Riyue Sunny Bao, PhD @RiyueSunnyBao Twitter profile

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Riyue Sunny Bao, PhD

8 months

Thrilled to co-organize our inaugural @sitcancer " #AI in #ImmunoOncology " Webinar @UPMCHillmanCC @RoswellPark @theNCI !! We have 9 spectacular courses on #AI , #clinical , #biomedical , #informatics , #LLM & data #privacy , #fairness , #disparities . Register:

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

3 years

When I dig out some old code and try to make it work #Bioinformatics

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

4 months

You know what sucks most in #academia ? It is when #faculty like us, want to hire highly talented candidates, and have the #money to provide a reasonable salary, but our institutional HR #blocks our offer cuz $$ we offered was too "high" considering the "number" of years of

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

1 year

Friendly reminder: #Research #Productivity is not the same in every #field . In some fields, students publish 10-30 pubs each year. In some fields, students publish 1 pub for their entire PhD. 1/n

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

3 years

Seq - a high-performance, #Python -based, compiled programming language geared toward #biology that combines the ease of use of high-level languages like Python or Matlab with the runtime performance of low-level languages like C or C++. @Evilution84

A Python-based programming language for high-performance computational genomics

Nature Biotechnology - A Python-based programming language for high-performance computational genomics

www.nature.com

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

2 years

Us #PI 's job is not to convince our students to stay in #academia or move to #industry , or vice versa. Our job is to present them #options to #choose , and be ready to answer the question - "What should I do if I want to be successful in [any area I want to be]"? #AcademicChatter

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

3 years

We should implement at least one permanent #Bioinformatics #PI position in each study section, same as #biostatistics . We have been talking #BigData for over a decade, yet no recognization for the important role of #Bioinformatics scientists. This makes me furious.

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

2 years

Our #R01 is awarded!!!🤩 @jasonlukemd @UPMCHillmanCC Thanks to our wonderful collab @RobertFerrisMD @BcellBruno @HSkinnerMDPhD , our @ImmunoTiil team Dr. Augustin @RyanAugustinMD Dr. Becky Dadey, Sarah Brodeur & more!! We r hiring! Find us #SITC2022 . Let's talk! #Immunotherapy

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

4 years

I am recruiting several BS/MS/PhD #bioinformatician #datascientists to join my group. Skills in #programming #omics #analysis + experience in #research preferred. #WFH until #inperson work is resumed. Official opening links 2 follow. DM me for details. @UPMCHillmanCC @PittTweet

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

4 years

`gtsummary` + `flextable` saved me so much time and energy coding up clinical summary tables tab1 <- tbl_summary(data.plot, by = Group) tab1.print <- tab1 %>% as_flex_table() save_as_docx(tab1.print, path = 'tab1.docx') done🤩 #Bionformatics

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

4 years

In #BioC2020 #BoF session "10 simple rules of #thriving in #bioinformatics #research ". Let's say NO to - isolated position - unrecognized contribution - neverending projs Let's say YES to - team environment - well-managed expectation - data-driven research @AcademicChatter

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

3 years

Germline HLA landscape does not predict efficacy of pembrolizumab monotherapy across solid tumor types: Immunity

Germline HLA landscape does not predict efficacy of pembrolizumab monotherapy across solid tumor...

Germline HLA diversity has been suggested as a biomarker of response to immune checkpoint inhibitors. Chhibber, Huang, Zhang et al. analyze 3,500 patients across 17 pembrolizumab clinical trials and...

www.cell.com

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

2 years

Thrilled that our #R01 #immunotherapy received 5%!! @TIILab @jasonlukemd #computational #singlecell #imaging #humanorganoid #mousemodel We r expanding at all levels! #bioinfo #drylab 21005251 22003119 #res #wetlab 22003062 22003374 #postdoc -pls DM/Email

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

3 years

Going through #NIH study sections and it is almost depressing to see so few #computational #PIs , while we are living in the #era of #bigdata w #singlecell , #multiomics , #imaging . Almost every grant proposes high-dimensional #data now. Who are going to analyze those data then?

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

4 years

@_applechew @AcademicChatter First author papers are only expected if you plan to stay in academia & have your own lab. Needless to say, that is a narrow road. Lots of other great #career #choices . The purpose of pursuing a #PhD is not papers, but to train your brain in order to be #successful in any career.

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

3 years

Spent 2.5 hours matching #sample #ids from 5 different systems from 5 labs, named by 5 different teams, with 5 different naming conventions. After some #ninja #skills , only found 2 samples with unmatched ids across all 5 systems. I call this a #win today 😂 #bioinformatics

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

4 years

I have started putting together a list of #virtual #conferences #workshops this year in #bioinformatics #biostatistics #computational #biology #medicine #mathmatical #statistical #MachineLearning #DeepLearning #AI #imaging check it out!! #AcademicChatter

GitHub - riyuebao/virtual-conferences-workshops: This repo collects the list of conferences/meeti...

This repo collects the list of conferences/meetings/workshops that have gone virtual in 2020. - riyuebao/virtual-conferences-workshops

github.com

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

4 years

As a huge #introvert , my default mode is to sit in the back seat , listen, smile, nod. If I accumulate enough courage, sweep off my cold sweat, take a deep breath to make an announcement - I am not #humblebrag ing. I am straight up #bragging . And it’s okay. #AcademicChatter

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

4 years

- formalize a problem and solve it - comprehend large amount of information in a short time - quickly find recourses, learn new skills, master it - understand failure is not the end, it is a process - proficient programming in at least one language #phdchat #AcademicChatter

Evelyne Deplazes

@DeplazesEvelyne

4 years

Challenge for #PhD people out there. @AcademicChatter Write down your top 5 transferable skills (yep, really. Write them down) If you are anything like me, they will sound pretty generic and use buzz words like 'problem solving', 'critical thinking', 'communication'. 1/2

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

9 months

Is there a #community that studies #organoids for #ImmunoOncology research? Esp co-culture with #Tcells #Macrophages to study #interactions . Our lab would love to join and make friends :) Please let us know! #immunotherapy #ICI #IO @ImmunoTiil @jasonlukemd

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

2 years

@GarmireGroup Maybe not every weekend, but not unusual. Wet lab experiments are timed and if falls on weekends, one would have to come in (e.g. cell lines, animal exp, etc.). For folks in my lab, I encourage them to take another weekday off if they have to come in on weekends. 1/2

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

3 years

Grant rejected Send cat pictures 😭 #Bioinformatics

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

3 years

We really should show #respect to #bioinformaticians & #biostatisticians when they say "I spent a lot of time+effort trouble shooting this analytical code" Same as when biologists say "I spent a lot of time+effort troubleshooting this experiment" We really do. #AcademicChatter

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

3 years

Paper accepted!!!!!!!!!!!!! This is the first time Reviewers accepted our revisions after the 1st round 🥳 Thanks to The Editor and Reviewers for the constructive suggestions and comments! Definitely encouraging news during the stressful grant submission time! #AcademicChatter

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

4 years

Super stoked to see this work sees the light !!!!🤩 We leveraged multiple #omics datasets #TCGA #CPTAC #ICGC identifying #targets associated w non-T cell-inflamed tumors. #Clinicaltrial #Immunotherapy ongoing! ***Looking for #bioinformatics #postdocs to join our lab #TIIL !!!

Jason Luke, MD, FACP

@jasonlukemd

4 years

Excited @GenomeMedicine paper out w @RiyueSunnyBao & our Translational Immuno-Informatics Lab @UPMCHillmanCC @PittDeptofMed Prior Tweetorial 👇 #ClinicalTrials & single cell validation coming! Looking for #bioinformatics post-docs!

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

6 months

Things I’ve learned after moving to a #leadership position: 1- some #decisions need to be made quick. Don’t drag. 2- most of time, providing a good enough #answer >>> spend days to come up w a perfect one (and it’s never perfect) 3- #trust is magical. 4- your #time is defined

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

3 years

@LisaMariaN91 never heard of it ... when I was in graduate school I went to lab on some weekends when I want my projects to move faster, but my PI never asked me to be there. Sometimes when I bumped into him on weekend in lab, he was like - WHY are you here don't you need sleep 😂

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

4 years

Predicting tissue-specific gene expression from whole blood transcriptome

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

3 years

Congrats to Dr. Ferris @RobertFerrisMD & team @AditiKulkarni91 @cornkuert Dr. Vujanovic on this brand new study #HNSCC #singlecell #TME !!! Glad to be part of it. 134k cells tumor-stroma-immune by T cell- #inflammation , #HPV status, & #heterogeneity .

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

3 years

Protip #Bioinformatics #1 Saying no up front is 100x better than saying yes& not deliver. #2 Build a network of whom you trust to work together is 100x fun than working alone. #3 Team science is a double-edge sword. Be clear of your expectation from others, &others from you.

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

2 years

@ZeynepHG I heard the hours are flexible … 😜

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

3 years

A collection of Excel tables != Databases A collection of shell/R scripts != Pipelines Fitting a line to data != AI and You don't need UMAP or t-SNE to visualize N=30 bulk samples #Bioinformatics

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

3 years

@toomanyspectra You are asking the right question, but to the wrong audience. The salary level is determined by university HR and funding agencies, not us faculty. In fact, even faculty wants to pay higher for their lab members, it gets rejected by HR and there is no mechanism to repeal.

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

3 years

@sridnona6 data available upon reasonable request #thenitneverhappens

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

3 years

We really have to start thinking of #Bioinformatics as a #discipline instead of a tool. And yes, it overlaps greatly with #compbio when it comes to #highdimensional data. #AcademicChatter

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

3 years

Our #Bioinformatics team is expanding!! I am opening two new positions in our #Cancer #Bioinformatics team @UPMCHillmanCC . We are leaders in #NGS #imaging #multiomics supporting large-scale P50 level grants. DM for details. Official job links soon to follow!

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

3 years

Are you interested in #bioinformatics #DataScience and enjoy collaboration with 400+ teams of scientists? Join my team at @UPMCHillmanCC #Pittsburgh !! Position open: We are looking for multiple candidates. DM me if you have any questions!!

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

2 years

Celebrate today. Not tomorrow. Not next month, or next year. There will always be another grant, another paper, another project . Happily placed a #bubbletea order for two 😎

Academic Chatter™

@AcademicChatter

2 years

..when I finish this paper ..when I submit that paper ..when I get this degree ..when I complete this task ..when I climb that ladder ..when I win this award The future is always busy. Don't forget to live now.

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

4 years

Super useful #Rstats package for generating tables that look like #NEJM papers (and others!) #gtsummary

Daniel Sjoberg

@statistishdan

5 years

🎊🎊We hit 1000 monthly CRAN downloads for {gtsummary} for the first time, woohoo 🎊🎊 @Margaret_Hannum @karissawhiting @zabormetrics #rstats #gt #reproducibility

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

4 years

#Bioinformatics

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

4 years

This has happened too many in grants - when a grant is cut, #bioinformatics is the first to be cut. You end up still doing 50% of the work but only get paid 5%. This will not change unless #NIH funds #bioinformatics as a separate discipline rather than an element of other grants.

Ming "Tommy" Tang

@tangming2005

4 years

Sad to see Defunding a bioinformatics core. How to make a core self-sufficient? What business models should a core deploy?

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

1 year

In reality, #good #science is #slow and often #frustrating . We have to repeat experiments to make sure obs is reproducible. We have to collect data to robustly test our hypothesis, to find something #true . #Science should not be rushed. Yet we are #rushing , all the time. 9/n

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

3 years

@jtleek The most painful is not the experience but the time and effort spent on doing data #cleaning - which nobody values except the person who is doing it. All eyes and prizes on #modeling but data #cleaning and #curation is most critical gatekeeper on reliable signal inputs!

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

4 years

Paper #accepted !! :) Felt a bit lifted by the positive news during a string of #rejections .... #academiclife #marchforward #WomenInSTEM #COVID19

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

5 years

What we see in tumor vs what we don't see in tumor. The negative part is equally, and sometimes more important. #science #statistical #inference

Lior Pachter

@lpachter

5 years

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

5 years

What are the best approaches to #manage and #track terabytes of #data & #results from different #omics #projects in one lab w #version #control ? Codes can be easily managed and commits tracked. But #data & #results ? Thinking of building a #centralized #repository for our lab 🤔

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

4 years

As #bioinformatician #biostatistician #DataScientist , have you ever felt you've done lots of work, yet achieved nothing? here is how to change that! A thread 👇 1/n

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

1 year

Major, real-time science rebuttals ongoing #cancer #microbiome Within 48 hours after ground breaking reports shared on preprint, rebuttal, rebuttal of rebuttal, and rebuttal of rebuttal of rebuttal have been published #code & #results This is the best of #ScienceTwitter .🦠🔬👩🏻‍🔬

Steven Salzberg 💙💛

@StevenSalzberg1

1 year

Major, fatal errors found in the data and methods of a 2020 paper in @Nature , including millions of reads mis-identified as bacteria. The "cancer microbiome" in this study was simply not there. @abrahamgihawi @elapertea @YuchenGe1 @JenniferLu717

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

6 months

Our lab has officially entered the "curse" of data generation speed >>> data analysis speed >>> paper publication speed 🫠 #AcademicChatter

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

3 months

T-cell inflamed versus non-T cell-inflamed HCC specimens from #HE images - first pass 🥳 #low #cost + #high #throughput ! #pathology #AI @ImmunoTiil

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

4 years

Critical skills for a successful #data #sciences #career : It is not fancy programs, amazing discoveries, or cool models. It is - #attention to #details , down to every number - #robustness for #quality - #rationale behind your every #CHOICE - always ask #WHY #Bioinformatics

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

3 years

@GooglingBioinfo If it’s raw data, start with basic Linux commands (sed, awk, etc.). Then find a tutorial and process a small set of data using Linux tools. If it’s processed data, start with basic R. Or, start with Python 🐍 , it’s a steeper climb but will be fun.

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

2 years

Our (inaugural!) #Spatial #Omics #Computational #Imaging Symposium had an amazing run! 150+ participants & 10 stellar speakers from @CMUCompBio @StanfordMed @PittTweet @HopkinsMedicine Thanks to all participants, organizers, and @UPMCHillmanCC #sponsorship .Stay tuned 2023!!

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

3 months

Very excited about our new prediction models on H&E images. Here is a close view of #lymphoid #aggregates adjacent to tumor, not mature TLS (yet!) #pathology #AI @ImmunoTiil

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

10 months

@saizhang0 Perfectly normal. One of the few opportunities in a year to take over the entire #cluster with zero #queue 🤣 and no, it has nothing to do with life/work balance. As a PhD student, young and motivated, you do whatever you want to make your projects work.

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

1 year

#singlecell twitter, recommendations on #companies who can take frozen cells and build 10x scRNAseq/scTCRseq/scBCRseq libraries? We had two failed runs during the past six months, and are exploring alternative options; before that all runs were great. Any tips are welcome!! :)

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

3 years

On this very emotional moment when we are left w only 24h of a wonderful winter break b4 work starts again... Did I accomplish writing goals? no Did I re-train model and made it better? no Did I finish analysis of 2m cells? also no We cooked &rested together, that was it 🥳😂🥟

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

4 years

Super excited to #share on the 1st day of 2021, I published my first (of the last decade ever) personal website. Check it out here 🥰🎉😈 #HappyNewYear2021 !!

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

3 years

What’s the best way to sort through your Twitter #bookmark , retrieve the #papers from tweets, and save to e.g. #zotero ? Do I have to do it one by one 😱 #AcademicChatter

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

4 years

Grant submitted! It's a small internal grant but fingers crossed!! #Bioinformatics #CloudComputing #Deeplearning

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

1 year

@AdrianoAguzzi I support everybody speaking their native tongue when having conversations amongst themselves. #Inclusion is not homogenous. It’s immigrants like us being comfortable speaking and sharing in a country where we were not born in.

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

3 years

Collaborators : would you like preprocessed data or raw data ? Me: raw data please. Fresh out of the machine, no processing. #Bioinformatics #trustissues 😏

Ijeamaka

@ijeamaka_a

3 years

People telling me that they are sending me clean data and the data *never* being clean is the source of all my trust issues.

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

2 years

Glad to have had the privilege teaching our #MSTP year 1 students ⁦ @PittDeptofMed ⁩ ⁦ @PittCMU_MSTP #biomedical #rmedicine #bioinformatics !! Our lab is at Shadyside and I always loved the opportunities to pop over to #UPitt campus any time 😆 ⁦ @ImmunoTiil ⁩

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

3 years

@drandersgs @sridnona6 We did not use your results so we would not include you on paper. Oh by the way thanks for sending all the results of that transcriptome assemblies, my PhD student used those sequences to run experiments.

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

11 months

Congrats to Dr. Becky Dadey, #postdow #fellow in our lab @ImmunoTiil on winning #10x #FFPE #Flex #pilot #award !! Becky is using #singlecell #compIO #multiomics to interrogate #tumor #immune microenv & #resistance to #immunotherapy in #liver #cancers . Go Becky!! @UPMCHillmanCC

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

2 years

We are continuing our latest hiring to expand our #bioinformatics team @UPMCHillmanCC !! Bioinfo - DataSci - Join us #Pittsburgh - Stable #funding , #family friendly #city life, superb #food , with 2 largest #nature #parks in town!

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

2 years

Things that us #academics could learn from our #industrial partners: - project #management - quarterly #milestones - #team science, no winner-take-all - company’s growth is #everybody ’s gain - proper #budget for proper operations - #promotion plan discussed at day 1 of hiring

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

2 years

@NinaSteele17 @mike_feigin @Momademia Find five senior , multi R01 funded PIs whom you trust, ask for 10 mins and present to them your hypothesis. If they don’t bite within first 1 min of your pitching , revisit your hypothesis, again, and again. Once the idea is solid, rest will flow.

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

6 years

Super excited to publish our work on #WNT #betaCatenin #immune #exclusion across 31 human solid tumors #TCGA #cancer w Dr. Tom Gajewski @jasonlukemd @RandySweisMD @stefanispranger @CCR_AACR @UCCancerCenter @UChicagoCRI twee-bstract to follow

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

4 years

Our lab is looking for #bioinformatics #scientist to join us! Apply here Check out our research projects here #Cancer #immunotherapy #singlecell #spatial #imaging #sequencing #compbio @jasonlukemd @ImmunoTiil @UPMCHillmanCC

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

3 years

@Nitasha__Sharma @AcademicChatter @OpenAcademics Students should be free to reach out to professors and not be judged! Professors might not respond if too busy, but hash responses like that are not professional. On the plus side, that is a clear sign for students to screen out which labs *not* to join at the first place.

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

2 years

The moment when senior faculty recommends speakers, they start w ‘X has two R01s, would be a good candidate’. Or ‘X published xxx CNS papers, I recommend them’. Shouldn’t we care more abt what we do to #improve #human ’s #lives , than specific metrics? #AcademicChatter #curecancer

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

5 years

@dgonzales1990 It's okay, I can assure you professional software developers might also have a hundred google tabs open.... sometimes it is equally important that you know where to find the answer, as knowing the answer yourself.

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

2 years

Believe it or not, we #bioinformatics scientists spend a good amount of time on a SUPER cool #name for any new algorithm or technology we develop (often themed after #food or cute #animals or cool #SpaceShip Innovation and creativity speaks there! #AcademicChatter 🤩

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

5 years

Have talked to many #bioinformatician #biostatistician friends we share the same frustration. We enjoy what we do but it's not helping our #career #dev cuz #academia only #rewards single #ownership rather than a #team . I have not found a solution but not giving up 💪 #WomenInSTEM

Dr. Elana J Fertig

@FertigLab

5 years

Thoughts on academic incentives. I am currently working on a program level grant with a core that's every bit as creative and involved as any of my grants as PI. But, the credit I will get should we win it will be way less.

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

3 years

#checkpoint party #SITC2021 rock n’ roll!!!!!!!!

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

4 years

#killer #Tcells : Determined, Precise, Persistent, Get job done Be like killer T cells #AcademicChatter

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

1 year

Dr. Robert Schreiber giving landmark lecture on cancer #immunoediting and #immunotherapy . Full house ! #SITC2023 #Tcells #myeloidcells #CTLA4 #imaging tracking cell composition and interactions #Codex @WUSTLmed

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

5 years

mosdepth by @brent_p processed my 3.5G #bam in 3m w 4 threads, could be faster if I do `-x`. Can run base-res+bin+threshold 1x,10x,20x +quantize mode sametime. I am switching all my #depth #calculation jobs to #mosdepth !! h/t @Evilution84 #bioinformatics

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

4 years

Huge #congrats to my friend &former colleague @Evilution84 @trevars @allig8r , all teams @UChicagoCTDS Dr. Grossman Dr. Staudt @NCIGDC_Updates on landmark papers @NatureGenet @NatureComms ! Being using #Genomic #Data #Commons throughout my career, I am so happy for all of you!!!

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

3 years

Which #computational #biology #bioinfo #sysbio #biomedical #informatics #conferences do you go to? I am most familiar w ISMB, ACMBCB, RECOMB, PSB. Others?? :) Calling for #twitterverse #wisdom !! #AcademicTwitter

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

6 years

New #deconvolution #algorithm from @IdoAmitLab @vikslab Eran Bacharach estimating #composition of #immune #nonimmune cells from bulk RNAseq leveraging #reference set built by #singlecell #RNAseq detailing the methodology. Cannot wait to try it out!

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

4 years

Bioinformatics : 20% parsing data 30% stats 50% making the figures that will go into a paper #AcademicChatter

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

1 year

Manually typed in 40+ author information on submission website The moment you click submit, website is down for maintenance I am done here #AcademicChatter

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

2 years

Looking forward to meeting everyone #SITC2022 #Boston !! 🥳 Our lab is hiring. If you have computational bgd and are interested in novel technology dev #singlecell #microscopyimaging #immunotherapy , happy to chat. I will be there for the whole week! @UPMCHillmanCC

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

3 years

and no, we do not do 5-mins heatmaps or 48-hour turnaround single cell results. Same as no PCR can be done within 5 mins, and no mouse experiments can be done within weeks, or sometimes months.

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

4 years

Does anybody else feel horrified to listen to their own recorded presentations or it was just me???? 🤣 After 5 tries and 2 cups of #midnight #coffee I finally got it. Poster and video uploaded!!! #ISMB2020 #TransMed #Bioinformatics

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

3 years

Recommendations for #ultrafast #splitting fastq.gz into smaller files? We have 100G WGS individual fastq.gz files; tried several tools, all single threaded and too slow, under a time crunch for grant submission 😱 The plan is splitting fq => bwamem => gatk chr #Bioinformatics

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

3 years

After two weeks of almost no break, we decided to take a rest and finally relax. We made Cheese Buldak, Chinese sausage fried rice, and blueberry pancake 🥰 #weekendcooking

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

6 months

@AtienzarSara it does not get easier, but you will develop strategies to manage it better. Most important is to build a support network to not feel alone :) grab coffee together and brainstorm ideas - always the most fun time as a PI! #AcademicChatter

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

4 years

@biobenkj @dccc_phd Statistics. Having a good understanding of #stats will go a long way in #Bioinformatics .

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

4 years

I have finished 16 tasks today ranging from #management to #grant to #scRNAseq #analysis to #sample #collection #logistics to #hiring to #mentoring , and it is only 4:30 PM. I have 11 more to go - feeling exhausted So I ordered #bubble #tea and #snacks 💪

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

4 years

To #survive #academia , find these five people - a friend who shares your rants & joy - an advisor who supports and points you the way - a partner who you recede to and always feel safe - a colleague who puts a stop to nonsense - an inner yourself who is not afraid of anything

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

5 years

@conTaminatedsci @GhadaHammad9 programming (the sort of class where you need to program in IDE on the fly in mid-terms/finals to pass) + probability (the sort of class where you need to do calculations on paper to pass) + linear algebra (yup calculations on paper too) will carry you a long way into science ...

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

3 years

Excited to share our work on #highrisk #neuroblastoma @jitcancer !! We report #peds patients w high T cell #inflamed signature & #neoantigen load show better #survival , and nominate #ASCL1 #SOX11 #KMT2A #activation asso w #cold tumors. #immunogenomics

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

2 years

5 #advice I received that changed my life - Guard your #time like guarding your bank account. - The most #successful people are experts in saying, "No". - Feeling angry is not productive. Find a #solution , then let go. - Build a #life outside of career. - Always set #Priorities .

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Riyue Sunny Bao, PhD

@RiyueSunnyBao

1 year

@RoxanaDaneshjou @AcademicChatter mistake: recruitment time too long. lessons learned: hire now, and hire early! even before starting a lab :)

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Riyue Sunny Bao, PhD

@RiyueSunnyBao