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PUBLICATION
⇒ Seema Khadirnaikar, Sudhanshu Shukla and SRM Prasanna (2023) Integration of pan-cancer multi-omics data for novel mixed subgroup identification using machine learning methods, PLoS One, DOI: 10.1371/journal.pone.0287176
⇒ Nikita Bhandari, Disha Acharya, Annesha Chatterjee, Lakshana Mandve, Pranjal Kumar, Shreesh Pratap, Pushkar Malakar & Sudhanshu K. Shukla (2023) Pan-cancer integrated bioinformatic analysis of RNA polymerase subunits reveal RNA Pol I member CD3EAP regulates cell growth by modulating autophagy, Cell Cycle, DOI: 10.1080/15384101.2023.2265676
⇒ Pushkar Malakar, Didhiti Singha, Debopriyo Choudhury & Sudhanshu Shukla (2023) Glutamine regulates the cellular proliferation and cell cycle progression by modulating the mTOR mediated protein levels of β-TrCP, Cell Cycle, DOI: 10.1080/15384101.2023.2260166
⇒ Patil PP, Kumar P, Khanal P, Patil VS, Darasaguppe HR, Bhandare VV, Bhatkande A, Shukla S, Joshi RK, Patil BM, Roy S. Computational and experimental pharmacology to decode the efficacy of Theobroma cacao L. against doxorubicin-induced organ toxicity in EAC-mediated solid tumor-induced mice. Front Pharmacol. (2023) May; 31;14:1174867. doi: 10.3389/fphar.2023.1174867. PMID: 37324470; PMCID: PMC10264642.
⇒ Khadirnaikar S, Shukla S, Prasanna SRM. Development of Machine Learning Model for Pan-cancer Subgroup Identification using Multi-omics Data. Scientific Reports doi: 13, 4636 (2023), doi.org/10.1038/s41598-023-31426-w
⇒ Joshi S, Kallappa S, Kumar P, Shukla S, Ghosh R. Simple diagnosis of cancer by detecting CEA and CYFRA 21‑1 in saliva using electronic sensors. Scientific Reports, 2022, (2022) 12:15315
⇒ Kumar P , Khadirnaikar S, Bhandari N, Chatterjee A and Shukla SK. An Epithelial-Mesenchymal plasticity signature identifies two novel LncRNAs with the opposite regulation. Frontiers in Cell and Developmental Biology, (2022), DOI: 10.3389/fcell.2022.885785.
⇒ Chatterjee A, Khadirnaikar S, Shukla SK. Development and validation of stemness associated LncRNA based prognostic model for lung adenocarcinoma patients. Cancer Biomarkers, (2021); doi: 10.3233/CBM-200687.
⇒ Khadirnaikar S, Chatterjee A, Shukla SK. Genetic and Epigenetic landscape of leukocyte infiltration identifies an immune prognosticator in lung adenocarcinoma. Cancer Biomarkers, 2021; doi: 10.3233/CBM-203071.
⇒ Khadirnaikar S, Chatterjee A, Shukla SK. Identification and characterization of senescence phenotype in Lung adenocarcinoma with high drug sensitivity. American Journal of Pathology. 2021;
⇒ Shukla S, Khadirnaikar S. RNA-Sequencing Analysis Pipeline for Prognostic Marker Identification in Cancer. Methods in Molecular Biology 2021;2174:119-131.
⇒ Khadirnaikar S, Chatterjee A, Kumar P, Shukla SK. A greedy algorithm-based stem cell LncRNA signature identifies a novel subgroup of lung adenocarcinoma patients with poor prognosis. Front Oncol. 2020.
⇒ Vo JN, Cieslik M, Zhang Y, Shukla S, Xiao L, Zhang Y, et al. The Landscape of Circular RNA in Cancer. Cell. 2019;176(4):869-81 e13.
⇒ Kumar P, Khadirnaikar S, Shukla SK. PILAR1, a novel prognostic LncRNA, reveals the presence of a unique subtype of lung adenocarcinoma patients with KEAP1 mutations. Gene. 2019;691:167-75.
⇒ Kumar P, Khadirnaikar S, Shukla SK. A novel LncRNA-based prognostic score reveals the TP53-dependent subtype of lung adenocarcinoma with poor survival. J Cell Physiol. 2019
⇒ Khadirnaikar S, Kumar P, Shukla SK. Development and validation of an immune prognostic signature for ovarian carcinoma. Cancer Reports.2019;2(1):e1166.
⇒ Khadirnaikar S, Kumar P, Pandi SN, Malik R, Dhanasekaran SM, Shukla SK. Immune associated LncRNAs identify novel prognostic subtypes of renal clear cell carcinoma. Mol Carcinog. 2019;58(4):544-53.
⇒ Zhang Y, Pitchiaya S, Cieslik M, Niknafs YS, Tien JC, Hosono Y, et al. Analysis of the androgen receptor-regulated lncRNA landscape identifies a role for ARLNC1 in prostate cancer progression. Nat Genet. 2018
⇒ Xiao L, Tien JC, Vo J, Tan M, Parolia A, Zhang Y, et al. Epigenetic Reprogramming with Antisense Oligonucleotides Enhances the Effectiveness of Androgen Receptor Inhibition in Castration-Resistant Prostate Cancer. Cancer Res. 2018;78(20):5731-40.
⇒ Shukla S. Unravelling the Long Non-Coding RNA Profile of Undifferentiated Large Cell Lung Carcinoma. Noncoding RNA. 2018;4(1).
⇒ Khadirnaikar S, Narayanan SP, Shukla SK. Decoding the LncRNA transcriptome of esophageal cancer: identification of clinically relevant LncRNAs. Biomark Med. 2018;12(10):1083-93.
Monitoring of microbial proteome dynamics using Raman stable isotope probing”JiroKarlo, AKDhillon, S Siddhanta,S.P.Singh, Journal of Biophotonics,16(4): e202200341, 2022.
Unraveling the Secrets of Colistin Resistance with Label-Free Raman Spectroscopy” Dimple Saikia, Priyanka Jadhav, Arti R Hole, C. Murali Krishna, and S.P. Singh, Biosensors, 12(9), 749, 2022.
Growth kinetics monitoring of Gram-negative pathogenic microbes using Raman spectroscopy” Dimple Saikia, Priyanka Jadhav, Arti R Hole, C. Murali Krishna, and S.P. Singh, Applied Spectroscopy, 2022 (10.1177/00037028221109624)
Green-Based Approach to Synthesize Silver Nanoparticles Using the FungalEndophyte Penicilliumoxalicum and Their Antimicrobial, Antioxidant, and In Vitro Anticancer Potential”PriyamvadaGupta, Nilesh Rai, Ashish Verma, Dimple Saikia,S. P. Singh, Rajiv Kumar, Santosh Kumar Singh, Deepak Kumar, and Vibhav Gautam ACS Omega7, 50, 46653-73, 2022.
Irradiation Induced Biochemical Changes in Human Mandibular Bone: A Raman Spectroscopic Study” Sridhar Reddy Padala, Dimple Saikia, Jopi J. W. Mikkonen, Emilia Uurasjarvi, Hannah Dekker, Engelbert A. J. M. Schulten, Nathalie Bravenboer, Arto Koistinen, Amrita Chauhan, S. P. Singh, Arja M. Kullaa, Applied Spectroscopy, 2022 (10.1177/00037028221109244)
Gene Expression and Characterization of Iturin A Lipopeptide Biosurfactant from Bacillus aryabhattai for Enhanced Oil Recovery” Deepak A. Yaraguppi, Zabin K. Bagewadi, Nilkamal Mahanta, S.P. Singh, T. M. Yunus Khan, Sanjay H. Deshpande, Chaitra Soratur, Simita Das and Dimple Saikia, Gels, 8, 403, 1-16, 2022.
Shortwave infrared otoscopy for diagnosis of middle ear effusions: a machine-learning-based approach” Rustin G. Kashani, Marcel C. Młyńczak, David Zarabanda, Paola Solis-Pazmino, David M. Huland, Iram N. Ahmad, S. P. Singh and Tulio A. Valdez, Scientific Reports 11, 12509, 2021.
Short-Wave Infrared Fluorescence Chemical Sensor for Detection of Otitis Media” Joshua J. Yim*, Surya Pratap Singh*, Anping Xia, Raana Kashfi-Sadabad, Martina Tholen, David M. Huland, David Zarabanda, Zhixin Cao, Paola Solis-Pazmino, Matthew Bogyo, and Tulio A. Valdez, ACS Sensors, 2020. (* equal contribution)
Spectrochemical Probing of microRNA duplex using spontaneous Raman Spectroscopy for Biosensing Applications” Preetham Ravi*, Surya Pratap Singh*, Jeon Woong Kang, Sarah Tran, Ramachandra Rao Dasari, Peter TC So, Dorian Liepmann, Kalpana S Katti, Dinesh Ramanath Katti, Venkatesan Renugopalakrishnan, Ramasamy Paulmurugan, Analytical Chemistry, 92, 21, 14423–431, 2020 (* equal contribution)
Cigarette smoke-induced changes in the murine vocal folds: a Raman spectroscopic observation” Elizabeth Erickson-DiRenzo, SP Singh, Joshua D Martinez, Santiago E Sanchez, Meena Easwaran, Tulio A Valdez, Analyst, 2020
Direct observation of glucose fingerprint using in vivo Raman spectroscopy”, Jeon Woong Kang, Yun Sang Park, Hojun Chang, Woochang Lee, S.P.Singh, Wonjun Choi, Luis H. Galindo, Ramachandra R. Dasari, Sung Hyun Nam, Jongae Park, Peter T. C. So, Sci ence Advances ,6, 2020. (MIT News)
Identification of early inflammatory changes in the tympanic membrane with Raman spectroscopy”, S.P.Singh, Anping Xia, Mahbuba Tusty, Andrey Malkovskiy, Meena Easwaran, David Zarabanda, Tulio A Valdez, Analyst, 144 (22), 6721-6728, 2019.
In vivo detection of drug-induced apoptosis in tumors using Raman spectroscopy” Oliver Jonas, Jeon Woong Kang, S.P. Singh, Alex Lammers, Freddy T. Nguyen, Ramachandra R. Dasari, PeterT.C. So, Robert Langer, Michael J. Cima, Analyst, 143,4836-39, 2018. (Cover Page Article)
Evaluation of accuracy dependence of Raman spectroscopic models on the ratio of calibration and validation points for non-invasive glucose sensing” S.P.Singh, Soumavo Mukherjee, LuisGalindo, Peter T. C. So, Ramachandra Rao Dasari, Uzma Zubair Khan, Raghuraman Kannan, Anandhi Upendran, Jeon Woong Kang, Anal Bioanal Chem, 410,6469-75, 2018. (NIH News)
Monitoring of microbial proteome dynamics using Raman stable isotope probing”JiroKarlo, AKDhillon, S Siddhanta,S.P.Singh, Journal of Biophotonics, 16(4): e202200341, 2022.
Unraveling the Secrets of Colistin Resistance with Label-Free Raman Spectroscopy” Dimple Saikia, Priyanka Jadhav, Arti R Hole, C. Murali Krishna, and S.P. Singh, Biosensors, 12(9), 749, 2022.
Growth kinetics monitoring of Gram-negative pathogenic microbes using Raman spectroscopy” Dimple Saikia, Priyanka Jadhav, Arti R Hole, C. Murali Krishna, and S.P. Singh, Applied Spectroscopy, 2022 (10.1177/00037028221109624)
Green-Based Approach to Synthesize Silver Nanoparticles Using the FungalEndophyte Penicilliumoxalicum and Their Antimicrobial, Antioxidant, and In Vitro Anticancer Potential”PriyamvadaGupta, Nilesh Rai, Ashish Verma, Dimple Saikia,S. P. Singh, Rajiv Kumar, Santosh Kumar Singh, Deepak Kumar, and Vibhav Gautam ACS Omega7, 50, 46653-73, 2022.
Irradiation Induced Biochemical Changes in Human Mandibular Bone: A Raman Spectroscopic Study” Sridhar Reddy Padala, Dimple Saikia, Jopi J. W. Mikkonen, Emilia Uurasjarvi, Hannah Dekker, Engelbert A. J. M. Schulten, Nathalie Bravenboer, Arto Koistinen, Amrita Chauhan, S. P. Singh, Arja M. Kullaa, Applied Spectroscopy, 2022 (10.1177/00037028221109244)
Gene Expression and Characterization of Iturin A Lipopeptide Biosurfactant from Bacillus aryabhattai for Enhanced Oil Recovery” Deepak A. Yaraguppi, Zabin K. Bagewadi, Nilkamal Mahanta, S.P. Singh, T. M. Yunus Khan, Sanjay H. Deshpande, Chaitra Soratur, Simita Das and Dimple Saikia, Gels, 8, 403, 1-16, 2022.
Shortwave infrared otoscopy for diagnosis of middle ear effusions: a machine-learning-based approach” Rustin G. Kashani, Marcel C. Młyńczak, David Zarabanda, Paola Solis-Pazmino, David M. Huland, Iram N. Ahmad, S. P. Singh and Tulio A. Valdez, Scientific Reports 11, 12509, 2021.
Short-Wave Infrared Fluorescence Chemical Sensor for Detection of Otitis Media” Joshua J. Yim*, Surya Pratap Singh*, Anping Xia, Raana Kashfi-Sadabad, Martina Tholen, David M. Huland, David Zarabanda, Zhixin Cao, Paola Solis-Pazmino, Matthew Bogyo, and Tulio A. Valdez, ACS Sensors, 2020. (* equal contribution)
Spectrochemical Probing of microRNA duplex using spontaneous Raman Spectroscopy for Biosensing Applications” Preetham Ravi*, Surya Pratap Singh*, Jeon Woong Kang, Sarah Tran, Ramachandra Rao Dasari, Peter TC So, Dorian Liepmann, Kalpana S Katti, Dinesh Ramanath Katti, Venkatesan Renugopalakrishnan, Ramasamy Paulmurugan, Analytical Chemistry, 92, 21, 14423–431, 2020 (* equal contribution)
Sublingual indocyanine green films for non-invasive swallowing assessment and inflammation detection through NIR/SWIR optical imaging” Beringhs André O’Reilly, Surya Pratap Singh, Tulio Alberto Valdez, Lu Xiuling, Scientific Reports, 10,1, 2020.
Cigarette smoke-induced changes in the murine vocal folds: a Raman spectroscopic observation” Elizabeth Erickson-DiRenzo, SP Singh, Joshua D Martinez, Santiago E Sanchez, Meena Easwaran, Tulio A Valdez, Analyst, 2020
Direct observation of glucose fingerprint using in vivo Raman spectroscopy”, Jeon Woong Kang, Yun Sang Park, Hojun Chang, Woochang Lee, S.P.Singh, Wonjun Choi, Luis H. Galindo, Ramachandra R. Dasari, Sung Hyun Nam, Jongae Park, Peter T. C. So, Sci ence Advances ,6, 2020. (MIT News)
Identification of early inflammatory changes in the tympanic membrane with Raman spectroscopy”, S.P.Singh, Anping Xia, Mahbuba Tusty, Andrey Malkovskiy, Meena Easwaran, David Zarabanda, Tulio A Valdez, Analyst, 144 (22), 6721-6728,2019.
Biochemical Changes in irradiated oral mucosa: A FTIR spectroscopic study”, HelenaUkkonen,Simo Vuokila, Jopi J. W. Mikkonen, Hannah Dekker, Engelbert A. J. M. Schulten, Elisabeth Bloemena, Arto Koistinen, Tulio A. Valdez, Arja M. Kullaa, S. P. Singh, Biosensors, 9,12, 2019.
In vivo detection of drug-induced apoptosis in tumors using Raman spectroscopy” Oliver Jonas, Jeon Woong Kang, S.P. Singh, Alex Lammers, Freddy T. Nguyen, Ramachandra R. Dasari, PeterT.C. So, Robert Langer, Michael J. Cima, Analyst, 143,4836-39, 2018. (Cover Page Article)
Evaluation of accuracy dependence of Raman spectroscopic models on the ratio of calibration and validation points for non-invasive glucose sensing” S.P.Singh, Soumavo Mukherjee, LuisGalindo, Peter T. C. So, Ramachandra Rao Dasari, Uzma Zubair Khan, Raghuraman Kannan, Anandhi Upendran, Jeon Woong Kang, Anal Bioanal Chem, 410,6469-75, 2018. (NIH News)