Ramana V. Davuluri

32 papers A* 1C 1Misc 2Journal 24Unranked 4
YearRankTypeTitle / Venue / Authors
2025 — conf
Augmenting DNABERT Embeddings with Multimodal DNA Features for Improved Regulatory Sequence Interpretation.
MLCB
Nimisha Papineni, Pratik Dutta, Max Chao, Orbin Acanto, Rekha Sathian, Pallavi Surana, Ramana V. Davuluri
2025 J jnl
DNABERT-S: pioneering species differentiation with species-aware DNA embeddings.
Bioinform.
Zhihan Zhou, Weimin Wu, Harrison Ho, Jiayi Wang, Lizhen Shi, Ramana V. Davuluri, Zhong Wang, Han Liu
2025 J jnl
DeepVRegulome: DNABERT-based deep-learning framework for predicting the functional impact of short genomic variants on the human regulome.
CoRR
Pratik Dutta, Matthew Obusan, Rekha Sathian, Max Chao, Pallavi Surana, Nimisha Papineni, Yanrong Ji, Zhihan Zhou, Han Liu, Alisa Yurovsky, Ramana V. Davuluri
2024 A* conf
DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genomes.
ICLR
Zhihan Zhou, Yanrong Ji, Weijian Li, Pratik Dutta, Ramana V. Davuluri, Han Liu
2024 J jnl
DNABERT-S: Learning Species-Aware DNA Embedding with Genome Foundation Models.
CoRR
Zhihan Zhou, Weimin Wu, Harrison Ho, Jiayi Wang, Lizhen Shi, Ramana V. Davuluri, Zhong Wang, Han Liu
2024 J jnl
TransTEx: novel tissue-specificity scoring method for grouping human transcriptome into different expression groups.
Bioinform.
Pallavi Surana, Pratik Dutta, Ramana V. Davuluri
2023 J jnl
DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome.
CoRR
Zhihan Zhou, Yanrong Ji, Weijian Li, Pratik Dutta, Ramana V. Davuluri, Han Liu
2021 J jnl
DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome.
Bioinform.
Yanrong Ji, Zhihan Zhou, Han Liu, Ramana V. Davuluri
2021 J jnl
ExTraMapper: exon- and transcript-level mappings for orthologous gene pairs.
Bioinform.
Abhijit Chakraborty, Ferhat Ay, Ramana V. Davuluri
2019 J jnl
Multivariate Analysis of Preoperative Magnetic Resonance Imaging Reveals Transcriptomic Classification of de novo Glioblastoma Patients.
Frontiers Comput. Neurosci.
Saima Rathore, Hamed Akbari, Spyridon Bakas, Jared Pisapia, Gaurav Shukla, Jeffrey D. Rudie, Xiao Da, Ramana V. Davuluri, Nadia Dahmane, Donald M. O'Rourke, Christos Davatzikos
2017 J jnl
Comparative evaluation of isoform-level gene expression estimation algorithms for RNA-seq and exon-array platforms.
Briefings Bioinform.
Matthew Dapas, Manoj Kandpal, Yingtao Bi, Ramana V. Davuluri
2015 — conf
Identification of candidate regulatory SNPs by integrative analysis for prostate cancer genome data.
BCB
Segun Jung, Hongjian Jin, Ramana V. Davuluri
2014 — conf
Comparison of data discretization methods for cross platform transfer of gene-expression based tumor subtyping classifier.
ICCABS
Segun Jung, Yingtao Bi, Ramana V. Davuluri
2013 J jnl
NPEBseq: nonparametric empirical bayesian-based procedure for differential expression analysis of RNA-seq data.
BMC Bioinform.
Yingtao Bi, Ramana V. Davuluri
2011 J jnl
Genome-wide mapping of RNA Pol-II promoter usage in mouse tissues by ChIP-seq.
Nucleic Acids Res.
Hao Sun, Jiejun Wu, Priyankara Wikramasinghe, Sharmistha Pal, Ravi Gupta, Anirban Bhattacharyya, Francisco J. Agosto-Perez, Louise C. Showe, Tim Hui-Ming Huang, Ramana V. Davuluri
2011 J jnl
IsoformEx: Isoform level gene expression estimation using weighted non-negative least squares from mRNA-Seq data.
BMC Bioinform.
Hyunsoo Kim, Yingtao Bi, Sharmistha Pal, Ravi Gupta, Ramana V. Davuluri
2011 J jnl
MPromDb update 2010: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-seq experimental data.
Nucleic Acids Res.
Ravi Gupta, Anirban Bhattacharyya, Francisco J. Agosto-Perez, Priyankara Wikramasinghe, Ramana V. Davuluri
2010 J jnl
Annotation of gene promoters by integrative data-mining of ChIP-seq Pol-II enrichment data.
BMC Bioinform.
Ravi Gupta, Priyankara Wikramasinghe, Anirban Bhattacharyya, Francisco A. Perez, Sharmistha Pal, Ramana V. Davuluri
2010 — conf
Data mining of mRNA-Seq and small RNA-Seq data to find microRNA targets.
BCB
Hyunsoo Kim, Ramana V. Davuluri
2010 C conf
Estimating the Expression of Transcript Isoforms from mRNA-Seq via Nonnegative Least Squares.
BIBE
Hyunsoo Kim, Yingtao Bi, Ramana V. Davuluri
2009 J jnl
An integrative ChIP-chip and gene expression profiling to model SMAD regulatory modules.
BMC Syst. Biol.
Huaxia Qin, Michael W. Y. Chan, Sandya Liyanarachchi, Curtis Balch, Dustin P. Potter, Irene J. Souriraj, Alfred S. L. Cheng, Francisco J. Agosto-Perez, Elena Nikonova, Pearlly Yan, Huey-Jen Lin, Kenneth P. Nephew, Joel H. Saltz, Louise C. Showe, Tim Hui-Ming Huang, Ramana V. Davuluri
2009 Misc conf
Session Introduction.
Pacific Symposium on Biocomputing
Michael F. Ochs, John Quackenbush, Ramana V. Davuluri, Habtom W. Ressom
2008 Misc conf
Session Introduction.
Pacific Symposium on Biocomputing
Michael F. Ochs, John Quackenbush, Ramana V. Davuluri
2006 J jnl
A mixture model-based discriminate analysis for identifying ordered transcription factor binding site pairs in gene promoters directly regulated by estrogen receptor-alpha.
Bioinform.
Lang Li, Alfred S. L. Cheng, Victor X. Jin, Henry H. Paik, Meiyun Fan, Xiaoman Li, Wei Zhang, Jason Robarge, Curtis Balch, Ramana V. Davuluri, Sun Kim, Tim Hui-Ming Huang, Kenneth P. Nephew
2006 J jnl
Genome-wide analysis of core promoter elements from conserved human and mouse orthologous pairs.
BMC Bioinform.
Victor X. Jin, Gregory A. Singer, Francisco J. Agosto-Perez, Sandya Liyanarachchi, Ramana V. Davuluri
2006 J jnl
MPromDb: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-chip experimental data.
Nucleic Acids Res.
Hao Sun, Saranyan K. Palaniswamy, Twyla T. Pohar, Victor X. Jin, Tim Hui-Ming Huang, Ramana V. Davuluri
2005 J jnl
OMGProm: a database of orthologous mammalian gene promoters.
Bioinform.
Saranyan K. Palaniswamy, Victor X. Jin, Hao Sun, Ramana V. Davuluri
2004 J jnl
HemoPDB: Hematopoiesis Promoter Database, an information resource of transcriptional regulation in blood cell development.
Nucleic Acids Res.
Twyla T. Pohar, Hao Sun, Ramana V. Davuluri
2004 J jnl
Java-based application framework for visualization of gene regulatory region annotations.
Bioinform.
Hao Sun, Ramana V. Davuluri
2003 J jnl
AGRIS: Arabidopsis Gene Regulatory Information Server, an information resource of Arabidopsis
BMC Bioinform.
Ramana V. Davuluri, Hao Sun, Saranyan K. Palaniswamy, Nicole Matthews, Carlos Molina, Mike Kurtz, Erich Grotewold
2001 J jnl
Identifying the 3'-terminal exon in human DNA.
Bioinform.
Jack E. Tabaska, Ramana V. Davuluri, Michael Q. Zhang
1999 J jnl
Evaluation of gene prediction software using a genomic data set: application to <$O_SSF>Arabidopsis thaliana<$C_SSF>sequences.
Bioinform.
Nathalie Pavy, Stephane Rombauts, Patrice Déhais, Catherine Mathé, Ramana V. Davuluri, Philippe Leroy, Pierre Rouzé