Nov 102017

I want to share some of my experiences balancing work and life and keeping our house organized. From the book “The life-changing magic of tidying up”, I learned a few things. Throwing away things I don’t use any more is the most important way to declutter, so only keep things that give me joy. A rule to decide whether to throw something away is to ask, “if I were to buy this thing at its current state, would I pay for it?” If not, then throw it away. For everything I keep, it needs to have a designated place in the house.

Recently, we started a cleanup routine in the kitchen. At the end of dinner, family members throw dice to determine who to perform which clean up tasks: clean up the table, take out the clean dishes from the dishwasher, put the dirty dishes in the dish washer, wash the pans, vacuum the floor, take out the trash, get and sort the mail. Kids throw first and select the first two tasks, and my husband and I will handle the rest. My kids used to always complain whatever task we assigned them was the hardest, but now we everyone gets different tasks by chance so no complains. Also, kids learned to do all the house chores.

From the book “How to manage your home without losing your mind”, I learned to use “the 10min pick up” rule for the family to work together to keep the house clean. Except myself, the rest of my family used to only clean up once in a while. As a result, they often don’t get the house organize and clean enough, even after spending significant time and efforts. So cleaning up the house has been a big burden for me and the rest of the family. The “10 min pick up” rule suggests that every family members should spend just 10 min each day to do some organizing and clean up, and leave the rest to the next day. Usually, each family member will work at their own pace to put jackets, backpacks, books, loose change, pens, nail clipper, medicine, scratch papers, candy wrappers, toys, dirty clothes in their proper place, or move one step further in the laundry washing, drying, and folding process. I still help kids a lot in their pick up process, but having 4 people each pick up 10min means 40 min of cleaning daily, which is sufficient to keep the house in order! Also, since family members appreciate each other for making the house a little bit cleaner and more organized even if it is not perfect, this task is now a pleasant experience for everyone!

So every evening after dinner, our family work together on 10 min cleaning in the kitchen and “10 min pick up” around the house. Then we do something fun, such as playing cards, board games (e.g. connect 4), ping pong, or foosball together. Even though the kids might still have unfinished homework and we always have even more unfinished work, we make sure to spend this family quality time together. Unfinished work can wait until after the quality time. Shouldn’t we always spare 15-30 min daily for the family? Even though my husband and I both have crazy work schedules, this evening routine has helped keep the house in order and maintain the happy family bond.

Sep 052017

I wrote this blog about 3 years ago, but never got to post it. Here it is:

I have been to several very interesting conferences in the last year. During many talks, I diligently took notes (I love Evernote) and downloaded relevant papers which I planned to read afterwards. However, upon returning from these conferences, I often had to deal with work that got piled up during my absence, and by time the crunch was over, the notes and papers to be read are forgotten.

At AACR, Myles Brown went to Rick Young‘s talk where Rick presented their in press Cell paper on super-enhancers. I immediately thought of stretched enhancer talk given by Francis Collins’ lab at the Welcome Trust disease epigenetics meeting. I went back to my notes, and saw the things I planned to ask lab members to check but never got to do. They could have given us 6 month lead on a dynamic ChIP-seq paper which we have been working on for publication.

Looking back, I should really spend sometime reviewing my notes after returning from each conference. First, I am highlighting my notes that are directly relevant to our work and things we should check in red now, so I can go back to it faster. Also, I will spend a couple of hours reviewing to make the conference really sink in.

The following is new: Sometimes these notes are extremely important, even if I don’t fully understand the material. Last year a new postdoc was designing an experimental study for using in vivo CRISPR screens to study immunotherapy response. I went back to my notes, and saw Nick Haining‘s talk a year ago, which had the identical experimental design. I am glad we didn’t embark on that study, because Nick’s study was published in Nature this summer.

Aug 252017

Over the years, I have an increasing appreciation of the cost effectiveness of tumor RNA-seq for precision cancer medicine research and clinical utility.

From TCGA tumor profiling, scientists have tried different clustering methods, from DNA mutations, mRNA-seq, miRNA expression, DNA methylation, and RPPA (proteomics). Although they often give different clustering results, the most informative in consensus clustering modeling of all the information together and tumor subtype classification is still probably RNA-seq. Of course, we can also learn a lot better how genes are differentially regulated in cancers, and Cistrome Cancer is one of our initial attempts. Sophisticated scientists can also investigate alternative splicing, RNA editing, non-coding RNA, or alternative polyadenylation .

How about tumor mutation analysis? The most functional oncogenic mutations can be directly detected from tumor RNA-seq. In recent neo-antigen prediction studies, the authors also only consider mutations that are highly expressed, which are detectable from RNA-seq. Unfortunately RNA-seq will miss tumor suppressor losses, but currently available cancer therapies are mostly targeting oncogene gain of function mutations instead of tumor suppressor loss, so RNA-seq will still be more informative to identifying targeted therapy.

To study tumor immune microenvironment, RNA-seq is quite informative in evaluating the immune infiltration and associating this with patient clinical features. There has been a number of papers published on this (CIBERSORT, CYT, TIMER, xCell), all based on tumor RNA-seq data. Also, we can obtain the patient HLA typing from tumor RNA-seq.

To obtain tumor immune repertoires, TCR-seq and BCR-seq are quite expensive and need separate assays for TCR alpha, beta, gamma, delta chains as well as BCR heavy and light chains. In contrast, RNA-seq can detect all of them from a single RNA-seq samples, at least the most abundant immune repertoire clones which are more likely to be recognizing tumor antigens. We have the TRUST algorithm to do this and are still improving the algorithm daily.

For therapy response biomarkers, traditionally oncologists use qPCR, small microarrays, and recently nano string. I wrote this blog about transcriptome as a biomarker in 2013, and I still believe in it 4 years later. Nowadays RNA-seq costs about $300 / sample (100M fragments of PE150) and the turn around time is usually one week, and these numbers continue to improve with sequencing technology development. RNA-seq provides much more information for an informative and robust biomarker.

One limitation is for RNA-seq is that sample quality is easier to maintain for DNA than for RNA especially for tumors obtained much longer before (e.g. in order to accumulate better survival information). However, physician scientists now are much more experienced with the processing or frozen storage of fresh tumors. Single-cell RNA-seq is gaining momentum in recent high profile studies, although it might be too costly and technically challenging to be adopted as a standard clinical assay, at least right now. Currently data analysis is still a bottle neck for many scientists, and here is one effort we made to streamline analysis. I hope the scientific community, including us, continue to develop the sample processing automation and data analysis algorithms and pipelines to help the coming of age for tumor RNA-seq.

Feb 122017

During the Christmas and New Year holidays, I read two books: The Miracle Morning and The One Thing. I tried to combine their recommendations in my daily activities, and the results have been quite impressive. I will start by explaining the The Miracle Morning first, which encourages people to establish a morning routine. There is a recommended routine, but the author encourages people to try different things to find something that fits them well. So here is mine:

1. Before going to bed at night, be determined to get up at a certain time in the morning. Depending on the time I go to bed, I decide the specific time I need to get up, but this doesn’t need to be crazy early, although going to bed early and around the same time daily helps.
2. Put the alarm away from arms reach, so I can really get up as soon as the alarm sounds.
3. Put on my fleece jacket, use the bathroom and brush my teeth. I feel much more refreshed after brushing my teeth.
4. Drink a cup of water I put next to my bed the night before. I put lemon juice and honey in the water which helps hydration in the morning.
5. My husband always takes a little longer, so I sit in bed, look over my new year resolution and the schedule for the day to wait for him (for meditation and exercise together). The new year resolution reminds me of my priorities, so I feel better saying no or delaying response to low priority activities. Checking my daily schedule ensures that I don’t forget important meetings that day. Also each day I give myself the top 1-2 things I need to get done (more details about The One Thing later).
6. Do 10 min meditation using Headspace or InsightTimer on my iPhone. Ariana Huffington recommended Headspace although there are many other mediation apps available. The Miracle Morning recommended “Affirmation” (kinda like going over our priorities) after meditation. However, if I don’t go over my priorities and schedules, my mind keeps on wandering over my priorities and schedules during the meditation. So I decide to mediate after I set my goal and schedule for the day.
7. Exercise for 30 min on yoga mat. We used to follow Sworkit, but recently we just sample some exercises from Sworkit ourselves. This really gets us warm and awake.
8. Take a shower, get dressed, do my writing. My husband gets the kids to school in the morning, while I pick up the kids in the afternoon. Depending on the time I have, this could be a productive time to get grants / papers written. No email at this time, although I need to be more disciplined here!
9. I take my vitamin and calcium pills and drink my breakfast while doing my writing. I prepare my breakfast the night before: add mixed bean porridge (16 mixed-bean bags from MarketBasket, cooked with high pressure cooker), yogurt, frozen fruits and vegetables, some nuts, and water, blend it into a fine mix. It looks disgusting but tastes great!
10. Go over my 3 daily SCRUM project meetings on Skype: 8am on immunology, 8:30am on CRISPR screens, and 9am on epigenetics. I am grateful to the dedication and hard work of my team, so we make progress every day!
11. Get more writing done alone at home, or prepare teaching on Tue / Thur teaching days.
12. Drive to work when there is no traffic, and listen to audiobooks on the drive. I don’t schedule meetings in the morning, so can drive in late. The Miracle Morning book recommends reading before writing, but writing is more important for me to get done in the morning, so I only “read” (aka listen) on my commute. Unfortunately audio books can’t be too serious (e.g. you can’t read scientific papers), but still could be very enlightening and fun.

The real “miracle” I have learned from this book is that these items (especially 5, 6, 7, 8) don’t always need to be the same length. Ideally, I get up at 6am and start my writing at 7am. However, if I sleep late and get up later in the morning, then I can shrink all the activities roughly proportionally: e.g. 1 min priorities, 3 min meditation, 10 min exercise, 15 min writing; or 30 sec priorities, 1 min medication, 5 min exercise, and 7 min writing. Even 5 min exercise is still better than no exercise. The key is to keep this routine every day! The habit, once established, could be very effective in making the whole day productive. Keeping the schedule makes me feel really good in the morning, so I am motivated to continue the habit. So now I really need to go to bed, so I can get up early to start My Miracle Morning tomorrow.

Jan 152017

In the last decade, Chinese government has drastically increased investment in education and research. One important initiative is the Chinese Scholarship Council (CSC) which sponsors graduate students to study for 1-2 years at top foreign research institutions. Our laboratory has hosted a number of talented visiting students, many of which achieved impressive research results during their visits. In Dec and Jan right before these scholarship applications are due, I often receive many email requests from candidates. Quite a few read something like this:

Dear Professor Xiaole Liu,

My name is AB, and I am 2nd year PhD student from C University in China. I work on the mechanism of X gene / complex in the Y developmental stage of Z organism. From my previous studies, I know techniques D, E, F and G and have published a paper in H, I, J journals. From your website, I read that you are a cancer and bioinformatics expert, and I really hope to learn more about both. Recently I have been awarded the CSC scholarship, which will sponsor me for travel and living cost to study in the US for one year. I hope to have the opportunity to study in your lab, so I urgently need to get an invitation letter from you.

I look forward to working with you!


Is there anything wrong with such a letter? Let’s analyze:

1. People usually say Dear Professor (or Doctor) Lastname, not first last. So I should be addressed as: Dear Professor Liu.

2. In most cases, the XYZ research has nothing to do with what my lab is doing. The applicant is just interested in learning cancer or bioinformatics, or both, but why would our lab be interested in hosting them? This is the same with postdoc applications as well. Is there something that the applicant could contribute, e.g. certain experimental technique, qualitative skills, biological knowledge, clinical sample resource, etc, which might be valuable to the host laboratory?

3. Usually the first letter just explores the possibility that a is interested in hosting his/her visit. The invitation letter request should be mentioned after the host lab has agreed to host. It is inappropriate to ask for the letter in the first email, let alone to ask for it “urgently”.

4. Every graduate student (of course postdoc and faculty as well) should actively maintain and update a CV, and include the CV in the attachment of such an email. Resume and CV are used for industry and academic job applications, respectively, and they have different lengths and formats. CV gives the host laboratory a lot more concrete ideas about the candidate, his educational histories, test scores, publications, awards, and other professional experiences, etc. Many people put their CV online, so it is easy to find good CV online and see how they are written. I often look at the CV of really successful experts in my field, and see what areas I need to grow. For example, seeing what papers these big shots published, grants and awards they obtained, courses they taught, other professional experiences they had at my stage is very inspiring. Anyway, always include CV when applying for PhD, postdocs, visiting scholarship, etc, which greatly increases the chance the application will be considered seriously.

Jan 082017

Recently, as I was looking up some answers to an immunology question, I came by this great YouTube Playlist of 35 short immunology videos by Armando Hasudungan. I will certainly be viewing all of these lectures!

From there, I also found the Aims Education list of 7 good BioMedical YouTube sites. Over the years working at DFCI, I have grown to admire doctors more and more, at least the Harvard MDs that I have worked with. I have meant to take some courses to learn more about medicine, such as the Harvard Medical School crash course to help physicians prepare for the board exam, but really haven’t found the time to do so. I guess this is a quick and easy start.

Technology is great, and god bless the people who spent the time to create educational resources for the world (e.g. contributors to Khan academy and Wikipedia).

Dec 152016

In the Dec 15, 2016 issue of Cell, three papers from Jonathan Weissman, Aviv Regev, and Ido Amit described this really cool technique called Perturb-seq. This is a technique to do focused CRISPRi screen (of ~100 sgRNAs) followed by Drop-seq. Basically they use CRISPRi to knockdown different genes in different cells, then examine the transcriptome outcome of the different knockdowns through single-cell RNA-seq. Very often after a genome-wide CRISPR screen, you often have many hits, so they can use CRISPRi to validate each hits and explore the mechanism of the KD effect. Although single-cell readout from Drop-Seq could be noisy, they sequence ~500 cells per CRISPRi, so the average from the ~500 should give a much more robust expression readout. Perturb-seq doesn’t have to be a validation step of a CRISPR screen, as I would be totally excited to see the transriptome in MCF7 after knocking down 100 different transcription factors, chromatin regulators, and kinases, as Aviv’s paper beautifully demonstrated. This is super cool!! For a long time we have been searching for a proper application for single-cell RNA-seq in translational cancer research. Perturb-seq really sold me on the practical value of Drop-seq.

Now, before we get too excited, we should examine the raw data from Perturb-seq. Seeing is believing! If the data quality is indeed excellent, then there will be opportunities to develop computational methods for the systematic modeling of gene regulatory networks. Aviv’s paper has some cool informatics modeling, but I am sure there are still good opportunities!!

I got an email the morning after I posted this blog, from my Stanford labmate Serge Saxonov. Turns out he is the CEO of 10X Genomics, the technology platform that enabled the Drop-seq part of Perturb-seq. What a happy surprise it is! I haven’t see Serge since I graduated. He started 23&me right after PhD, and now is the CEO of 10X Genomics, wow!!

Dec 082016

When I was traveling this fall, I watched the movie Me Before You over two flights. A dashing rich young Will Traynor became paralyzed from a car accident. Despite his family members and caregivers trying to cheer him up, he didn’t see his condition improving so asked his family to end his life (sorry for the spoiler). The ending was a surprise, which really got me thinking. Recently I also had a good discussion about it with my girlfriends. They thought Will was good and real, but I didn’t think very highly of him. His brain was still very sharp, and he had good connections to make a difference in the world. If he wasn’t so rich, had a wife and kids to support, could he afford to die?

Today at the San Antonio Breast Cancer Symposium, Eric Winer gave the William L. McGuire Memorial Lecture. He discussed the recent development and challenges of breast cancer treatment. At the end he talked about his own history. He was born with hemophilia and frequented hospitals as a child, at a time when the life expectancy of hemophilia patients was 20. When he was 13, Factor VIII became available which with injections every 5 days, he could be symptom free. This motivated him to be a doctor. Since Factor VIII was isolated from blood donors, he got HIV infection in 1989 and was kicked out by his dentist. With the development of HAART, a cocktail taken daily for HIV patients, he can live with HIV. Then it turns on HIV infection from blood donors also often accompanies hepatitis C, so he had to take 2 more years of interferon and ribaviron to treat hepatitis C. In 2003, he got GI vascular shunt from the HIV treatment and liver necrosis, which he had to take a surgery to bypass. Despite these harrowing experiences, he now has a lovely family with 3 successful kids, and appears as healthy and energetic as ever. He thanked biomedical research, also the US healthcare system for giving him access to newest drugs to treat his conditions. So the hope for cancer patients, at least in US, is also that with advances in biomedical research, cancer treatment will advance significantly in the coming years.

It was such a moving and motivational talk! Before I only knew Eric as the preeminent breast cancer oncologist, the head of our breast cancer SPORE, who always appears happy and confident. I didn’t know he had to live through so much, and even now has to regularly take the Factor VIII injection and HAART medication. He has all the excuses in the world to complain about his fate, and yet he has the optimism and grit to achieve so much in life. Actually looking around, many of my very successful relatives and colleagues have had personal or family tragedies, divorce, illness, or death (of loved ones), etc. And yet they had the optimism and grit to pull themselves together and try their best. Eric mentioned that growing up with hemophilia shaped him, so he was able to deal with later challenges in life. Compared to them, I feel so lucky and want to give my best to my work and the world.

So now I am even more convinced that Will should not commit suicide. Christopher Reeve didn’t commit suicide, instead he made his last 9 years of paralyzed life worthwhile and did so much good to the world. Even though Will’s illness was not curable at the time, there is always hope that a cure will be found with new biomedical research and development.

Dec 012016

Just finished NIKE founder Phil Knight’s book Shoe Dog. An absolute must read, not only for its content, but also for its humor! The true stories about real people are infinitely more fascinating than novels, you see the laughs and the tears in their experiences.

When I read books about Steve Jobs, Jeff Bezos, and Elon Musk, I felt that these people are geniuses way beyond my league. They knew exactly where they want and are going from the start. But Phil Knight is more like us mortals, improvising as he went along, and just trying his best. His advice was quite intriguing: “Let everyone else call your idea crazy, just keep going. Don’t stop, don’t even think about stopping until you get there, and don’t give much thought towards where there is.” Indeed, in work, I wish we plan strategically and do the right things towards the goals, but very often we end up in a different place from where we thought there is.

NIKE was able to keep most of its founding team for many years, especially those who love sports or running. It boosted my respect for runners who have that grit and optimism. I bought new NIKE free running shoes. Time to get back to regular exercise!

Sep 282016

When I was a graduate student at Stanford, fellow graduate students hang out together all the time, going to social activities, consulting on class or research projects, or gossiping about different advisors or laboratories. One topic we discuss often is how long it takes for our respective advisors to revise our manuscripts. A common complaint from students is, “I have sent this manuscript to my advisor for two weeks, and still haven’t heard a word from my advisor about it. What is s/he doing??”. Having been a faculty for 14 years, I finally understand the answer to this question.

First of all, I appreciated how busy a faculty’s schedule is, and it gets busier as the faculty becomes more senior. Since I wrote the “Fit Tasks to Schedules” blog, I feel much less guilty saying No to people who requests me to review papers / grants or write letters of references / evaluations on a short notice. Also, I now categorize manuscripts from my trainees into 4 categories based on how important and well written the ms is.

A. For ms that is very important (clever method, significant finding, potential for high profile publication) and well written, I am extremely motivated to revise it as soon as I receive it. I am very happy to use my skills and knowledge to improve the writing of the ms, and check it off my to-do list.

B. For a ms that is well written but not very important, or not so central to the research program in my group, I usually take a quick look and give some brief feedback quickly, and mostly rely on the first and senior authors to revise the ms in detail.

C. For a ms that is very important and yet not so well written, I feel strongly that the ms has potential but also the pain associated with the revision / rewriting. It would take the trainees persistence to find time and work with me on the revision, and my perseverance to revise the ms to a good shape in a couple weeks or months.

D. For a ms that is not so important and not so well written, it usually languish on my computer for months. The ms is often not in shape for submission but it will take too much time and efforts to revise it.

So when trainees wonder why their advisors still haven’t revised their ms, it is often because their ms is in category C or D. When this happens, the trainees often feel that the ball is in the court of the advisors (I already give the ms to her, and it is her responsibility to revise it), but in fact it is still in the court of the trainees (I better revise this ms myself more so it is in better shape for my advisor to revise). So trainee should take the initiatives and schedule a time (e.g. 30-60 min) to talk to the advisors about the ms to get some quick comments, or to sit and work on the revision together with the advisor. After all, if a ms drags on too long or never gets published, it probably hurts the trainees more than the advisors.