Nov 212012

For years, I didn’t consider Kindle. Recently my husband told me that I could download the Kindle software to read Kindle books on my MacBookPro.

For many years I have been trying to learn speed reading. I bought some books on this but wasn’t even able to finish reading them. My friend Liping Wei and I used to joke that these books certainly were not very successful in teaching me speed reading.

So I tried again, this time on a book called Breakthrough Rapid Reading on Kindle. It turned out it was much easier to read on Kindle than on paper, since I can change the font, columns, and width to fit my reading habit. The book asked me to think about 5 books to read if I only have 6 months to live, and mentioned that I might be able to finish reading them in the next 6 months without dying :). I thought of Shakespeare, Mark Twain, Jane Austin, Plutarch, and Harry Porter, but where can I find these books?

Turned out Amazon has all these books in Kindle format. What’s more, you won’t believe the price, the complete works of Shakespeare, Mark Twain, Jane Austin, for just $2.99!! Wow, I should really clean up my bookshelves. The cool thing is that these Kindle books can automatically sync with my iPhone, so I can read it anywhere with my iPhone when I have a few minutes. Kindle also has many free children’s books, many with nice pictures too.

Technology is really changing the world!

Nov 202012

We have been processing all the publicly available ChIP-seq and DNase-seq data in human and mouse. With that in place, Hanfei Sun made a very nice interface called CistromeFinder. Curious about whether factor X has binding sites near gene Y? CistromeFinder can help you evaluate specific ChIP-seq/DNase-seq dataset and give you the answer to this question.

Nov 142012

A lab member started using HTML KickStart to design the web interface for one of our projects. I think the main page explains it really well, “HTML KickStart is an ultra–lean set of HTML5, CSS, and jQuery (javascript) files, layouts, and elements designed to give you a headstart and save you 10’s of hours on your next web project.” I really like the clean and sleek interface. These are the wonders of technology!

Nov 102012

Many scientists in the chromatin field had biochemical background, which I didn’t appreciated enough. Several weeks ago, Yi Zhang gave a seminar at our Center of Functional Cancer Epignetics. I have heard Yi’s talks at scientific conferences, where he only had ~20 min to discuss recent findings. In this seminar, he explained his career paths from studying histone mehtylating enzymes (HMTs), to histone demethylating enzymes (KDMs), to DNA demethylating enzymes (TET family proteins). I came to appreciate his biochemical background a lot better, which motivated him to extend to exciting new research directions. Suddenly the connections clicked in my mind. Basically from protein structure, he could foresee the similarity between enzymes doing the histone demethylation and DNA methylation. I also see him move from biochemistry to stem cell biology, and learn many new techniques and expertise to answer important questions. I have seen many famous scientists before, but scientists who are deep thinkers, who continue to challenge themselves by building on their existing strength, learning new things, answering the next important questions are far fewer. I now have new found respect for Yi Zhang. Too bad he is not working on cancer epigenetics.

Nov 092012

My group is recently looking into the 12 cancer driver pathways that Vogelstein mentioned, and we found that many pathways have really nice and intuitive YouTube videos.








Epigenetics (these although are not about cancers):

Cell cycle:

The following do not have good hits:
DNA damage repair

Actually through this I found a series of nice videos introducing basic biology concepts:

Nov 092012

This afternoon, the Postdoc and Graduate Student Affairs Office at DFCI hosted a seminar on “Habits of an Effective Scientist”. Kudos to our newest postdoc Wei Li, here are the notes:

Levi Garraway

  1. get to work early in the morning
    Plan experiments days/weeks ahead and stick to the plan
    Expect to invest some (but not all) evenings and weekends
    Use time wisely
  2. pick a great mentor
    Academically outstanding
    Worthy of emulation (professionally and personally)
    Has time for you
  3. pick projects that are both salient and have a high likelihood to success
    “Bayesian principle”
    Nobel prize can come later… but keep it interesting!
  4. be true to the science; be evidence based
    Objectivity and critical thinking
    Openness to new directions
    Willingness to accept failures
    Ability to recognize when you might be wrong
  5. chance favors the prepared mind; master writing and communication, presentation
  6. decide what you want out of your career and what sacrifices you are willing to make
    What does success mean to you?
    How long to delay gratification?
    “Down time” (or lack thereof)
  7. always prioritize that which matters most

Jean Zhao

  1. setting goals and timelines
  2. inspiration vs perspiration
    “Genius is one percent inspiration and ninety-nine percent perspiration” (Thomas Edison)
  3. be truthful
    “Being busy does not always mean real work.The object of all work is production or accomplishment and to either of these ends there must be forethought, system, planning, intelligence, and honest purpose, as well as perspiration.”
    “Seeming to do is not doing”
  4. careful planning
  5. persistence
  6. be resourceful
    “Our greatest weakness lies in giving up.The most certain way to succeed is always to try just one more time.”
    “Just because something doesn’t do what you planned it to do doesn’t mean it’s useless”
  7. common sense
    “The three great essentials to achieve anything worthwhile are: hard work, stick-to-itiveness, and common sense”
  8. focus
    “To explain all nature is too difficult a task for any one man or even for any one age. It’s much better to do a little with certainty and leave the rest for others that come after you, than to explain all things by conjecture without make sure of any thing.” (Issac Newton)
  9. collaboration
  10. be positive
    “I have not failed. I’ve just found 10,000 ways that won’t work.”
  11. balancing vs managing
Nov 082012

My son started playing the violin this fall, and spent the first 3 weeks learning to hold the violin and the bow and putting his fingers correctly on the strings. The violin teacher told him to imagine building a big house. The early practices on posture, fingering, and bow movement just lay the foundation for later building the house.

I have had experimental biology students asking whether they could do a rotation in my laboratory to learn the basics of Bioinformatics. In the long run, they hope to be proficient in both genomics experiments as well as bioinformatics analysis, under the co-supervision of me and another experimental biologists. I am often enthusiastic about such requests, as it is important for experimental biologists using genomics approaches to understand high throughput data analysis. Frankly, what is genomics without bioinformatics? Actually at Harvard, we have a class STAT115/215 that teaches the basic algorithms and skills for bioinformatics data analysis as well as python and R programing. I believe these lay a good foundation for learning the basics of Bioinformatics.

Dilemmas arise when occasionally the rotation students say, “During this rotation, I am very keen on bringing along a dataset from my experimental advisor’s lab to analyze in your lab, and we would like to see this paper out soon.” I have been thinking hard about how to best respond to such requests until I see this beautifully done documentary: Jiro Dreams of Sushi.

Imagine Master Jiro getting this request from an apprentice at a top French restaurant, “I have a passion for the culinary art, and have been learning a lot from this top French restaurant. I would like to do an apprenticeship at your restaurant, because I heard you are the world-famous sushi master”. The apprentice continues, “And by the way, I will be bringing my own fish to this apprenticeship. The French restaurant I have been learning from will be hosting a great wedding dinner in 3 months for a prominent Japanese family. In addition to the exquisite French dishes, we would really like to use the fish I bring to learn making sushi from you that we could serve at this wedding”. Knowing that apprentices at Master Jiro’s restaurant spend 10 years laying solid foundations before they can make an egg sushi with Master Jiro, I now know how to respond: although bioinformatics research takes at least as much skills and experiences as making sushi, since you are a really smart Harvard graduate student, I will give you a break and ask for only 5 years :).

Nov 062012

Ever since I got promoted to full professor, the number reference letter requests (for training grant mentors, job applications, promotion evaluations) have quadrupled. Usually I ask the applicants for their CV, academic statement (which summarizes the research, teaching, community service, grants and awards), and representative papers. In addition to reading these, I also would like to check out the person’s My Citations profile on Google Scholar. To my amazement, many professors don’t have a profile on Google Scholar.

Every scientist can create a Google Scholar profile to keep track of your papers, citations, and H-index. More interestingly, it gives recommendations on what new papers you might be interested in reading, and these recommendations are quite accurate! It is really easy to setup, and Google scholar is actually quite amazing in finding your previous publications. The update could be tricky for Chinese PIs (so set “manual update”), since Google often mistakenly identify papers that are published by other people with the same last name and first initial. For older papers, Google often sorts things out better, probably from the website of the PI and his/her collaborators (co-authors).

Since the Google Scholar My Citations profiles are setup by the authors themselves (instead of Wikipedia which could be setup by your admirers), there are two types of PIs who don’t have a profile. The first type are big shots: they are so busy that they don’t have time to set this up, but they are so famous that you should just know their papers. The other type are country pumpkins, or more appropriately in Chinese 土人. So if you are a PI but don’t have a Google Scholar profile yet don’t belong to the first type, do yourself a favor and setup one.

Nov 042012

I have this crazy hypothesis, which I told many other colleagues: If a faculty has 3 kids or more, s/he will be very successful academically. This hypothesis doesn’t have very good sensitivity, meaning that you can still do well without have 3 kids or more. But it has excellent specificity, meaning that if you have 3 kids or more, oh, then you will definitely do well! If someone can handle 3 kids in her personal life, I mean it, she is in control of her academic life!

Actually all my colleagues with 3 kids or more are very successful, Kevin Struhl, Sunney Xie (for both, their 2nd and 3rd are twins), David Fisher, Fritz Roth, Linda Chin, Mark Daley, Russ Altman, Eran Segal, Ben Ebert, Laurie Glimcher, Catherine Wu, Howard Chang, and many others… I still remembered when Evan Johnson first discussed with me about doing a PhD thesis in spring of 2005. I had a meeting with him and his other PhD advisor Jun Liu about a potential project. A couple of months passed, and I didn’t hear from him. So I thought, “OK, maybe he wasn’t that serious about doing a thesis with me”. Then in June 2005, he emailed me to say that he had been thinking about the project I told him. His wife just had the 3rd baby after a complicated pregnancy, and he would like to meet again and really work on this project in the summer. A light went on in my head, “3 kids! OK I am going to take this student!” Later, it turned out that Evan was a Mormon :), but he still confirmed my hypothesis: Evan did great work in my lab, finished PhD in 4 years, got a faculty position right after, had his 4th child, was the 1st of all my trainees to get an NIH R01, and is doing really interesting work at BU now.

So I hope you are convinced. If not, look around you (i.e. if you are not in China :), and I bet you will see cases validating this hypothesis. So far the only false positive I am aware of is Amy Bishop from University of Alabama. During her promotion evaluation, she pulled out a gun and killed her committee members. What will happen to her poor five kids! I am glad she is not in my department, and I acknowledge the hypothesis doesn’t apply to anyone literally crazy!

Nov 022012

I listen to audiobooks on my long commute to work every day. It keeps me awake while I drive. A great place to buy audiobooks is Audible. For $20 / month, you can buy two audio books (any two) a month, and sometimes I buy a lot when they have many books on sale for only $5-6 each. For two books a month, you could really learn a lot over time! I don’t usually read fiction, most of the time I listen to biography, history, science, self help books, and audible professor (recorded lectures).

A while ago, I “read” (listened to the audible version of) The Emperor of All Maladies: A Biography of Cancer. It is a wonderful book about the history of cancer research. Being at the Dana-Farber Cancer Institute which was started by Sidney Farber who invented chemotherapy, it was wonderful to learn about our history here and the early lessons on chemotherapy. I also tremendously enjoyed reading all the science history about basic research, e.g. review of work by Varmus, Weinberg, and many others. It was really exciting, and I listened to it back to back twice. I told lab members about this book, and bought one for the lab.

Recently one lab member told me that he tried to read it, but got so bored he couldn’t finish. Apparently another lab member also tried but couldn’t pass the first few pages. It occurred to me that indeed the beginning of this book wasn’t as interesting. So I looked at the table of content on Amazon. The fun starts around page 18 when the author introduced Sidney Farber. Actually from the book preview on Amazon, I noticed that each chapter is often divided by sections. If one section is boring, just jump a section ahead. Hope this will help other readers go beyond the first few pages. Enjoy reading!