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@article{DBLP:journals/corr/abs-2402-08777, author = {Zhihan Zhou and Weimin Wu and Harrison Ho and Jiayi Wang and Lizhen Shi and Ramana V. Davuluri and Zhong Wang and Han Liu}, title = {{DNABERT-S:} Learning Species-Aware {DNA} Embedding with Genome Foundation Models}, journal = {CoRR}, volume = {abs/2402.08777}, year = {2024}, url = {https://doi.org/10.48550/arXiv.2402.08777}, doi = {10.48550/ARXIV.2402.08777}, eprinttype = {arXiv}, eprint = {2402.08777}, timestamp = {Fri, 16 Feb 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/corr/abs-2402-08777.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/corr/abs-2306-15006, author = {Zhihan Zhou and Yanrong Ji and Weijian Li and Pratik Dutta and Ramana V. Davuluri and Han Liu}, title = {{DNABERT-2:} Efficient Foundation Model and Benchmark For Multi-Species Genome}, journal = {CoRR}, volume = {abs/2306.15006}, year = {2023}, url = {https://doi.org/10.48550/arXiv.2306.15006}, doi = {10.48550/ARXIV.2306.15006}, eprinttype = {arXiv}, eprint = {2306.15006}, timestamp = {Mon, 03 Jul 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/corr/abs-2306-15006.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/ChakrabortyAD21, author = {Abhijit Chakraborty and Ferhat Ay and Ramana V. Davuluri}, title = {ExTraMapper: exon- and transcript-level mappings for orthologous gene pairs}, journal = {Bioinform.}, volume = {37}, number = {20}, pages = {3412--3420}, year = {2021}, url = {https://doi.org/10.1093/bioinformatics/btab393}, doi = {10.1093/BIOINFORMATICS/BTAB393}, timestamp = {Wed, 15 Dec 2021 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bioinformatics/ChakrabortyAD21.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/JiZLD21, author = {Yanrong Ji and Zhihan Zhou and Han Liu and Ramana V. Davuluri}, title = {{DNABERT:} pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome}, journal = {Bioinform.}, volume = {37}, number = {15}, pages = {2112--2120}, year = {2021}, url = {https://doi.org/10.1093/bioinformatics/btab083}, doi = {10.1093/BIOINFORMATICS/BTAB083}, timestamp = {Thu, 14 Jul 2022 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bioinformatics/JiZLD21.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/ficn/RathoreABPSRDDD19, author = {Saima Rathore and Hamed Akbari and Spyridon Bakas and Jared Pisapia and Gaurav Shukla and Jeffrey D. Rudie and Xiao Da and Ramana V. Davuluri and Nadia Dahmane and Donald M. O'Rourke and Christos Davatzikos}, title = {Multivariate Analysis of Preoperative Magnetic Resonance Imaging Reveals Transcriptomic Classification of de novo Glioblastoma Patients}, journal = {Frontiers Comput. Neurosci.}, volume = {13}, pages = {81}, year = {2019}, url = {https://doi.org/10.3389/fncom.2019.00081}, doi = {10.3389/FNCOM.2019.00081}, timestamp = {Mon, 05 Feb 2024 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/ficn/RathoreABPSRDDD19.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bib/DapasKBD17, author = {Matthew Dapas and Manoj Kandpal and Yingtao Bi and Ramana V. Davuluri}, title = {Comparative evaluation of isoform-level gene expression estimation algorithms for RNA-seq and exon-array platforms}, journal = {Briefings Bioinform.}, volume = {18}, number = {2}, pages = {260--269}, year = {2017}, url = {https://doi.org/10.1093/bib/bbw016}, doi = {10.1093/BIB/BBW016}, timestamp = {Thu, 04 Jun 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bib/DapasKBD17.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@inproceedings{DBLP:conf/bcb/JungJD15, author = {Segun Jung and Hongjian Jin and Ramana V. Davuluri}, title = {Identification of candidate regulatory SNPs by integrative analysis for prostate cancer genome data}, booktitle = {Proceedings of the 6th {ACM} Conference on Bioinformatics, Computational Biology and Health Informatics, {BCB} 2015, Atlanta, GA, USA, September 9-12, 2015}, pages = {278--285}, publisher = {{ACM}}, year = {2015}, url = {https://doi.org/10.1145/2808719.2808748}, doi = {10.1145/2808719.2808748}, timestamp = {Tue, 06 Nov 2018 00:00:00 +0100}, biburl = {https://dblp.org/rec/conf/bcb/JungJD15.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@inproceedings{DBLP:conf/iccabs/JungBD14, author = {Segun Jung and Yingtao Bi and Ramana V. Davuluri}, title = {Comparison of data discretization methods for cross platform transfer of gene-expression based tumor subtyping classifier}, booktitle = {{IEEE} 4th International Conference on Computational Advances in Bio and Medical Sciences, {ICCABS} 2014, Miami, FL, USA, June 2-4, 2014}, pages = {1--2}, publisher = {{IEEE} Computer Society}, year = {2014}, url = {https://doi.org/10.1109/ICCABS.2014.6863918}, doi = {10.1109/ICCABS.2014.6863918}, timestamp = {Thu, 23 Mar 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/conf/iccabs/JungBD14.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bmcbi/BiD13, author = {Yingtao Bi and Ramana V. Davuluri}, title = {NPEBseq: nonparametric empirical bayesian-based procedure for differential expression analysis of RNA-seq data}, journal = {{BMC} Bioinform.}, volume = {14}, pages = {262}, year = {2013}, url = {https://doi.org/10.1186/1471-2105-14-262}, doi = {10.1186/1471-2105-14-262}, timestamp = {Sun, 15 Mar 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bmcbi/BiD13.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bmcbi/KimBPGD11, author = {Hyunsoo Kim and Yingtao Bi and Sharmistha Pal and Ravi Gupta and Ramana V. Davuluri}, title = {IsoformEx: Isoform level gene expression estimation using weighted non-negative least squares from mRNA-Seq data}, journal = {{BMC} Bioinform.}, volume = {12}, pages = {305}, year = {2011}, url = {https://doi.org/10.1186/1471-2105-12-305}, doi = {10.1186/1471-2105-12-305}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bmcbi/KimBPGD11.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/nar/GuptaBAWD11, author = {Ravi Gupta and Anirban Bhattacharyya and Francisco J. Agosto{-}Perez and Priyankara Wikramasinghe and Ramana V. Davuluri}, title = {MPromDb update 2010: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-seq experimental data}, journal = {Nucleic Acids Res.}, volume = {39}, number = {Database-Issue}, pages = {92--97}, year = {2011}, url = {https://doi.org/10.1093/nar/gkq1171}, doi = {10.1093/NAR/GKQ1171}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/nar/GuptaBAWD11.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/nar/SunWWPGBASHD11, author = {Hao Sun and Jiejun Wu and Priyankara Wikramasinghe and Sharmistha Pal and Ravi Gupta and Anirban Bhattacharyya and Francisco J. Agosto{-}Perez and Louise C. Showe and Tim Hui{-}Ming Huang and Ramana V. Davuluri}, title = {Genome-wide mapping of {RNA} Pol-II promoter usage in mouse tissues by ChIP-seq}, journal = {Nucleic Acids Res.}, volume = {39}, number = {1}, pages = {190--201}, year = {2011}, url = {https://doi.org/10.1093/nar/gkq775}, doi = {10.1093/NAR/GKQ775}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/nar/SunWWPGBASHD11.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bmcbi/GuptaWBPPD10, author = {Ravi Gupta and Priyankara Wikramasinghe and Anirban Bhattacharyya and Francisco A. Perez and Sharmistha Pal and Ramana V. Davuluri}, title = {Annotation of gene promoters by integrative data-mining of ChIP-seq Pol-II enrichment data}, journal = {{BMC} Bioinform.}, volume = {11}, number = {{S-1}}, pages = {65}, year = {2010}, url = {https://doi.org/10.1186/1471-2105-11-S1-S65}, doi = {10.1186/1471-2105-11-S1-S65}, timestamp = {Sat, 30 Sep 2023 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bmcbi/GuptaWBPPD10.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@inproceedings{DBLP:conf/bcb/KimD10, author = {Hyunsoo Kim and Ramana V. Davuluri}, editor = {Aidong Zhang and Mark Borodovsky and Gultekin {\"{O}}zsoyoglu and Armin R. Mikler}, title = {Data mining of mRNA-Seq and small RNA-Seq data to find microRNA targets}, booktitle = {Proceedings of the First {ACM} International Conference on Bioinformatics and Computational Biology, {BCB} 2010, Niagara Falls, NY, USA, August 2-4, 2010}, pages = {499--501}, publisher = {{ACM}}, year = {2010}, url = {https://doi.org/10.1145/1854776.1854871}, doi = {10.1145/1854776.1854871}, timestamp = {Tue, 06 Nov 2018 00:00:00 +0100}, biburl = {https://dblp.org/rec/conf/bcb/KimD10.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@inproceedings{DBLP:conf/bibe/KimBD10, author = {Hyunsoo Kim and Yingtao Bi and Ramana V. Davuluri}, title = {Estimating the Expression of Transcript Isoforms from mRNA-Seq via Nonnegative Least Squares}, booktitle = {10th {IEEE} International Conference on Bioinformatics and Bioengineering, {BIBE} 2010, Philadelphia, Pennsylvania, USA, May 31-June 3 2010}, pages = {296--297}, publisher = {{IEEE} Computer Society}, year = {2010}, url = {https://doi.org/10.1109/BIBE.2010.61}, doi = {10.1109/BIBE.2010.61}, timestamp = {Fri, 24 Mar 2023 00:00:00 +0100}, biburl = {https://dblp.org/rec/conf/bibe/KimBD10.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bmcsb/QinCLBPSCANYLNSSHD09, author = {Huaxia Qin and Michael W. Y. Chan and Sandya Liyanarachchi and Curtis Balch and Dustin P. Potter and Irene J. Souriraj and Alfred S. L. Cheng and Francisco J. Agosto{-}Perez and Elena Nikonova and Pearlly Yan and Huey{-}Jen Lin and Kenneth P. Nephew and Joel H. Saltz and Louise C. Showe and Tim Hui{-}Ming Huang and Ramana V. Davuluri}, title = {An integrative ChIP-chip and gene expression profiling to model {SMAD} regulatory modules}, journal = {{BMC} Syst. Biol.}, volume = {3}, pages = {73}, year = {2009}, url = {https://doi.org/10.1186/1752-0509-3-73}, doi = {10.1186/1752-0509-3-73}, timestamp = {Tue, 05 May 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/bmcsb/QinCLBPSCANYLNSSHD09.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/LiCJPFLZRBDKHN06, author = {Lang Li and Alfred S. L. Cheng and Victor X. Jin and Henry H. Paik and Meiyun Fan and Xiaoman Li and Wei Zhang and Jason Robarge and Curtis Balch and Ramana V. Davuluri and Sun Kim and Tim Hui{-}Ming Huang and Kenneth P. Nephew}, title = {A mixture model-based discriminate analysis for identifying ordered transcription factor binding site pairs in gene promoters directly regulated by estrogen receptor-alpha}, journal = {Bioinform.}, volume = {22}, number = {18}, pages = {2210--2216}, year = {2006}, url = {https://doi.org/10.1093/bioinformatics/btl329}, doi = {10.1093/BIOINFORMATICS/BTL329}, timestamp = {Mon, 02 Mar 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bioinformatics/LiCJPFLZRBDKHN06.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bmcbi/JinSALD06, author = {Victor X. Jin and Gregory A. Singer and Francisco J. Agosto{-}Perez and Sandya Liyanarachchi and Ramana V. Davuluri}, title = {Genome-wide analysis of core promoter elements from conserved human and mouse orthologous pairs}, journal = {{BMC} Bioinform.}, volume = {7}, pages = {114}, year = {2006}, url = {https://doi.org/10.1186/1471-2105-7-114}, doi = {10.1186/1471-2105-7-114}, timestamp = {Sun, 15 Mar 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bmcbi/JinSALD06.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/nar/SunPPJHD06, author = {Hao Sun and Saranyan K. Palaniswamy and Twyla T. Pohar and Victor X. Jin and Tim Hui{-}Ming Huang and Ramana V. Davuluri}, title = {MPromDb: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-chip experimental data}, journal = {Nucleic Acids Res.}, volume = {34}, number = {Database-Issue}, pages = {98--103}, year = {2006}, url = {https://doi.org/10.1093/nar/gkj096}, doi = {10.1093/NAR/GKJ096}, timestamp = {Sun, 17 May 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/nar/SunPPJHD06.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/PalaniswamyJSD05, author = {Saranyan K. Palaniswamy and Victor X. Jin and Hao Sun and Ramana V. Davuluri}, title = {OMGProm: a database of orthologous mammalian gene promoters}, journal = {Bioinform.}, volume = {21}, number = {6}, pages = {835--836}, year = {2005}, url = {https://doi.org/10.1093/bioinformatics/bti119}, doi = {10.1093/BIOINFORMATICS/BTI119}, timestamp = {Mon, 02 Mar 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bioinformatics/PalaniswamyJSD05.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/SunD04, author = {Hao Sun and Ramana V. Davuluri}, title = {Java-based application framework for visualization of gene regulatory region annotations}, journal = {Bioinform.}, volume = {20}, number = {5}, pages = {727--734}, year = {2004}, url = {https://doi.org/10.1093/bioinformatics/btg476}, doi = {10.1093/BIOINFORMATICS/BTG476}, timestamp = {Mon, 02 Mar 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bioinformatics/SunD04.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/nar/PoharSD04, author = {Twyla T. Pohar and Hao Sun and Ramana V. Davuluri}, title = {HemoPDB: Hematopoiesis Promoter Database, an information resource of transcriptional regulation in blood cell development}, journal = {Nucleic Acids Res.}, volume = {32}, number = {Database-Issue}, pages = {86--90}, year = {2004}, url = {https://doi.org/10.1093/nar/gkh056}, doi = {10.1093/NAR/GKH056}, timestamp = {Sun, 17 May 2020 01:00:00 +0200}, biburl = {https://dblp.org/rec/journals/nar/PoharSD04.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bmcbi/DavuluriSPMMKG03, author = {Ramana V. Davuluri and Hao Sun and Saranyan K. Palaniswamy and Nicole Matthews and Carlos Molina and Mike Kurtz and Erich Grotewold}, title = {{AGRIS:} Arabidopsis Gene Regulatory Information Server, an information resource of Arabidopsis \emph{cis}-regulatory elements and transcription factors}, journal = {{BMC} Bioinform.}, volume = {4}, pages = {25}, year = {2003}, url = {https://doi.org/10.1186/1471-2105-4-25}, doi = {10.1186/1471-2105-4-25}, timestamp = {Sun, 15 Mar 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bmcbi/DavuluriSPMMKG03.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/TabaskaDZ01, author = {Jack E. Tabaska and Ramana V. Davuluri and Michael Q. Zhang}, title = {Identifying the 3'-terminal exon in human {DNA}}, journal = {Bioinform.}, volume = {17}, number = {7}, pages = {602--607}, year = {2001}, url = {https://doi.org/10.1093/bioinformatics/17.7.602}, doi = {10.1093/BIOINFORMATICS/17.7.602}, timestamp = {Mon, 02 Mar 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bioinformatics/TabaskaDZ01.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
@article{DBLP:journals/bioinformatics/PavyRDMDLR99, author = {Nathalie Pavy and Stephane Rombauts and Patrice D{\'{e}}hais and Catherine Math{\'{e}} and Ramana V. Davuluri and Philippe Leroy and Pierre Rouz{\'{e}}}, title = {Evaluation of gene prediction software using a genomic data set: application to {\textless}{\textdollar}O{\_}SSF{\textgreater}Arabidopsis thaliana{\textless}{\textdollar}C{\_}SSF{\textgreater}sequences}, journal = {Bioinform.}, volume = {15}, number = {11}, pages = {887--899}, year = {1999}, url = {https://doi.org/10.1093/bioinformatics/15.11.887}, doi = {10.1093/BIOINFORMATICS/15.11.887}, timestamp = {Mon, 02 Mar 2020 00:00:00 +0100}, biburl = {https://dblp.org/rec/journals/bioinformatics/PavyRDMDLR99.bib}, bibsource = {dblp computer science bibliography, https://dblp.org} }
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