Bo Xia @BoXia7 Twitter profile | Pikagi

Pikagi

Bo Xia

@BoXia7

2,124

Followers

1,803

Following

36

Media

476

Statuses

Junior Fellow @Harvard Society of Fellows | @GRO_Broad Fellow & PI @broadinstitute . Study the genome: how we develop, what causes diseases, what makes us human

Cambridge/Boston, MA

https://t.co/pUWYPm3uTE

Joined March 2018

Don't wanna be here? Send us removal request.

Pinned Tweet

@BoXia7

Bo Xia

4 months

A true curiosity-driven journey, fulfilling one of my childhood dreams! The tail loss marks a pivotal evolutionary step towards humans and apes. But how did it happen? @ItaiYanai @JefBoeke

@ItaiYanai

Itai Yanai

4 months

How did we lose our tail? A simple question.. but it wasn't really asked before! We discovered a plausible scenario for the genetic mechanism that led to tail loss. Amazing that such a big change may have been caused by such a small genetic event. @BoXia7

Tweet media one

98

781

3K

23

95

472

Last Seen Profiles

@pengen_stw

@noe_generaption

@KemppainTa

@HerrudHerr

@EliasAmare

@TeamHeretics

@amines110

@karim_zzz8

@Billys_Bets

@sarafamous7

@ded_tyt

@tatyebt

@Elton_PE

@archedinburgh

@Julia_in_Winter

@soobsgfz

@Projectj0220

@MsgToken

@mina_edennosono

@shortkia1

@science06211

@Goddess_Sindra

@coach_G63

@JaylenC97955716

@StefanoBusani

@Angelique9523

@alkhbr_mmhwnh

@hyzlhs

@Secunda11656206

@AlexMasterman0

@ASEANNOWTH

@davebhuvan

@sjad10017098

@AveMacmull

@mr_beha

@PoaDMDuluth

@BoXia7

Bo Xia

4 years

Here is the transcriptomics insight: the bulk RNA-seq (Fig 1), single-cell RNA-seq (Fig. 2), spatial transcriptomics (Fig. 3), and the original organ (Fig. 4). (Feel free to cite with image credit to Bo Xia)

Tweet media one

Tweet media two

Tweet media three

Tweet media four

40

457

2K

@BoXia7

Bo Xia

3 years

OK, I'm finally able to share this exciting research that has been in my head for years, or literally almost my whole life. "The Genetic Basis of Tail-loss Evolution in Humans and Apes".

@ItaiYanai

Itai Yanai

3 years

Losing our tail had big consequences for our ancestors, but how did it happen? In our paper, led by @BoXia7 , and with @JefBoeke , we propose that tail-loss involved the insertion of a single transposable element, with implications for our health today.

47

271

1K

19

62

383

@BoXia7

Bo Xia

3 years

Just received the new year gift from @10xGenomics . Thanks so much! It’s amazing that they made my Lego brain (aka lego spatial transcriptomics concept) into a gift box that you can replicate it 100%. Have fun with it!

Tweet media one

15

14

259

@BoXia7

Bo Xia

2 years

I’m super excited to start my new journey as @GRO_Broad Fellow @broadinstitute and a Junior Fellow of the Society of Fellows @Harvard . I will lead an independent group to study the principles and mechanisms of genome organization underlying development, disease, and evolution.

15

8

252

@BoXia7

Bo Xia

2 months

This is the moment when I truly understood that a PI going to lab only causes trouble (by interrupting their experiments)😌

Tweet media one

7

3

164

@BoXia7

Bo Xia

2 years

Our C.Origami work is online @NatureBiotech ! A tour de force by @tan_jimin and a wonderful collaboration with @artsinyc . Check out how we use high-throughput in silico genetic screen to discover new regulation of genome organization. Full manuscript here:

@NatureBiotech

Nature Biotechnology

2 years

Cell-type-specific prediction of 3D chromatin organization enables high-throughput in silico genetic screening

Tweet media one

0

23

95

6

26

147

@BoXia7

Bo Xia

3 months

UCSC @GenomeBrowser is an ‘eBible’ (whatever it means) for geneticists. They even made a tutorial using our discovery as a case study - I will teach it in undergrad genetics/bio course. . Happy to do guest lectures, too. Just DM or email me.

@ItaiYanai

Itai Yanai

3 months

The UCSC @GenomeBrowser is a free user-friendly browser for anyone curious to study a genome. “Tracks” of annotation are shown in parallel, showing genes, transcripts, other genomes, and functional information. You can zoom in & out to study the genome at different scales. (2/13)

Tweet media one

1

6

49

2

20

142

@BoXia7

Bo Xia

2 years

Super excited & grateful to receive the 2022 NIH Director's Early Independence Award (DP5)! Thank you @NIH_CommonFund for supporting our work studying gene and genome regulation @GRO_Broad @broadinstitute and @Harvard . We're recruiting - join us for exciting science and more!

@NIH_CommonFund

NIH Common Fund

@NIH_CommonFund

2 years

What behavioral and #BiomedicalResearch will this year’s #NIHHighRisk awardees conduct? From #HealthDisparities to #ReproductiveHealth , see the award-winning, innovative projects early career and seasoned #scientists proposed:

Tweet media one

0

8

17

9

5

121

@BoXia7

Bo Xia

2 years

I’m very honored and grateful to be one of the recipients of the 2022 @WeintraubAward ! This award is also presented to my two great mentors, @ItaiYanai and @JefBoeke , who share the same spirit of being caring, supportive & inspiring mentors as Dr. Hal Weintraub.

@HutchBasicSci

Hutch Basic Sciences

2 years

Our biggest congratulations to the recipients of the 2022 @WeintraubAward ! These thirteen exceptional graduate students exemplify the bold, creative, and pioneering spirit embodied by Dr. Hal Weintraub. Learn more:

0

2

16

14

3

110

@BoXia7

Bo Xia

2 years

Having problems with experimental Hi-C protocol and its cost? What if you can instead do in silico Hi-C with a tool that accurately predicts a high-resolution and cell type-specific chromatin interaction map? And even enables in silico perturbations and screening? Here you go!1/6

@biorxivpreprint

bioRxiv

@biorxivpreprint

2 years

Cell type-specific prediction of 3D chromatin architecture #bioRxiv

0

4

26

1

20

83

@BoXia7

Bo Xia

4 years

Very excited to share our latest work published on @CellCellPress ! With @ItaiYanai , we address long-standing mystery that testis has the most widespread transcriptome. We proposed that ‘transcriptional scanning’ modulates gene mutation rates, and ultimately gene evolution rates!

Tweet media one

@CellCellPress

Cell

4 years

Happy Thursday! Our issue unveils a brand new look for @CellPressNews & is full of exciting science, including 🐍 venom gland #organoids , #proteomics in #cancer & #neuroscience , #purine #metabolism , #Toxoplasma & more

Tweet media one

2

9

34

8

15

71

@BoXia7

Bo Xia

7 months

Our lab finished the wonderful year in the past week by welcoming Dr. Xinyu Ling @Dennislxy formal onboarding, a fun lab meeting with interesting science and games&gifts, and a lab dinner of celebration and appreciation! Very much look forward to the exciting new year! #XiaLab

Tweet media one

Tweet media two

1

2

51

@BoXia7

Bo Xia

4 years

I feel extremely honored and grateful for sharing the 2020 Regeneron Prize for Creative Innovation. It was a fun and fulfilling journey, especially during this difficult time. Science and Innovations can be – and should be – the solution to many problems we are facing right now.

@Regeneron

Regeneron

4 years

Congrats to the recipients of the eighth annual Regeneron Prize for Creative Innovation, which celebrates and rewards cutting-edge thinking from the next generation of young #scientists . Read about their winning proposals here:

Tweet media one

0

2

11

10

0

47

@BoXia7

Bo Xia

2 years

This truly made my day! Dr. Pääbo’s work on FoxP2 is one of my all-time favorite, and a big reason attracting me to the field of evolutionary genetics. We learn from the past to guide our way forward!

@NobelPrize

The Nobel Prize

2 years

BREAKING NEWS: The 2022 #NobelPrize in Physiology or Medicine has been awarded to Svante Pääbo “for his discoveries concerning the genomes of extinct hominins and human evolution.”

Tweet media one

531

14K

41K

0

0

46

@BoXia7

Bo Xia

1 month

So much fun learning about all the amazing stories behind the science in celebration of @JefBoeke ’s 70th birthday and >40 years as a scientist and a fantastic mentor! This fireside chat with Jef, moderated by @ItaiYanai , was unparalleled!!

Tweet media one

0

4

41

@BoXia7

Bo Xia

9 months

I'm super excited to welcome my PhD mentor, @ItaiYanai , to visit @broadinstitute next Monday and give TWO presentations: one at CC&E on some exciting ongoing research, and another Art-of-Science Seminar on one of Itai's favorites: Night Science!! @GRO_Broad @nightsciencepod

Tweet media one

0

1

40

@BoXia7

Bo Xia

2 years

Me watching droplet flowing when working with inDrop/Drop-seq single-cell RNA-seq. People nowadays working with 10X or other platform scRNAseqs won’t have such fun😉

@erin_rod_phd

Erik A. Rodriguez

2 years

😲Me watching live cell imaging videos!😲

2

95

910

1

3

36

@BoXia7

Bo Xia

5 months

How proud should I be as a new PI&mentor?! Two students are applying for graduate schools this year and both of them are accepted to some top programs around the country! Stayed tuned!

0

0

35

@BoXia7

Bo Xia

3 months

Why we take undergrads? NOT for an extra pair of hands!!! But because they are curious; they are creative; they are fearless; they are not constrained; and more importantly they are the future! They do need some protection during exploration sometimes so choose good mentors!

@DalalSci

Dalal Hamad

3 months

Why do PIs take on undergraduates in their lab? Why would someone who has ongoing big projects decide, 'I’m going to take someone who is inexperienced in research and has a high chance of messing up, to help me with it'? Genuinely interested

357

42

503

2

1

30

@BoXia7

Bo Xia

3 years

So proud of our rising star Eric!

@10xGenomics

10x Genomics

3 years

Single cell #CRISPR screens are informing novel therapeutic approaches to acute myeloid leukemia. Learn how Dr. Eric Wang of @sloan_kettering identified regulators of leukemia differentiation in this upcoming webinar. Register today: #AML #ECCITEseq

Tweet media one

1

4

27

1

0

29

@BoXia7

Bo Xia

6 months

Absolutely fantastic to see this work led by @AndrewPountain and @ItaiYanai out in Nature today. I had the luck to see its full journey from early fun observations (e.g.🅾️❎🈁) of gene exp pattern along bacterial genome to insights in transcription-replication regulation! 🥂 🎉

@ItaiYanai

Itai Yanai

6 months

Our paper is out today in @Nature ! Imagine getting this plot when studying single-cell data of growing bacteria! Could it be the cell cycle?! We found that a gene’s response to its replication reveals gene regulation on a genomic scale. @AndrewPountain

Tweet media one

39

253

1K

2

3

27

@BoXia7

Bo Xia

3 years

This has been an incredible journey in the late stage of my Ph.D. Words can't express how much I appreciate the tremendous support from my dear mentors @ItaiYanai and @JefBoeke . If you are looking for models of fantastic mentors, here they are!!

2

0

26

@BoXia7

Bo Xia

6 months

Nothing in bioinformatics makes sense except in the light of experimental validation. Joke aside, it's worth thinking about what true discoveries&principles&theories we can make beyond computational observations and modeling.

0

0

21

@BoXia7

Bo Xia

4 months

@TDCapellini @ItaiYanai @CrumpLab I’d be happy to grab coffee together and talk if that works. I’m also thinking of organizing a Zoom discussion and inviting people who are interested in this topic and want to discuss more and/or may have additional questions/comments/suggestions.

2

1

22

@BoXia7

Bo Xia

3 years

I literally watched this video with tears in my eyes. The past year has been really tough for Asians - especially Chinese - in America, and I don’t know how long this toughness will last. I lived with fear last year, completely different from what I felt when I came here in 2015.

Tweet media one

@POTUS

President Biden

3 years

From the Biden family to yours, happy #LunarNewYear . We wish you happiness, health, and prosperity in the Year of the Ox.

7K

10K

90K

1

1

20

@BoXia7

Bo Xia

4 months

@ItaiYanai @JefBoeke @WEIMINZHANG6 @BroshRan This journey marked my PhD-to-PI transition @broadinstitute . My lab @GRO_Broad now develops technologies that can accelerate our discoveries towards principles and mechanisms of genome regulation during cell fate transitions in development and diseases.

www.boxialab.org

0

0

21

@BoXia7

Bo Xia

2 years

@GRO_Broad @broadinstitute @Harvard @YiChengqi @ItaiYanai @JefBoeke @REMLehmann @xinjin @giladevrony @zz_zhaozhang @LiamHoltLab @JeremyDasen @artsinyc @iannisaifantis1 @jane_skok @KVRamachandran5 @TristanLi_Lab @buck_trible The best way I can think of to thank them is to pass on their generosity, kindness, and support to more people. We are recruiting brilliant postdoc fellows, research associates, and undergrad interns passionate about genome sciences and exciting research.

Xia Laboratory - Join Us!

We are actively recruiting talented people to join our group at the Broad Institute of MIT and Harvard! Please contact Bo for new opportunities: boxialab{at}gmail.com

www.boxialab.org

1

2

19

@BoXia7

Bo Xia

1 year

Possibly unpopular opinion: “progress in science depends on new ideas, new techniques, and new discoveries, more likely in that order”

1

0

17

@BoXia7

Bo Xia

3 years

@SageJulien @ItaiYanai @JefBoeke That was the biggest challenge in the project😂

0

0

17

@BoXia7

Bo Xia

4 years

Yes we are! We made kits for making DIY N95-equivalent masks!! Every one can make 10 masks in ~1h!

Tweet media one

Tweet media two

@JefBoeke

Jef Boeke

4 years

#isg team led by @LiliBlumenberg and @boxia7 leading effort to fab hundreds of diy n95 masks to protect the hi thruput testing swat teams at #isg #NYULAngone . proud!!! ⁦ @DavidFenyo ⁩ ⁦ @meghanokeefe ⁩

Tweet media one

6

9

51

1

5

16

@BoXia7

Bo Xia

4 months

In the intron of TBXT, I found a hominoid-specific Alu element that was hidden there to be discovered for 3 decades. In fact, it is just one out of >1 million copies of Alu in our genome - people would say it's not functional due to its location in the middle of nowhere - intron.

1

3

15

@BoXia7

Bo Xia

4 months

@TDCapellini @ItaiYanai I appreciate Terry for bringing up these thoughts, and agree that Terry’s comments are worth thinking about and discussing with the community. Let me explain:

1

2

15

@BoXia7

Bo Xia

2 years

This has been a quite long wait and finally! Click chemistry is just magic!!Guess for Sharpless, clearly there is another life right after Nobel Prize - waiting for another one as a laureate 😆And this wait is 20 years…

@NobelPrize

The Nobel Prize

2 years

BREAKING NEWS: The Royal Swedish Academy of Sciences has decided to award the 2022 #NobelPrize in Chemistry to Carolyn R. Bertozzi, Morten Meldal and K. Barry Sharpless “for the development of click chemistry and bioorthogonal chemistry.”

Tweet media one

368

10K

28K

1

1

15

@BoXia7

Bo Xia

4 years

As suggested, here is the analogy of a developmental system (e.g. spermatogenesis) that single cells form a continuum - pseudotime - in the tSNE visualization. Of course, there may be some somatic cell types (isolated clusters), for example, niche cells or epithelia.

Tweet media one

0

2

15

@BoXia7

Bo Xia

3 years

Thank you Carl @carlzimmer for telling the back stories. It’s really exciting to see the puzzle as a kid can be addressed. I’m looking forward to the future work which will be even more interesting.

@carlzimmer

Carl Zimmer

3 years

In non-covid news: why don’t we have tails? Your humble correspondent is ON IT.

5

38

140

0

0

15

@BoXia7

Bo Xia

4 months

@ItaiYanai As scientists we care about evidence&facts, and welcome civil and scientific discussion. This scientist accused us of 3 main criticisms, using insulting words repeatedly. I present some scientific evidence along with his (non-insulting) words so that the community can see:

Tweet media one

1

3

15

@BoXia7

Bo Xia

4 years

@AnnaYeaton Both. I made a lego brain, took a picture, and then photoshopped to refine the edges.

0

0

14

@BoXia7

Bo Xia

4 years

Do you have any moment that a very wild idea suddenly strikes you out of the blue? If that happens, write it down immediately, even on a table napkin. Here is how I'm doing with my 'napkin ideas':

Tweet card media

How to turn a Eureka moment into a research project

From ‘napkin idea’ to published paper.

1

1

14

@BoXia7

Bo Xia

5 years

It was a great experience working on this ‘Periodic Table of Cell Types’ with @ItaiYanai and with Development @Dev_journal . Check the Hypothesis piece and let us know how you think about it.

Tweet media one

@ItaiYanai

Itai Yanai

5 years

Bo Xia and I propose that cell types can be aligned according to their developmental stages and represented as a periodic table. @BoXia7

1

12

33

1

3

14

@BoXia7

Bo Xia

3 years

My parents always taught me to cherish food because they truly know what starvation is. Mr. Yuan #YuanLongPing #袁隆平 led the ‘Green Revolution’ in China by the development of high-yielding hybrid rice which has saved countless lives since 1970s.

1

0

12

@BoXia7

Bo Xia

3 years

Congratulations Dr.Barkley @BarkleyDalia It was an exciting journey to be your baymate and watching you grow over the years. Look forward to seeing what you will achieve next!

@ItaiYanai

Itai Yanai

3 years

Please welcome the brilliant Dr. @BarkleyDalia who defended her thesis on the 'Recurrence of cancer cell states across diverse tumors and their interactions with the microenvironment'. It was a joy to serve as her mentor. Keep an eye out for the wonderful things she will do next!

Tweet media one

Tweet media two

0

1

33

0

0

13

@BoXia7

Bo Xia

9 months

Congratulations Jason @JD_Buenrostro !! A true genius, a humble person, and a wonderful mentor!

@macfound

MacArthur Foundation

9 months

Jason Buenrostro ( @JD_Buenrostro ) is a cellular and molecular biologist and 2023 MacArthur Fellow investigating the mechanisms that regulate gene expression. #MacFellow Explore his work and all the 2023 MacArthur Fellows on our website!

8

29

202

0

1

12

@BoXia7

Bo Xia

6 months

Basic science is not just a foundation. It’s encouraging to read this inspiring piece by @REMLehmann ⁩ . Ruth has always been a role model to me!

Tweet card media

Basic science is not just a foundation

Nature Cell Biology - Intellectual freedom for scientists, unconstrained by commercial interests and direct application, fuels unexpected discoveries. Curiosity-driven, basic science has yielded a...

0

1

11

@BoXia7

Bo Xia

2 months

Glad to contribute to the investigation of xenotransplantation through leading the single-cell and time-resolved transcriptomic monitoring of xenograft-recipient interactions! Online @MedCellPress

@MedCellPress

Med by Cell Press

2 months

Online Now: Cellular dynamics in pig-to-human kidney xenotransplantation

0

0

1

1

1

12

@BoXia7

Bo Xia

8 months

Congratulations to the Sc2.0 @SynGenome team on complete synthesizing all chromosomes of yeast. This is an international collaboration achieved through the dedicated leadership, ingenuity, and perseverance by my comentor @JefBoeke . A true inspiration!

@DarkMatterDNA

The Dark Matter Project

8 months

Huge day for synthetic biology! The completion and publication of all Sc2.0 synthetic yeast chromosomes 🧬IT'S THE END OF THE BEGINNING🧬 @SynGenome #syntheticbiology

0

7

21

1

0

12

@BoXia7

Bo Xia

2 years

I’m so happy to learn that one friend just received a highly prestigious fellowship and they thought my tiny piece of suggestions really helped!

1

0

12

@BoXia7

Bo Xia

3 years

Why I don't have a tail? I used to ask this 'stupid' question when I was a little kid, seeing almost all other animals having tails but not me. 2/n

1

0

12

@BoXia7

Bo Xia

5 years

Fantastic symposium #NYCHumanGenetics at the National History museum! So many exciting talks @BlumaLeuch @erichjarvis @mason_lab and the poster session in the Hall of Ocean Life is just amazing. See the huge blue whale and the little white posters!

Tweet media one

1

1

10

@BoXia7

Bo Xia

3 years

What exactly does this hominoid-specific Alu insertion do? It turned out that this Alu element insertion is able to induce a unique alternative splicing isoform of TBXT which is sufficient to induce shortened tail or no-tail. 7/n

1

1

11

@BoXia7

Bo Xia

4 months

Congratulations to the new cohort of @WeintraubAward awardees —especially my friends Olivia Harringmeyer and @BingxuL — for their creative and pioneering spirit!

@WeintraubAward

Weintraub Graduate Student Award

@WeintraubAward

4 months

A huge congratulations to the recipients of the 2024 @FredHutch @WeintraubAward ! These twelve exceptional graduate students exemplify the bold, creative, and pioneering spirit embodied by Dr. Hal Weintraub:

Tweet media one

2

14

64

1

1

11

@BoXia7

Bo Xia

4 months

Embarking on this journey of curiosity has been remarkable, but what stands out is the incredible support from @ItaiYanai and @JefBoeke , and collaboration and help from @WEIMINZHANG6 , Guisheng Zhao, Xinru Zhang, @BroshRan , Jiangshan Bai, Matt Maurano, Sang Y. Kim, and many more!

1

0

11

@BoXia7

Bo Xia

4 years

Thank you to @Regeneron for funding and organizing the “dream” proposal challenge. Thank you to my great mentors, @JefBoeke and @ItaiYanai , and many friends who have supported me all the way through my career in science.

1

0

10

@BoXia7

Bo Xia

8 months

Congratulations @WEIMINZHANG6 and @DarkMatterDNA and @JefBoeke on this exciting work! The mSWAP-in tool greatly expands the capacity for routinely synthesizing large DNA and integrating it into the genome for functional studies and more.

@DarkMatterDNA

The Dark Matter Project

8 months

Out in @Nature ! @WEIMINZHANG6 and the @DarkMatterDNA team developed an efficient method to (biallelically) overwrite the mouse genome with any DNA🧬Huge step to mammalian SynBio. Oh, they also made a COVID-19 mouse model🤧

Tweet media one

0

36

111

0

2

9

@BoXia7

Bo Xia

4 months

The true Eureka or Night Science @nightsciencepod moment came when I noticed that this AluY element, distinctively hominoid-specific, is uniquely positioned in a head-to-head arrangement with another Alu element found in various monkey species, all of which possess tails!

Tweet media one

1

0

10

@BoXia7

Bo Xia

7 months

A great discussion @slavov_n & @anshulkundaje . Interpreting large bio data for discoveries requires both thorough domain expertise and a deep understanding of e.g. ML tools. However those who mastered both are few, and huge barriers still block true collaboration across expertise

@slavov_n

Prof. Nikolai Slavov

7 months

What are the bottlenecks of interpreting biological data?

24

7

41

0

0

10

@BoXia7

Bo Xia

4 months

@ItaiYanai @JefBoeke I got the ‘luxury’ to revisit this childhood curiosity after a tailbone injury. Inspired by the foundational works in developmental biology and comparative genomics, my attention turned to a gene called TBXT (aka T or Brachyury, which in Greek means ‘short tail’! @tbxt_brachyury )

1

0

10

@BoXia7

Bo Xia

3 years

BTW, no one thinks of @JimCameron 's Avatar @officialavatar ? Na'vi people use their tails for communication.😎

Tweet media one

0

0

10

@BoXia7

Bo Xia

1 year

Such a wonderful day, with great science delivered by amazing speakers! Looking forward to the coming year of great science around!

@GRO_Broad

Gene Regulation Observatory

1 year

Thank you to the GRO community for a fantastic day of scientific discussion @broadinstitute yesterday for our 2nd Annual GRO Retreat! Inspiring talks from all levels of scientists & great conversation throughout. Photo by our own @labronic_mike

Tweet media one

0

12

50

0

0

9

@BoXia7

Bo Xia

9 months

Congratulations to the new cohort of Early Independence Awardees!! Especially, congratulations to my dear friend, grad school classmate, and fellow @JefBoeke labmate @sudpinglay on this prestigious award!! Sud will rock with his lab at the amazing @uwgenome !!

@NIH_CommonFund

NIH Common Fund

@NIH_CommonFund

9 months

Did you know that the @NIHDirector ’s Early Independence Award supports junior #scientists to launch independent careers? Look at how this year’s awardees are “skipping the postdoc” and will pursue their own #biomedical and #BehavioralResearch #NIHHighRisk

Tweet media one

8

16

106

1

0

10

@BoXia7

Bo Xia

3 years

Trying to look at the method in a 2019 paper. It says: XXX was performed according to a 2015 paper. I was curious and dug deeper but consistently got "XXX was performed according to" 2015->2012->2009->2007, and finally to a 1999 paper with full method description. Good job!👏

1

0

9

@BoXia7

Bo Xia

2 years

@GRO_Broad @broadinstitute @Harvard @YiChengqi @ItaiYanai @JefBoeke Special thanks to Drs. Chuan He, Richard Tsien, @REMLehmann , @xinjin , @giladevrony , @zz_zhaozhang , @LiamHoltLab , @JeremyDasen , @artsinyc , @iannisaifantis1 , @jane_skok , Matt Maurano, @KVRamachandran5 , @TristanLi_Lab , @buck_trible and more, for their kindness and support.

1

0

10

@BoXia7

Bo Xia

2 years

Congrats @BarkleyDalia ! Exciting work of recurrent cancer states across cancer types finally came out online after a long wait!!

@ItaiYanai

Itai Yanai

2 years

Paper is finally out in @NatureGenet ! "Cancer cell states recur across tumor types and form specific interactions with the tumor microenvironment" Check out our catalog of conserved cancer cell states defined by scRNA-Seq & ST. Congrats @BarkleyDalia !

Tweet media one

16

171

773

0

0

10

@BoXia7

Bo Xia

2 years

Never too late to learn new tricks from Itai, though I still hope to have learned this one earlier...

@ItaiYanai

Itai Yanai

2 years

The secret to staying calm as you prepare to give a good presentation is to remind yourself that you want to explain, not to impress.

8

49

678

0

0

9

@BoXia7

Bo Xia

4 months

@TDCapellini @ItaiYanai Last, as @CrumpLab and many more pointed out, our study raises more questions, including those mentioned above by Terry, and functions of isoforms, downstream gene regulation, transposon biology, etc. The answers to these questions will lead us to a much deeper understanding.

1

0

9

@BoXia7

Bo Xia

2 years

Can’t agree more!!! We have way underestimated how much a good mentorship contributes to the advancement of science, both directly and indirectly. That’s why I consider myself so lucky during graduate school!

@ItaiYanai

Itai Yanai

2 years

When looking for a mentor, remember that a career in science is a 1000 times easier if you have a mentor who will - time after time - make the phone calls, write the letters, and enable opportunities for you.. Be sure to choose a mentor you can easily imagine doing that for you.

30

340

2K

0

0

9

@BoXia7

Bo Xia

1 year

I’ve been lucky enough during my training - and would sincerely spread these words to those who are looking for mentors.

@ItaiYanai

Itai Yanai

1 year

Scientists-in-training: find the mentor that is right for you. Here are my guidelines for how to do that 🧵 1. Make sure to choose a mentor who will be deeply committed to your career; someone who will continue advising and supporting you well after your time working together.

7

211

902

0

0

9

@BoXia7

Bo Xia

2 years

In this work, we present Origami, a deep neural network architecture for genomics, and leveraged its power for predicting 3D chromatin conformation - C.Origami. 2/6

Tweet media one

1

1

9

@BoXia7

Bo Xia

4 years

mainly because of my expired visa. If I leave the country, I’m risking my Ph.D. career of not being able to renew my visa, meaning not able to come back to US. I know so many more students who are in the same situation! Not being able to reunion with my family really sucks!!!!!

0

0

8

@BoXia7

Bo Xia

4 months

Cannot agree more! It’s exciting to see many CS/math people joining bio field - teaming up with people with a deep understanding of the biological question and the underlying logic will probably have the best chance to make a true impact.

@anshulkundaje

Anshul Kundaje (anshulkundaje@bluesky)

4 months

To all budding compbio & ML folks interested in bio: Don't just only run behind the latest ML model hype train. The greatest long run impact will come by really assimilating prior bio/compbio literature with the goal of really understanding strategies for how to model biology. 1/

8

129

788

0

0

8

@BoXia7

Bo Xia

2 years

Game changer sequencing technology that enables so many!

@seankenneths

Sean Simmons

2 years

Excited to share our preprint: how to use @UltimaGenomics new sequencing technology for massive single cell genomics: with @UltimaGenomics (esp Doron Lipson, Gilad Almogy, Florian Oberstrass, Gila Yanai) and Aviv Regev and @jzlevin groups @broadinstitute

3

20

65

0

0

8

@BoXia7

Bo Xia

4 months

@nightsciencepod So it takes TWO to make an impact! The unique alignment of a pair of Alu elements is crucial; without it, neither element would have significance. This inspired me to propose that hominoid-specific alternative splicing (AS) of TBXT influences tail development in hominoids.

Tweet media one

1

0

8

@BoXia7

Bo Xia

4 months

@TDCapellini @ItaiYanai With analyses and rationale interpretation, we presented our top pick: an AluY insertion in TBXT. With explainable genetics, mol-bio, & dev-bio results, we provided the first plausible genetic mechanism for this long-sought curiosity - we discussed in the Discussion of the paper.

Tweet media one

1

0

6

@BoXia7

Bo Xia

4 years

Almost every single East Asian knew the asymptomatic spread at least TWO MONTHS AGO!! Learn from what happened outside the US! Again: weakness and ignorance are not barriers to survival, but arrogance is! (By Cixin Liu, in The Three-Body Problems)

@jaketapper

Jake Tapper

4 years

Bill de Blasio Rejects Claim U.S. Knew Asymptomatic People Could Spread the Virus: Only Learned That 'In the Last 48 Hours’ via @mediaite

2K

822

3K

0

1

8

@BoXia7

Bo Xia

3 years

“He had a bad day”, but those eight people - including six Asians - lost their lives! All Asians SUFFERED a bad day! #StopAsianHate

@JoyYWu

Joy Wu, MD, PhD

3 years

OK I found my words. I am howling with rage tonight at the rising tide of violence and hate crimes directed towards Asians in America, punctuated by the horrific shootings yesterday in Georgia at 3 Asian-owned business that claimed 8 lives, including those of 6 Asian women.

34

229

1K

0

0

7

@BoXia7

Bo Xia

4 months

@nightsciencepod In fact, it is the secondary structure - rather than the specific Alu sequences - that plays a crucial role. By engineering a reverse complementary pair with Alu-independent sequences, we observed identical alternative splicing, underscoring the structural significance.

1

0

7

@BoXia7

Bo Xia

4 months

This journey culminated in a stunning cover image, thanks to @amanraghuwanshi ( @aman_raghu__ on Instagram), with edits by Bailey Tischer and myself. Find out the deep, philosophical emotion captured in the gaze of the two bonnet macaques.

Nature - Tale of tails

One of the most notable changes along the evolutionary lineage to apes and humans is the loss of the tail — an attribute that distinguishes them from...

2

0

8

@BoXia7

Bo Xia

3 years

Detect-seq! Latest work from my undergrad research mentor, a chem-bio tool to amplify detection efficiency of base editing-targeted sites! It’s amazing to see my own work years ago is now applied to a totally different field. Sometimes a small chemistry makes a big difference!

@naturemethods

Nature Methods

3 years

Our June issue is live! 🎉 On the cover, Detect-seq from @YiChengqi and colleagues, a method to detect genome-wide off-target sites induced by cytosine base editors.

Tweet media one

0

7

25

0

1

8

@BoXia7

Bo Xia

4 months

@TDCapellini @ItaiYanai First, pinpointing genetic change(s) corresponding to a deep evolutionary trait is way more challenging than most may think. Specifically between hominoids and old-world monkeys, there are tens of millions of hominoid-specific mutations - probably impossible to test them all.

1

1

7

@BoXia7

Bo Xia

3 years

It still blows my mind to think that such a little Alu element - one out of >1 million Alu copies in our genome - may just do such a crazy thing. 9/n

2

0

8

@BoXia7

Bo Xia

3 months

Great to see @zhou_jian ’s beautiful work online in @ScienceMagazine A fantastic case of how we can use model to enable&accelerate discoveries! I thought about bidirectional TF motif contributed to bidi transcription many years ago - feeling so pleased to see it turned out true.

@zhou_jian

Jian Zhou

3 months

Glad that our sequence model of promoters in human genome is now published in @ScienceMagazine . Check out the paper for a deep dive into the sequence basis of transcription initiation at the basepair level:

15

85

339

0

0

6

@BoXia7

Bo Xia

4 years

Team work with new roomate @ Halloween night. Here are the questions: who did better and who will win?

Tweet media one

0

0

7

@BoXia7

Bo Xia

3 years

Surprisingly, I found a hominoid(humans and apes)-specific Alu element, a common repeat sequence of ~300 base pairs, was inserted into the center of an intron in a gene called TBXT, also called T or Brachyury. 5/n

1

0

7

@BoXia7

Bo Xia

3 years

Congratulations Chenxu, and welcome to NYC!! I’ve been lucky to have collaborated with Chenxu in the lab of @YiChengqi ! An amazing scientist and a great human being! If you’re interested in single cell genomics and beyond, you’d reach out to him ASAP!

@chenxuzhu

Chenxu Zhu

3 years

I am thrilled to announce that I will join @nygenome and @WeillCornell in 2022! I cannot wait to join these fantastic communities and work with the amazing scientists!! My future lab will focus on single-cell tech dev, and postdoc positions are available:

14

23

212

1

1

7

@BoXia7

Bo Xia

4 months

Congratulations @Anders_S_Hansen and @deWitLab labs on the careful examination of ZNF143! Pioneering work in ENCODE enabled many discoveries and advances about the genome. But we always have to be careful in interpreting the data, especially in the AI era.

@Anders_S_Hansen

Anders Sejr Hansen

@Anders_S_Hansen

4 months

(1/14) Excited to share our new work on ZNF143/ZFP143 by @DomenicNarducci ZNF143 has been widely reported to be a general loop factor Instead we and @deWitLab in a companion preprint show that ZNF143 is a TF with no loop function:

Tweet media one

Tweet media two

Tweet media three

Tweet media four

9

78

282

0

0

6

@BoXia7

Bo Xia

4 years

I have a joke about White House’s anti-COVID plan, but but it never existed.

0

0

6

@BoXia7

Bo Xia

4 months

Brachyury/TBXT has a deep history in dev bio. The mouse mutant was first identified in 1920s by Nadine Dobrovolskaya-Zavadskaya, a Kyiv-born Russian French scientist; and its gene was cloned in 1990 by Bernhard Herrmann @MPI_MolGen . More about “Never-ending story of Brachyury”.

2

0

7

@BoXia7

Bo Xia

2 years

This is clearly the right thing to do! Thank you @Princeton for taking the lead! More importantly, I will speak loud for postdoc fellows, who are in their best years of scientific productivity but are paid unbelievably low! Saw so many great people leaving academia because of it.

@Princeton

Princeton University

2 years

#PrincetonU will increase graduate fellowship and stipend rates by an average of 25% to about $40,000 for doctoral candidates during the 10-month academic year. It is the University’s largest one-year increase in graduate student stipend rates.

15

160

844

1

1

7

@BoXia7

Bo Xia

2 years

Thank you @cegs_ica for highlighting our C.Origami model for de novo prediction of chromatin organization and in silicon genetic screening (ISGS) framework for discovering novel regulations in 3D genome. An updated version below, and more to come soon!

Tweet card media

Cell type-specific prediction of 3D chromatin organization enables high-throughput in silico...

The mammalian genome is spatially organized in the nucleus to enable cell type-specific gene expression. Investigating how chromatin organization determines this specificity remains a challenge....

www.biorxiv.org

@cegs_ica

Center for Integrated Cellular Analysis

2 years

1/10 Today we highlight C.Origami, a deep learning model from @artsinyc , @BoXia7 , & @tan_jimin that takes into account DNA sequence, CTCF binding, and chromatin accessibility profiles to effectively predict de novo cell type-specific chromatin architecture

2

15

45

0

0

7

@BoXia7

Bo Xia

5 years

#ASHG2019 kickoff in Houston!

Tweet media one

1

0

6

@BoXia7

Bo Xia

2 years

@GRO_Broad @broadinstitute @Harvard Truly honored and grateful for this special opportunity. This won’t be possible w/o the tremendous amount of support and help from mentors, colleagues, and friends. I’m very lucky to have @YiChengqi as my undergrad research mentor, and @ItaiYanai and @JefBoeke as my PhD mentors.

1

0

6

@BoXia7

Bo Xia

8 months

A tour de force by @jengreitz lab and collaborators across ENCODE teams for building an encyclopedia of human enhancer-promoter regulatory interactions! This would serve and empower so many disease investigations and beyond! Congratulations!!

@jengreitz

Jesse Engreitz

8 months

Excited to share our collaboration with ENCODE to map enhancer-gene regulatory interactions across the human genome! We developed a new model that beats ABC by incorporating additional information on promoter class and enhancer-enhancer interactions. Thread 👇

3

35

195

0

1

5

@BoXia7

Bo Xia

2 years

@ItaiYanai And thinking about science in a shower😉.

0

0

6

@BoXia7

Bo Xia

2 years

Congrats again Eric!! So proud of you and look forward to your new exciting discoveries! If you are looking for a great mentor and exciting cancer research, better reach out to Eric ASAP!!

@ewang2323

Eric Wang

2 years

I’m very excited to announce that I’ll be starting my laboratory at @jacksonlab as an Assistant professor! Thanks to all my amazing mentors @AbdelWahablab , @iannisaifantis1 and @ChrisVakoc . The Wang lab will open its doors Fall of 2022, stay tuned for future job postings!

60

16

318

1

0

6

@BoXia7

Bo Xia

2 years

Such impactful words from @CarolynBertozzi ! This is truly inspiring especially for junior scientists! #DiversityandInclusion #NotPlayingbyRules

@malycat03

Maly Cosco

2 years

Impactful words by @CarolynBertozzi today on how diversity in her trainees enabled creativity, not playing by the rules, and ultimately the work that built the field of bioorthogonal chemistry. Diverse science leads to better science!

57

2K

7K

0

0

6

@BoXia7

Bo Xia

3 years

For those who are not familiar, Brachyury was derived from Greek, meaning 'short tail'. But humans and apes have complete and almost identical TBXT coding sequences compared to other long-tailed monkeys. 6/n

1

0

6

@BoXia7

Bo Xia

3 years

Luckily, this accident led me to recap the question in my head about the tail, but in a more biological way: what is the genetic basis of our tail-loss evolution? 4/n

1

0

6

@BoXia7

Bo Xia

4 months

Beyond the molecular and developmental impact of the AluY insertion, we also delved into the implications for modern human health and our evolutionary trajectory. Read more from our paper and a great News&Views in Nature

1

0

6

@BoXia7

Bo Xia

4 months

@TDCapellini @ItaiYanai Four, reg. Terry’s concerns about the mouse models - I believe the answers are already in the manuscript. Reg 11-13), the phenotype is explained by the relative levels of short transcript Tbxt-dE6 expressed at the embryonic tail bud - in Fig 4e. …

1

0

5

@BoXia7

Bo Xia

4 years

Want to read a book during this special time? Highly recommend the Hugo Award-winning sci-fi: THE THREE-BODY PROBLEM. So many insightful thoughts. Here is one of my favorite sentences: Weakness and ignorance are not barriers to survival, but arrogance is. !

The Three-Body Problem

The inspiration for the Netflix series 3 Body Problem!WINNER OF THE HUGO AWARD FOR BEST NOVELOver 1 million copies sold in North America“A mind-bending epi...

us.macmillan.com

0

0

6