Sep 062015
 

Just finished a book, The Hiding Place. It tells the story of a family who helped and hid the Jews during WWII. The book teaches us to be grateful in whatever situation and help the less fortunate people. Recently in my habit monitoring tool, I added an item to be grateful for all the good things in my life. There are so many things I should be grateful for, for our good health and comfortable wealth, happy family, smart and hard working lab members, wonderful colleagues, our town, our kids’ teachers, my friends and relatives. The book made me realize that even if things don’t work well or my luck turns, I should still face life with optimism, appreciation and grace. When scientists commit suicide, sabotage other people’s study, or even poison their colleagues, they often feel they had nothing to be happy about or no other choices in life. In fact, we all have things to be grateful, even in dire circumstances. In the Hiding Place, Corrie and Betsy have inspired people to be grateful and pray for their captors even in concentration camps. What I found especially surprising is that after the war, the heroine opened her house and forgave the people who betrayed the patriots to the Germans. I could and should always find enough reasons to be grateful in life, but to pray for the enemies? Hmm… That takes a lot more hearts.

Aug 282015
 

Developing scientific reputation relies on publishing impactful discoveries, developing widely used algorithms, but probably equally importantly delivering insightful scientific talks. In some conferences, I am often chagrined or amused by talks in the following styles (sometimes a talk could combine the 3 styles which is quite a sight to behold :):

A speaker goes over all the major publications (Nature, Science, New England JM, Lancet, you name it) to demonstrate that a new direction (often following a US or EU initiative) is important, although none were their own study. It is like a 科普 journal club which treats the other scientists in the audiences like school children. Actually such talks are often good for student audiences who may not be as well informed about the new trend, so are quite informative and inspiring. Also such talks often signal that the government will be spending major $ on this new direction, so we should start to scheme and get a slice of the pie :).

A speaker says “the computational method is very complicated, so I won’t go into the details, but trust me, here is our finding”. Then a list of biological observations is given, and the speaker says “we don’t know what this means” or “I don’t really understand the biology”. It is possible that these methods are good and the discoveries are true. However, for these results to be taking seriously, the data / method need to be explained to earn credibility, computational biologists should learn the domain biology and talk more professionally about the biological findings.

A speaker says, “the method is very simple la! so I won’t go over the details, but we have boat loads of money to generate tons of data, and we integrated everything, so here is our results”. Then to the abhorrence of the audiences, the “results” presented are “we filed a patent or developed a kit”, “we obtained some major government awards or venture capital funding”, “this method can really be used to solve all biomedical questions, which can be demonstrated by the following 100 published papers from our group”, or “we found a new use of an old drug or a new drug combination, some have clinical trials ongoing, but for intellectual property reasons I can’t tell you what it is”. Such talks are often super effective ;), since naive audiences often fall head over heels to join the speaker’s lab.

A good scientific talk should focus on one coherent biological study, start from the motivation, explain what data is used, how the computational method works (at least the key intuition), then present specific biological findings with thoughtful biological interpretations and full appreciation of potential limitations. If the talk is a computational method, then explain why and how it is developed, what the main functional features and advantages are, where the method can be downloaded for use. The audiences could learn how a study progresses from a logical flow, how to a use tool / website / database to speed up their analysis and hypothesis generation, how to use the thinking of the presented method to develop their own methods, how to use the presented biological findings to inform their next experiments. It is OK to present published studies, but probably even better studies under preparation, review, or revision (many reputable international conferences encourage speakers to present unpublished work).

I hope that with more and more great scientists getting into computational biology, the field becomes more mature, our scientists could learn to deliver professional, more informative and insightful scientific talks in scientific conferences. At least I hope speakers at the Young Bioinformatics PI Workshop try their best to give good talks. Only when we can do so can computational biologists be respected by experimental biologists, can Chinese scientists earn international reputation.

P.S. Recently Xiaowei Zhuang gave a talk at our CFCE retreat. She talked about many different studies and papers from her group, but was super clear on the intuition as well as the significance behind each study. You could see how their technology progresses over time, and could really learn a lot which was very exciting. I guess it is possible to cover many topics in one talk and still do a great job, but Xiaowei’s scientific expertise as well as her talk style (which I am sure take a lot of hard work to hone) is quite a different league!

Aug 182015
 

Recently I finished The Wright Brothers book. One sentence struck me: The best dividends on the labor invested have invariably come from seeking more knowledge rather than more power. Science will be a better place if scientists can all follow this… The brothers were stoic, diligent, resilient, and detail oriented. Reading the book not only inspired me about future research, but also brought back some sweet memories of our past research. There were a few times in my life when we were learning a lot and making good progress in research, such as the time we were developing MDscan, understanding epigenetics from analyzing the data Keiji Zhao (Barski et al Cell 2007), and recently learning about CRISPR screens. Despite the setbacks, the excitement from new knowledge or good results kept us going. The book was heart warming, and gave me the confidence that with careful and hard work, everything is possible.

However, a few days after I read the Wright Brothers book, I read about Howard Armstrong (Dreamers and Deceivers). Very few people heard about Armstrong, but he made seminal inventions, most notably regenerative circuits for radio amplifiers and FM radio transmission. However, Armstrong lost the patent lawsuit of the first to Lee Forest (under the backing of AT&T), then the FM patent lawsuit to RCA. Even though experts completely credited Armstrong with these inventions, his patent losses caused both financial and emotional exhaustion, and Armstrong committed suicide. It was a very sad story, and I almost want to give up on science.

After reading the two stories, I thought about why the inventions between Wright brothers and Armstrong came to so different outcomes. Here are three reasons I came up with:

1. The Wright brothers had each other for support, whereas Armstrong worked kind of alone. In science, we need enough colleagues who are our close friends for support us in science, career development, and occasionally in personal life.

2. The Wright brothers understood the power of public relationship, and knew how to time their flights in order to generate enough public Wow! Armstrong was going against the PR machine of AT&T and RCA so lost his cases. In science, institutional PR department could certainly help, but for us well prepared papers and talks are our most effective PR.

3. The Wright brothers grew up in a cultured environment, and their father was a bishop. Despite their simple life, the brothers have refined taste and wide knowledge, what Hart Berg called “capital Exhibit A”, which inspires confidence. I sometimes marvel at my colleagues’ talents and knowledge outside science, such as art (Nelly Polyak), music (David Fisher), literature (Judy Garber), and social (Myles Brown) matters.

So scientific genius and hard work are necessary, but without the other important components, we could end up a sad story like Armstrong.

Jul 162015
 

This afternoon I attended the DFCI Annual Female Faculty Retreat. It was actually very good, especially the panel discussion. There were a few points the panelists raised which I thought quite thought provoking and would like to share.

  • Teach people how to treat you, and don’t be the victim of other people’s stereotyping
  • Compartmentalize your schedule and make time for yourself (either work or life)
  • Instead of over-committing on community services, focus on very few important initiatives that you can really make an impact and leave a legacy
  • Keep bicycling at the back of the pack, but don’t fall off the bike (for female faculty with family obligations)
  • Guilt is a wasted emotion
Jul 122015
 

Recently a graduate student in my group asked for advices on looking for postdoctoral labs and advisors. Here are my thoughts…

Do some research and find an research area that you find very interesting and promising. It is actually a good thing for postdocs to try a new direction in postdoc different from their PhD study to learn new things, as long as their PhD expertise can still contribute to the postdoc training and the postdoc lab. Read some good papers (recommend using Gnosis to search for papers) and check some website. I don’t like postdocs who come to interview at say, “I am happy to do any project you ask me to do”, or “I have been doing A and realize how important B is which I am really lacking, so I would like to come to your lab and learn B”. I would be much more interested if a postdoc come with, “I am very interested in area B that you are an expert, and I am especially curious whether my expertise in A could be used to investigate this particular question in B”. It is possible that even with all the HW you have done, your proposed project still looks hopeless or naive in the expert eyes of the professor, but at least s/he will appreciate that you made this much effort in learning a new direction, thinking of a potential problem, and writing it out (actually this proposal is a good way for the PI to see how well you can write).

Carefully prepare your CV and a good interview talk. Start preparing your CV at the beginning of your graduate school. Download the CV of some scientists you admire and see what they have on their CV. Is there a way you could accumulate some of the experiences on their CV (award, talk in conferences, review papers for journals, organize some smaller scale meeting or conference tutorials, join professional organizations, and of course publish well). Also learn to give effective research talks as early as possible in your career (understand your audience, explain clearly, how to draw audience attention, let your message sink with the audiences), as this is one of the most useful skills! Work hard and seriously on every possible talk opportunity (lab meeting, department colloquial, conference talks / tutorials, defense) during your to hone your skills. I told lab members they need to give 30-50 talks / year to give good talks, so if a beginning graduate only gets to give 3-5 lab meeting talks / year, they should rehearse each talk 10 times themselves before giving it formally.

Obtain 3-4 reference letters. Graduate students should think about this at the beginning of their graduate school: besides my own research advisor, which other professors in our institutes (e.g. you got to know them from serving as TA on courses, giving department colloquial talks, qualify or thesis defense talks), which collaborators (e.g. establish a good collaboration with a group where you could have meaningful interactions with the collaborating PI), and which other professors (e.g. you got to know them from conferences or their research seminars). Give your letter writers plenty of time (2-3 months) before the due date so they have time to write a good letter.

When looking for advisors, check whether the lab has a high success rate (number and probably more importantly percent) of sending previous trainees to successful (esp faculty) careers. If the advisor is relatively junior, then the meeting with the professor will be important. Does s/he care about your career development and success, does s/he inspire you from the discussion, does s/he treat you like a future star or only care about “just do what I tell you to do”. For bioinformatics students looking for postdocs, if your future postdoc advisor is an experimental biologist, it would help if s/he has a good informatics collaborator that you could work with and learn from. Make sure the lab could respect your background and reserve some time for you to develop your own methodology research, rather than being a data janitor to all the data generated in your advisor’s laboratory. When applying, write a personalized email, explain your background, why the lab interests you, what you can contribute. When I see an application where the email could be sent to just about any lab (except for the “Dear Dr. X”), I would totally ignore their application.

Apply for multiple laboratories, even if you are most interested in just joining one. If you get multiple offers or were interviewed by multiple laboratories, each lab that are interested in you will find you more valuable. At least by talking to more labs, you can learn the potential future field better. Read the papers from the lab more carefully before the interview. Dress professionally and look sharp, be on time for interview meetings. Some labs might give you a Skype interview first before on site interviews, so prepare for the Skype interview as well. Give a good talk, and be objective in answering questions. This is the opportunity to act like a star, be knowledgable, confident, and relaxed. Talk to the lab members to find out the style of the advisor (how do they work together, is the advisor nice, etc) and see whether this is a good fit for you.

Postdoc application is extremely important for a student’s future career. Take it seriously and prepare, prepare, prepare… A lot of these preparations are also useful for later job search as well.

Jul 112015
 

When you search for papers on PubMed, it usually gives the results in chronological order so many new but irrelevant papers are on the top. When you search papers on Google Scholar, it usually gives results ranked by citations, so will miss the newest exciting finding. Students in my lab recently made a very simple but useful tool Gnosis. It ranks all the PubMed hits by (Impact Factor of the journal + Year), so you get the newest and most important papers first. The sorted results (either in html or attached .txt format), including the PMID, link to paper, paper title, first / last author, journal, year, citation on PMC, are sent to authors by email. When I tried to learn a new field or keep updated on new important findings in my area, I use Gnosis.

Suggestions welcome!

Jul 042015
 

I just finished an audio book called “Better Than Before”. A while ago, I read a book about the importance of habit (The Power of Habit: Why We Do What We Do in Life and Business). I agree what we can achieve in life is the product of our habits, yet The Power of Habit book didn’t explain how to form good habits. “Better Than Before” instead gave a lot of good advices on how to establish good habits. I also realized that some of the things that bother me were because of bad habits. It mentioned 4 fundamental habits: sleep more, eat less, exercise more, and unclutter. I heard Terry Speed say recently exercise is the solution to all his health problems :), but I think these four are probably all quite useful. While the book discussed the importance of monitoring habits, it occurred to me there must be a good Apple App for it. Indeed I found this App called Way of Life, and have been using it to monitor the good habits I want to have (a little harder lately due to my travel). I would recommend both the book and the App.

Jul 012015
 

Sometimes when things occupy my mind, I like to write it down. If I don’t mind sharing it with others, I will put this on my blog. However, when I have manuscripts or grants due (actually, when do we ever not have ms or grants due?), I often feel guilty writing blogs (didn’t you have more important work to do?).

Recently I talked to Terry Speed about this. He thought that writing blog could be a healthy activity if: 1) I can get the thoughts out of my mind so I can focus on other important issues; 2) if I find writing blogs relaxing (can’t always be so stretched with writing grants and papers); and 3) if the blogs could be beneficial to other readers. I guess I can consider writing blog like doing exercise or reading for fun, and don’t need to feel guilty for writing blogs. Writing is especially helpful when I travel. Sometimes sitting in the plane / train / taxi when it is a bit bumpy, I have a lot in my mind yet I don’t have wireless internet, or if I get lost in a conference / seminar talk but don’t feel like focused enough to revise a paper or write a grant, I can type my thoughts without looking closely about what I write, and it feels good to get my thoughts filed away.

Jun 242015
 

For years, I have been trying to have regular physical exercise without much success. I tried to run or swim, but between the unpredictable weather, my travel schedules, and monthly cycles, it is hard to keep a daily practice. I also tried the 7MWC. It is fast, but so hard and painful it is challenging for me to keep up.

I took some Yoga class during graduate days, but for some reason never liked it. For many years, I considered Yoga not real exercise. Recently I started doing YogaStudio from my iPhone, since it had amazing reviews. It has 15min, 30min, or 60min readymade classes, focusing on different things at different levels. This is something I can reliably do daily either in the morning or at night (actually nice to do right before bed). At the beginning, my mind kept on wandering around, thinking about some research problems, family errands, the need to buy something or write an email. But recently I did the Yoga studio with a friend, and noticed her smooth and deep breathing. I tried to mimic her, and realized that the long and even breathing naturally keeps my mind focused and relaxed. It has been great, and I now bring my yoga mat even when I travel.

Another colleague mentioned that it is important to have some daily exercises that will get our heart rate to > 150 beats / min. I started practicing climbing stars, as it definitely jumps by heart rate. I often park at P4 and my office is at the 11th floor, so going up and down 15 floors is becoming a routine. I read from a book “Better Than Before” that the benefit of exercise doesn’t have to come from rigorous exercise, rather the basic movement of walking, stretching, wiggling, going up stairs could be most beneficial. This is definitely encouraging, so I am trying to keep these simple things when I have a min or so.

P.S. Learning that a lot of the successful colleagues that I admire, e.g. Bing Ren, Terry Speed, Peter Jones, routinely run, I am trying to give running another try. I am surprised to find that after my recent stair exercises, getting back into running is not that painful.

Jun 102015
 

Recently I noticed something. For a popular software tool that handles big data, like RMA, BWA, DESeq, or MACS2, the community usually gives it enough credit, because users often cite these tools in their studies. However, for web database resources that people can quickly look up, they are often extremely widely used and yet not get enough credit from citation. Examples include: UCSC genome browser, CBioPortal, and BioGPS. They provide user-friendly visualization of public data, so people can refine their hypothesis or check things quickly. Unfortunately these tools (unless bundled with another biological study), rarely get published well beyond NAR. However, in terms of their value to the scientific community, how are they not as good as a Cell Resource paper? I hope the community will consider the number of visits / queries in evaluating the value of such web resources, instead of their published journals and citations by others.