Saptarshi Pyne

Journal articles

1. Inference of cell type-specific gene regulatory networks on cell lineages from single cell omic datasets. Zhang S, Pyne S, Pietrzak S, Halberg S, McCalla SG, Siahpirani AF, Sridharan R, Roy S. Nature Communications, vol. 14, no. 1, pp. 1-25, May 27, 2023. Publisher's site  
2. Identifying strengths and weaknesses of methods for computational network inference from single cell RNA-seq data. McCalla SG^, Siahpirani AF^ (^joint first authors), Li J, Pyne S (third author), Stone M, Periyasamy V, Shin J, and Roy S. G3: Genes Genomes Genetics, vol. 13, no. 3, pp. jkad004, March 2023. Publisher's site  
3. Rapid Reconstruction of Time-varying Gene Regulatory Networks with Limited Main Memory. Pyne S, Anand A. IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 18, no. 4, pp. 1608-1619, Jul-Aug 1, 2021. Publisher's site   Preprint  Code & data
4. Impact of the Continuous Evolution of Gene Ontology on the Performance of Similarity Measures for Scoring Confidence of Protein Interactions. Paul M, Anand A, Pyne S. SN Computer Science, Springer Nature (SN), vol. 1, article 351, no. 6, 2020. Publisher's site  
5. Rapid Reconstruction of Time-varying Gene Regulatory Networks. Pyne S, Kumar AR, Anand A. IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 17, no. 1, pp. 278-291, 1 Jan-Feb, 2020. Publisher's site   Preprint  Code & data

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Conferences

1. Impact of the Continuous Evolution of Gene Ontology on Similarity Measures. Paul M, Anand A, Pyne S. Presented in Pattern Recognition and Machine Intelligence (PReMI) 2019, Tezpur, India. Published in Lecture Notes in Computer Science, vol. 11942, pp. 122-129, Springer. Publisher's site

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Posters

1. Single-cell Omics to Examine the Cell Type-specific Gene Regulatory Programs of Mucilage Production in Sorghum bicolor. Venado RE, Pyne S (joint first author), Pereira WJ, Dervinis C, Kirst M, Roy S, Anè JM. Genomic Science Program Annual Principal Investigator Meeting, 2023, Washington, DC, USA.
2. Towards Genome-scale Disease Progression Modeling. Pyne S, Kumar AR, Anand A. 17th International Conference on Bioinformatics (InCoB) 2018, New Delhi, India. PDF

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Software

1. CRAN R Package ‘TGS’ [CRAN URL]: Rapid Reconstruction of Time-Varying Gene Regulatory Networks.

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Thesis

• Improving Reconstruction Efficiency of Time-varying Gene Regulatory Networks, Abstract, Full, 2020.

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