2023

February:

• Our recent single-cell RNA editing paper is highlighted by Cancer Research. 

​January: 

• Congratulations to Carlos for receiving a diversity grant from NIH!
• Carlos gave a fantastic presentation at at UCLA's riboforum!
• We welcome rotation students Anna Fraser and Haley De Ocampo to our lab!

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2022

December: 

• Our paper on "Single-cell analysis in lung adenocarcinoma implicates RNA editing in cancer innate immunity and patient prognosis" is published at Cancer Research. A great collaboration with the Boutros lab. Congratulations to Tracey and Jack in our lab!

November: 

• We are glad to have contributed to the RIbonomics consortium led by the Hoffmann lab at UCLA. Check out the recent consortium publication on "Kinetics of mRNA nuclear export regulate innate immune response gene expression" at Nature Communications!  Congratulation to the team including our lab members (Jae, Ashley, Esther)!
• Congratulations to Mudra for an outstanding dissertation defense, a fantastic wrap-up of her superb PhD research!
• Our collaborative paper with Dr. Desmond Smith's lab is now on BioRxiv: "Genetic pathways regulating the longitudinal acquisition of cocaine self administration in mice". Congratulations to Carlos, Tadeo and Mudra, and everyone in the Smith lab!
• The lab bid farewell to Zhiheng. Best wishes to Zhiheng for the next chapter of his career!

October: ​

• Ting delivered a fantastic platform presentation on our MPRA study at the ASHG! 
• Elaine and Ryo presented posters on their projects at the ASHG!  

​
September: ​

• We welcome rotation students Christian, Clara, Lena and Lynn to our lab!
• Congratulations to Kofi for giving a fantastic presentation at the QCBio Retreat!
• Congratulations to Elaine for winning the Poster Award at the QCBio Retreat!
• Our scAllele paper is published at Science Advances! Read it  here. 
• We received a new NIH R01 grant to support our work in double-stranded RNAs in Alzheimer's disease!

August: ​

• Congratulations to Ting for an outstanding dissertation defense, a fantastic wrap-up of her superb PhD research!
• Check out the final version of our PODXL paper here.
• The Zebra Finch transcriptome paper, in collaboration with the Schlinger, Whitelegge and White labs, is published in Gene. Check it out here.  Congratulations to Jingyan, Ting and Ling in our lab and our co-authors!​

​
July: ​

• Our PODXL paper is accepted at iScience, Congratulations Ting, Tracey, and Jae. A great collaboration with Dr. Amy Rowat and her lab.
• Our scAllele paper is accepted at Science Advances, Congratulations Giovanni, Ting and Tracey!  Pre-print is here. 
• Our lab hosted a BIG Summer Happy Hour! 

June: ​

• We welcome BIG summer students Raymond Benitez and Rohan Chatterjee  to our lab!
• We received an NIH R01 grant to support our work in RNA editing in cancer!
• Congratulations to Sari for receiving the CMB training grant!
• Congratulations to Lindsey for receiving the CMB training grant!
• Congratulations to Jonatan for receiving the iDISCOVERY training grant! 
• Ryo Yamamoto joined our lab under joint mentorship with Dr. Noah Zaitlen! Welcome, Ryo!!

May: ​

• Congratulations to Giovanni for winning the Collaboratory T-shirt design contest.  What a cool design! Check it out here on Twitter. 
• Jack Dodson joined our lab under joint mentorship with Dr. Paul Boutros!  Welcome, Jack!!
• Lindsey Dudley joined our lab! Welcome, Lindsey!!

​
April: ​

• Congratulations to Elaine for receiving the NSF Graduate Research Fellowship (GRFP)!
• Get to know the 2022 NSF GRFP awardees of UCLA Life Sciences.

March: ​

• Our paper "scAllele: a versatile tool for the detection and analysis of variants in scRNA-seq" is online at BioRxiv. Congratulations to Giovanni, Ting and Tracey!
• ​Check out the scAllele software on our github page.
• We welcome rotation students Jack Dodson, Lindsey Dudley and Ryo Yamamoto to our lab!
• Sari Terrazas joined our lab!  Welcome, Sari!!
• Our paper "L-GIREMI uncovers RNA editing sites in long-read RNA-seq" is online at BioRxiv! Congratulations to Zhiheng, Giovanni, Ting and Mudra! A great collaboration with Dr. Ali Mortazavi's group.
• Check out the L-GIREMI software on our github page. ​
• Congratulations to Elaine for receiving the GATP training grant!

February: 

• We received an NIH R01 grant to support our work in "Systematic analysis of functional 3’ UTR genetic variants and their relevance to Alzheimer’s Disease".

​January: 

• Congratulations to Giovanni for receiving the QCB Collaboratory Postdoctoral Fellowship!
• We welcome rotation student Sari Terrazas to our lab!​
• We welcome undergraduate students Ryan Barney, Duncan Croll, Alison King and Melinda Luo to our lab!

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2021

December: 

• Congratulations to Jonatan for successfully advancing to PhD candidacy!

November: 

• Ting gave a fantastic presentation at at UCLA's riboforum!

October: 

• Congratulations to Kiku for an outstanding dissertation defense, a fantastic wrap-up of her superb PhD research!
• Giovanni gave a fantastic presentation at the QCBio Research Seminar series!
• Carlos gave a fantastic presentation at the ERGR journal club!

September: 

• Congratulations to Ting and Kofi for winning the Poster Presentation award at the QCBio retreat!
• Congratulations to Giovanni for an outstanding dissertation defense, a tour de force of new algorithms and biological insights!
• Tracey and I are very glad to have contributed to this interesting study published at JCI Insight: "Lipin 1 modulates mRNA splicing during fasting adaptation in liver.", a collaboration with Dr. Karen Reue's group at UCLA.
• Congratulations to Carlos for being awarded the Hyde Fellowship!
• Congratulations to Tracey for an outstanding dissertation defense, a fantastic wrap-up of her superb PhD research!

June: 

• Congratulations to Carlos for advancing to PhD candidacy!
• Congratulations to Elaine for contributing to this interesting collaboration now published in PLoS Genetics, check it out: "Genetics of white color and iridophoroma in “Lemon Frost” leopard geckos"!
• We welcome Elaine Huang to our lab as a PhD student!
• Congratulations to Ting Fu for being awarded the Dissertation Year Fellowship!

May: 

• Mudra gave a fantastic presentation at UCLA's riboforum!

March: 

• We welcome rotation student Allison Schiffman to our lab!

February: 

• Stephen and I are very happy to have contributed to this interesting study "Long-term maturation of human cortical organoids matches key early postnatal transitions", a collaboration with Dr. Dan Geschwind and other groups.

January: ​

• Elaine and I are glad to have contributed to this interesting study by Dr. Leonid Kruglyak's group "Genetics of white color and iridophoroma in “Lemon Frost” leopard geckos". 
• Our paper "Allele-specific alternative splicing and its functional genetic variants in human tissues" is published at Genome Research. Congratulations to Kofi, Esther, Jae, Yiwei, Christina, Boon and Ei-Wen!
• We welcome rotation students Patricia Mendez and Mark Xiang to our lab!

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2020

December: 

• We received an NIH R01 grant to support our work in "Systematic approaches to deciphering regulation and function of RNA editing in brain".

November: 

• Kiku and I are glad to have contributed to this interesting study by Dr. Yong Kim's group: "Molecular consequences of fetal alcohol exposure on amniotic exosomal miRNAs with functional implications for stem cell potency and differentiation".
• Tadeo awarded the UCLA CARE fellowship.

October: 

• Our paper “RNA editing in cancer impacts mRNA abundance in immune response pathways” is published in Genome Biology. Congratulations to Tracey, Ting, Jae, Giovanni and all coauthors!  
• Our paper "Extracellular microRNA 3’ end modification across diverse body fluids" is published in Epigenetics.  Congratulations to Kiku and Jae!

September: 

• We welcome rotation students to our lab, Auriana Arabpour, Elaine Huang, and Nguyen Phi! Looking forward to an exciting quarter (despite virtually)!

August: 

• We welcome undergraduate student, Tadeo Spencer, to our lab!
• Congratulations to Ting Fu for receiving the Hyde Fellowship!
• Congratulations to Jonatan Hervoso for receiving funding as a Diversity Scholar!
• UCLA's 2020 Bruins-in-Genomics (BIG) Summer program wraps up this month. We are grateful to the program directors and the administrative team for stellar organizations of the first-ever remote BIG Summer! What a great achievement for the student mentees and mentors!!!  We say farewell to our trainees Bridget and Tori, and we congratulate them on receiving the Research Excellence Award.  We also congratulate Kofi for serving as a fantastic mentor to Bridget and Tori and receiving the Outstanding Mentor Award!
• We welcome Dr. Zhiheng Liu to our lab!
• ​AUG 1, happy RNA day!

July: 

• Introducing the ENCODE 3 landing page at Nature.   Enjoy reading the consortium paper and the companions!
• We are delighted to have been part of the ENCODE 3 consortium (and the current ENCODE 4 consortium).  Congratulations to Giovanni, Ei-Wen and Esther for your contributions as ENCODE3 consortium members. We are grateful for the inclusion of two of our papers on the Nature landing page!

​
June: 

• Check out  this interesting study by Dr. Yibin Wang's group: "p38 mitogen-activated protein kinase regulates chamber specific perinatal growth in heart" published at the Journal of Clinical Investigation. We are glad to have contributed to this work.
• UCLA's 2020 Bruins-in-Genomics (BIG) Summer program kicks off this month!  We welcome two BIG Summer students to our lab: Tori Concepcion and Bridget Phillips!
• Congratulations to Carlos Gonzalez-Figueroa for receiving the Cellular and Molecular Biology Training Grant!
• We welcome Jonatan Hervoso to our lab!

​
May: 

• While sheltering at home, our lab members have been hard-at-work! Our manuscript "Allele-specific alternative splicing in human tissues" is now on BioRxiv. Congratulations Kofi, Jae, Esther, Yiwei, Christina, Boon, Ei-Wen!

​
March: 

• We welcome Carlos Gonzalez-Figueroa to our lab!
• Our manuscript "Extracellular microRNA 3' end modification across diverse body fluids" is now on BioRxiv. Congratulations Kiku and Jae!
• Our manuscript "Differential RNA editing between epithelial and mesenchymal tumors impacts mRNA abundance in immune response pathways" is now on BioRxiv. This work was spearheaded by two graduate students, Tracey Chan and Ting Fu, and in collaboration with Dr. Chonghui Cheng at Baylor College of Medicine!

​
February: 

• Kiku and I are glad to have contributed to this interesting study by Dr. Feng Guo's lab: "Fe(III) heme sets an activation threshold for processing distinct groups of pri-miRNAs in mammalian cells".

​
January: 

• Our paper describing the new statistical methods, named REDITs, to analyze differential RNA editing is published at Bioinformatics!  Congratulations, Stephen!
• The REDITs package is available for download at our lab's GitHub page.
• We welcome rotation students Carlos Gonzalez-Figueroa and Jonatan Hervoso to our lab!

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2019

November:

• Congratulations to Kofi for successfully advancing to PhD candidacy. Great job, Kofi!

September:

• We received an NIH R56 grant to support our work on Alzheimer's disease.
• Our paper "mountainClimber identifies alternative transcription start and polyadenylation sites in RNA-seq" is online at Cell Systems. 

August:

• Stephen delivered a fantastic dissertation defense seminar! Congratulations, Dr. Tran!
• We received a Program Vision Leader Award to support our research in cancer. We thank the JCCC of UCLA for this award.
• Our research is featured in the UCLA College Magazine - "The Future of Aging, Disease, Brain Health, Biodiversity & more" ​https://www.college.ucla.edu/the-future-of/

July: 

• Our manuscript "mountainClimber identifies alternative transcription start and polyadenylation sites in RNA-seq" is accepted to Cell Systems. Congratulations, Ashley!  
• Check out mountainClimber at our gitHub page: https://github.com/gxiaolab/mountainClimber
• We welcome BIG Summer student Peter Nekrasov to our lab!

June: 

• Mudra is awarded the Biomedical Big Data Training grant. Congratulations, Mudra!

May: 

• Congratulations to Mudra for winning the Best Poster Award at the 2019 GATP-BWF-BBD Joint Symposium!
• Congratulations to Ei-Wen for delivering a fantastic lightning talk at the ITCR meeting!

April: 

• Our collaborative paper with Dr. Tao Jiang's group "DeepPASTA: Deep neural network based polyadenylation site analysis" is published at Bioinformatics!
• Check out the publication by The Extracellular RNA Communication Consortium: Establishing foundational knowledge and technologies for extracellular RNA research. We are pleased to contribute through Dr. David Wong's group.
• Congratulations to Ei-Wen for winning a travel award to the ITCR annual meeting!​

March: 

• Our paper "Allele-specific binding of RNA-binding proteins reveals functional genetic variants in the RNA" is published at Nature Communications.​ Congratulations to Ei-Wen, Jae, Esther, Boon, Yiwei, Ting and Giovanni!

January: 

• Check out the various coverages on our Autism study, e.g.: UCLA News Room, Ars Technica, Spectrum
• Our paper “Regulation of RNA editing by RNA-binding proteins in human cells” is published at Communications Biology. Congratulations to Giovanni, Stephen, Hyun-Ik, Jae, Ei-Wen and Anneke!
• Congratulations to Kofi for winning the Poster Award at the 2019 ENCODE Consoritum meeting!

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2018

December:

• Our paper “Widespread RNA editing dysregulation in brains from autistic individuals.” is published at Nature Neuroscience. Congratulations Stephen, Hyun-Ik, Jae, Adel, Esther!
• Congratulations to Christina for successfully advancing to PhD candidacy. Great job, Christina!
• Congratulations to Ting for successfully advancing to PhD candidacy. Great job, Ting!

November:

• Our collaborative paper with Dr. Kosuri’s lab “A multiplexed assay for exon recognition reveals that an unappreciated fraction of rare genetic variants cause large-effect splicing disruptions” is published at Molecular Cell.  Congratulations, Christina and Esther!
• Congratulations to Mudra for successfully advancing to PhD candidacy. Great job, Mudra!

October:

• Our paper “Widespread RNA editing dysregulation in Autism Spectrum Disorders” is now on BioRxiv. Congratulations to all co-authors!

September:

• Quantitative Biology ‘s Special Issue on RNA Processing and Regulation edited by Dr. Xiao and Dr. Chaolin Zhang is now online.

• Congratulations to Ashley, Ei-Wen, Giovanni, Kofi, and Yi-Wei for presenting their work at the QCBio retreat!

August:

• Our paper analyzing ENCODE eCLIP-Seq data: “Allele-specific binding of RNA-binding proteins reveals functional genetic variants in the RNA” is now on BioRxiv. Check it out!
• Ashley presented a fantastic dissertation defense seminar! Congratulations, Dr. Cass!
• Michele Ramos and Elaine Huang wrapped up their BIG summer research with us, and they won the poster award at BIG summer poster session. Thanks to Kiku for great mentoring!

July:

• Our collaborative paper with Dr. Chonghui Cheng’s group Co-regulation of alternative splicing by hnRNPM and ESRP1 during EMT. is published at RNA. 
• We welcome BIG summer students Michele Ramos and Elaine Huang to our lab!

June:

• Mudra Choudhury is awarded a Biomedical Big Data Training grant! Congratulations, Mudra!
• Esther delivered a fantastic dissertation defense seminar and with that, completed her PhD study! Congratulations, Dr. Hsiao!  

May:

• Congratulations to Giovanni for successfully advancing to PhD candidacy!
• Kiku Koyano is awarded the Eureka Scholarship!  Congratulations, Kiku!
• Our collaborative paper with Dr. Bill Lowry’s group Loss of MECP2 Leads to Activation of P53 and Neuronal Senescence. is published at Stem Cell Reports. Congratulations, Stephen!
• Check out the news coverage on the study “Human tRNA-derived small RNAs modulate host-oral microbial interactions”!
• Our paper “RNA editing in nascent RNA affects pre-mRNA splicing” is online at Genome Research. Congratulations, Esther, Jae, Yun, Andrew, Stephen, Ei-Wen, Giovanni!

April:

• Our collaborative paper with Dr. David Wong’s group “Human tRNA-derived small RNAs modulate host-oral microbial interactions” is published at the Journal of Dental Research. Congratulations, Kiku!
• Our collaborative paper with Dr. David Wong’s group “Characterization of Human Salivary Extracellular RNA by Next-generation Sequencing” is published at Clinical Chemistry. Congratulations, Kiku and Ken!

March:

• Congratulations to Kiku and Tracey for successfully advancing to PhD candidacy!!

February:

• Our collaborative paper with Dr. Tao Jiang’s lab “TAPAS: Tool for Alternative Polyadenylation Site Analysis” is published at Bioinformatics. Available online now! 

 January:

• ​Our collaborative paper with Dr. Stephanie White’s lab “FoxP2 isoforms delineate spatiotemporal transcriptional networks for vocal learning in the zebra finch” is published at eLife.  Congratulations, Zach!