2024

• Nature communications Biology

cis-and trans-regulatory contributions to a hierarchy of factors influencing gene expression variation

https://doi.org/10.1038/s42003-024-07255-6

Siddhant Kalra, Stephen Lanno, Guadalupe Sanchez and Joseph D. Coolon

• Frontiers in Microbiomes

Searching for bacterial plastitrophs in modified Winogradsky columns

https://doi.org/10.3389/frmbi.2024.1303112

Fatai A. Olabemiwo , Claudia Kunney , Rachel Hsu , Chloe De Palo , Thaddeus Bashaw , Kendall Kraut , Savannah Ryan , Yuting Huang , Will Wallentin, Siddhant Kalra , Valerie Nazzaro and Frederick M. Cohan

2023

• Genomics

Genome-wide gene expression responses to experimental manipulation of Saccharomyces cerevisiae repressor activator protein 1 (Rap1) expression level

https://doi.org/10.1016/j.ygeno.2023.110625

S. Kalra, R. Peyser, J. Ho, C. Babbin, N. Bohan, A. Cortes, J. Erley, M. Fatima, J. Flinn, E. Horwitz, R. Hsu, W. Lee, V. Lu, A. Narch, D. Navas, K. Okoroafor, E. Ouanemalay, S. Ross, F. Sowole, E. Specht and J.D. Coolon

2022

• Cancer Gene Therapy

MiR-330-5p and miR-1270 target essential components of RNA polymerase I transcription and exhibit a novel tumor suppressor role in lung adenocarcinoma

https://doi.org/10.1038/s41417-022-00544-4

Sheetanshu Saproo, Shashanka S Sarkar, Ekta Gupta, Sourav Chattopadhyay, Aarzoo Charaya, Siddhant Kalra, Gaurav Ahuja, and Srivatsava Naidu

2021

• Briefings in Bioinformatics

EcTracker: Tracking and elucidating ectopic expression leveraging large-scale scRNA-seq studies

https://doi.org/10.1093/bib/bbab237

Vishakha Gautam, Aayushi Mittal, Siddhant Kalra, Sanjay Kumar Mohanty, Krishan Gupta, Komal Rani, Srivatsava Naidu, Tripti Mishra, Debarka Sengupta, and Gaurav Ahuja

• Bioinformatics

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

https://doi.org/10.1093/bioinformatics/btaa1104

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, and Gaurav Ahuja

• The FEBS Journal

Challenges and possible solutions for decoding extranasal olfactory receptors

https://doi.org/10.1111/febs.15606

Siddhant Kalra, Aayushi Mittal, Manisha Bajoria, Tripti Mishra, Sidrah Maryam, Debarka Sengupta, and Gaurav Ahuja

• Briefings in bioinformatics

The cellular basis of loss of smell in 2019-nCoV-infected individuals

https://doi.org/10.1093/bib/bbaa168

Krishan Gupta, Sanjay Kumar Mohanty, Aayushi Mittal, Siddhant Kalra, Suvendu Kumar, Tripti Mishra, Jatin Ahuja, Debarka Sengupta, and Gaurav Ahuja

2020

• Nature Communications biology

Analysis of single-cell transcriptomes links enrichment of olfactory receptors with cancer cell differentiation status and prognosis

https://doi.org/10.1038/s42003-020-01232-5

Siddhant Kalra, Aayushi Mittal, Krishan Gupta, Vrinda Singhal, Anku Gupta, Tripti Mishra, Srivatsava Naidu, Debarka Sengupta, and Gaurav Ahuja

• Informatics in Medicine Unlocked

LEPStr: A database for Mycobacterium leprae short tandem repeats

https://doi.org/10.1016/j.imu.2020.100322

Partha Sarathi Mohanty, Dimple Saikia, Siddhant Kalra, Farah Naaz, Avi Kumar Bansal. Harpeet Singh Pawar, Keshar Kunja Mohanty, Sandeep Sharma, Manju Shukla, and Shripad A. Patil.

2019

• Book Chapter: Essentials of Bioinformatics, Volume I

Modeling and Optimization of molecular biosystems to generate predictive models

https://doi.org/10.1007/978-3-030-02634-9_17

Ankush Bansal, Siddhant Kalra, Babajan Banaganapalli, and Tiratha Raj Singh

2017

• International Journal of Computational Biology

Structural bioinformatics and big data analytics: a mini review

https://doi.org/10.34040/IJCB.6.1.2017.86

Pulkit Anupam Srivastava, Siddhant Kalra, and Raghu Yennamalli

• MOJ Proteomics and Bioinformatics

Computational tools and resources for CRISPR/Cas9 genome editing method:a mini review

https://doi.org/10.15406/mojpb.2017.05.00164

Ragothaman M Yennmalli, Siddhant Kalra, Pulkit Anupam Srivastava, and Vijay Kumar Garlapati