Scientific Writing Retreat Course

Repeat Visitor: Pau Creixell

Photo provided by Pau Creixell

Photo provided by Pau Creixell

Pau Creixell of the Koch Institute for Integrative Cancer Research at MIT is the next scientist to be featured in the 2018 edition of our Repeat Visitor series. Pau is a postdoctoral fellow in Michael Yaffe’s lab, which is part of the MIT Center Precision Cancer Medicine. In the thirteen months since October 2017, Pau trained in three of our courses: X-Ray Methods in Structural Biology, Workshop on Leadership in Bioscience, and Scientific Writing Retreat. And with the Network Biology meeting and courses on Cryoelectron Microscopy and Synthetic Biology in his sights, we will likely be seeing Pau again. In the meantime, we reached out to Pau to discuss his experiences so far and learn what keeps him coming back to Cold Spring Harbor.

Talk us through your research interests and how you made them the focus of your work.

Using both computational and experimental quantitative approaches, I am interested in understanding how specific cancer mutations perturb protein function and cause disease. The focus of my work is protein kinases, a subset of proteins highly mutated in cancer and targeted by many therapeutic agents. I find cellular signaling and protein kinases fascinating because even though they have been studied for decades, we are still discovering new molecular functions for them and learning how they are perturbed in cancer. The degree of regulation and functional diversification in protein kinases is very interesting to me, and the amount of sequencing and functional information that we have for them now allows for more systematic studies. It’s a field that has repeatedly shown how fundamental discoveries in molecular biology can lead to effective targeted therapies that benefit patients.

How did your scientific journey begin?

When I was young, a family member was diagnosed with cancer and that had a big impact on me. Since then, I decided that by doing research I could try to contribute to our understanding of the disease which, in turn, could result in better therapies. I was also very fortunate to have a supportive home and school environment, where my curiosity was encouraged by my parents, grandparents, and teachers.

As I was finishing my undergraduate studies in biology, the Human Genome Project was being completed and a number of cancer genome projects were starting. I quickly realized that to address fundamental biological questions, we would need to not only generate quantitative data, but also integrate and decode large and diverse sources of data. This inspired me to pursue a PhD in computational systems biology. Since my ultimate goal is to lead an interdisciplinary lab, I wanted to complement my computational training with expertise in cancer biology. Thus for my postdoc, I purposely transitioned into a lab where I could improve my experimental skills in biochemistry and molecular/cellular cancer biology.

Your most recent course at CSHL was last month’s Scientific Writing Retreat. Can you tell us what attracted you to the retreat?

Scientific Writing Retreat Class of 2018

Scientific Writing Retreat Class of 2018

Given the time scientists invest in writing and the number of versions every manuscript, grant, or application goes through, I always felt that the process of writing could be improved and made more enjoyable. I wanted to learn more about scientific writing in general and how the process may change depending on the purpose of each document. A major takeaway from the retreat is to focus on the audience and how it will interpret your writing. The audience is often broader and more diverse than most of us appreciate; keeping this in mind ensures that key information is presented clearly and your writing is easy to understand.

Since part of the retreat is devoted to practicing on your own work, I returned from it with much-improved versions of abstracts for two manuscripts as well as a research statement. I also learned how to give better feedback on the scientific documents of others, and I increased my understanding of how scientific stories are crafted, submitted, and published. I picked up general writing strategies (e.g., given the limited space in titles, abstracts, and summaries, one has to use the most meaningful words and avoid superfluous ones) and became aware of my major writing weakness (referred to as “your kryptonite” in the retreat). Communicating your science effectively is required to become a successful scientist, and I would like to thank the great instructors, coaches, and my fellow participants for their help.

It’s becoming more common for trainees of the Scientific Writing Retreat to also participate in the Workshop on Leadership in Bioscience. In fact, you are among six recent alums who participated in both the retreat and leadership workshop. Was there something specific about the leadership workshop that led you to apply for it?

I think it is no coincidence that several trainees attend both the leadership workshop and writing retreat as these skills are critical for those transitioning to scientific independence.

I have found there to be little leadership training for scientists, who are supposed to run labs without any formal training on how to successfully manage and lead others. Similar to how I looked for both computational and experimental training opportunities during my PhD and postdoc, I attended the leadership workshop because, in my mind, it was important to be as prepared as possible if I want to effectively lead my own interdisciplinary laboratory in the future.

Workshop on Leadership in Bioscience Class of 2018

Workshop on Leadership in Bioscience Class of 2018

Generally speaking, any starting junior faculty will want to set up an exciting, fun, and creative lab environment but, as covered in the workshop, this will ultimately depend on hiring the right people and setting the right lab environment and expectations. Another important takeaway from the workshop is to recognize that no one is infallible and everyone makes mistakes when running a lab. You have to be open to feedback from everyone and ready to learn from your own mistakes so you can fix them as soon as they are detected. By establishing consistent and objective parameters during the hiring stage and requesting independent feedback from everyone in the lab, one can aim to counteract intrinsic biases and group-thinking, thereby cultivating a diverse and creative lab.

Though I currently have limited opportunities to manage others, I have already implemented some of the aspects I learned and have been working to overcome some of my weaknesses as a leader. The facilitators of the workshop are incredibly knowledgeable and I plan to stay in touch with them as my leadership skills develop. I, along with the facilitators and other workshop participants, have joined a LinkedIn group where we keep in touch and share our ideas.

Finally, the laboratory short course on X-Ray Methods in Structural Biology: Was there something specific that led you to apply for this course?

For my postdoc, I was interested in learning techniques that would allow me to better characterize the molecular effects of mutations in proteins. During a meeting with my PI, he recommended this course, which he himself attended and enjoyed twenty years prior.

From my participation in the course, I took away an appreciation for the physical principles behind x-ray crystallography. It is extremely exciting to be able to learn the fundamentals from those who pioneered the field and developed the technologies and software that are now commonplace. I crystallized many different proteins and learned how to explore different crystallization conditions. I also emerged from the course clearly understanding how diffraction data are interpreted so that structural models can be derived. Being able to transition from raw data to a model and back to the data is an important skill, so that one doesn’t simply take the structural model as the only solution. As I am working on solving structures for protein kinases in complex with specific substrate peptides, this has allowed me to critically evaluate the different research options moving forward. Coming from a computational background, it is also appealing to consider that a research project can now begin by mining millions of cancer somatic mutations, and finish by resolving the molecular differences between mutant and wild-type proteins at atomic resolution.

The overall format of your three courses are different. What differences or similarities did you pick up, and what advice can you share with future participants?

All three of the courses had a direct impact on the way I now look at scientific problems and the scientific process in general. The training was intense but extremely worthwhile, and I learned something new every day. In all cases it also felt like the more effort you put in, the more knowledge you get out, so I would certainly encourage future attendees to complete any assignments that are suggested by the instructors.

An aspect easily overlooked about these courses is that they offer a great opportunity to build community. The topics, formats, duration, location (Banbury versus CSHL main campus), instructors, and attendees were obviously different in the courses I took, but they all had a similar feeling of being part of a community. My memories include laughing and sharing experiences with participants and instructors of diverse origins and backgrounds, going for morning runs together, and relaxing in the basement of Robertson House and on a sailing trip. When one is an early-stage scientist like I am, often competing with peers, it is important to remember that the vast majority of us are driven by shared interests in addressing thought-provoking scientific questions and contributing positively to society.

Pau received financial support from the Convergence Scholars Program, Helen Hay Whitney Foundation, Helmsley Charitable Trust, National Cancer Institute, and National Institute of General Medical Sciences. On behalf of Pau, we would like to thank these organizations and agencies for continuing to support and enable our young scientists to attend a CSHL course where they expand their skills, knowledge, and network.

The three courses Pau took part in - Workshop on Leadership in Bioscience, X-Ray Methods in Structural Biology, and Scientific Writing Retreat - will again be offered at CSHL in 2019. All three courses have already begun to accept applications, and applications for the leadership workshop are due by January 15, 2019 here.

Thank you to Pau for sharing with us his experience, and we look forward to having him back at the Laboratory again. To meet other featured scientists - and discover the wide range of science that takes part in a CSHL meeting or course - go here and here.

Visitor of the Week: Oscar Perez


Meet Oscar Perez, director of the Developmental Biology Laboratory 113 in the Pontificia Universidad Católica del Ecuador’s School of Biological Sciences, a graduate student in Dr. Federico Brown’s lab at the University of Sao Paulo, and the Ecuadorian representative in the Latin American Society for Development Biology Board. Oscar was on campus for two courses this year – Scientific Writing Retreat followed by Computational Genomics – but his history with CSHL started twelve years ago when he took his first CSHL course. We caught up with him to ask what keeps him coming back.

What are your research interests? What are you working on?
I am interested in the evolutionary comparison of reproductive strategies and early development of Ecuadorian chordates. My research is currently focused in the plasticity of oocyte organization and how this can modify the embryological events. I apply the comparative method in order to find molecular variations in oogenesis and embryogenesis of the Ecuadorian megadiverse fauna.

How did you decide to make this the focus of your research?
Since an early age, I was always interested in nature and I was fortunate to have a childhood surrounded by forests and open fields. I clearly remember hearing the Quito frogs singing in the cold nights and looking for bugs under the stones in the morning. I have to thank my mother for showing me a marvelous chicken birth and what I consider my very first exposure to embryology. Every child should have a similar opportunity.

How did your scientific journey begin?
I had the great fortune of working with great mentors with Dr. Eugenia del Pino, Dr. Richard Elinson, and Dr. Luis Coloma being the most influential to my scientific formation. I became extremely interested in embryological events while working with the outstanding Ecuadorian embryologist Dr. Eugenia del Pino. In her lab, I had the opportunity to be involved – for the first time – in the diverse and fascinating area of embryology by studying the embryos of Ecuadorian frogs which began my fascination for this almost unknown field of biology. My love for molecular techniques, evolution, and direct development came from Dr. Elinson’s expertise, and my passion for reproductive biology and ecology came from scientific interaction with the brilliant herpetologist Dr. Luis Coloma.

Was there something specific about the Computational Genomics course that drew you to apply?
There were three main reasons I applied for the Computational Genomics course in CSHL: 1) My previous experience in the CSHL Xenopus and live imaging training courses were brilliant; 2) The outstanding instructors listed for the genomics course; and 3) CSHL is considered one of the most prestigious scientific institutes in the world.

What and/or how will you apply what you've learned from the course to your work?
Undoubtedly, all the information I acquired from the course will be of great help in my research and institution. I have to say that my research in the non-model science world. Ecuadorian alternative models such as frogs, ascidians, and sea slugs do not have standardized molecular tools as in mice, Xenopus, or the human. Fortunately, in this course I learned of alternative ways to take advantage of modern computational tools to analyze transcriptomic data from my non-model species and still get informative results despite the absence of reference genomes and other existing tools that are easily obtained in human and mouse. Institutionally, my Computational Genomics training is very important because these skills can be shared with other laboratories and groups in collaborative investigations.

What is your key takeaway from the course?
The take-home message from the Computational Genomics course is that genomics is a flexible tool that can offer several alternative strategies to solve one single question. The experience of the genomics experts and mentors were extremely useful to learn how to effectively extract many hidden results from your data.

If someone curious in attending this course asked you for feedback or advice on it, what would you tell him/her?
My answer would say to complete all the homework sent by the instructors before the course. Even when you are not required to be an expert in the field, you must have a certain level of knowledge in order to get in the fast lane of learning. Also, bring data. If you have an unsolved problem in this regard, the Computational Genomics course is the right place to solve it.

How many CSHL courses have you attended?
Computational Genomics, 2018
Scientific Writing Retreat, 2018
Immunocytochemistry, In Situ Hybridization & Live Cell Imaging, 2009
Cell & Developmental Biology of Xenopus, 2006

Thinking back on your course at CSHL (Cell & Developmental Biology of Xenopus in 2006), did you notice differences or similarities between that course and Computational Genomics?
I still clearly remember how intense and diverse the training was at the Xenopus course in 2006 and, even after 12 years, that same level intensity and high quality of the courses in CSHL has remained the same. Although, considering the tasks sent weeks before the course started, preparation of a poster, and the mid-term test, I could even say that Computational Genomics might be more demanding than the 2006 course.

Since your first two CSHL courses, your career stage has changed. Given your present position, did your experience in the course change in any way?
Course features such as intensity and quality of the knowledge offered are contrastable; however, it is without doubt that CSHL offers first-rate courses instructed by leaders in the field of science. Over the years, my capacity of appreciating this knowledge has evolved. When I was a younger researcher, I did not fully appreciate how great an opportunity it was to train and be trained in one the most prestigious scientific institutes in the world. But, as my experience has expanded, I have become more aware of the magnitude of having opportunities to learn and to learn from such a source.

What do you like most about your time at CSHL?
The confidence that you acquire by mastering specific techniques. The rate of learning in CSHL is very high as is the demand and complexity of the courses. It is great to have the opportunity to ask your questions to pioneers, leaders, and scientific experts that collaborate with CSHL to teach and share their knowledge. 

Oscar received a fellowship from Pontificia Universidad Catolica del Ecuador (PUCE). On behalf of Oscar, thank you to the PUCE for supporting and enabling our scientists to attend a CSHL course where they expand their skills, knowledge, and network.

Thank you to Oscar for being this week's featured visitor. To meet other featured scientists - and discover the wide range of science that takes part in a CSHL meeting or course - go here.

Visitor of the Week: Tatiana Moiseeva

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Meet Tatiana Moiseeva of the University of Pittsburgh. The Russian national is a postdoctoral associate in Dr. Christopher Bakkenist’s lab. She returned to campus for her first CSHL course: Scientific Writing Retreat.

What are your research interests? What are you working on?
I study how human cells initiate the replication of their DNA and how they suppress the majority of the available replication origins that should only be used in the event of stress. Certain drugs that are currently in clinical trials can induce excessive replication initiation and make cells more prone to toxic DNA damage.

How did you decide to make this the focus of your research?
I have always been interested in basic science questions. The Bakkenist lab focuses on using certain kinase inhibitors to sensitize cancer cells to ionizing radiation, and we found an unexpected effect of a drug that was supposed to be inert in the absence of DNA damage. My natural curiosity took over and I had to figure out what happens exactly, and it turned out that I can use this drug to answer some basic science questions, so I couldn’t resist.

How did your scientific journey begin?
I completed my undergraduate and graduate degrees in St. Petersburg, Russia. I had amazing professors in the Polytechnical University who inspired me, encouraged discussion, critical thinking, taught me the importance of constant self-education, and really shaped my scientific mind. Doing research in Russia was not easy but they, by example, showed me that nothing is impossible if you put your mind to it. I have switched a few research topics since then, but I think my education is what defined my scientific path.

Was there something specific about the Scientific Writing Retreat course that drew you to apply?
Scientific writing is a critical part of working in academia. To date, I have written multiple manuscripts and grant proposals that I asked my PIs to look over. They always provided feedback but they weren’t always able explain why I should write something in a certain way. My goal in attending this course is to become more independent in my writing and improve this valuable skill for future work as an independent researcher.

What and/or how will you apply what you've learned from the course to your work?
Ask several people to read your text before submitting it. Getting feedback, even from non-experts, can help a lot.

What is your key takeaway from the course?
For any piece of scientific writing, proper structure is key. Whether it is a seven-figure paper or three-sentence abstract, the order of the messages is what matters the most.

How many CSHL courses have you attended? How about meetings at CSHL?
This is my first course but I am very curious about the Workshop on Leadership in Bioscience. I attended the Cell Cycle meeting in 2012 and DNA Replication meetings in 2015 and 2017. I am planning to attend the 2019 Eukaryotic DNA Replication & Genome Maintenance meeting.

If someone curious in attending this course asked you for feedback or advice on it, what would you tell him/her?
This course is very useful, informative, and intensive. Before coming to the retreat, think about the general and specific writing problems you are having because the time at the retreat is very tight. Anything can be solved, you will see the progress immediately. Also, the course is always the week before Thanksgiving - be ready for the snow!

What do you like most about your time at CSHL?
A chance to meet new people from very different backgrounds (that we don’t really get at scientific conferences), learn about their experiences and make new friends. Also, very good dinners. 

Thank you to Tatiana for being this week's featured visitor. To meet other featured scientists - and discover the wide range of science that takes part in a CSHL meeting or course - go here.

Repeat Visitor: Sumangala Shetty


Every so often, we host a course trainee multiple times in a year. One such trainee from 2017 is Sumangala “Suma” Shetty, a research and teaching specialist at Paul Copeland’s lab in Robert Wood Johnson Medical School – Rutgers University. 

Suma made her debut at CSHL Meetings & Courses six years ago when she attended the 2012 Translational Control meeting. She still clearly remembers being surprised by the “talks [going] past 10 PM” and that “attendance was still at its peak during the evenings”. Last year, Suma returned to CSHL to attend three courses – The Genome Access Course, Scientific Writing Retreat, and Computational Genomics – and from our conversation it doesn’t seem like we’ve seen the last of her. 

Tell us about your research interests and what you’re working on. 
My research focuses on understanding the mechanism of synthesis for a specialized group of proteins referred to as selenoproteins. Selenoproteins play a crucial role in cellular homeostasis, thyroid hormone metabolism, redox regulation, storage and transport of selenium, protein folding, and signaling skeletal muscle regeneration.

The Genome Access Course, Fall Session, 2017

The Genome Access Course, Fall Session, 2017

We offer roughly 30 courses per year and you participated in three of those courses last year. How did you decide which courses to apply for?
In concert with my want to transition into an independent scientist, I have been focusing on developing new skill sets to keep pace with emerging data mining techniques and high-throughput screening methods for genomic data analysis. Since independent research relies on grant funding, I was interested in a workshop that focused on grant writing. Similarly, I surveyed for courses on bioinformatics and data analysis tools. There are several online tools and resources, and I have acquired several online certificates for data analysis as well as developed programming skills using Python. But I was longing for face-to-face interaction with fellow beginners to discuss pitfalls and potentials, and, most importantly, get feedback. 

Keeping in mind my two goals and learning environment criteria, I consulted my mentors for advice. In addition, in December 2016, I attended a CRISPR workshop by NIH where I met Dr. Vielka Selezar. At that point in time she had just joined Cape Breton University (Canada) as a new faculty member and was in a similar situation as me so I asked her for advice. She shared with me her learning experience at CSHL’s Computational Genomics course and highly recommended it. Interestingly, when I visited the CSHL website, I found several other courses that suited my needs and I narrowed down the list to the three most relevant for my career. 

What is your key takeaway from each of the three courses?
I totally enjoyed each of the courses, especially given their highly-interactive setups. The Genome Access Course exposed me to a rich collection of databases and tools. It was so engrossing and involved that I didn’t even need my second shot of caffeine in the afternoon! Totally loved it and, in fact, I think The Genome Access Course should be made mandatory for all graduate students.

Scientific Writing Retreat, 2017

Scientific Writing Retreat, 2017

My second course was the Scientific Writing Retreat. This workshop was an eye opener for several reasons: 1) It taught me how to overcome writer’s block and clean a draft for clarity; 2) I learned inside information on how a manuscript submitted to a journal is reviewed and how to improve the chances of it being accepted; 3) I chatted with a grant writing expert; and 4) The one-on-one review of my manuscript draft was, in my opinion, the best feature of this course. At the end, I felt like my fellow participants, the mentors, and I had become a tight-knit network that I could always approach with any of my tough writing issues. Charla and Steve thank you very, very much. 

And finally, Computational Genomics was the most intense and most exciting seven-day course I have ever attended. We were in class almost all day till midnight and still every one of us showed up at 9:00 the next morning. It was highly informative and full of new tools to explore. My favorite part was working in teams on our take-home midterm exam and also on our final project, because I learnt a lot from my course mates. Also, through an online course on genomic data analysis by Johns Hopkins University, I had heard lectures from James Taylor and Jeff Leek but it was cool and an honor to meet and hear them in person at the course. They were extremely helpful, very humble, and the course was much more fun than an online course. 

One similarity I noticed that was consistent in the three courses is that all of the course mentors were highly motivated and inspiring. They were extremely helpful, always available, and their enthusiasm was infectious.

Have you already applied what you learned from each course to your work?
I am using the data analysis tools on our pre-existing RNA-seq and proteomics data, and currently, we are storyboarding some new applications for our project using genome analysis tools. Also, tips from the Scientific Writing Retreat enabled me to finish my manuscript. 

Computational Genomics, 2017

Computational Genomics, 2017

If someone interested in a CSHL course asked you for advice, what would that be?
After my experience, I strongly believe that CSHL courses are a crucial resource for learning current techniques under the direct supervision of the experts. I think a stronger awareness about CSHL courses should be raised among graduate students and postdocs; and therefore, I would strongly encourage those interested in a CSHL course to apply. A number of the courses post their past lectures online so it’s easy to browse the content and analyze if the course will suit your needs.

Our readers are curious about how course tuitions are funded. Would you like to share how you were able to pay for three courses in one year? 
I am fortunate in that my PI, Paul Copeland, strongly supports my career growth. We both agreed that expanding my skill set will add new insights to our current projects and, therefore, I received financial support for my courses from Paul.

What did you like most about your time at CSHL? 
The intensity and enthusiasm of everyone I met. More importantly, the one-on-one interaction and personalized discussion with experts on our individual projects.

Do you have any future plans to attend another course or, perhaps, a meeting at CSHL?
Absolutely yes. The CSHL Meetings & Courses website is in my browser favorite list, and I am already planning to apply for the Statistical Methods for Functional Genomics course. 

Thank you to Suma for sharing with us her experience. We look forward to having her back at the Laboratory soon. To meet other featured scientists - and discover the wide range of science that takes part in a CSHL meeting or course - go here.

Visitor of the Week: Yi-Jyun Luo


Meet Yi-Jyun Luo of Harvard University. Having recently graduated from the Okinawa Institute of Science and Technology Graduate University (Japan), Yi-Jyun joined Mansi Srivastava's lab this past September as a postdoctoral fellow. He is affiliated with the Department of Organismic and Evolutionary Biology and returns to CSHL to attend his second CSHL course in two years. This year, Yi-Jyun is training at the 2017 Scientific Writing Retreat which is held annually in the Banbury Conference Center. 

What are your research interests? What are you working on?
I am interested in evolutionary developmental biology, and my research interests are in animal body patterning and cell fate regulation during evolution. I am working on stem cell regulation in a new regeneration model: acoel Hofstenia miamia.

Was there something specific about the Scientific Writing Retreat course that drew you to apply?
Writing is an essential aspect of doing science in terms of getting publications and grants. As a non-native English speaker, I am always working to improve my English writing and to better communicate my ideas and research. From my past experience of attending CHSL meetings and courses, I knew this course would be an excellent opportunity for me to learn scientific communication skills.

What is your key takeaway from the Course?
The diversity in the attendees, and the encouraging environment fostered by the Course to share and speak with those from different fields, are awesome. I have picked up a lot of new ideas on how to deliver my work to a target audience and to lay people. 

How many CSHL courses and meetings have you attended?
This is my third time at CSHL but this is my first time at the Banbury Center. I attended the Biology of Genomes meeting in 2015 and the Programming for Biology course in 2016.

If someone curious in attending a future iteration of the Scientific Writing Retreat course asked you for feedback or advice on it, what would you tell him/her?
I highly recommend this course as it is very rewarding in terms of scientific and personal experiences. The course is exceptional for learning written communication know-how from the best, and it is also an excellent networking opportunity to meet editors face-to-face. Also, the Banbury Center is a lovely setting for this course.

What do you like most about your time at CSHL?
I really enjoy the unique and inspiring atmosphere at CSHL. Both the Banbury Center and Main Campus are full of natural scenery and academic history, and are all about cutting-edge technology and science communication. Also, people are friendly and there are plenty of opportunities to interact with fellow scientists and journal editors.

Yi-Jyun received a stipend from the National Institute of General Medical Sciences (NIGMS) to cover a portion of his course tuition. On behalf of Yi-Jyun, thank you to NIGMS for supporting and enabling our young scientists to attend a CSHL course where they expand their skills, knowledge, and network.

Thank you to Yi-Jun for being this week's featured visitor. To meet other featured scientists - and discover the wide range of science that takes part in a CSHL meeting or course - go here