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Pseudo-grading of tumor subpopulations from single-cell transcriptomic data using Phenotype Algebra

Namrata Bhattacharya, Anja Rockstroh, Sanket Suhas Deshpande, Sam Koshy Thomas, Anunay Yadav, Chitrita Goswami, Smriti Chawla, Pierre Solomon, Cynthia Fourgeux, Gaurav Ahuja, Brett G Hollier, Himanshu Kumar, Antoine Roquilly, Jeremie Poschmann, Melanie Lehman, Colleen C Nelson*, Debarka Sengupta*

https://doi.org/10.7554/eLife.98469.1

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Marker-free characterization full-length transcriptomes of single live circulating tumor cell

Sarita Poonia, Anurag Goel, Smriti Chawla, Namrata Bhattacharya, Priyadarshini Rai, Yi Fang Lee, Yoon Sim Yap, Jay West, Ali Asgar Bhagat, Juhi Tayal, Anurag Mehta, Gaurav Ahuja, Angshul Majumdar*, Naveen Ramalingam*, Debarka Sengupta*

Genome Res. (2022)

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Microfluidic system-based time-course tracking of physical proximity between cells and its effect on gene expression for elucidating live single cancer-immune cell interactions

Bianca C. T. Flores, Smriti Chawla, Ning Ma, ..., Naveen Ramalingam*, Debarka Sengupta*, Stefanie Jeffery*

Comms. Bio. (2022)

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Gene expression based inference of cancer drug sensitivity

Smriti Chawla, Anja Rockstroh, Melanie Lehman, Ellca Ratther, Atishay Jain, Anuneet Anand, Apoorva Gupta, Namrata Bhattacharya, Sarita Poonia, Priyadarshini Rai, Nirjhar Das, Angshul Majumdar, Jayadeva Jayadeva, Gaurav Ahuja, Brett Hollier, Colleen Nelson*, Debarka Sengupta*

Nature Comms. 13, Article number: 5680 (2022)

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A new deep learning technique reveals the exclusive functional contributions of individual cancer mutations

Prashant Gupta, Aashi Jindal, Gaurav Ahuja, Jayadeva*, Debarka Sengupta*

J Biol Chem. https://doi.org/10.1016/j.jbc.2022.102177

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Artificial intelligence uncovers carcinogenic human metabolites

Aayushi Mittal, Sanjay Kumar Mohanty, Vishakha Gautam, Sakshi Arora, Sheetanshu Saproo, Ria Gupta, Roshan Sivakumar, Prakriti Garg, Anmol Aggarwal, Padmasini Raghavachary, Nilesh Kumar Dixit, Vijay Pal Singh, Anurag Mehta, Juhi Tayal, Srivatsava Naidu, Debarka Sengupta* & Gaurav Ahuja*

Nature Chem. Bio. https://doi.org/10.1038/s41589-022-01110-7

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Quantification of Age-Related Decline in Transcriptional Homeostasis

Krishan Gupta, Princey Yadav, Sidrah Maryam, Gaurav Ahuja*, Debarka Sengupta*

J Mol Biol. 2021 Sep 17;433(19):167179.

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Modeling expression ranks for noise-tolerant differential expression analysis of scRNA-seq data

Krishan Gupta, Manan Lalit, Aditya Biswas, Chad D. Sanada, Cassandra Greene, Kyle Hukari, Ujjwal Maulik, Sanghamitra Bandyopadhyay, Naveen Ramalingam, Gaurav Ahuja, Abhik Ghosh, Debarka Sengupta*

Genome Res. 2021 Apr; 31(4): 689–697.

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UniPath: a uniform approach for pathway and gene-set based analysis of heterogeneity in single-cell epigenome and transcriptome profiles

Smriti Chawla, Sudhagar Samydurai, Say Li Kong, Zhengwei Wu, Zhenxun Wang, Wai Leong Tam, Debarka Sengupta*, Vibhor Kumar*

Nucleic Acids Res. 2021 Feb 22;49(3):e13.

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Machine-OlF-Action: A unified framework for developing and interpreting machine-learning models for chemosensory research

Anku Gupta, Mohit Choudhary, Sanjay Kumar Mohanty, Aayushi Mittal, Krishan Gupta, Aditya Arya, Suvendu Kumar, Nikhil Katyayan, Nilesh Kumar Dixit, Siddhant Kalra, Manshi Goel, Megha Sahni, Vrinda Singhal, Tripti Mishra, Debarka Sengupta*, Gaurav Ahuja*

Bioinformatics. 2021 Jan 8;btaa1104.

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Molecular signature comprising 11 platelet-genes enables accurate blood-based diagnosis of NSCLC

Chitrita Goswami, Smriti Chawla, Deepshi Thakral, Himanshu Pant, Pramod Verma, Prabhat Singh Malik, Jayadeva, Ritu Gupta*, Gaurav Ahuja*, Debarka Sengupta*

BMC Genomics. 2020 Oct 27;21(1):744.

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Integrative Analysis and Machine Learning based Characterization of Single Circulating Tumor Cells

Arvind Iyer, Krishan Gupta, Shreya Sharma, Kishore Hari, Yi Fang Lee, Neevan Ramalingam, Yoon Sim Yap, Jay West, Ali Asgar Bhagat, Balaram Vishnu Subramani, Burhanuddin Sabuwala, Tuan Zea Tan, Jean Paul Thiery, Mohit Kumar Jolly, Naveen Ramalingam*, Debarka Sengupta*

J Clin Med. 2020 Apr 22;9(4):1206.

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Improved dropClust R package with integrative analysis support for scRNA-seq data

Debajyoti Sinha, Pradyumn Sinha, Ritwik Saha, Sanghamitra Bandyopadhyay*, Debarka Sengupta*

Bioinformatics. 2019 Nov 6;btz823.

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Staging System to Predict the Risk of Relapse in Multiple Myeloma Patients Undergoing Autologous Stem Cell Transplantation

Chitrita Goswami, Sarita Poonia, Lalit Kumar*, Debarka Sengupta*

Front Oncol. 2019; 9: 633.

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Discovery of rare cells from voluminous single cell expression data

Aashi Jindal, Prashant Gupta, Jayadeva*, Debarka Sengupta*

Nat Commun. 2018 Nov 9;9(1):4719.

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CellAtlasSearch: a scalable search engine for single cells

Divyanshu Srivastava, Arvind Iyer, Vibhor Kumar*, Debarka Sengupta*

Nucleic Acids Res. 2018 Jul 2;46(W1):W141-W147.

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dropClust: efficient clustering of ultra-large scRNA-seq data

Debajyoti Sinha, Akhilesh Kumar, Himanshu Kumar, Sanghamitra Bandyopadhyay*, Debarka Sengupta*

Nucleic Acids Res . 2018 Apr 6;46(6):e36.

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