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Urminder Singh

Bioinformatician

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Publications

Overview

Please see my Google scholar page for most up-to-date list of publications.

Preprints

  • Urminder Singh, Kyle Hernandez, Bruce Aronow, and Eve S Wurtele. African Americans and European Americans exhibit distinct gene expression patterns across tissues and tumors that are associated with immunologic and infectious functions and environmental exposures. ResearchSquare, 2020.

  • Urminder Singh, Jing Li, Arun S Seetharam and Eve S Wurtele. pyrpipe: a python package for rna-seq workfows. bioRxiv, page 925818, 2020.

  • Arun S Seetharam, Urminder Singh, Jing Li, Priyanka Bhandary, Zebulun Arendsee, and Eve Syrkin Wurtele. Maximizing prediction of orphan genes in assembled genomes. bioRxiv, 2019.

  • Jing Li, Urminder Singh, Zebulun Arendsee, and Eve Syrkin Wurtele. Landscape of the Dark Transcriptome Revealed through Re-mining Massive RNA-Seq Data. bioRxiv, 2020.

  • Zebulun Arendsee, Andrew Wilkey, Urminder Singh, Jing Li, Manhoi Hur, and Eve Syrkin Wurtele. synder: inferring genomic orthologs from synteny maps. BioRxiv(2019): 554501.

Peer-reviewed

  • Urminder Singh, and Eve S Wurtele. orfipy: a fast and flexible tool for extracting ORFs. Bioinformatics, 2020.

  • Urminder Singh, Manhoi Hur, Karin Dorman, Eve Syrkin Wurtele. MetaOmGraph: a workbench for interactive exploratory data analysis of large expression datasets. Nucleic acids research 48.4 (2020): e23-e23.

  • Urminder Singh and Eve Syrkin Wurtele. Genetic novelty: How new genes are born. Elife 9 (2020): e55136.

  • Zebulun Arendsee, Jing Li, Urminder Singh, Priyanka Bhandary, Arun Seetharam, and Eve Syrkin Wurtele. Fagin: synteny-based phylostratigraphy and finer classification of young genes. BMC bioinformatics 20.1 (2019): 1-14.

  • Ananya Neogy, Tushar Garg, Anil Kumar, Anuj K Dwivedi, Harshita Singh, Urminder Singh, Zeenu Singh, Kalika Prasad, Mukesh Jain, Shri Ram Yadav. Genome-Wide Transcript Profiling Reveals an Auxin-Responsive Transcription Factor, OsAP2/ERF-40, Promoting Rice Adventitious Root Development. Plant and Cell Physiology 60.10 (2019): 2343-2355.

  • Zebulun Arendsee, Jing Li, Urminder Singh, Arun Seetharam, Karin Dorman, and Eve Syrkin Wurtele. phylostratr: A framework for phylostratigraphy. Bioinformatics, 35(19):3617–3627, 2019.

  • Urminder Singh, Kushal Shah, Suman Dhar, Vinod Singh, and Annangarachari Krishnamachari. ORIS: An interactive software tool for prediction of replication origin in prokaryotic genomes. Journal of Open Source Software 4.40 (2019): 1589.

  • Urminder Singh, Niraj Khemka, Mohan Singh Rajkumar, Rohini Garg, and Mukesh Jain. PLncPRO for prediction of long non-coding RNAs (lncRNAs) in plants and its application for discovery of abiotic stress-responsive lncRNAs in rice and chickpea. Nucleic acids research 45.22 (2017): e183-e183.

  • Urminder Singh, Sucheta Chauhan, A Krishnamachari, and Lovekesh Vig. Ensemble of deep long short term memory networks for labelling origin of replication sequences. 2015 IEEE International Conference on Data Science and Advanced Analytics (DSAA). IEEE, 2015.

Book chapters

  • Niraj K Khemka, Urminder Singh, Anuj K Dwivedi, and Mukesh Jain. Machine Learning-Based Annotation of Long Noncoding RNAs Using PLncPRO. Legume Genomics. Humana, New York, NY, 2020. 253-260.