Mixture modelling of gene expression data from microarray experiments. - Debashis Ghosh; Arul M. Chinnaiyan (Bioinform., 2002)

Internet-based profiler system as integrative framework to support translational research. - Robert Kim; Francesca Demichelis; Jeffery Tang; Alberto Riva; Ronglai Shen; Doug F. Gibbs; Vasudeva Mahavishno; Arul M. Chinnaiyan; Mark A. Rubin (BMC Bioinform., 2005)

Eigengene-based linear discriminant model for tumor classification using gene expression microarray data. - Ronglai Shen; Debashis Ghosh; Arul M. Chinnaiyan; Zhaoling Meng (Bioinform., 2006)

A Latent Variable Approach for Meta-Analysis of Gene Expression Data from Multiple Microarray Experiments. - Hyungwon Choi; Ronglai Shen; Arul M. Chinnaiyan; Debashis Ghosh (BMC Bioinform., 2007)

From Bytes to Bedside: Data Integration and Computational Biology for Translational Cancer Research. - Jomol P. Mathew; Barry S. Taylor; Gary D. Bader; Saiju Pyarajan; Marco Antoniotti; Arul M. Chinnaiyan; Chris Sander; Steven J. Burakoff; Bud Mishra (PLoS Comput. Biol., 2007)

ProbeMatch: rapid alignment of oligonucleotides to genome allowing both gaps and mismatches. - You Jung Kim; Nikhil Teletia; Victor Ruotti; Christopher A. Maher; Arul M. Chinnaiyan; Ron M. Stewart; James A. Thomson; Jignesh M. Patel (Bioinform., 2009)

HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data. - Zhaohui S. Qin; Jianjun Yu; Jincheng Shen; Christopher A. Maher; Ming Hu 001; Shanker Kalyana-Sundaram; Jindan Yu; Arul M. Chinnaiyan (BMC Bioinform., 2010)

ChimeraScan: a tool for identifying chimeric transcription in sequencing data. - Matthew K. Iyer; Arul M. Chinnaiyan; Christopher A. Maher (Bioinform., 2011)

Gene Fusion Markup Language: a prototype for exchanging gene fusion data. - Shanker Kalyana-Sundaram; Achiraman Shanmugam; Arul M. Chinnaiyan (BMC Bioinform., 2012)

Oculus: faster sequence alignment by streaming read compression. - Brendan A. Veeneman; Matthew K. Iyer; Arul M. Chinnaiyan (BMC Bioinform., 2012)

rSeqNP: a non-parametric approach for detecting differential expression and splicing from RNA-Seq data. - Yang Shi; Arul M. Chinnaiyan; Hui Jiang 002 (Bioinform., 2015)

Two-pass alignment improves novel splice junction quantification. - Brendan A. Veeneman; Sudhanshu Shukla; Saravana M. Dhanasekaran; Arul M. Chinnaiyan; Alexey I. Nesvizhskii (Bioinform., 2016)

Integrative clinical genomics of metastatic cancer. - Dan R. Robinson; Yi-Mi Wu; Robert J. Lonigro; Pankaj Vats; Erin Cobain; Jessica Everett; Xuhong Cao; Erica Rabban; Chandan Kumar-Sinha; Victoria Raymond; Scott Schuetze; Ajjai Alva; et al. (Nat., 2017)

MechRNA: prediction of lncRNA mechanisms from RNA-RNA and RNA-protein interactions. - Alexander Gawronski; Michael Uhl; Yajia Zhang; Yen-Yi Lin; Yashar S. Niknafs; Varune R. Ramnarine; Rohit Malik; Felix Feng; Arul M. Chinnaiyan; Colin C. Collins; Süleyman Cenk Sahinalp; Rolf Backofen (Bioinform., 2018)

A systematic overview of single-cell transcriptomics databases, their use cases, and limitations. - Mahnoor N. Gondal; Saad Ur Rehman Shah; Arul M. Chinnaiyan; Marcin Cieslik (Frontiers Bioinform., 2024)