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<h1>Cai Lab</h1>
<p> < Single Cell Biology | Machine Learning > </p>
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<dl>
<dt>11/13/2024</dt>
<dd>Dr. Cai speaks at the NTU-TAMU Bilateral Symposium in Taipei.</dd>
<dt>11/12/2024</dt>
<dd>Dr. Cai speaks at National Chung Hsing University in Taichung.</dd>
<dt>11/11/2024</dt>
<dd>Dr. Cai speaks at the 11th GEAR-UP Forum - Norman Borlaug Lecture Series in Taichung.</dd>
<dt>11/01/2024</dt>
<dd>VMBS TODAY // Fall 2024 - <a href="https://indd.adobe.com/embed/02409bb3-bf7d-4e24-97e5-1498d3c02156?startpage=23&allowFullscreen=true">Quantum Leaps in Single-Cell Science</a> (Story by Courtney Price).</dd>
<dt>10/12/2024</dt>
<dd>Selim speaks at the <a href="https://icibm2024.iaibm.org/">International Conference on Intelligent Biology and Medicine (ICIBM 2024)</a> in Houston.</dd>
<dt>10/05/2024</dt>
<dd>Dr. Cai speaks at the 2024 Texas Taiwanese Biotechnology Association (TTBA) 10th Annual Symposium, TMC Innovation, Houston.</dd>
<dt>09/20/2024</dt>
<dd>Dr. Cai speaks at the <a href="https://sbmi.uth.edu/">McWilliams School of Biomedical Informatics</a> in the Houston Texas Medical Center.</dd>
<dt>09/19/2024</dt>
<dd>Cristhian presents the <a href="https://doi.org/10.48550/arXiv.2206.15362">quantum GRN model</a> in the ECEGSA Graduate Student Seminar.</dd>
<dt>09/16/2024</dt>
<dd>Dr. Cai presents at the VTPB Seminar.</dd>
<dt>08/21/2024</dt>
<dd>Dr. Cai speaks at the <a href="https://acs.digitellinc.com/live/32/page/1049">ACS Fall 2024 Conference (Quantum Computing, AI & Quantum AI to Elevate Chemical Discoveries)</a> in Denver, Colorado.</dd>
<dt>06/28/2024</dt>
<dd>Dr. Cai speaks at the <a href="https://icsa.zuel.edu.cn/index.html">ICSA 2024 China Conference</a> in Wuhan, China.</dd>
<dt>06/07/2024</dt>
<dd>Dr. Cai speaks at the <a href="https://www.csh-asia.org/?content/2349">DNA Metabolism, Genomic Stability and Human Disease Conference</a> in Suzhou, China.</dd>
<dt>05/28/2024</dt>
<dd>Dr. Cai speaks in the <a href="https://hkumicro.hku.hk/">Department of Microbiology</a> and in the <a href=https://www.sbms.hku.hk/event/seminar-2024-05-28>School of Biomedical Sciences</a>, University of Hong Kong.</dd>
<dt>05/23/2024</dt>
<dd>Dr. Cai speaks at the <a href="https://www.iddst.com/iddst2024/default.asp">IDDST</a>, Osaka, Japan.</dd>
<dt>03/21/2024</dt>
<dd>Dr. Cai speaks at the <a href="https://tamids.tamu.edu/event/ai-health-workshop/">TAMIDS Machine Learning, AI, and Health Collaborations Workshop</a> -- Unveiling the Cellular Universe: Where Machine Learning Meets Single-Cell Biology.</dd>
<dt>03/20/2024</dt>
<dd>Shreyan speaks at the <a href="https://www.mdanderson.org/research/research-resources/core-facilities/cprit-single-core/events.html">Texas Single Cell (TXSC) Working Group Seminar</a> -- Beyond Averages: Exploring the Individuality and Meaningful Chaos of Single-Cell Gene Expression.</dd>
<dt>01/11/2024</dt>
<dd>Dr. Cai participates as a panelist at the <a href="https://content.mathworks.com/viewer/658099992da96fca8f1f060b">MathWorks Biomed Roundtable</a>, discussing how computation is changing the life sciences.</dd>
<dt>12/11/2023</dt>
<dd>Dr. Cai speaks in the <a href="https://calendar.tamu.edu/research/event/310799-exploring-advanced-frontiers-in-single-cell">Seminar Series - Regional Center for Excellence in Cancer Research</a> at TAMU.</dd>
<dt>11/20/2023</dt>
<dd>TAMU Today News -- <a href="https://today.tamu.edu/2023/11/20/researchers-use-quantum-computing-to-predict-gene-relationships/">Researchers Use Quantum Computing To Predict Gene Relationships</a>.</dd>
<dt>10/18/2023</dt>
<dd>Cai lab is at the <a href="https://drive.google.com/drive/folders/1W7ScLOQEGcrr9vqOGePbRYJTTLPACExm?usp=sharing">2023 GCC Single-Cell Symposium</a>.</dd>
<dt>10/13/2023</dt>
<dd>Dr. Cai speaks at the Distinguished Speaker Seminar in the Department of Electrical & Computer Engineering.</dd>
<dt>09/29/2023</dt>
<dd>Dr. Cai is interviewed on the YouTube channel <a href="https://youtu.be/WlN1zQ8a7kA?si=Tl_gUPv62yUo1Phr">NiklasOPF</a> talking about quantum gene regulatory network.</dd>
<dt>08/25/2023</dt>
<dd>Shreyan receives TAMU Walter W. Lechner Estate Scholarship!</dd>
<dt>07/29/2023</dt>
<dd>Dr. Cai presents at <a href="https://icml.cc/virtual/2023/workshop/21483">ICML 2023 Workshop on Computational Biology</a>.</dd>
<dt>07/24/2023</dt>
<dd>Shreyan presents his research to the SURGe students taking the GENE 657 Command Line Skills course and Professional Development Session #5: Bioinformatics in Genetics Research, on West Campus.</dd>
<dt>07/19/2023</dt>
<dd>Dr. Cai speaks at the International Conference on Intelligent Biology and Medicine (<a href="https://icibm2023.iaibm.org/">ICIBM 2023</a>).</dd>
<dt>07/13/2023</dt>
<dd>Our latest research on "Quantum gene regulatory networks" has just been published in @Nature_NPJ Quantum Information. Read it here: <a href="https://rdcu.be/dgIpu">https://rdcu.be/dgIpu</a>.</dd>
<dt>07/12/2023</dt>
<dd>Yongjian starts doing internship at <a href="https://www.modernatx.com/">Moderna</a>.</dd>
<dt>06/24/2023</dt>
<dd>Yongjian speaks at the Artificial Intelligence and Biomedicine Society (<a href="https://ai2healthcare.github.io/news/2023/06/18/Dr.Yongjian_Yang">AI2Health)</a>. Check out the <a href=https://youtu.be/AKwP9rzrbVU>recording</a>.</dd>
<dt>05/22/2023</dt>
<dd>Dr. Cai speaks at Texas A&M Cancer Research Symposium at The George in Century Square.</dd>
<dt>05/08/2023</dt>
<dd>Yongjian publishes Gene Knockout Inference (<a href="https://github.com/yjgeno/GenKI">GenKI</a>) at <a href="https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkad450/7184155">NAR</a>.</dd>
<dt>04/16/2023</dt>
<dd>Yongjian attends <a href="http://recomb2023.bilkent.edu.tr/">RECOMB 2023</a>, Istanbul, Turkey. Check out <a href="https://twitter.com/RECOMBconf">@RECOMBconf</a>.</dd>
<dt>03/21/2023</dt>
<dd>Dr. Cai speaks at <a href="https://www.asneurochem.org/Past-Meetings">ASN 2023</a>, Lexington, KY. Download <a href="https://www.asneurochem.org/resources/2023.03.03%20-%20ASN2023%20-%20Program%20Book.pdf">full program book</a>.</dd>
<dt>02/24/2023</dt>
<dd>The GENE Executive Committee approved <a href="https://sites.google.com/genomezoo.net/cailab/teaching/vibs675">VIBS 675: Single-cell Data Analysis via Machine Learning</a> as a GENE elective. It is under the area of Statistics and Bioinformatics competency (<a href="https://genetics.tamu.edu/current-students/required-courses/">https://genetics.tamu.edu/current-students/required-courses/</a>).</dd>
<dt>02/18/2023</dt>
<dd>Dr. Cai speaks at the <a href="https://immunity.health.tamu.edu/">Texas Symposium on Critical Topics in Immunology</a>, Texas A&M Hotel and Conference Center, College Station, Texas. <a href="https://immunity.health.tamu.edu/wp-content/uploads/2023/01/Symposium-on-Critical-Topics-in-Immunology-Schedule-1-25-23.pdf">View agenda</a>.</dd>
<dt>02/15/2023</dt>
<dd>We are generously supported by the CPRIT <a href="https://www.cprit.state.tx.us/grants-funded/grants/rp230204">RP230204</a> to create and run a single cell 'omics core.</dd>
<dt>02/01/2023</dt>
<dd>FOX 44 News: <a href="https://www.fox44news.com/news/local-news/brazos/grant-to-assist-am-researchers-in-developing-cancer-drug/">Grant to assist A&M researchers in developing cancer drug</a>.</dd>
<dt>01/17/2023</dt>
<dd>Dr. Cai starts teaching VIBS675/689 - <a href="https://sites.google.com/genomezoo.net/cailab/teaching/vibs675">Single-Cell Data Analysis via Machine Learning</a>.</dd>
<dt>12/19/2022</dt>
<dd>Yongjian publishes <a href="https://www.cell.com/cell-systems/fulltext/S2405-4712(23)00030-3">research article</a> describing <a href="https://github.com/cailab-tamu/scTenifoldXct">scTenifoldXct</a> at <i>Cell Systems</i>. Visit his <a href="https://twitter.com/yjyang027/status/1650579470128955392">twitter thread</a>.</dd>
<dt>12/01/2022</dt>
<dd>AgriLife E-Newsletter: <a href="https://agrilifetoday.tamu.edu/2022/11/30/1-19-million-grant-will-leverage-single-cell-sequencing-technology/">$1.19 million grant will leverage single-cell sequencing technology</a>.</dd>
<dt>11/08/2022</dt>
<dd>Yongjian speaks at the <a href="https://sciml.tamids.tamu.edu/2022/10/29/tamids-2022-sciml-workshop/">TAMIDS 2022 Scientific Machine Learning (SciML) Workshop</a>.</dd>
<dt>10/26/2022</dt>
<dd>Yongjian and Dr. Cai presents at the <a href="https://sco2022.blogs.rice.edu/">3rd GCC Single Cell Omics Symposium</a>. <a href="https://twitter.com/hashtag/gccsco2022">More</a>...</dd>
<dt>10/13/2022</dt>
<dd>Dr. Cai speaks at the <a href="https://www.ftz.czu.cz/en">Czech University of Life Sciences Prague (CZU)</a> in <a href="https://www.idnes.cz/zpravy/domaci/fakulta-tropickeho-zemedelstvi-nova-budova-predstaveni.A200923_115858_domaci_lre">Budova Tropického Zemědělství</a>.</dd>
<dt>10/12/2022</dt>
<dd>Dr. Cai speaks at the <a href="https://www.icsb2022.berlin/">ICSB 2022</a>, Berlin, Germany. Final program is <a href="https://easychair.org/smart-program/ICSB2022/index.html">here</a>.</dd>
<dt>10/04/2022</dt>
<dd>AgriLife E-Newsletter: <a href="https://agrilifetoday.tamu.edu/2022/10/04/agrilife-research-led-study-examines-nonalcoholic-fatty-liver-disease/">AgriLife Research-led study examines nonalcoholic fatty liver disease</a>. </dd>
<dt>09/27/2022</dt>
<dd>Dr. Cai speaks at the <a href="https://www.mdanderson.org/research/research-resources/core-facilities/cprit-single-core/events.html">Single Cell Omics Data Workshop</a> at <a href="https://brc.rice.edu/">BioScience Research Collaborative</a>. <a href="https://twitter.com/nicholas_navin/status/1574813390706544640?s=20&t=ATEIlEXrz0hvClJLBgjcdg">More</a>...</dd>
<dt>08/15/2022</dt>
<dd>Qian starts working as an intern in <a href="https://www.jnj.com/">Johnson & Johnson</a>.</dd>
<dt>08/09/2022</dt>
<dd>Yongjian speaks at the International Conference on Intelligent Biology and Medicine (<a href="https://icibm2022.iaibm.org/">ICIBM 2022</a>) on "GenKI: a variational graph autoencoder based virtual knockout tool for gene function predictions via single-cell gene regulatory network."</dd>
<dt>08/02/2022</dt>
<dd>Yongjian receives the travel award provided by <a href="https://tamids.tamu.edu/2019/01/24/texas-am-institute-of-data-science-graduate-travel-grants-program/">Texas A&M Institute of Data Science Graduate Travel Grants Program</a>. Thanks, TAMIDS!</dd>
<dt>07/13/2022</dt>
<dd>Cristhian presents the <a href="https://doi.org/10.48550/arXiv.2206.15362">quantum GRN model</a> in the 2nd Cycle of International Conferences about hosted by Universidad Mayor de San Simon (Bolivia) and University of Cincinnati (USA).</dd>
<dt>07/12/2022</dt>
<dd>Cristhian presents the <a href="https://doi.org/10.48550/arXiv.2206.15362">quantum GRN model</a> in the seminar Experiences in Scientific Research Processes hosted by Universidad Nacional de Ingenieria (Peru).</dd>
<dt>06/30/2022</dt>
<dd>Quantum gene regulatory networks <a href="https://doi.org/10.21203/rs.3.rs-1785614/v1">preprint</a> is on. See also in <a href="https://doi.org/10.48550/arXiv.2206.15362">arXiv:2206.15362 </a>[cs.ET].</dd>
<dt>06/17/2022</dt>
<dd>We are hiring! See <a href="https://www.linkedin.com/pulse/phd-position-machine-learning-single-cell-biology-2022-james-cai/">PhD Position in Machine Learning and Single-Cell Biology</a>.</dd>
<dt>06/06/2022</dt>
<dd>Qian starts first intern in <a href="https://www.bms.com/">Bristol Myers Squibb</a>.</dd>
<dt>06/03/2022</dt>
<dd>Dr. Cai speaks at the <a href="https://www.uh.edu/nsm/biology-biochemistry/news-events/stegg/">Southeast Texas Evolutionary Genetics and Genomics (STEGG) 2022 Symposium</a>.</dd>
<dt>05/17/2022</dt>
<dd>Qian wins the Flash Talk Award (1st Place) in the 2022 CVMBS Trainee Research Symposium.</dd>
<dt>05/11/2022</dt>
<dd>Dr. Cai speaks at <a href="https://www.toxicology.org/events/shm/cct/FutureToxV.asp">FutureTox V</a>, Chapel Hill, NC.</dd>
<dt>04/15/2022</dt>
<dd>Qian's article "Association of pyroptosis and severeness of COVID-19 as revealed by integrated single-cell transcriptome data analysis" published in ImmunoInformatics is <a href="https://doi.org/10.1016/j.immuno.2022.100013">online</a>.</dd>
<dt>04/12/2022</dt>
<dd>Special Issue "<a href="https://www.mdpi.com/journal/genes/special_issues/Single-cell_Bioinformatics">Single-Cell Bioinformatics and Machine Learning</a>" has been published in our open access journal Genes (ISSN 2073-4425).</dd>
<dt>03/01/2022</dt>
<dd>SCGEATOOL is online at <a href="https://scgeatool.github.io/">https://scgeatool.github.io</a>.</dd>
<dt>02/18/2022</dt>
<dd>Qian's article "scInTime: A Computational Method Leveraging Single-Cell Trajectory and Gene Regulatory Networks to Identify Master Regulators of Cellular Differentiation" is published in Genes as part of the Special Issue Single-Cell Bioinformatics and Machine Learning and is available <a href="https://www.mdpi.com/2073-4425/13/2/371">online</a>.</dd>
<dt>02/01/2022</dt>
<dd>scTenifoldKnk paper is online in <a href="https://www.cell.com/patterns/fulltext/S2666-3899(22)00001-0"><i>Patterns</i></a>.</dd>
<dt>12/09/2021</dt>
<dd>Dr. Cai speaks at <a href="https://tamids.tamu.edu/2021/10/27/tamids-2021-research-conference-program/">TAMIDS Research Conference</a>.</dd>
<dt>11/10/2021</dt>
<dd>Yongjian publishes at <a href="https://cancerpreventionresearch.aacrjournals.org/content/early/2021/11/22/1940-6207.CAPR-21-0378.abstract">Cancer Prevention Research</a>.</dd>
<dt>10/07/2021</dt>
<dd>Yongjian speaks at the <a href="https://sco2021.blogs.rice.edu/agenda/">2nd Annual Gulf Coast Consortia (GCC) Single Cell Omics Cluster Symposium</a>.</dd>
<dt>07/28/2021</dt>
<dd>Daniel's new tool <a href="https://cran.r-project.org/web/packages/rPanglaoDB/index.html"><i>rPanglaoDB</i></a> is made public.</dd>
<dt>04/01/2021</dt>
<dd>Daniel will be joining the <a href="https://www.kuijjerlab.org/">Kuijjer lab</a> at <a href="https://www.uio.no/">University of Oslo</a> as a postdoctoral fellow through the Marie Curie Scientia Fellows II program to work on regulatory network modeling in single-cell data. Here's a <a href="https://vetmed.tamu.edu/news/press-releases/daniel-osorio-fellowship/">CVM News</a> to learn more.</dd>
<dt>03/23/2021</dt>
<dd>Preprint "<a href="https://www.biorxiv.org/content/10.1101/2021.03.22.436484v1">scTenifoldKnk: a machine learning workflow performing virtual knockout experiments on single-cell gene regulatory networks</a>" is posted at BioRxiv.</dd>
<dt>03/08/2021</dt>
<dd>Dr. Cai presents at the <a href="https://www.drugabuse.gov/research/research-data-measures-resources/genetics-epigenetics-ccrt/nida-genetics-consortium-ngc/nida-genetic-consortium-meetings-abstracts">2021 Genetics and Epigenetics Cross-Cutting Research Team (GECCRT) Meeting</a>.</dd>
<dt>02/04/2021</dt>
<dd>Daniel receives <a href="https://ec.europa.eu/research/mariecurieactions/">Marie Skłodowska-Curie Actions</a> <a href="https://marie-sklodowska-curie-actions.ec.europa.eu/actions/postdoctoral-fellowships">Postdoctoral Fellowship</a>. <a href="https://marie-sklodowska-curie-actions.ec.europa.eu/actions/how-to-apply#postdoctoral">How to apply</a>?</dd>
<dt>12/10/2020</dt>
<dd>Dr. Cai speaks at the 3rd Workshop on Computational Advances for Single-Cell Omics Data Analysis (<a href="https://iccabs.engr.uconn.edu/workshop.html">CASCODA 2020</a>).</dd>
<dt>12/03/2020</dt>
<dd>Dr. Cai speaks at the <a href="https://iac.nchu.edu.tw/en/12/new20191106/2020-12-03-7th-GEAR-UP-Forum-6971424">7th NCHU GEAR UP forum</a>.</dd>
<dt>11/29/2020</dt>
<dd>Dr. Cai speaks at the 2020 TAMU-NCHU research forum.</dd>
<dt>11/05/2020</dt>
<dd>scTenifoldNet is published online in <a href="https://www.cell.com/patterns/fulltext/S2666-3899(20)30187-2"><i>Patterns</i></a>.</dd>
<dt>10/08/2020</dt>
<dd>Dr. Cai speaks at the <a href="http://scoc2020.blogs.rice.edu/agenda/">1st Annual Gulf Coast Consortia (GCC) Single Cell Omics Cluster Symposium</a>.</dd>
<dt>09/25/2020</dt>
<dd>Dr. Cai speaks at <a href="https://eustm-2020.heysummit.com/speakers/prof-james-cai/">EUSTM-2020</a> on COVID-19 - 7th Annual Congress of the European Society for Translational Medicine on Covid-19 (EUSTM-2020 21-25 September, 2020 (Virtual Congress).</dd>
<dt>08/25/2020</dt>
<dd>Daniel publishes on <a href="https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaa751/5896986"><i>Bioinformatics</i></a>.</dd>
<dt>07/19/2020</dt>
<dd>Preprint: Single-cell gene regulatory network analysis reveals potential mechanisms of action of antimalarials against SARS-CoV-2. [<a href="https://osf.io/va7ux/">https://osf.io/va7ux/</a>] [<a href="https://www.researchgate.net/publication/342927096_Single-cell_gene_regulatory_network_analysis_reveals_potential_mechanisms_of_action_of_antimalarials_against_SARS-CoV-2">ResearchGate</a>.]</dd>
<dt>04/14/2020</dt>
<dd><i>npj Schizophrenia</i> paper published: <a href="https://www.nature.com/articles/s41537-020-0097-5">Overdispersed gene expression in schizophrenia</a></dd>
<dt>11/01/2019</dt>
<dd>Dr. Cai speaks at <a href="https://www2.aeplan.co.jp/icsb2019/index.html">The 20th International Conference on Systems Biology (ICSB2019)</a>.</dd>
<dt>06/04/2019</dt>
<dd><a href="https://www.linkedin.com/post/edit/phd-position-human-geneticscomputational-science-james-jing-cai">Opening</a> for graduate student is available.</dd>
<dt>04/09/2019</dt>
<dd>Dr. Cai speaks at the <a href="https://www.eventbrite.com/e/2019-10x-user-group-meeting-houston-registration-56386105359">10x Genomics User Group meeting in Houston</a>.</dd>
<dt>03/11/2019</dt>
<dd>We release three preprints: [<a href="https://doi.org/10.1101/544163">bioRxiv 544163</a>] [<a href="https://doi.org/10.1101/548115">bioRxiv 548115</a>] and [<a href="https://doi.org/10.1101/574426">bioRxiv 574426</a>].</dd>
<dt>10/13/2018</dt>
<dd>Preprint '<a href="https://www.biorxiv.org/content/10.1101/441527v1">Overdispersed gene expression characterizes schizophrenic brains</a>' posted at BioRxiv.</dd>
<dt>07/08/2018</dt>
<dd>Dr. Cai attends <a href="https://smbe.org/smbe/SMBE2018Meeting/">SMBE18</a> in Yokohama.</dd>
<dt>09/25/2017</dt>
<dd>Ahmad publishes <a href="https://github.com/ahmad-alkawam/vGWAS-simu">vQTL/vGWAS simulator</a> at BMC Genomics.</dd>
<dt>09/01/2017</dt>
<dd>Welcome to new members of the team, Daniel and Ahmad!</dd>
<dt>08/15/2017</dt>
<dd>Guangzao, as lead author, publishes at <a href="https://pubs.rsc.org/en/content/articlelanding/2017/an/c7an00944e">Analyst</a>.</dd>
<dt>07/06/2017</dt>
<dd>We attend <a href="https://www.smbe.org/smbe/MEETINGS/2017Meeting.aspx">SMBE17</a> in Austin.</dd>
<dt>06/09/2017</dt>
<dd>We are part of <a href="http://www.google.com/url?q=http%3A%2F%2Fwww.txgen.tamu.edu%2Fporecamp_usa%2F&sa=D&sntz=1&usg=AFQjCNGpJZx2PkDoIXW83DMI272zew_Adw">PoreCamp USA 2017</a>. Read The Eagle <a href="http://www.google.com/url?q=http%3A%2F%2Fwww.theeagle.com%2Fnews%2Flocal%2Ftexas-a-m-workshop-offers-students-researchers-training-with-new%2Farticle_af9f3b5a-6eb7-5af5-83dc-f9863ce8e7e1.html&sa=D&sntz=1&usg=AFQjCNGuJmNd2yMMfAo2nppY0F-4DY94HQ">report</a>.</dd>
<dt>06/02/2017</dt>
<dd>We participate the 2nd Southeast Texas Evolutionary Genetics and Genomics (<a href="http://www.google.com/url?q=http%3A%2F%2Fwww.tamug.edu%2Fstegg%2F&sa=D&sntz=1&usg=AFQjCNHfjy6l-vZYA9tWS5ML5zhBmHv3FA">STEGG</a>) Symposium at Texas A&M University at Galveston.</dd>
<dt>05/01/2017</dt>
<dd><a href="https://www.genomezoo.net/people">Postdoc position</a> is available immediately.</dd>
<dt>04/28/2017</dt>
<dd><a href="https://www.genomezoo.net/people">Opening</a> for graduate student is available.</dd>
<dt>04/27/2017</dt>
<dd>This new lab website is launched. Lab news on the old site is still accessible <a href="https://sites.google.com/a/genomezoo.net/www/home/home_old">here</a>.</dd>
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Our research lies at the interface of human genetics, computational statistics, and data science. Current research focuses on understanding diverse behaviors of cells using machine learning, network theory, and quantum computation. We develop analytical frameworks to study single-cell omics data gathered from various types of cells. We also study the genetic basis of phenotypic variability in the human population and develop computational tools to identify variants underlying susceptibility to genetic disorders.
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<h3>Journal Articles</h3>
<ol>
<li>Gupta S, Cai JJ.
<strong>Gene Function Revealed at the Moment of Stochastic Gene Silencing.</strong>
<em><u>bioRxiv [Preprint]</u></em>.
2024/01/01; 2024.07.16.603770-.
doi:<a href="https://doi.org/10.1101/2024.07.16.603770">10.1101/2024.07.16.603770</a>.</li>
<span class="__dimensions_badge_embed__" data-doi="10.1101/2024.07.16.603770" data-style="small_rectangle"></span><br>
<li class="highlighted">Gatlin V, Gupta S, Romero S, Chapkin RS, Cai JJ.
<strong>Beyond Differential Expression: Embracing Cell-to-Cell Variability in Single-Cell Gene Expression Data Analysis.</strong>
<em><u>bioRxiv [Preprint]</u></em>.
2024/01/01; 2024.08.08.607086-.
doi:<a href="https://doi.org/10.1101/2024.08.08.607086">10.1101/2024.08.08.607086</a>.</li>
<span class="__dimensions_badge_embed__" data-doi="10.1101/2024.08.08.607086" data-style="small_rectangle"></span><br>
<audio controls src="wav/x10_1101_2024_08_08_607086.wav" style="height: 30px;"></audio>
<li>Tanaka J, Kondo Y, Sakurai M, Sawada A, Hwang Y, Miura A, Shimamura Y, Shimizu D, Hu Y, Sarmah H, Ninish Z, Cai J, Wu J, Mori M.
<strong>Ephrin Forward Signaling Controls Interspecies Cell Competition in Pluripotent Stem Cells.</strong>
<em><u>bioRxiv [Preprint]</u></em>.
2024 Jun 3:2024.
doi: <a href="https://doi.org/10.1101/2024.06.02.597057">10.1101/2024.06.02.597057</a>.
PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/38895424">38895424</a>.</li>
<span class="__dimensions_badge_embed__" data-doi="10.1101/2024.06.02.597057" data-style="small_rectangle"></span><br>
<li>Madhu LN, Kodali M, Upadhya R, Rao S, Shuai B, Somayaji Y, Attaluri S, Kirmani M, Gupta S, Maness N, Rao X, Cai J, Shetty AK.
<strong>Intranasally Administered EVs from hiPSC-derived NSCs Alter the Transcriptomic Profile of Activated Microglia and Conserve Brain Function in an Alzheimer's Model.</strong>
<em><u>bioRxiv [Preprint]</u></em>.
2024 Jan 19:2024.
doi: <a href="https://doi.org/10.1101/2024.01.18.576313">10.1101/2024.01.18.576313</a>.
PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/38293018">38293018</a>.</li>
<span class="__dimensions_badge_embed__" data-doi="10.1101/2024.01.18.576313" data-style="small_rectangle"></span><br>
<li>Ferrer P, Upadhyay S, Cai JJ, Clement TM.
<strong>Novel Nuclear Roles for Testis-Specific ACTL7A and ACTL7B Supported by In Vivo Characterizations and AI Facilitated In Silico Mechanistic Modeling with Implications for Epigenetic Regulation in Spermiogenesis.</strong>
<em><u>bioRxiv [Preprint]</u></em>.
2024 Feb 29:2024.
doi: <a href="https://doi.org/10.1101/2024.02.29.582797">10.1101/2024.02.29.582797</a>.
PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/38464253">38464253</a>.</li>
<span class="__dimensions_badge_embed__" data-doi="10.1101/2024.02.29.582797" data-style="small_rectangle"></span><br>
<li class="highlighted">Romero S, Gupta S, Gatlin V, Chapkin RS, Cai JJ.
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