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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}
}

@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}
}

@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}
}

@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}
}

@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}
}

@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}
}

@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    = {{BCB}},
  pages        = {278--285},
  publisher    = {{ACM}},
  year         = {2015}
}

@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    = {{ICCABS}},
  pages        = {1--2},
  publisher    = {{IEEE} Computer Society},
  year         = {2014}
}

@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}
}

@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}
}

@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}
}

@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}
}

@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}
}

@inproceedings{DBLP:conf/bcb/KimD10,
  author       = {Hyunsoo Kim and
                  Ramana V. Davuluri},
  title        = {Data mining of mRNA-Seq and small RNA-Seq data to find microRNA targets},
  booktitle    = {{BCB}},
  pages        = {499--501},
  publisher    = {{ACM}},
  year         = {2010}
}

@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    = {{BIBE}},
  pages        = {296--297},
  publisher    = {{IEEE} Computer Society},
  year         = {2010}
}

@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}
}

@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}
}

@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}
}

@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}
}

@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}
}

@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}
}

@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}
}

@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}
}

@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}
}

@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}
}