times of the day.
- I am usually the senior author (and corresponding author) on publications that emerge from projects led by my trainees, and that are funded by my group. There are sometimes exceptions to this, for example for projects that are entirely the work of trainees, though this is rare.
- I seek to foster and encourage an atmosphere of exploration, learning, productivity, and good communication, and a positive, motivating, safe, and respectful work environment.
- I must approve all conference abstracts, posters, or presentations, and all manuscripts, or any other product, that is a representation of the research that comes from the lab.
- I seek to offer timely, conscientious, and constructive feedback on abstracts, posters, presentations, and manuscripts.
- I try to always be available to talk about, and comment on, student and post-doc research ideas and grant applications.
- I will be timely in writing letters of recommendation, especially when I am given sufficient notice.
- We sometimes use live animals in our research, and I consider it a solemn duty to ensure that animals are used judiciously, and treated ethically.
- I strive to uphold the values of our group, and uphold the highest principles of ethical behavior and research integrity.
- I strive to achieve work-life balance, though this is often elusive, and what that means shifts over time. I have interests outside of academia, I am not a happy or effective person when those interests are neglected, and I will sometimes be hard to reach when engaged in those activities.
Expectations for mentees:
- Conscientiously strive to uphold the values of our group, and uphold the highest principles of ethical behavior and research integrity.
- If your project involves live animals, then you are responsible for those animals, even if others are assigned day-to-day care. Animal care is a solemn duty. I expect trainees to respect the lives of their research animals, to ensure that animals are used judiciously, and that they are treated ethically.
- Strive to be a good colleague, and a good group citizen. I expect you to cultivate strong professional relationships with your lab colleagues, and with others in your program. These relationships should be supportive and not competitive. Indeed, many of the friendships that you make during your time here will extend far beyond your tenure here. Just as you seek guidance from your colleagues especially early in your tenure, you should also strive to be generous with guidance and advice later in your tenure.
- Be responsible for your own schedule, but expect to work the absolute minimum of a 40-hour work week (usually more). Sometimes off-hours participation (e.g., evenings, weekends) will be necessary (e.g., depending on the needs of experiments, animal care, or other deadlines). I expect trainees to learn and practice effective time-management and task-prioritization skills. In fact, these are critically important skills that gain in importance as you progress, and will serve you well throughout your career. I am happy to help with this.
- Strive to be flexible and periodically willing and available to work outside of your typical personal schedule, for example to help your colleagues, or during emergencies, time-sensitive experiments, or in the face of looming deadlines. Sometimes our research animals dictate the hours that we work, because of inherent features of their biology (breeding schedule, circadian rhythms, etc.).
- Our laboratory group is committed to open and transparent science. That means that trainees must be committed to maintaining detailed and thorough notes of research (wet lab, computational) activities. For computational work you should maintain a digital notebook, and organize project-specific workflows in a GitHub repository. Raw data must be backed up, and sequence data should be uploaded to public repositories soon after receipt. Intermediate data files (e.g. VCF files, read count files) should accompany manuscripts, and be made available as published supplemental materials or in public repositories that assign a doi. All materials needed to reproduce the work must be retained and organized. All trainees must be committed to regular backing-up of their work, and ensure durable backing up of raw and intermediate data (e.g., on the cloud and on external hard drives).
- I expect everyone to be present and actively engage in laboratory group functions (e.g., lab meetings, and laboratory personnel recruitment activities).
- When encountering challenges with the science or bench work, first sit down and think about solutions yourself, then look for answers in books or the literature, then solicit advice from fellow lab-mates, students, and post-docs, then seek advice of the PI. I (the PI) am always happy to talk about troubleshooting or the science, but show that you have thought about the issues before you come see me. There is a balance to be struck between figuring it out on your own and seeking guidance/advice from others: Be careful not to get stuck down rabbit holes for too long for fear of appearing incompetent. But in order to mature you need to spend some time in rabbit holes. Regular communication with your colleagues and with me will help you to find this balance.
- I encourage and expect you to write and apply for fellowships and grants throughout your tenure – for research money, stipend funds, travel funds, etc.
- You are encouraged to attend research conferences, especially in the last few years of your tenure. Typically, the Lab will cover the costs (if funds are available) if you are the primary author and presenter (platform talk or poster). Even if this is the case, you are expected to still apply for travel funds from external sources.
- You are encouraged to engage in mentorship activities yourself, where you are responsible for training and mentoring others (e.g., new students, visiting scholars, REU students, junior colleagues, collaborators, etc.).
- As you mature during your tenure, you are expected to expand your independence. You are also expected to embrace greater leadership responsibilities within and beyond the group, including training junior colleagues, engaging in public outreach, engaging in service to their communities, establishing and leading collaborations, etc. As you mature you should gain some freedom and confidence in being able to establish new collaborations, either with my assistance, or on your own.
- Students who are co-advised by me and another faculty member benefit from our expanded expertise, but are often challenged to accommodate different mentorship styles and philosophies. Navigating this requires honest awareness and excellent communication between all parties, which should be primarily facilitated by the student, especially as they mature during their tenure in the program.
- See the Whitehead lab Code of Conduct for some additional details and resources.
- I expect you to regularly and effectively communicate with me (PI Whitehead) about your research progress. Some of this will be during group meetings (e.g., lab meeting) but also one-on-one. You are free to come by my office any time, but it is sometimes better to arrange for a dedicated meeting time. Whether one-on-one meetings are regular or arranged on an as-needed basis will depend on what works best between us, and that may change over time. For one-on-one meetings, I ask that trainees prepare a brief agenda, and create notes during or after the meeting. The agenda and notes are organized in a shared Google doc, so we can both keep track of progress and goals. If you shared slides or worksheets or figures during our meeting, links to those materials should be embedded in the Google doc, and if we did a lot of scribbling on the white board, you should snap a photo of the white board and also embed that in the Google doc. I keep a separate “meeting notes” Google doc for each trainee. These docs are updated with each new meeting, so they eventually represent a nice record of your progress.
- I expect everyone to actively engage in (weekly or bi-weekly) laboratory group meetings. These meetings are regular during the academic year, but are typically more irregular during the summer. This is primarily the trainee’s time to leverage our collective “hive mind” to enrich their scientific and professional development. Lab meeting organization and activities are organized and led mainly by trainees.
- I expect trainees to respectfully engage with all laboratory members, including visiting scholars and outside collaborators (see Collaborators section below).
- Receiving critical feedback: Research is difficult, and failure is part of the game. Some experiments will fail, some analyses won’t work, many fellowship and grant applications will be rejected, and manuscripts will receive critical feedback and perhaps be rejected. This is all part of the scientific enterprise. Failure should be expected. But that doesn’t mean that you should develop a pessimistic outlook. I think that it is best to approach the scientific enterprise with optimism, but to also anticipate difficulties, such that you can develop the emotional resilience to learn from challenge and failure. You should expect to receive critical feedback from me, other professors, and your peers. You should expect that this feedback is offered with the best of intentions in mind – in order to enable your growth and maturity as a research scientist, educator, and communicator. I seek to communicate feedback that is constructive, effective, and delivered with kindness. We must all strive to “criticize the ideas, not the person”. You should seek to develop tools and skills that will help you to receive critical feedback, embrace it, learn from it, and convert it into activities and behaviors that make you better at your craft. That being said, you will also achieve many successes, and we will celebrate all of those – the small ones and the big ones – as a group!
- Peer-reviewed research publications are academic currency. They are the widgets that we make. Your academic credit is therefore judged in large part by your inclusion as an author of publications, and the quality and quantity of those publications. It is therefore important to form a sense of what kinds of contributions warrant authorship, and to be as open and transparent about authorship expectations as possible.
- One may consider 6 key elements that contribute to publications: 1) project conceptualization and securing of funding, 2) design of experiments (usually accompanies item 1), 3) data collection, 4) data analysis, 5) data interpretation, 6) writing the manuscript.
- Very generally speaking, a reasonable rule of thumb is that if an individual is involved in any two or more of the above contributions, this should earn them authorship. But this “rule of thumb” is only a guiding principle. Sometimes a massive contribution to only one of the contributions is sufficient. Often the bar for authorship is lower for more junior folks (e.g., undergraduate students) compared to more senior folks (e.g., postdocs).
- Conversations about inclusion as an author should be explicit and happen early during a project. Some participants may have different opinions and expectations about what contributions warrant authorship (e.g., help with a bioinformatics script, help with training, running some gels or PCRs, advice with data interpretation, etc.). We should be willing to contribute assistance and advice to our colleagues without always expecting authorship to follow. That being said, project leads should be generous with authorship, being mindful not to abuse or diminish the value and meaning of being an author. if you feel that your contributions have or will warrant authorship, then those conversations need to happen soon, and the PI should likely be involved. Many journals have useful guidance on criteria for authorship.
- Usually the identity of the first author is obvious (the lead student or postdoc) and the senior (last) and corresponding author is the senior faculty member who guides the research program (e.g., the lab PI). Collaborators and other contributors are included as additional authors, and their order of inclusion is sometimes important. Sometimes, more than one primary participant contributes equally (meriting first authorship), and/or more than one senior supervisor contributes equally, such that decisions about who is first and senior/corresponding author are fraught. This may become tricky when manuscripts emerge from highly collaborative research efforts. In these cases we need to be especially mindful of arriving at solutions where everyone, especially junior participants, receive the credit that they deserve. Sometimes this involves splitting one manuscript into two or more publications, where different participants are primary/senior authors on different publications. Alternatively, sometimes solutions involve two or more participants sharing primary authorship or senior authorship on a single publication.
- If you are included as an author you carry an obligation to review, edit, and approve the final manuscript, and you should be willing and able to articulate and defend the core findings.
- For any contribution that does not rise to the level of authorship, those should all be included in the acknowledgements section of the manuscript.
- I expect that many/most trainees will have interests that have nothing to do with academia (e.g., athletic, artistic, family time, etc.), and I acknowledge that engaging in these activities holds immense value in making us whole, happy, and effective people (and productive academics). I encourage trainees to seek a balance between their academic pursuits and other pursuits, while recognizing that this can be difficult given the heavy demands of academic training.
- If you have difficulties in your personal life that affect your personal well-being and/or academic performance, then please seek help. Help can come from your established friends and family, but also from your program/lab colleagues including me. Importantly, excellent professional help is available through many programs at UC Davis, as detailed in our Whitehead Laboratory Code of Conduct. I as the lab PI do not need to know the details of your personal life, but if you are struggling to meet your obligations then it may help to communicate with me at some level – a trusted health care professional can offer good guidance on whether/how to share with me.
Special expectations for mentees depending on their role/title:
- Funding: I usually only recruit new students after I receive new research funding. This is so that I have funds to support student stipend/tuition/fees for at least part of their tenure. No grant extends for the full duration of most student’s tenure, such that most students are not supported with grant funds during their entire tenure. As such, students are encouraged to apply for grants, fellowships, and traineeships. This serves several complementary purposes. It offers training in writing, which is a core academic skill. If successful, this is an important and noticeable addition to your CV. If successful, it frees up laboratory and program funds to expand the scope of our work. Even if unsuccessful, the iterative work of receiving critical feedback, incorporating feedback, and thereby improving your writing skills, fulfills a core learning objective of your graduate training. Support is also secured through teaching assistantships. TA-ships provide teaching training, which fulfills another core learning objective of your graduate training. Though this is a fluid process, and it requires some planning and flexibility, no student ever goes unsupported for any period of time during grad school. Even though your grad school offers of admission may or may not include language that explicitly “guarantees” funding for the full grad school duration, pretty much every recruit achieves full funding through some combination of support vehicles as indicated above.
- In my group, graduate students are typically assigned to projects for the first 1-2 years of their tenure for training purposes, and to help fulfill the research objectives of funded projects. During the training period of the first 1-2 years, students are encouraged to develop their own research ideas. These ideas may be acted upon if feasible, if they are of mutual interest with the PI, and if they fall under the broader umbrella of our group’s research agenda. Ideas and projects that explore beyond the scope of funded projects are strongly encouraged, but not necessary, and tend to require additional funding that is pursued by the trainee. If dissertation projects beyond the first two years remain within the general scope of funded projects, this is fine (and common), but the student is still expected to take ownership, exhibit leadership, and contribute their own creativity.
- Graduate students should aim for three or more chapters to their dissertation and produce at least three first-authored publications. The student may or may not be first author on papers to which they contribute during their 1st or 2nd year training period, depending on the scope of their contribution. Collaboration on side-projects is encouraged, since it adds depth to your experience and training, and may expand your professional network. But it is easy to get over-extended and get off-track, so side-projects should be carefully considered in consultation with the PI.
- Postdocs are typically hired to work on a specific project, where their goal should be to earn primary authorship of emergent publications.
- Side projects are possible and encouraged as long as either 1) the project for which they were hired is complete or rapidly progressing, or 2) the postdoc secures their own research funding. Since it is easy to get over-extended and off-track with side-projects, they should be carefully considered in consultation with the PI.
- Staff Research Associates are typically committed to a contracted number of weekly work hours. As such, the requirements for them to attend all laboratory functions (e.g., lab meetings, etc.) may be relaxed.
- If they work beyond regularly-scheduled hours, for example during emergencies, then their hours will be compensated during non-critical periods.
- Work on self-inspired or self-motivated projects is possible and encouraged, as long as they are of mutual interest, and only if assigned duties are fulfilled.
- Laboratory work will initially involve duties that support the work of RAs, students, and post-docs. Self-sufficient projects are the goal, but may take some time (e.g., a couple of years) to be realized. Assignment of an individual project is possible only after several quarters of dedicated work in supporting roles, sufficient demonstration of commitment, enthusiasm, independence, and good attention to detail. Opportunities may arise to be included as an author on publications that emerge from lab contributions when appropriate; for many students this is an appropriate and important goal.
- Rarely, opportunities may arise to attend off-campus research conferences; the Lab may cover the costs (if there are available funds) as long as the student is primary author and is the presenter. There are also regular on-campus research conferences where students are encouraged to attend and present.
Some guidance for working with Whitehead Lab collaborators
- Please be aware that the Whitehead Lab collaborates with several other research groups, and their participation with our group is of strategic importance to the short- and long-term success of our research program. Indeed, many of your research projects only exist because of these long-term collaborations. Many of our collaborators are my (PI Whitehead) personal friends and long-time colleagues.
- All interactions with collaborators should be respectful; if your interactions with collaborators starts to have problems, please seek the counsel of PI Whitehead immediately. I expect collaborators to also treat you with kindness, consideration, and respect. Often, collaborators can become important additions to your growing professional network.
- In the interest of maintaining long-term relationships and to advance the science, we often do things for collaborators that do not appear to be of immediate benefit to ourselves. Reciprocally, they often do things for us, which are sometimes not obvious, or may predate your participation. Because many of these collaborations are long term, but your tenure within the group is shorter, it is easy to lose sight of the broader benefits to our program, including previous, current, and future trainees.
- Collaborators have agendas and obligations of their own that may extend beyond our immediate mutual interests, and we must be mindful of those (because we also have our own agendas).
- Effective communication is critical for maintaining active and fruitful collaboration. This includes timely distribution of presentation abstracts and manuscript drafts, and mindful inclusion of comments from collaborators, and distribution of data as it emerges (where appropriate) so that everyone can contribute their particular expertise to analysis, interpretation, and deciding what to do next.
- We must be careful to avoid considering collaborators as powerless middle authors that only exist to advance our own agendas. That is, “win-win” thinking is critical.
Whitehead Lab Values Statement and Code of Conduct
Updated: May 2022
[NOTE: please feel free to use/modify these materials for your own purposes, with attribution]
We value science as a powerful method for understanding how nature works, and we value the role that science can play in promoting a world that is more just for humans and for non-human creatures. We strive for rigorous, transparent, important, and reproducible research. While conducting our scientific inquiry, we are committed to providing a safe, supportive, inclusive, and harassment-free environment for everyone. We value freedom of expression while respecting the views of others. We strive for critical thinking and discussion, but try to be mindful of how our unique experiences and privilege shape our world view, and seek to be thoughtful, considerate, and compassionate toward others. We strive for work-life balance. We value diversity in its many forms (gender, ethnic, disability, economics), in part because we believe that diversity enriches the scientific enterprise, but more importantly because embracing people for who they are and where they come from is of deep intrinsic moral value.
Laboratory Code of Conduct:
All members of the Whitehead lab commit themselves to:
- Treating others with dignity, respect, and consideration, regardless of identity (e.g., gender, age, sexual orientation, (dis)ability, race, ethnicity, politics, and religion (or lack thereof)). We seek to create a laboratory culture that is safe and inclusive for everyone.
- Upholding the highest principles of ethics and integrity during our academic pursuits (learning and research). The academic enterprise is based upon a foundation of trust and of shared values; these values include Honesty (convey information truthfully and honoring commitments), Accuracy (report findings precisely and take care to avoid errors), Efficiency (use resources wisely and avoid waste), and Objectivity (let the facts speak for themselves and avoid improper bias) – from the NIH “What is research integrity” https://grants.nih.gov/policy/research_integrity/what-is.htm
- Producing scientific research that is compelling, relevant, reproducible, transparent, and rigorous.
- Diligently keeping paper and/or digital lab notebooks, and if digital making sure that it is backed up. Commit to regularly backing up all digital materials and resources that are relevant to Whitehead lab activities.
- Promoting an environment where occupational laboratory safety is prioritized; e.g., where safety training is up to date, and we are complying at all times with safety regulations.
- Avoiding the use of sexual language and imagery, unless in the context of biological reproduction.
- If inter-personal disputes arise between laboratory members, please consider the following steps for resolution
- Take some time apart to reach a state of calm, and to thoughtfully reflect on the nature of the dispute and possible solutions that could include compromise.
- On neutral ground, attempt calm and deliberate dialogue with each other that is considerate and respectful.
- If the dispute cannot be settled between the two parties, and an outside mediator appears to be necessary, engaging other laboratory members could be appropriate. However, sometimes this may be inappropriate especially if other lab members feel pressured into “taking sides”. In this case, please engage with PI Whitehead. (ETHICS, SAFETY_). USE JUDGEMENT – ASKING AND ENGAGING
- PI Whitehead will then meet with each party separately, then likely together, to seek solutions that are fair and equitable.
- If the dispute is with PI Whitehead, then consider starting with the first suggestion in this section (item 1. And 2. above – seek to resolve the dispute with each other). However, given the power imbalance at play, this may not be feasible. In this case, then trainees should seek support from any of the following resources:
- CONSULT PEERS – make sure expectations are reasonable/alighend with lab norms.
- Faculty that are members of their guidance committee or dissertation committee.
- The University Ombuds Office (https://ombuds.ucdavis.edu/). “The UC Davis Ombuds Office is a confidential, independent, impartial, and informal problem-solving and conflict management resource for all members of the UC Davis and UC Davis Health campus communities. We invite students, staff, and faculty, with university-related issues and concerns, to visit our office. The Ombuds can assist by listening to concerns, clarifying issues, identifying policies and resources, and providing coaching and communication strategies.”
- The Graduate Group or Department chairperson.
- If the dispute involves suspicion of academic/research misconduct, then this should be immediately reported to PI Whitehead, and confidentiality will be protected to the greatest extent possible. Breaches of academic integrity hurt us all – it is damaging to the reputation of individuals, research groups, institutes, and the broader scientific enterprise. It must be avoided/prevented, or dealt with swiftly and appropriately, including due-process.
- In the event of harassment/sexual misconduct, the PI is required to report the claim to the University following Title IX. There are also a number of routes to report misconduct or request support that do not include the PI:
- Here is contact information for dealing with harassment and discrimination:
- Harassment and Discrimination Assistance and Prevention Program (HDAPP)
Other Campus Resources:
- UC Davis Ombuds Office: https://ombuds.ucdavis.edu/ (530-754-7233)
- UC Davis Center for Advocacy, Resources & Education (CARES): https://care.ucdavis.edu/ (530-752-3299)
- UC Davis Academic and Staff Assistance Program (ASAP): https://hr.ucdavis.edu/departments/asap (530-752-2727)
- UC Davis Counseling Services: https://shcs.ucdavis.edu/counseling-services (530-752-0871)
- UC Davis LGBTQIA Resource Center: http://lgbtqia.ucdavis.edu/ (530-752-2452)
- UC Davis Women’s Resources and Research Center: http://wrrc.ucdavis.edu/ (530-752-3372)
- UC Davis Diversity, Equity & Inclusion: https://diversity.ucdavis.edu/how-do-i
- UC Davis Harassment & Discrimination Assistance and Prevention Program (HDAPP): https://hdapp.sf.ucdavis.edu/report-incident
- HDAPP Resources: https://hdapp.sf.ucdavis.edu/resources
- Understanding the process for formal complaints to HDAPP: https://hdapp.sf.ucdavis.edu/process
- Guidelines for using inclusive language: https://www.linguisticsociety.org/resource/guidelines-inclusive-language
- Gender decoder: check language for gender-specific coding: http://gender-decoder.katmatfield.com/
- UC Davis Graduate Student Association: https://gsa.ucdavis.edu/
- University of California Postdoc and Academic Researchers Union UAW Local 5810 http://uaw5810.org/welcome-new-postdocs/
- Links to campus resources to help you navigate centers, programs, and additional resources designed to support your academic career: https://ebeler.faculty.ucdavis.edu/resources/faq-student-resources/.
- Lots of additional resources (UC Davis, DEI, Grad school advice, research, bioinformatics, funding, career development, etc.) on the Whitehead lab website: https://whiteheadresearch.wordpress.com/links/