A multi-expert system for the automatic detection of protein domains from sequence information. - Niranjan Nagarajan; Golan Yona (RECOMB, 2003)

A Faster Reliable Algorithm to Estimate the p-Value of the Multinomial llr Statistic. - Uri Keich; Niranjan Nagarajan (WABI, 2004)

Automatic prediction of protein domains from sequence information using a hybrid learning system. - Niranjan Nagarajan; Golan Yona (Bioinform., 2004)

Computing the P-value of the information content from an alignment of multiple sequences. - Niranjan Nagarajan; Neil Jones; Uri Keich (ISMB (Supplement of Bioinformatics), 2005)

Apples to apples: improving the performance of motif finders and their significance analysis in the Twilight Zone. - Patrick Ng; Niranjan Nagarajan; Neil Jones; Uri Keich (ISMB (Supplement of Bioinformatics), 2006)

Statistical Techniques for Biological Motif Discovery. - Niranjan Nagarajan (2007)

Uncovering Genomic Reassortments among Influenza Strains by Enumerating Maximal Bicliques. - Niranjan Nagarajan; Carl Kingsford (BIBM, 2008)

FAST: Fourier transform based algorithms for significance testing of ungapped multiple alignments. - Niranjan Nagarajan; Uri Keich (Bioinform., 2008)

Scaffolding and validation of bacterial genome assemblies using optical restriction maps. - Niranjan Nagarajan; Timothy D. Read; Mihai Pop (Bioinform., 2008)

Reliability and efficiency of algorithms for computing the significance of the Mann-Whitney test. - Niranjan Nagarajan; Uri Keich (Comput. Stat., 2009)

Parametric Complexity of Sequence Assembly: Theory and Applications to Next Generation Sequencing. - Niranjan Nagarajan; Mihai Pop (J. Comput. Biol., 2009)

Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples. - James Robert White; Niranjan Nagarajan; Mihai Pop (PLoS Comput. Biol., 2009)

Alignment and clustering of phylogenetic markers - implications for microbial diversity studies. - James Robert White; Saket Navlakha; Niranjan Nagarajan; Mohammadreza Ghodsi; Carl Kingsford; Mihai Pop (BMC Bioinform., 2010)

Finding Biologically Accurate Clusterings in Hierarchical Tree Decompositions Using the Variation of Information. - Saket Navlakha; James Robert White; Niranjan Nagarajan; Mihai Pop; Carl Kingsford (J. Comput. Biol., 2010)

Opera: Reconstructing Optimal Genomic Scaffolds with High-Throughput Paired-End Sequences. - Song Gao 004; Wing-Kin Sung; Niranjan Nagarajan (J. Comput. Biol., 2011)

FinIS: Improved in silico Finishing Using an Exact Quadratic Programming Formulation. - Song Gao 004; Denis Bertrand; Niranjan Nagarajan (WABI, 2012)

@MInter: automated text-mining of microbial interactions. - Kun Ming Kenneth Lim; Chenhao Li; Kern Rei Chng; Niranjan Nagarajan (Bioinform., 2016)

Predicting Cancer Drug Response using a Recommender System. - Chayaporn Suphavilai; Denis Bertrand; Niranjan Nagarajan (Bioinform., 2018)

Task Uncertainty Loss Reduce Negative Transfer in Asymmetric Multi-task Feature Learning. - Rafael Peres da Silva; Chayaporn Suphavilai; Niranjan Nagarajan (CoRR, 2020)

Task Uncertainty Loss Reduce Negative Transfer in Asymmetric Multi-task Feature Learning (Student Abstract). - Rafael Peres da Silva; Chayaporn Suphavilai; Niranjan Nagarajan (AAAI, 2021)

TUGDA: task uncertainty guided domain adaptation for robust generalization of cancer drug response prediction from in vitro to in vivo settings. - Rafael Peres da Silva; Chayaporn Suphavilai; Niranjan Nagarajan (Bioinform., 2021)

BEEM-Static: Accurate inference of ecological interactions from cross-sectional microbiome data. - Chenhao Li; Tamar Vered Av-Shalom; Jun Wei Gerald Tan; Junmei Samantha Kwah; Kern Rei Chng; Niranjan Nagarajan (PLoS Comput. Biol., 2021)

CREAMMIST: an integrative probabilistic database for cancer drug response prediction. - Hatairat Yingtaweesittikul; Jiaxi Wu; Aanchal Mongia; Rafael Peres; Karrie Ko; Niranjan Nagarajan; Chayaporn Suphavilai (Nucleic Acids Res., 2023)

Floria: fast and accurate strain haplotyping in metagenomes. - Jim Shaw; Jean-Sébastien Gounot; Hanrong Chen; Niranjan Nagarajan; Yun William Yu (Bioinform., 2024)

Comparative analysis of metagenomic classifiers for long-read sequencing datasets. - Josip Maric; Kresimir Krizanovic; Sylvain Riondet; Niranjan Nagarajan; Mile Sikic (BMC Bioinform., 2024)

MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes. - Rafael Peres da Silva; Chayaporn Suphavilai; Niranjan Nagarajan (BMC Bioinform., 2024)