| HMM-ModE–Improved classification using profile hidden Markov models by optimising the discrimination threshold and modifying emission probabilities with negative training sequences PK Srivastava, DK Desai, S Nandi, AM Lynn BMC bioinformatics 8, 1-17, 2007 | 55 | 2007 |
| A genome-wide steroid response study of the major human fungal pathogen Candida albicans D Banerjee, N Martin, S Nandi, S Shukla, A Dominguez, ... Mycopathologia 164, 1-17, 2007 | 51 | 2007 |
| Comparison of theoretical proteomes: identification of COGs with conserved and variable pI within the multimodal pI distribution S Nandi, N Mehra, AM Lynn, A Bhattacharya BMC genomics 6, 1-12, 2005 | 36 | 2005 |
| Serological microarray for a paradoxical diagnostic of Whipple’s disease CJ Bonhomme, P Renesto, S Nandi, AM Lynn, D Raoult European journal of clinical microbiology & infectious diseases 27, 959-968, 2008 | 34 | 2008 |
| Discovery, optimization and validation of an optimal DNA-binding sequence for the Six1 homeodomain transcription factor Y Liu, S Nandi, A Martel, A Antoun, I Ioshikhes, A Blais Nucleic acids research 40 (17), 8227-8239, 2012 | 32 | 2012 |
| Alignment-free method for DNA sequence clustering using Fuzzy integral similarity AK Saw, G Raj, M Das, NC Talukdar, BC Tripathy, S Nandi Scientific reports 9 (1), 3753, 2019 | 29 | 2019 |
| ModEnzA: accurate identification of metabolic enzymes using function specific profile HMMs with optimised discrimination threshold and modified emission probabilities DK Desai, S Nandi, PK Srivastava, AM Lynn Advances in bioinformatics 2011, 2011 | 29 | 2011 |
| Identification of cis-regulatory modules in promoters of human genes exploiting mutual positioning of transcription factors S Nandi, A Blais, I Ioshikhes Nucleic acids research 41 (19), 8822-8841, 2013 | 24 | 2013 |
| Alignment-free similarity analysis for protein sequences based on fuzzy integral AK Saw, BC Tripathy, S Nandi Scientific reports 9 (1), 2775, 2019 | 17 | 2019 |
| ProkSeq for complete analysis of RNA-Seq data from prokaryotes AKMF Mahmud, N Delhomme, S Nandi, M Fällman Bioinformatics 37 (1), 126-128, 2021 | 14 | 2021 |
| Optimizing the GATA-3 position weight matrix to improve the identification of novel binding sites S Nandi, I Ioshikhes BMC genomics 13, 1-17, 2012 | 12 | 2012 |
| PTE, a novel module to target Polycomb Repressive Complex 1 to the human cyclin D2 (CCND2) oncogene SR Cameron, S Nandi, TG Kahn, JI Barrasa, P Stenberg, YB Schwartz Journal of Biological Chemistry 293 (37), 14342-14358, 2018 | 8 | 2018 |
| Alternatives of Buchholz relay and more robust schemes for transformer internal fault protection N Kumar, S Majumdar, V Prakash, T Mulo, S Nandi Proc. 3rd Int. Conf. on Innovations in Computers, Information and …, 2012 | 3 | 2012 |
| Fuzzy code on RNA secondary structure AK Saw, S Nandi, BC Tripathy International Journal of Pure and Applied Mathematics 114 (3), 483-501, 2017 | 2 | 2017 |
| Detection of differential expression of miRNAs in computerized tomography-guided lung biopsy A Singh, R Kant, S Nandi, N Husain, M Naithani, AA Mirza, TS Saluja, ... Journal of Cancer Research and Therapeutics 18 (1), 231-239, 2022 | 1 | 2022 |
| Identification of the conserved long non-coding RNAs in myogenesis A Bhattacharya, S Champramary, T Tripathi, D Thakur, I Ioshikhes, ... BMC genomics 22 (1), 336, 2021 | 1 | 2021 |
| PTE, a novel module of mammalian Polycomb Response Elements SR Cameron, S Nandi, TG Kahn, JI Barrasa, P Stenberg, YB Schwartz bioRxiv, 2017 | 1 | 2017 |
| Combined promoter-capture Hi-C and Hi-C analysis reveals a fine-tuned regulation of 3D chromatin architecture in colorectal cancer AK Saw, A Madhok, A Bhattacharya, S Nandi, S Galande bioRxiv, 2022.11. 08.515643, 2022 | | 2022 |
| Exploring a Drosophila Transcription Factor Interaction Network to Identify Cis-Regulatory Modules AKMF Mahmud, D Yang, P Stenberg, I Ioshikhes, S Nandi Journal of Computational Biology 27 (8), 1313-1328, 2020 | | 2020 |
| ProkSeq for complete analysis of RNA-Seq data from prokaryotes Bioinformatics, 2020 | | 2020 |
