From IIT Dharwad

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21.  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

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20.  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

 

19. 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

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18.  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.

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17. 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

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16. 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

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15. 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.

 

14. 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.

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13. 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.

 

12.  Khadirnaikar S, Chatterjee A, Shukla SK. Identification and characterization of senescence phenotype in Lung adenocarcinoma with high drug sensitivity. American Journal of Pathology. 2021; doi.org/10.1016/j.ajpath.2021.07.005

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11. Shukla S, Khadirnaikar S. RNA-Sequencing Analysis Pipeline for Prognostic Marker Identification in Cancer. Methods in Molecular Biology 2021;2174:119-131.

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10. 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.

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9. 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.

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8. 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.

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7. 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.

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6. Khadirnaikar S, Kumar P, Shukla SK. Development and validation of an immune prognostic signature for ovarian carcinoma. Cancer Reports. 2019;2(1):e1166.

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5. 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.

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4. 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;50(6):814-24.

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3. 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.

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2. Shukla S. Unravelling the Long Non-Coding RNA Profile of Undifferentiated Large Cell Lung Carcinoma. Noncoding RNA. 2018;4(1).

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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.

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From The University of Michigan

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1.         Skala SL, Xiao H, Udager AM, Dhanasekaran SM, Shukla S, Zhang Y, et al. Detection of 6 TFEB-amplified renal cell carcinomas and 25 renal cell carcinomas with MITF translocations: systematic morphologic analysis of 85 cases evaluated by clinical TFE3 and TFEB FISH assays. Mod Pathol. 2018;31(1):179-97.

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2.       Wang L, Harms PW, Palanisamy N, Carskadon S, Cao X, Siddiqui J, et al. Age and Gender Associations of Virus Positivity in Merkel Cell Carcinoma Characterized Using a Novel RNA In Situ Hybridization Assay. Clin Cancer Res. 2017;23(18):5622-30.

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3.       Shukla S, Evans JR, Malik R, Feng FY, Dhanasekaran SM, Cao X, et al. Development of a RNA-Seq Based Prognostic Signature in Lung Adenocarcinoma. J Natl Cancer Inst. 2017;109(1).

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4.       Mahajan K, Malla P, Lawrence HR, Chen Z, Kumar-Sinha C, Malik R, et al. ACK1/TNK2 Regulates Histone H4 Tyr88-phosphorylation and AR Gene Expression in Castration-Resistant Prostate Cancer. Cancer Cell. 2017;31(6):790-803 e8.

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5.       Wang L, He Y, Liu W, Bai S, Xiao L, Zhang J, et al. Non-coding RNA LINC00857 is predictive of poor patient survival and promotes tumor progression via cell cycle regulation in lung cancer. Oncotarget. 2016;7(10):11487-99.

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6.       Veeneman BA, Shukla S, Dhanasekaran SM, Chinnaiyan AM, Nesvizhskii AI. Two-pass alignment improves novel splice junction quantification. Bioinformatics. 2016;32(1):43-9.

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7.       Shukla S, Zhang X, Niknafs YS, Xiao L, Mehra R, Cieslik M, et al. Identification and Validation of PCAT14 as Prognostic Biomarker in Prostate Cancer. Neoplasia. 2016;18(8):489-99.
 

8.       Mehra R, Vats P, Cieslik M, Cao X, Su F, Shukla S, et al. Biallelic Alteration and Dysregulation of the Hippo Pathway in Mucinous Tubular and Spindle Cell Carcinoma of the Kidney. Cancer Discov. 2016;6(11):1258-66.

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9.       Falzarano SM, McKenney JK, Montironi R, Eble JN, Osunkoya AO, Guo J, et al. Renal Cell Carcinoma Occurring in Patients With Prior Neuroblastoma: A Heterogenous Group of Neoplasms. Am J Surg Pathol. 2016;40(7):989-97.

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From Indian Institute of Science

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1.       Pal J, Patil V, Mondal B, Shukla S, Hegde AS, Arivazhagan A, et al. Epigenetically silenced GNG4 inhibits SDF1alpha/CXCR4 signaling in mesenchymal glioblastoma. Genes Cancer. 2016;7(3-4):136-47.

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2.       Shukla S, Patric IR, Patil V, Shwetha SD, Hegde AS, Chandramouli BA, et al. Methylation silencing of ULK2, an autophagy gene, is essential for astrocyte transformation and tumor growth. J Biol Chem. 2014;289(32):22306-18.

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3.       Jha P*, Pia Patric IR*, Shukla S*, Pathak P, Pal J, Sharma V, et al. Genome-wide methylation profiling identifies an essential role of reactive oxygen species in pediatric glioblastoma multiforme and validates a methylome specific for H3 histone family 3A with absence of G-CIMP/isocitrate dehydrogenase 1 mutation. Neuro Oncol. 2014;16(12):1607-17. * equal authors

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4.       Shukla S, Pia Patric IR, Thinagararjan S, Srinivasan S, Mondal B, Hegde AS, et al. A DNA methylation prognostic signature of glioblastoma: identification of NPTX2-PTEN-NF-kappaB nexus. Cancer Res. 2013;73(22):6563-73.

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5.       Arimappamagan A, Somasundaram K, Thennarasu K, Peddagangannagari S, Srinivasan H, Shailaja BC, et al. A fourteen gene GBM prognostic signature identifies association of immune response pathway and mesenchymal subtype with high risk group. PLoS One. 2013;8(4):e62042.

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6.       Thota B, Shukla SK, Srividya MR, Shwetha SD, Arivazhagan A, Thennarasu K, et al. IDH1 mutations in diffusely infiltrating astrocytomas: grade specificity, association with protein expression, and clinical relevance. Am J Clin Pathol. 2012;138(2):177-84.

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7.       Suri V, Jha P, Agarwal S, Pathak P, Sharma MC, Sharma V, et al. Molecular profile of oligodendrogliomas in young patients. Neuro Oncol. 2011;13(10):1099-106.

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