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Publications

TOBF1 modulates mouse embryonic stem cell fate through regulating alternative splicing of pluripotency genes

CriSNPr: a single interface for the curated and de novo design of gRNAs for CRISPR diagnostics using diverse Cas systems

Capturing nucleic acid variants with precision using CRISPR diagnostics.

Rhythm Phutela, Sneha Gulati, Manoj Kumar, Souvik Maiti, Debojyoti Chakraborty.

Multiplex Biomarker Techniques, Springer (2022).

Commentary: Artificial intelligence-based screening of retina

Mayank Bansal, Krithika Rangarajan

Indian Journal of Opthalmology (2022).

FnCas9 Editor Linked Uniform Detection Assay for COVID 19.

Rhythm Phutela, Sneha Gulati, Manoj Kumar, Souvik Maiti, Debojyoti Chakraborty.

Multiplex Biomarker Techniques, Springer (2022).

Engineered PAM-flexible FnCas9 variants for robust and specific genome editing and diagnostics.

Sundaram Acharya, Asgar Ansari, Seiichi Hirano, Deepanjan Paul, Riya Rauthan, Manoj Kumar, Rhythm Phutela, Sajal Sarkar, Sneha Gulati, Sudipta Mahato, Savitri Maddileti, Vinay Pulimamidi, Indumathi Mariappan, Hiroshi Nishimasu, Osamu Nureki, Souvik Maiti, Debojyoti Chakraborty. Research Square (2021).

FnCas9 based CRISPR diagnostic for rapid and accurate detection of major SARS-CoV2 variants on a paper strip.

Manoj Kumar*, Sneha Gulati*, Asgar H Ansari, Rhythm Phutela, Sundaram Acharya, Mohd Azhar,  Jayaram Murthy, Poorti Kathpalia, Akshay Kanakan, Ranjeet Maurya, Janani Srinivasa Vasudevan, Aparna Murali, Rajesh Pandey, Souvik Maiti, Debojyoti Chakraborty. eLife (2021).

 

2021

RAY: CRISPR diagnostic for rapid and accurate detection of SARS-CoV2 variants on a paper strip. Manoj Kumar, Sneha Gulati, Asgar Hussain Ansari, Rhythm Phutela, Sundaram Acharya, Poorti Kathpalia, Akshay Kanakan, Ranjeet Maurya, Janani Srinivasa Vasudevan, Aparna Murali, Rajesh Pandey, Souvik Maiti, Debojyoti Chakraborty. MedRxiv (2021). https://doi.org/10.1101/2021.02.01.21250900

 

Rapid and accurate nucleobase detection using FnCas9 and its application in COVID-19 diagnosis. Mohd Azhar, Rhythm Phutela, Manoj Kumar, Asgar Hussain Ansari, Riya Rauthan, Sneha Gulati, Namrata Sharma, Dipanjali Sinha, Saumya Sharma, Sunaina Singh, Sundaram Acharya, Sajal Sarkar, Deepanjan Paul, Poorti Kathpalia, Meghali Aich, Paras Sehgal, Gyan Ranjan, Rahul C Bhoyar, Genetic Epidemiology IndiCovGEN Consortium, Khushboo Singhal, Harsha Lad, Pradeep Kumar Patra, Govind Makharia, Giriraj Ratan Chandak, Bala Pesala, Debojyoti Chakraborty, Souvik Maiti. Biosensors and Bioelectronics (2021). https://doi.org/10.1016/j.bios.2021.113207

 

CRISPR Cas9 based genome editing in inherited retinal dystrophies. Mayank Bansal, Sundaram Acharya, Saumya Sharma, Rhythm Phutela, Riya Rauthan, Souvik Maiti, Debojyoti Chakraborty. Ophthalmic Genetics (2021).  https://doi.org/10.1080/13816810.2021.1904421

Low-cost CRISPR diagnostics for resource-limited settings. Sneha Gulati, Souvik Maiti, Debojyoti Chakraborty. Trends in Genetics (2021). https://doi.org/10.1016/j.tig.2021.05.001

Voices of biotech research. Annabi N, Baker M, Boettiger A, Chakraborty D, Chen Y, Corbett KS, Correia B, Dahlman J, de Oliveira T, Ertuerk A, Yanik MF, Henaff E, Huch M, Iliev ID, Jacobs T, Junca H, Keung A, Kolodkin-Gal I, Krishnaswamy S, Lancaster M, Macosko E, Martínez-Núñez MA, Miura K, Molloy J, Cruz AO, Platt RJ, Posey AD Jr, Shao H, Simunovic M, Slavov N, Takebe T, Vandenberghe LH, Varshney RK, Wang J. Nature Biotechnology (2021). https://doi.org/10.1038/s41587-021-00847-1 

​Rapid identification and tracking of SARS-CoV-2 variants of concern. Debojyoti Chakraborty, Anurag Agrawal, Souvik Maiti. The Lancet (2021). https://doi.org/10.1016/S0140-6736(21)00470-0

2020

Ophthalmic genetics practice and research in India: Vision in 2020. Mayank Bansal, Radhika Tandon, Rohit Saxena, Arundhati Sharma, Sagnik Sen, Alisha Kishore, Pradeep Venkatesh, Souvik Maiti, Debojyoti Chakraborty. American Journal of Medical Genetics. Partc C, seminars in Medical Genetics (2020). https://doi.org/10.1002/ajmg.c.31827

Terminal uridylyl transferase-mediated site-directed access to clickable chromatin employing CRISPR-dCas9. Jerrin Thomas George, Mohd. Azhar, Meghali Aich, Dipanjali Sinha, Uddhav B Ambi, Souvik Maiti, Debojyoti Chakraborty, and Seergazhi G Srivatsan. Journal of the American Chemical Society (2020). https://doi.org/10.1021/jacs.0c06541

Role of lncRNAs in stem cell maintenance and differentiation. Meghali Aich, Debojytoi Chakraborty. (2020). Current Topics in Developmental Biology (2020). https://doi.org/10.1016/bs.ctdb.2019.11.003

The Paf1 complex positively regulates enhancer activity in mouse embryonic stem cells. Li Ding, Maciej Paszkowski-Rogacz, Jovan Mircetic, Debojyoti Chakraborty, Frank Buchholz. Life Science Alliance (2020). https://doi.org/10.26508/lsa.202000792

 

2019


Francisella novicida Cas9 interrogates genomic DNA with very high specificity and can be used for mammalian genome editing. Sundaram Acharya*, Arpit Mishra*, Deepanjan Paul*, Asgar Hussain Ansari, Mohd. Azhar, Manoj Kumar, Riya Rauthan, Namrata Sharma, Meghali Aich, Dipanjali Sinha, Saumya Sharma, Shivani Jain, Arjun Ray, Suman Jain, Sivaprakash Ramalingam, Souvik Maiti, and Debojyoti Chakraborty. Proceedings of the National Academy of Sciences (2019). https://doi.org/10.1073/pnas.1818461116

 

2018


Novel internal regulators and candidate miRNAs within miR-379/miR-656 miRNA cluster can alter cellular phenotype of human glioblastoma. Subhashree Nayak, Meghali Aich, Anupam Kumar, Suman Sengupta, Prajakta Bajad, Parashar Dhapola, Deepanjan Paul, Kiran Narta, Suvendu Purkrait, Bharati Mehani, Ashish Suri, Debojyoti Chakraborty, Arijit Mukhopadhyay, Chitra Sarkar. Scientific Reports (2018). https://doi.org/10.1038/s41598-018-26000-8

 
A G-quadruplex motif at the 3’ end of sgRNAs improves CRISPR-Cas9-based genome editing efficiency. Smita Nahar, Paras Sehgal, Mohd. Azhar, Manish Rai, Amrita Singh, Sridhar Sivasubbu, Debojyoti Chakraborty, and Souvik Maiti. Chemical Communications (2018). 

https://doi.org/10.1039/C7CC08893K

2017


LncRNA Panct1 maintains mouse embryonic stem cell identity by recruiting TOBF1 to Oct-Sox sequences in early G1. Debojyoti Chakraborty, Maciej Paszkowski-Rogacz, Nicolas Berger, Li Ding, Jovan Mircetic, Jun FuVytautas Iesmantavicius, Chunaram ChoudharyKonstantinos AnastassiadisA Francis StewartFrank Buchholz. Cell Reports (2017).

https://doi.org/10.1016/j.celrep.2017.11.045

CRISPR-Cas9: a new tool for gene therapy. Saumya Sharma, Souvik Maiti, Debojyoti Chakraborty. eLS (2017). 

https://doi.org/10.1002/9780470015902.a0026629

2016


CRISPR/Cas9: a historical and chemical biology perspective of targeted genome engineering. Amrita Singh, Debojyoti Chakraborty, and Souvik Maiti. Chemical Society Reviews (2016). https://doi.org/10.1039/C6CS00197A

Inactivation of cancer mutations utilizing CRISPR/Cas9. Christina Gebler, Tim Lohoff, Maciej Paszkowski-Rogacz, Jovan Mircetic, Debojyoti Chakraborty, Aylin Camgoz, Martin V Hamann, Mirko Theis, Christian Thiede, Frank Buchholz. Journal of the National Cancer Institute (2016). https://doi.org/10.1093/jnci/djw183


Directed evolution of a recombinase that excises the provirus of most HIV-1 primary isolates with high specificity. Janet Karpinski, Ilona Hauber, Jan Chemnitz, Carola Schäfer, Maciej Paszkowski-Rogacz, Debojyoti Chakraborty, Niklas Beschorner, Helga Hofmann-Sieber, Ulrike C Lange, Adam Grundhoff, Karl Hackmann, Evelin Schrock, Josephine Abi-Ghanem, M Teresa Pisabarro, Vineeth Surendranath, Axel Schambach, Christoph Lindner, Jan van Lunzen, Joachim Hauber, and Frank Buchholz. Nature Biotechnology (2016).

https://doi.org/10.1038/nbt.3467

2015


Targeting Human Long-Noncoding Transcripts by Endoribonuclease-prepared siRNAs. Mirko Theis, Maciej Paszkowski-Rogacz, Ina Weisswange, Debojyoti Chakraborty, Frank Buchholz. Journal of Biomolecular Screening (2015).

https://doi.org/10.1177/1087057115583448

Systems Analyses Reveal Shared and Diverse Attributes of Oct4 Regulation in Pluripotent Cells. Li Ding, Maciej Paszkowski-Rogacz, Maria Winzi, Debojyoti Chakraborty, Mirko Theis, Sukhdeep SinghGiovanni Ciotta, Ina Poser, Assen Roguev, Wai Kit Chu, Chunaram Choudhary, Matthias Mann, A. Francis Stewart, Nevan Krogan, Frank Buchholz. Cell Systems (2015).

https://doi.org/10.1016/j.cels.2015.08.002

Before 2015


Universal Tre (uTre) recombinase specifically targets the majority of HIV-1 isolates. Janet Karpinski, Jan Chemnitz, Ilona Hauber Josephine Abi-Ghanem, Maciej Paszkowski-Rogacz, Vineeth Surendranath, Debojyoti Chakraborty,  Niklas BeschornerHelga Hofmann-SieberUlrike C LangeAdam GrundhoffKarl HackmannEvelin SchrockJosephine Abi-GhanemM Teresa PisabarroVineeth SurendranathAxel SchambachChristoph LindnerJan van LunzenJoachim HauberFrank Buchholz. Journal of the International AIDS Society (2014). https://doi.org/10.7448/IAS.17.4.19706


Combined RNAi and localization for functionally dissecting long noncoding RNAs. Debojyoti Chakraborty, Dennis Kappei, Mirko Theis, Anja Nitzsche, Li Ding, Maciej Paszkowski-Rogacz et al. Nature Methods (2012). https://doi.org/10.1038/nmeth.1894

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