Indranil Mukhopadhyay

Avatar for Indranil Mukhopadhyay

Indranil Mukhopadhyay

Professor Statistics University of Nebraska-Lincoln

Contact

Address
HARH 342A
Lincoln, NE 68583-0963
Phone
402-472-7214 On-campus 2-7214
Email
imukhopadhyay2@unl.edu
Website

AREA OF EXPERTISE

Genomic data integration, Single-cell data analytics, Machine learning, Time series analysis, Public health dynamics, Statistical inference.

RESEARCH INTEREST

Indranil's research interests encompass statistical genetics and genomics, time series analysis, machine learning, public health, and statistical inference. His recent work primarily focuses on developing novel statistical methods for genomic data integration and single-cell analytics, with an emphasis on real-world applications.

PUBLICATION

Book:

Statistical Methods in Human genetics, (jointly with Prof. Partha Pratim Majumder) (2023), Springer

Manuscript submitted:

Mritunjoy Barman, Madeline Morrison, Nikhitha Gangavarapu, Thomas Davis, Jeff Bradshaw, Nathan Mueller, Stephen Wegulo, Indranil Mukhopadhyay, Gary Hein, Satyanarayana Tatineni, Shaonpius Mondal (2025): Incidence of Wheat Curl Mite-Transmitted Viruses in Major Cereal Crops: Potential Roles of Cover and Forage Cereal Crops in the Continuum of Wheat Streak Mosaic Disease Complex. Submitted to Plant Disease.

All publications:

  1. Kiruthiga Mone, Shraddha Singh, Fatema Abdullatif, Meghna Sur, Mahima T. Rasquinha, Javier Seravalli, Denise K. Zinniel, Indranil Mukhopadhyay, Raul G. Barletta, Teklab Gebregiworgis, Jay Reddy (2025): Immunization with Complete Freund’s Adjuvant Reveals Trained Immunity-like Features in A/J Mice. Vaccines; 13(7):768. https://doi.org/10.3390/vaccines13070768.
  2. Nilanjan Chatterjee, Indranil Mukhopadhyay, Parag Nigam, Bilal Habib (2023): Predicting carrying capacity of a large carnivore from prey densities: a new approach. PeerJ. 11:e15914. doi: 10.7717/peerj.15914. PMID: 38025689; PMCID: PMC10676078
  3. Tristan Mary-Huard, Sarmistha Das, Indranil Mukhopadhyay, Stephane Robin (2022): Querying multiple sets of P-values through composed hypothesis testing. Bioinformatics. 38(1):141-148. https://doi.org/10.1093/bioinformatics/btab59
  4. Sanjib Kumar Gupta, Indranil Mukhopadhyay, Aditya Chatterjee (2022): Two-dimensional extended warranty length design from incomplete warranty data based on a new price curve considering different maintenance policies. Computers and Industrial Engineering. 170:108323
  5. Sarmistha Das, Indranil Mukhopdhyay (2021): TiMEG: an integrative statistical method for partially missing multi-omics data. Scientific Reports.11(1):24077. doi:10.1038/s41598-021-03034-z
  6. Pronoy Kanti Mondal, Udit Surya Saha, Indranil Mukhopadhyay (2021): PseudoGA: Cell pseudotime reconstruction based on genetic algorithm. Nucleic Acids Research. 49(14)
  7. Sarmistha Das, Pramit Ghosh, Sandip Banerjee, Saumyadipta Pyne, Indranil Mukhopadhyay (2021): Determination of critical community size from an HIV/AIDS model. PLOS ONE. 16(1): e0244543
  8. Rasmika Billa, Mohammad Abdul Razzaq, Indranil Mukhopadhyay, Santanu Mandal (2021): Scheduling for healthcare centre for COVID-19: deep learning and genetic algorithm approach. 2021 IEEE International Conference on Health, Instrumentation & Measurement, and Natural Sciences (InHeNce), IEEE | DOI: 10.1109/InHeNce52833.2021.9537264 
  9. Bikram Karmakar, Indranil Mukhopadhyay (2020): Statistical Validity and Consistency of Big Data Analytics: A General Framework. Statistics and Applications. 18(2):369-381.
  10. Meghana Aruru, Raanan Gurewitsch, Sarmistha Das, Pramit Ghosh, Bandana Sen, Indranil Mukhopadhyay, Saumyadipta Pyne (2020): A data-driven approach to COVID-19: Resources, policies, and best practices. BLDE University Journal of Health Sciences. 5(2):226-231.
  11. Sarmistha Das, Pramit Ghosh, Bandana Sen, Saumyadipta Pyne, Indranil Mukhopadhyay (2020): Critical Community Size for COVID-19: A Model Based Approach for Strategic Lockdown Policy. Statistics and Applications. 18(1):181-196. 
  12. Bikram Karmakar, Sarmistha Das, Soham Bhattacharya, Rohan Sarkar, Indranil Mukhopadhyay (2019): Tight clustering for large datasets with an application to gene expression data. Scientific Reports. 9:3053, https://doi.org/10.1038/S41598-019-39459-W
  13. Bikram Karmakar, Indranil Mukhopadhyay (2019): Risk Efficient Sequential Estimation of Multivariate Random Coefficient Autoregressive Process. Sequential Analysis. 38(1): 26-45.
  14. Sarmistha Das, Partha Pratim Majumder, Raghunath Chatterjee, Aditya Chatterjee, Indranil Mukhopadhyay (2019): A powerful method to integrate genotype and gene expression data for dissecting the genetic architecture of a disease. Genomics. 11: 1387-1394. https://doi.org/10.1016/j.ygeno.2018.09.011
  15. Sk Shahid Nadim, Sudip Samanta, Nikhil Pal, Ibrahim M. Elmojtaba, Indranil Mukhopadhyay, Joydev Chattopadhyay (2018): Impact of predator signals on the stability of a predator-prey system - a Z-control approach. Differential Equations and Dynamical Systems. https://doi.org/10.1007/s12591-018-0430-x
  16. Sarmistha Das, Pronoy Kanti Mondal, Saurabh Ghosh, Indranil Mukhopadhyay (2018): Family based genome wide association of inflammation biomarkers and fenofibrate treatment response in GOLDN study. BMC Proceedings (Suppl 9):41. doi: 10.1186/s12919-018-0146-5
  17. Hemant Kulkarni, Indranil Mukhopadhyay, Saurabh Ghosh (2018): Transmission-based association mapping of triglyceride levels in a longitudinal framework using quasi-likelihood. BMC Proceedings 12 (Suppl 9):39 https://doi.org/10.1186/s12919-018-0147-4
  18. Bikram Karmakar, Indranil Mukhopadhyay (2017): Risk efficient estimation of fully dependent random coefficient autoregressive models of general order. Communications in Statistics-Theory and Methods, 47(17): 4242-4253. https://doi.org/10.1080/03610926.2017.1371758
  19. Das Ghosh D, Mukhopadhyay I, Bhattacharya A, Roy Chowdhury R, Mandal NR, Roy S, Sengupta S (2017): Impact of genetic variations and transcriptional alterations of HLA class I genes on cervical cancer pathogenesis. International Journal of Cancer, 140(11), 2498-2508, doi: 10.1002/ijc.30681.
  20. Aditi Chandra, Anirudhya Lahiri, Swapan Senapati, Baidehi Basu, Saurabh Ghosh, Indranil Mukhopadhyay, Akhilesh Behra, Somenath Sarkar, Gobinda Chatterjee, Raghunath Chatterjee (2016): Increased Risk of Psoriasis due to combined effect of HLA-Cw6 and LCE3 risk alleles in Indian population. Scientific Reports, 6, doi:10.1038/srep24059
  21. Suddhasil Mookherjee, Deblina Banerjee, Subhadip Chakraborty, Indranil Mukhopadhyay, Abhijit Sen, Kunal Ray (2016): Evaluation of the IL1 Gene Cluster Single Nucleotide Polymorphisms in Primary Open-Angle Glaucoma Pathogenesis. Genetic Testing and Molecular Biomarkers, DOI: 10.1089/gtmb.2015.034
  22. Amrendra Kumar, Sudipta Das, Anurag Agrawal, Indranil Mukhopadhyay, Balaram Ghosh (2015): Genetic association of key Th1/Th2 pathway candidate genes, IRF2, IL6, IFNGR2, STAT4 and IL4RA, with atopic asthma in the Indian population. Journal of Human Genetics, 2015 May 21. doi: 10.1038/jhg.2015.45.
  23. Sayantan Datta, Anindita Ray, Richa Singh, Pinaki Mondal, Analabha Basu, Navonil De Sarkar, Mousumi Majumder, Guruparasad Maiti, Aradhita Baral, Ganga Nath Jha, Indranil Mukhopadhyay, Chinmay Panda, Shantanu Chowdhury, Saurabh Ghosh, Susanta Roychoudhury, Bidyut Roy (2015): Sequence and expression variations in 23 genes involved in mitochondrial and non-mitochondrial apoptotic pathways and risk of oral leukoplakia and cancer. Mitochondrion, 25, 28–33
  24. Gopaldeb Chattopadhyay, Indranil Mukhopadhyay (2015): On a class of partially sequential two-sample test procedures for multivariate continuous data. Statistics, 49 (2), http://dx.doi.org/10.1080/02331888.2014.960868
  25. Navonil De Sarkar, Roshni Roy, Jit Kumar Mitra, Sandip Ghose, Arnab Chakraborty, Ranjan Rashmi Paul, Indranil Mukhopadhyay, Bidyut Roy (2014): A quest for miRNA bio-marker: a track back approach from gingivo buccal cancer to two different types of precancers. PLoS ONE, 9(8), e104839
  26. Roshni Roy, Navonil De Sarkar, Sandip Ghose, Ranjan R Paul, Anindita Ray, Indranil Mukhopadhyay, Bidyut Roy (2014): Association between risk of oral precancer and genetic variations in microRNA and related processing genes. Journal of Biomedical Science, 21:48, http://www.jbiomedsci.com/content/21/1/48
  27. Piyali Datta Chakraborty, Sutapa Goswami, Sudipta Bera, Indranil Mukhopadhyay (2014): Quantitation of polydeoxyribonucletides (PDRNs) in human placental extract
    by fluorescence spectroscopy using ethidium bromide. American Journal of Analytical Chemistry, 5, 784-795, http://dx.doi.org/10.4236/ajac.2014.512087
  28. Prithwijit Ghosh, Damayanti Das Ghosh, Amita Majumdar (Giri), Sharmila Sengupta, Chandana Das, Indranil Mukhopadhyay (2014): Polymerase chain reaction and deoxyribonucleic acid-sequencing based study on distribution of human papillomavirus 16/18 among histopathological types of cervical intra-epithelial neoplasia and primary invasive cervical carcinoma: A scenario in North Bengal, India. Journal of Mid-life Health, 5(1), 14-22, doi:10.4103/0976-7800.127786
  29. Majumdar A, Mukhopadhyay I, Ghosh S (2014) Association mapping of blood pressure levels in a longitudinal framework using binomial regression. BMC Proceedings 8 (Suppl 1): S 74, http://www.biomedcentral.com/1753-6561/8/S1/S74
  30. Haldar T, Mukhopadhyay I, Ghosh S (2014) A Novel Transmission-based Test of Association for Multivariate Phenotypes: An Application to Systolic and Diastolic Blood Pressure Levels. BMC Proceedings 8 (Suppl 1): S71, http://www.biomedcentral.com/1753-6561/8/S1/S71
  31. Anurag Satpathy, Shivamurthy Ravindra, Amit Porwal, Abhaya C. Das, Manoj Kumar, Indranil Mukhopadhyay (2013): Effect of alcohol consumption status and alcohol concentration on oral pain induced by alcohol-containing mouthwash. Journal of Oral Science, 55(2), 99-105
  32. Madhumita Basu, Tania Das, Alip Ghosh, Subhadipa Majumder, Ardhendu Kumar Maji, Sumana Datta Kanjilal, Indranil Mukhopadhyay, Susanta Roychowdhury, Soma Banerjee, Sanghamitra Sengupta (2012): Gene-gene interaction and functional impact of polymorphisms on innate genes in controlling Plasmodium falciparum blood infection level. PLoS ONE, 7(10), e46441
  33. Neelanjana Roy, Indranil Mukhopadhyay, Kausik das, Pratap Pandit, Partha P. Majumder, Amal Santra, Simanti Datta, Soma Mukherjee, Abhijit Chowdhury (2012): Genetic variants of TNFα, IL10, IL1β, CTLA4 and TGFβ1 modulate the indices of alcohol- induced liver injury in East Indian population. Gene, Nov 1; 509(1): 178-188; doi: 10.1016/j.gene.2012.07.077. Epub 2012 Aug 10 
  34. Damayanti Das Ghosh, Bornali Bhattacharjee, Shrinka Sen, Laikangbam Premi, Indranil Mukhopadhyay, Rahul Roy Chowdhury, Sudipta Roy, Sharmila Sengupta (2012): Some novel insights on HPV16 related cervical cancer pathogenesis based on analyses of LCR methylation, viral load, E7 and E2/E4 expressions. PLoS ONE, 7(9), e44678 
  35. Anbupalam Thalamuthu, Jingyuan Zhao, Garrett Teoh Hor Keong, Venkateswarlu Kondragunta, Indranil Mukhopadhyay (2011): Association tests for rare and common variants based on genotypic and phenotypic measures of similarity between individuals. BMC Proceedings, 5 (Suppl 9):S89, http://www.biomedcentral.com/1753-6561/5/S9/S89
  36. Mukhopadhyay I, Saha S, Ghosh S (2011): Integrating binary traits with quantitative phenotypes for association mapping. BMC Proceedings, 5 (Suppl 9):S73, http://www.biomedcentral.com/1753-6561/5/S9/S73
  37. Indranil Mukhopadhyay, Souvik Kumar Bandyopadhyay, Aditya Chatterjee (2011): Prioritisation of the determinants of customer satisfaction: A simultaneous equation approach in ordinal endogenous set-up. Total Quality Management & Business Excellence, 22(1), 117:130, URL: http://dx.doi.org/10.1080/14783363.2010.545558
  38. Suddhasil Mookherjee, Deblina Banerjee, Subhadip Chakraborty, Antara Banerjee, Indranil Mukhopadhyay, Abhijit Sen, Kunal Ray (2010): Association of IL1A and IL1B loci with primary open angle glaucoma. BMC Medical Genetics, 11:99, PMID: 20565898
  39. Indranil Mukhopadhyay, Eleanor Feingold, Daniel E Weeks, Anbupalam Thalamuthu (2010): Association tests using kernel-based measures of multi-locus genotype similarity between individuals. Genetic Epidemiology, 34(3), 213-221, PMID: 19697357.
  40. Damayanti Das, Bornali Bhattacharjee, Shrinka Sen, Indranil Mukhopadhyay, Sharmila Sengupta (2010): Association of viral load with HPV16 positive cervical cancer pathogenesis: Causal relevance in isolates harboring intact viral E2 gene. Virology, 402,197–202, PMID: 20394955
  41. Gopaldeb Chattopadhyay, Indranil Mukhopadhyay (2010): Progressive censoring under inverse sampling for nonparametric multi-sample location problem. Test, 19, 325-341
  42. Shirley Y. Hill, Eric K. Hoffman, Nicolas Rezza, Anbupalam Thalamuthu, Daniel E. Weeks, Abigail G. Mathews, Indranil Mukhopadhyay (2008): Dopaminergic mutations: within family and linkage in multiplex alcohol dependence families. American Journal Medical Genetics B, Neuropsychiatric Genetics, 147B, 517-26, PMID: 17948902
  43. Indranil Mukhopadhyay, Sudipta Chatterjee, Aditya Chatterjee (2007):  Enhancement of economy of a thermal power generating system through prediction of plant efficiency parameters. Journal of Applied Statistics, 34(3), 249-259.
  44. Anbupalam Thalamuthu*, Indranil Mukhopadhyay*, Xiaojing Zheng, George C. Tseng (2006): Evaluation and comparison of gene clustering methods in microarray analysis. Bioinformatics, 22 issue 19, 2405-2412, PMID: 16882653, http://bioinformatics.oxfordjournals.org/content/vol22/issue19/index.dtl
  45. Indranil Mukhopadhyay, Eleanor Feingold, Tao Wang, Robert C. Elston, Daniel E. Weeks (2006): Treatment of uninformative families in mean allele sharing tests for linkage. Statistical Applications in Genetics and Molecular Biology, 5(1), Article 13. http://www.bepress.com/sagmb/vol5/iss1/art13, PMID: 17049024
  46. Indranil Mukhopadhyay, Anup Som, Satyabrata Sahoo (2006): Word organization in coding DNA: A mathematical model. Theory in Biosciences, 125(1), 1-17, PMID: 17046370
  47. Anbupalam Thalamuthu*, Indranil Mukhopadhyay*, Amrita Ray, Daniel E. Weeks (2005): A comparison between microsatellite and single-nucleotide polymorphism markers with respect to two measures of information content. BMC Genetics, 6(Suppl 1): S27. http://www.biomedcentral.com/1471-2156/6/S1/S27. PMID: 16451636
  48. Indranil Mukhopadhyay, Eleanor Feingold, Daniel E. Weeks (2004): No  ‘bias’ toward the null hypothesis in most conventional multipoint nonparametric linkage analysis. American Journal of Human Genetics, 75, 716-718, PMID: 17049024
  49. Indranil Mukhopadhyay, Aditya Chatterjee, S.K.Maitra, Ruma Dey (2004): Histophysiological appraisal of ovarian activity in an Indian major carp in relation to climatological variables: a data based approach. Calcutta Statistical Association Bulletin, 55, No. 217-218.
  50. A. Som, S. Sahoo, I. Mukhopadhyay, J. Chakrabarti, R. Chaudhury (2003): Scaling violations in coding DNA. Europhysics Letters, 62, No. 2, 271-277.
  51. A. K. Basu, Indranil Mukhopadhyay (2003): On sequential estimation and confidence sequences for random coefficient autoregressive parameter. Stochastic Modelling and Applications, 6, No. 2. 
  52. A. K. Basu, Indranil Mukhopadhyay (2000): On Darling-Robbins type confidence sequences and sequential tests for AR(1) model. Perspectives in Statistical Science, Eds. J. K. Ghosh, P. K. Sen & A. K. Basu, 37-46, Oxford University Press, New Delhi. 
  53. A. K. Basu, Indranil Mukhopadhyay (1999): Sequential estimation of the   autoregressive parameters in general vector autoregressive model. Sankhya Series A, 61, 241-253. 
  54. A. K. Basu, Indranil Mukhopadhyay (1999): On Darling-Robbins type confidence    sequences and sequential tests with power one for parameters of an autoregressive process. Statistics and Probability Letters 45, 205-214.
  55. A. K. Basu, Indranil Mukhopadhyay (1998): Sequential shrinkage estimation of the autoregressive parameters in vector autoregressive model. Stochastic Modelling and Applications, 1, 72-91.

  56. A. K. Basu, Indranil Mukhopadhyay (1998): Fixed width sequential simultaneous confidence intervals for the parameters in AR(p) model. Frontiers in Probability and Statistics, Eds. S. P. Mukherjee, S. K. Basu & B. K. Sinha, 25-34, Narosa Publishing House, New Delhi.

    * equal contribution

Patent:

Biomarker and an in-vitro method for head & neck cancer prognosis (2019); Application No.: 201811018135 A. India.

Teaching experience

At University of Nebraska-Lincoln, USA

  1. STAT 883 (Mathematical Statistics II – Statistical Inference): Spring 2024
  2. STAT 877 (Introduction to Mixed Model Analysis): Fall 2024
  3. STAT 801A (Statistical Methods in Research: Non Calculus): Spring 2025
  4. STAT 983 (Statistical Learning): Fall 2025

At Indian Statistical Institute, Kolkata, India

  1. Statistical Methods in Biomedical Research
  2. Statistical Genetics I
  3. Statistical Genetics II
  4. Multivariate Analysis
  5. Applied Multivariate Analysis
  6. Statistical Methods I
  7. Statistical Methods II
  8. Statistical Methods III
  9. Statistical Methods IV
  10. Linear Statistical Models
  11. Time Series Analysis
  12. Statistics (MSQE)

At University of Burdwan, Burdwan, India

  1. Probability Theory
  2. Linear Models
  3. Regression Analysis
  4. Queueing Theory
  5. Game Theory
  6. Inventory Analysis
  7. Computer Programming

At St. Xavier’s College, Kolkata, India

  1. Linear Algebra
  2. Descriptive Statistics
  3. Probability Distributions
  4. Sampling Distribution
  5. Statistical Inference
  6. Testing of Hypothesis
  7. Sequential Analysis
  8. Multivariate Analysis
  9. Large Sample Theory
  10. Analysis of Variance (including Regression Analysis, and ANOCOVA)