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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.
<strong>Quantum Annealing for Enhanced Feature Selection in Single-Cell RNA Sequencing Data Analysis.</strong>
<em><u>arXiv [Preprint]</u></em>.
2024/08/28;(2408.08867).
doi:<a href="https://doi.org/10.48550/arXiv.2408.08867">10.48550/arXiv.2408.08867</a>.</li>
<span class="__dimensions_badge_embed__" data-doi="10.48550/arXiv.2408.08867" data-style="small_rectangle"></span><br>
<audio controls src="wav/x10_48550_arXiv_2408_08867.wav" style="height: 30px;"></audio>
<li>Guo X, Li H, Zhu B, Wang X, Xu Q, Aquino E, Koo M, Li Q, Cai J, Glaser S, Wu C.
<strong>HFD feeding for seven months abolishes STING disruption-driven but not female sex-based protection against hepatic steatosis and inflammation in mice.</strong>
<em><u>J Nutr Biochem</u></em>.
2024 Sep 14;135:109770.
doi: <a href="https://doi.org/10.1016/j.jnutbio.2024.109770">10.1016/j.jnutbio.2024.109770</a>.
PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/39284534">39284534</a>.</li>
<span class="__dimensions_badge_embed__" data-doi="10.1016/j.jnutbio.2024.109770" data-style="small_rectangle"></span><br>
<li>Zhong Y, Cui S, Yang Y, Cai JJ.
<strong>Controlled Noise: Evidence of epigenetic regulation of Single-Cell expression variability.</strong>
<em><u>Bioinformatics</u></em>.
2024 Jul 17;40(7):btae457.
doi: <a href="https://doi.org/10.1093/bioinformatics/btae457">10.1093/bioinformatics/btae457</a>.
PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/39018178">39018178</a>.</li>
<span class="__dimensions_badge_embed__" data-doi="10.1093/bioinformatics/btae457" data-style="small_rectangle"></span><br>
<li>Yan X, Li C, Liu K, Zhang T, Xu Q, Li X, Zhu J, Wang Z, Yusuf A, Cao S, Peng X, Cai JJ, Zhang X.
<strong>Parallel degradome-seq and DMS-MaPseq substantially revise the miRNA biogenesis atlas in Arabidopsis.</strong>
<em><u>Nat Plants</u></em>.
2024 Jul;10(7):1126-1143.
doi: <a href="https://doi.org/10.1038/s41477-024-01725-9">10.1038/s41477-024-01725-9</a>.
PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/38918606">38918606</a>.</li>
<span class="__dimensions_badge_embed__" data-doi="10.1038/s41477-024-01725-9" data-style="small_rectangle"></span><br>
<li>Hanson BS, Hailemariam A, Yang Y, Mohamed F, Donati GL, Baker D, Sacchettini J, Cai JJ, Subashchandrabose S.
<strong>Identification of a copper-responsive small molecule inhibitor of uropathogenic Escherichia coli.</strong>
<em><u>J Bacteriol</u></em>.
2024 Jul 25;206(7):e0011224.
doi: <a href="https://doi.org/10.1128/jb.00112-24">10.1128/jb.00112-24</a>.
PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/38856220">38856220</a>.</li>
<span class="__dimensions_badge_embed__" data-doi="10.1128/jb.00112-24" data-style="small_rectangle"></span><br>
<li>Bazan HA, Bhattacharjee S, Reid MM, Jun B, Polk C, Strain M, St Pierre LA, Desai N, Daly PW, Cucinello-Ragland JA, Edwards S, Recio J, Alvarez-Builla J, Cai JJ, Bazan NG.
<strong>Transcriptomic signature, bioactivity and safety of a non-hepatotoxic analgesic generating AM404 in the midbrain PAG region.</strong>
<em><u>Sci Rep</u></em>.
2024 May 15;14(1):11103.
doi: <a href="https://doi.org/10.1038/s41598-024-61791-z">10.1038/s41598-024-61791-z</a>.
PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/38750093">38750093</a>.</li>
<span class="__dimensions_badge_embed__" data-doi="10.1038/s41598-024-61791-z" data-style="small_rectangle"></span><br>
<li>Ahmad I, Gupta S, Faulkner P, Mullens D, Thomas M, Sytha SP, Ivanov I, Cai JJ, Heaps CL, Newell-Fugate AE.
<strong>Single-nucleus transcriptomics of epicardial adipose tissue from female pigs reveals effects of exercise training on resident innate and adaptive immune cells.</strong>
<em><u>Cell Commun Signal</u></em>.
2024 Apr 26;22(1):243.
doi: <a href="https://doi.org/10.1186/s12964-024-01587-w">10.1186/s12964-024-01587-w</a>.
PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/38671495">38671495</a>.</li>
<span class="__dimensions_badge_embed__" data-doi="10.1186/s12964-024-01587-w" data-style="small_rectangle"></span><br>
<li>Chen B-J, Lin C-H, Wu H-Y, Cai JJ, Chao D-Y.
<strong>Experimental and analytical pipeline for sub-genomic RNA landscape of coronavirus by Nanopore sequencer.</strong>
<em><u>Microbiol Spectr</u></em>.
2024 Apr 2;12(4):e0395423.
doi: <a href="https://doi.org/10.1128/spectrum.03954-23">10.1128/spectrum.03954-23</a>.
PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/38483513">38483513</a>.</li>
<span class="__dimensions_badge_embed__" data-doi="10.1128/spectrum.03954-23" data-style="small_rectangle"></span><br>
<li>Yang Y, Lin YT, Li G, Zhong Y, Xu Q, Cai JJ.
<strong>Interpretable modeling of time-resolved single-cell gene-protein expression with CrossmodalNet.</strong>
<em><u>Brief Bioinform</u></em>.
2023 Sep 22;24(6):bbad342.
doi: <a href="https://doi.org/10.1093/bib/bbad342">10.1093/bib/bbad342</a>.
PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/37798250">37798250</a>.</li>
<span class="__dimensions_badge_embed__" data-doi="10.1093/bib/bbad342" data-style="small_rectangle"></span><br>
<li class="highlighted">Roman-Vicharra C, Cai JJ.
<strong>Quantum gene regulatory networks.</strong>
<em><u>npj Quantum Inf</u></em>.
2023/07/13;9(1)1-8.
doi:<a href="https://doi.org/10.1038/s41534-023-00740-6">10.1038/s41534-023-00740-6</a>.</li>
<span class="__dimensions_badge_embed__" data-doi="10.1038/s41534-023-00740-6" data-style="small_rectangle"></span><br>
<audio controls src="wav/x10_1038_s41534_023_00740_6.wav" style="height: 30px;"></audio>
<li>Chang H, Cai JJ, Zhou Q.
<strong>Order-based structure learning without score equivalence.</strong>
<em><u>Biometrika</u></em>.
2024/05/13;111(2)551-572.
doi:<a href="https://doi.org/10.1093/biomet/asad052">10.1093/biomet/asad052</a>.</li>
<span class="__dimensions_badge_embed__" data-doi="10.1093/biomet/asad052" data-style="small_rectangle"></span><br>
<li>Yang W, Kim DM, Jiang W, Ai W, Pan Q, Rahman S, Cai JJ, Brashear WA, Sun Y, Guo S.
<strong>Suppression of FOXO1 attenuates inflamm-aging and improves liver function during aging.</strong>
<em><u>Aging Cell</u></em>.
2023 Oct;22(10):e13968.
doi: <a href="https://doi.org/10.1111/acel.13968">10.1111/acel.13968</a>.
PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/37602516">37602516</a>.</li>
<span class="__dimensions_badge_embed__" data-doi="10.1111/acel.13968" data-style="small_rectangle"></span><br>
<li class="highlighted">Yang Y, Li G, Zhong Y, Xu Q, Chen BJ, Lin YT, Chapkin RS, Cai JJ.
<strong>Gene knockout inference with variational graph autoencoder learning single-cell gene regulatory networks.</strong>
<em><u>Nucleic Acids Res</u></em>.
2023 Jul 21;51(13):6578-6592.
doi: <a href="https://doi.org/10.1093/nar/gkad450">10.1093/nar/gkad450</a>.
PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/37246643">37246643</a>.</li>
<span class="__dimensions_badge_embed__" data-doi="10.1093/nar/gkad450" data-style="small_rectangle"></span><br>
<audio controls src="wav/x37246643.wav" style="height: 30px;"></audio>
<li class="highlighted">Yang Y, Li G, Zhong Y, Xu Q, Lin YT, Roman-Vicharra C, Chapkin RS, Cai JJ.
<strong>scTenifoldXct: A semi-supervised method for predicting cell-cell interactions and mapping cellular communication graphs.</strong>
<em><u>Cell Syst</u></em>.
2023 Apr 19;14(4):302-311.
doi: <a href="https://doi.org/10.1016/j.cels.2023.01.004">10.1016/j.cels.2023.01.004</a>.
PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/36787742">36787742</a>.</li>
<span class="__dimensions_badge_embed__" data-doi="10.1016/j.cels.2023.01.004" data-style="small_rectangle"></span><br>
<audio controls src="wav/x36787742.wav" style="height: 30px;"></audio>
<li>Li H, Zheng J, Xu Q, Yang Y, Zhou J, Guo X, Cai Y, Cai JJ, Xie L, Awika J, Han X, Li Q, Kennedy L, Francis H, Glaser S, Huo Y, Alpini G, Wu C.
<strong>Hepatocyte Adenosine Kinase Promotes Excessive Fat Deposition and Liver Inflammation.</strong>
<em><u>Gastroenterology</u></em>.
2023 Jan;164(1):134-146.
doi: <a href="https://doi.org/10.1053/j.gastro.2022.09.027">10.1053/j.gastro.2022.09.027</a>.
PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/36181835">36181835</a>.</li>
<span class="__dimensions_badge_embed__" data-doi="10.1053/j.gastro.2022.09.027" data-style="small_rectangle"></span><br>
<li>Doke M, McLaughlin JP, Cai JJ, Pendyala G, Kashanchi F, Khan MA, Samikkannu T.
<strong>HIV-1 Tat and cocaine impact astrocytic energy reservoirs and epigenetic regulation by influencing the LINC01133-hsa-miR-4726-5p-NDUFA9 axis.</strong>
<em><u>Mol Ther Nucleic Acids</u></em>.
2022 Jul 6;29:243-258.
doi: <a href="https://doi.org/10.1016/j.omtn.2022.07.001">10.1016/j.omtn.2022.07.001</a>.
PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/35892093">35892093</a>.</li>
<span class="__dimensions_badge_embed__" data-doi="10.1016/j.omtn.2022.07.001" data-style="small_rectangle"></span><br>
<li>Chen J, Tang S, Ke S, Cai JJ, Osorio D, Golovko A, Morpurgo B, Guo S, Sun Y, Winkle M, Calin GA, Tian Y.
<strong>Ablation of long noncoding RNA MALAT1 activates antioxidant pathway and alleviates sepsis in mice.</strong>
<em><u>Redox Biol</u></em>.
2022 Aug;54:102377.
doi: <a href="https://doi.org/10.1016/j.redox.2022.102377">10.1016/j.redox.2022.102377</a>.
PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/35763934">35763934</a>.</li>
<span class="__dimensions_badge_embed__" data-doi="10.1016/j.redox.2022.102377" data-style="small_rectangle"></span><br>
<li>Ni N, Fang X, Mullens DA, Cai JJ, Ivanov I, Bartholin L, Li Q.
<strong>Transcriptomic Profiling of Gene Expression Associated with Granulosa Cell Tumor Development in a Mouse Model.</strong>
<em><u>Cancers (Basel)</u></em>.
2022 Apr 27;14(9):2184.
doi: <a href="https://doi.org/10.3390/cancers14092184">10.3390/cancers14092184</a>.
PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/35565312">35565312</a>.</li>
<span class="__dimensions_badge_embed__" data-doi="10.3390/cancers14092184" data-style="small_rectangle"></span><br>
<li class="highlighted">Osorio D, Zhong Y, Li G, Xu Q, Yang Y, Tian Y, Chapkin RS, Huang JZ, Cai JJ.
<strong>scTenifoldKnk: An efficient virtual knockout tool for gene function predictions via single-cell gene regulatory network perturbation.</strong>
<em><u>Patterns (N Y)</u></em>.
2022 Feb 1;3(3):100434.
doi: <a href="https://doi.org/10.1016/j.patter.2022.100434">10.1016/j.patter.2022.100434</a>.
PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/35510185">35510185</a>.</li>
<span class="__dimensions_badge_embed__" data-doi="10.1016/j.patter.2022.100434" data-style="small_rectangle"></span><br>
<audio controls src="wav/x35510185.wav" style="height: 30px;"></audio>
<li>Xu Q, Yang Y, Zhang X, Cai JJ.
<strong>Association of pyroptosis and severeness of COVID-19 as revealed by integrated single-cell transcriptome data analysis.</strong>
<em><u>Immunoinformatics (Amst)</u></em>.
2022 Jun;6:100013.
doi: <a href="https://doi.org/10.1016/j.immuno.2022.100013">10.1016/j.immuno.2022.100013</a>.
PMID: <a href="https://pubmed.ncbi.nlm.nih.gov/35434695">35434695</a>.</li>
<span class="__dimensions_badge_embed__" data-doi="10.1016/j.immuno.2022.100013" data-style="small_rectangle"></span><br>
<li>Willis SC, Saenz DE, Wang G, Hollenbeck CM, Portnoy DS, Cai JJ, Winemiller KO.
<strong>Gill transcriptome of the yellow peacock bass (Cichla ocellaris monoculus) exposed to contrasting physicochemical conditions.</strong>
<em><u>Conservation Genet Resour</u></em>.
2022/12;14(4)391-401.
doi:<a href="https://doi.org/10.1007/s12686-022-01284-1">10.1007/s12686-022-01284-1</a>.</li>
<span class="__dimensions_badge_embed__" data-doi="10.1007/s12686-022-01284-1" data-style="small_rectangle"></span><br>
<li>Zhou F, He K, Cai JJ, Davidson LA, Chapkin RS, Ni Y.
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