Publications

By date:

2022:

Integrating multimodal data through interpretable heterogeneous ensemblesLi, Yan Chak; Wang, Linhua; Law, Jeffrey; Murali, TM; Pandey, Gaurav. Bioinformatics Advances, Volume 2, Issue 1, vbac065.

Signal from Noise: Using Machine Learning to Distil Knowledge from Data in Biological Psychiatry, Quinn, Thomas P.; Hess,Jonathan L.; Marshe, Victoria S.;Barnett, Michelle M.;Hauschild, Anne-Christin;Maciukiewicz, Malgorzata; Elsheikh, Samar S.M.; Men, Xiaoyu; Trakadis, Yannis J.; Breen, Michael S.; Barnett, Eric J.; Zhang-James, Yanli; Ahsen, Mehmet Eren;Cao, Han; Chen, Junfang; Asif, Salekin ; Hou, Jiahui; Lin, Ping-I; Nicodemus, Kristin K.; Meyer-Lindenberg, Andreas; Bichindaritz, Isabelle; Faraone, Stephen V.; Cairns, Murray J.; Pandey, Gaurav; Muller, Daniel J.; Glatt, Stephen J.. PsyArXiv. 

Can you hear me now? Clinical applications of audio recordings, Kumar, Anish; Jaquenoud, Theo; Becker, Jacqueline Helcer; Cho, Dayeon; Mindt, Monica Rivera; Federman, Alex; Pandey, Gaurav. medRxiv. 

2021:

Machine learning-driven identification of early-life air toxic combinations associated with childhood asthma outcomes. Li, Yan-Chak; Hsu, Hsiao-Hsien Leon; Chun, Yoojin; Chiu, Po-Hsiang; Arditi, Zoe; Claudio, Luz; Pandey, Gaurav; Bunyavanich, Supinda. The Journal of Clinical Investigation. 131(22).  

Predicting youth diabetes risk using NHANES data and machine learning. Vangeepuram, Nita; Liu, Bian; Chiu, Po-hsiang; Wang, Linhua; Pandey, Gaurav. Scientific reports. 11(11212).  

Developing parsimonious ensembles using predictor diversity within a reinforcement learning framework. Stanescu, Ana; Pandey, Gaurav. arXiv preprint arXiv:2102.07344.  

Predicting Individual Cell Division Events from Single-Cell ERK and Akt Dynamics. Stern, Alan D; Smith, Gregory R; Santos, Luis C; Sarmah, Deepraj; Zhang, Xiang; Lu, Xiaoming; Iuricich, Federico; Pandey, Gaurav; Iyengar, Ravi; Birtwistle, Marc R. bioRxiv.  

Developing better digital health measures of Parkinson’s disease using free living data and a crowdsourced data analysis challenge. Sieberts, Solveig K; Borzymowski, Henryk; Guan, Yuanfang; Huang, Yidi; Matzner, Ayala; Page, Alex; … Li, Yan-Chak; … ; Stanescu, Ana; … ; Pandey, Gaurav; Shawen, Nicholas; Synder, Phil; Omberg, Larsson. medRxiv.  

An interpretable connectivity-based decoding model for classification of chronic marijuana use. Kulkarni, Kaustubh R; Schafer, Matthew; Berner, Laura; Fiore, Vincenzo G; Heflin, Matt; Hutchison, Kent; Calhoun, Vince; Filbey, Francesca; Pandey, Gaurav; Schiller, Daniela. bioRxiv.  

2020:

Computational performance of heterogeneous ensemble frameworks on high-performance computing platforms. Wang, Linhua; Timsina, Prem; Pandey, Gaurav. IEEE International Conference on Big Data (Big Data).  

MetaClean: a machine learning-based classifier for reduced false positive peak detection in untargeted LC-MS metabolomics data. Chetnik, Kelsey; Petrick, Lauren; Pandey, Gaurav. Metabolomics. 16(11).  

Clinical features of COVID-19 mortality: development and validation of a clinical prediction model. Yadaw, Arjun S; Li, Yan-chak; Bose, Sonali; Iyengar, Ravi; Bunyavanich, Supinda; Pandey, Gaurav. The Lancet Digital Health. 2(10).  

Unravelling the architecture of membrane proteins with conditional random fields. Lukov, Lior; Chawla, Sanjay; Liu, Wei; Church, Brett; Pandey, Gaurav. arXiv preprint arXiv:2008.02467.

Clinical predictors of COVID-19 mortality. Yadaw, Arjun S; Li, Yan-chak; Bose, Sonali; Iyengar, Ravi; Bunyavanich, Supinda; Pandey, Gaurav. medRxiv.  

Evaluation of combined artificial intelligence and radiologist assessment to interpret screening mammograms. Schaffter, Thomas; Buist, Diana SM; Lee, Christoph I; Nikulin, Yaroslav; Ribli, Dezső; Guan, Yuanfang; Lotter, William; Jie, Zequn; Du, Hao; Wang, Sijia; … ; Pandey, Gaurav (the DM DREAM Consortium) . JAMA network open. 3(3).

Pharmacological Silencing of MicroRNA-152 Prevents Pressure Overload-Induced Heart Failure. LaRocca, Thomas J; Seeger, Timon; Prado, Maricela; Perea-Gil, Isaac; Neofytou, Evgenios; Mecham, Brigham H; Ameen, Mohamed; Chang, Alex Chia Yu; Pandey, Gaurav; Wu, Joseph C. Circulation: Heart Failure. 13(3).  

Radiogenomics consortium genome-wide association study meta-analysis of late toxicity after prostate cancer radiotherapy. Kerns, Sarah L; Fachal, Laura; Dorling, Leila; Barnett, Gillian C; Baran, Andrea; Peterson, Derick R; Hollenberg, Michelle; Hao, Ke; Narzo, Antonio Di; Ahsen, Mehmet Eren; Pandey, Gaurav; … ; Ostrer, Harry; Rosenstein, Barry. JNCI: Journal of the National Cancer Institute. 112(2).  

Tissue-resident PDGFRα+ progenitor cells contribute to fibrosis versus healing in a context-and spatiotemporally dependent manner. Santini, Maria Paola; Malide, Daniela; Hoffman, Gabriel; Pandey, Gaurav; D’Escamard, Valentina; Nomura-Kitabayashi, Aya; Rovira, Ilsa; Kataoka, Hiroshi; Ochando, Jordi; Harvey, Richard P. Cell reports. 30(2).  

Data integration through heterogeneous ensembles for protein function prediction. Wang, Linhua; Law, Jeffrey; Murali, TM; Pandey, Gaurav. bioRxiv.

2019:

NeTFactor, a framework for identifying transcriptional regulators of gene expression-based biomarkers. Ahsen, Mehmet Eren; Chun, Yoojin; Grishin, Alexander; Grishina, Galina; Stolovitzky, Gustavo; Pandey, Gaurav; Bunyavanich, Supinda. Scientific Reports. 9(12970).

Objective risk stratification of prostate cancer using machine learning and radiomics applied to multiparametric magnetic resonance images. Varghese, Bino; Chen, Frank; Hwang, Darryl; Palmer, Suzanne L; De Castro Abreu, Andre Luis; Ukimura, Osamu; Aron, Monish; Aron, Manju; Gill, Inderbir; Duddalwar, Vinay; Pandey, Gaurav. Scientific Reports. 9(1570).  

Assessing computational predictions of the phenotypic effect of cystathionine-beta-synthase variants. Kasak, Laura; Bakolitsa, Constantina; Hu, Zhiqiang; Yu, Changhua; Rine, Jasper; Dimster-Denk, Dago F; Pandey, Gaurav; De Baets, Greet; Bromberg, Yana; Cao, Chen. Human mutation. 40(9).  

Radiogenomics. Rosenstein, Barry S; Pandey, Gaurav; Speers, Corey W; Oh, Jung Hun; West, Catharine ML; Mayo, Charles S. Big Data in Radiation Oncology.

A machine learning approach predicts essential genes and pharmacological targets in cancer. Gilvary, Coryandar; Madhukar, Neel S; Gayvert, Kaitlyn; Foronda, Miguel; Perez, Alexendar; Leslie, Christina S; Dow, Lukas; Pandey, Gaurav; Elemento, Olivier. bioRxiv.  

2018:

Radiation therapy outcomes models in the era of radiomics and radiogenomics: uncertainties and validation. El Naqa, Issam; Pandey, Gaurav; Aerts, Hugo; Chien, Jen-Tzung; Andreassen, Christian Nicolaj; Niemierko, Andrzej; Ten Haken, Randall K. International journal of radiation oncology, biology, physics. 102(4).  

A crowdsourced analysis to identify ab initio molecular signatures predictive of susceptibility to viral infection. Fourati, Slim; Talla, Aarthi; Mahmoudian, Mehrad; Burkhart, Joshua G; Klén, Riku; Henao, Ricardo; Yu, Thomas; Aydın, Zafer; Yeung, Ka Yee; Ahsen, Mehmet Eren; … ; Ana Stanescu; … ; Pandey, Gaurav; … ; Mangravite, Lara M. ; … ; Sieberts, Solveig K. Nature communications. 9(1).  

A nasal brush-based classifier of asthma identified by machine learning analysis of nasal RNA sequence data. Pandey, Gaurav; Pandey, Om P; Rogers, Angela J; Ahsen, Mehmet E; Hoffman, Gabriel E; Raby, Benjamin A; Weiss, Scott T; Schadt, Eric E; Bunyavanich, Supinda. Scientific reports. 8(1).  

Large-scale protein function prediction using heterogeneous ensembles. Wang, Linhua; Law, Jeffrey; Kale, Shiv D; Murali, TM; Pandey, Gaurav. F1000Research. 7  

2017:

Using machine learning to identify air pollution exposure profiles associated with early cognitive skills among us children. Stingone, Jeanette A; Pandey, Om P; Claudio, Luz; Pandey, Gaurav. Environmental Pollution. 230  

Analysis of transcriptional variability in a large human iPSC library reveals genetic and non-genetic determinants of heterogeneity. Carcamo-Orive, Ivan; Hoffman, Gabriel E; Cundiff, Paige; Beckmann, Noam D; D’Souza, Sunita L; Knowles, Joshua W; Patel, Achchhe; Papatsenko, Dimitri; Abbasi, Fahim; Reaven, Gerald M; Whalen, Sean; … ; Pandey, Gaurav; Chang, Rui R; Quertermous, Thomas ; Lemischka, Ihor. Cell stem cell. 20(4).  

Learning parsimonious ensembles for unbalanced computational genomics problems. Stanescu, Ana; Pandey, Gaurav. PACIFIC SYMPOSIUM ON BIOCOMPUTING 2017.  

2016 or before:

Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis. Sieberts, Solveig K; Zhu, Fan; García-García, Javier; Stahl, Eli; Pratap, Abhishek; Pandey, Gaurav; Pappas, Dimitrios; Aguilar, Daniel; Anton, Bernat; Bonet, Jaume. Nature communications. 2016. 7(1).  

Endothelial to mesenchymal transition is common in atherosclerotic lesions and is associated with plaque instability. Evrard, Solene M; Lecce, Laura; Michelis, Katherine C; Nomura-Kitabayashi, Aya; Pandey, Gaurav; Purushothaman, K-Raman; d’Escamard, Valentina; Li, Jennifer R; Hadri, Lahouaria; Fujitani, Kenji. Nature communications. 2016. 7(1).  

Breast imaging in the era of big data: structured reporting and data mining. Margolies, Laurie R; Pandey, Gaurav; Horowitz, Eliot R; Mendelson, David S. AJR. American journal of roentgenology. 2016. 206(2).  

Predicting protein function and other biomedical characteristics with heterogeneous ensembles. Whalen, Sean; Pandey, Om Prakash; Pandey, Gaurav. Methods. 2016. 93  

Microbiota regulate the ability of lung dendritic cells to induce IgA class-switch recombination and generate protective gastrointestinal immune responses. Ruane, Darren; Chorny, Alejo; Lee, Haekyung; Faith, Jeremiah; Pandey, Gaurav; Shan, Meimei; Simchoni, Noa; Rahman, Adeeb; Garg, Aakash; Weinstein, Erica G. Journal of Experimental Medicine. 2016. 213(1).  

Prediction of genetic interactions using machine learning and network properties. Madhukar, Neel S; Elemento, Olivier; Pandey, Gaurav. Frontiers in bioengineering and biotechnology. 2015. 3  

Prediction of human population responses to toxic compounds by a collaborative competition. Eduati, Federica; Mangravite, Lara M; Wang, Tao; Tang, Hao; Bare, J Christopher; Huang, Ruili; Norman, Thea; Kellen, Mike; Menden, Michael P; Yang, Jichen; … ; The NIEHS-NCATS-UNC DREAM Toxicogenetics Collaboration (Whalen, Sean & Pandey, Gaurav); … ; Xie, Y; Saez-Rodriguez, Julio. Nature biotechnology. 2015. 33(9).  

Guest editorial for special section on BIOKDD2013. Pandey, Gaurav; Rangwala, Huzefa. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2014. 11(5).  

Enhancing the functional content of eukaryotic protein interaction networks. Pandey, Gaurav; Arora, Sonali; Manocha, Sahil; Whalen, Sean. PloS one. 2014. 9(10).

A comparative analysis of ensemble classifiers: case studies in genomics. Whalen, Sean; Pandey, Gaurav. 2013 IEEE 13th International Conference on Data Mining. 2013.  

Improving breast cancer survival analysis through competition-based multidimensional modeling. Bilal, Erhan; Dutkowski, Janusz; Guinney, Justin; Jang, In Sock; Logsdon, Benjamin A; Pandey, Gaurav; Sauerwine, Benjamin A; Shimoni, Yishai; Moen Vollan, Hans Kristian; Mecham, Brigham H. PLoS computational biology. 2013. 9(5).  

A large-scale evaluation of computational protein function prediction. Radivojac, Predrag; Clark, Wyatt T; Oron, Tal Ronnen; Schnoes, Alexandra M; Wittkop, Tobias; Sokolov, Artem; Graim, Kiley; Funk, Christopher; Verspoor, Karin; Ben-Hur, Asa; … ; Pandey, Gaurav; … ; Friedberg Iddo . Nature methods. 2013. 10(3).  

Decoding dendritic cell function through module and network analysis. Pandey, Gaurav; Cohain, Ariella; Miller, Jennifer; Merad, Miriam. Journal of immunological methods. 2013. 387(01-Feb).  

Predicting submicron air pollution indicators: a machine learning approach. Pandey, Gaurav; Zhang, Bin; Jian, Le. Environmental Science: Processes & Impacts. 2013. 15(5).  

Proceedings of the 12th International Workshop on Data Mining in Bioinformatics (BIOKDD 2013): Chicago, USA, August 2013. Pandey, Gaurav; Rangwala, Huzefa. 2013.  

Enhancing the functional content of protein interaction networks. Pandey, Gaurav; Manocha, Sahil; Atluri, Gowtham; Kumar, Vipin. arXiv preprint arXiv:1210.6912. 2012.  

Deciphering the transcriptional network of the dendritic cell lineage. Miller, Jennifer C; Brown, Brian D; Shay, Tal; Gautier, Emmanuel L; Jojic, Vladimir; Cohain, Ariella; Pandey, Gaurav; Leboeuf, Marylene; Elpek, Kutlu G; Helft, Julie. Nature immunology. 2012. 13(9).  

Computational approaches to protein function prediction. Pandey, Gaurav; Kumar, Vipin; Steinbach, Michael; Meyers, Chad L. 2012.  

Putting genetic interactions in context through a global modular decomposition. Bellay, Jeremy; Atluri, Gowtham; Sing, Tina L; Toufighi, Kiana; Costanzo, Michael; Ribeiro, Philippe Souza Moraes; Pandey, Gaurav; Baller, Joshua; VanderSluis, Benjamin; Michaut, Magali. Genome research. 2011. 21(8).  

Mining low-support discriminative patterns from dense and high-dimensional data. Fang, Gang; Pandey, Gaurav; Wang, Wen; Gupta, Manish; Steinbach, Michael; Kumar, Vipin. IEEE Transactions on Knowledge and Data Engineering. 2010. 24(2).  

An integrative multi-network and multi-classifier approach to predict genetic interactions. Pandey, Gaurav; Zhang, Bin; Chang, Aaron N; Myers, Chad L; Zhu, Jun; Kumar, Vipin; Schadt, Eric E. PLoS computational biology. 2010. 6(9).  

Protein Secondary Structure Prediction with Conditional Random Fields. Lukov, Lior; Chawla, Sanjay; Liu, Wei; Church, Brett; Pandey, Gaurav. School of Information Technologies, University of Sydney. 2010.  

Data mining techniques for enhancing protein function prediction. Pandey, Gaurav. PhD thesis, University of Minnesota. 2010.  

Discovering coherent value bicliques in genetic interaction data. Atluri, Gowtham; Bellay, Jeremy; Pandey, Gaurav; Myers, Chad; Kumar, Vipin. Proceedings of 9th International Workshop on Data Mining in Bioinformatics (BIOKDD10). 2010.

Subspace differential coexpression analysis: problem definition and a general approach. Fang, Gang; Kuang, Rui; Pandey, Gaurav; Steinbach, Michael; Myers, Chad L; Kumar, Vipin. Pacific Symposium on Biocomputing 2010. 2010.  

Scientific Data Analysis. Kamath, Chandrika; Wale, Nikil; Karypis, George; Pandey, Gaurav; Kumar, Vipin; Rajan, Krishna; Samatova, Nagiza F; Breimyer, Paul; Kora, Guruprasad; Pan, Chongle. Scientific Data Management. 2009.  

Incorporating functional inter-relationships into protein function prediction algorithms. Pandey, Gaurav; Myers, Chad L; Kumar, Vipin. BMC bioinformatics. 2009. 10(1).  

Structure extraction from unstructured documents. Daga, Rakshit; Pandey, Gaurav. 2009.  

Two-Dimensional Association Analysis For Finding Constant Value Biclusters In Real-Valued Data. Atluri, Gowtham; Bellay, Jeremy; Pandey, Gaurav; Myers, Chad L; Kumar, Vipin. 2009.  

An association analysis approach to biclustering. Pandey, Gaurav; Atluri, Gowtham; Steinbach, Michael; Myers, Chad L; Kumar, Vipin. Proceedings of the 15th ACM SIGKDD international conference on Knowledge discovery and data mining. 2009.  

Association analysis techniques for analyzing complex biological data sets. Pandey, Gaurav; Atluri, Gowtham; Fang, Gang; Gupta, Rohit; Steinbach, Michael; Kumar, Vipin. 2009 IEEE International Workshop on Genomic Signal Processing and Statistics. 2009.  

Association analysis techniques for bioinformatics problems. Atluri, Gowtham; Gupta, Rohit; Fang, Gang; Pandey, Gaurav; Steinbach, Michael; Kumar, Vipin. International Conference on Bioinformatics and Computational Biology. 2009.  

Association rules network: Definition and applications. Pandey, Gaurav; Chawla, Sanjay; Poon, Simon; Arunasalam, Bavani; Davis, Joseph G. Statistical Analysis and Data Mining: The ASA Data Science Journal. 2009. 1(4).  

Scientific data analysis. Kamath, Chandrika; Wale, Nikil; Karypis, George; Pandey, Gaurav; Kumar, Vipin; Rajan, Krishna; Samatova, Nagiza F; Breimyer, Paul; Kora, Guruprasad; Pan, Chongle. Scientific Data Management: Challenges, Technology, and Deployment. 2009.  

Systematic evaluation of scaling methods for gene expression data. Pandey, Gaurav; Ramakrishnan, Lakshmi Naarayanan; Steinbach, Michael; Kumar, Vipin. 2008 IEEE International Conference on Bioinformatics and Biomedicine. 2008.  

Association analysis techniques for discovering functional modules from microarray data. Pandey, Gaurav; Atluri, Gowtham; Steinbach, Michael; Kumar, Vipin. Nature Precedings. 2008.  

Determination of document similarity. Daga, Rakshit; Pandey, Gaurav. 2008.  

Association analysis for real-valued data: Definitions and application to microarray data. Pandey, Gaurav; Atluri, Gowtham; Steinbach, Michael; Myers, Chad L; Kumar, Vipin. 2008.  

Association analysis-based transformations for protein interaction networks: a function prediction case study. Pandey, Gaurav; Steinbach, Michael; Gupta, Rohit; Garg, Tushar; Kumar, Vipin. Proceedings of the 13th ACM SIGKDD international conference on Knowledge discovery and data mining. 2007.  

Comparative study of various genomic data sets for protein function prediction and enhancements using association analysis. Gupta, Rohit; Garg, Tushar; Pandey, Gaurav; Steinbach, Michael; Kumar, Vipin. SIAM Workshop on Data Mining for Biomedical Informatics. 2007.  

Incorporating functional inter-relationships into algorithms for protein function prediction. Pandey, Gaurav; Kumar, Vipin. ISMB/ECCB Special Interest Group meeting on Automated Function Prediction. 2007.  

On extracting structured knowledge from unstructured business documents. Pandey, Gaurav; Daga, Rakshit. Proc IJCAI Workshop on Analytics for Noisy Unstructured Text Data. 2007.  

Systematic evaluation of normalization methods for gene expression data. Pandey, Gaurav; Ramakrishnan, Lakshmi Naarayanan; Steinbach, Michael; Kumar, Vipin. 2007.  

Computational approaches for protein function prediction: A survey. Pandey, Gaurav; Kumar, Vipin; Steinbach, Michael. 2006.  

Computational approaches for protein function prediction. Pandey, Gaurav; Kumar, Vipin; Steinbach, Michael. A Survey. 2006.  

Enhancing data analysis with noise removal. Xiong, Hui; Pandey, Gaurav; Steinbach, Michael; Kumar, Vipin. IEEE Transactions on Knowledge and Data Engineering. 2006. 18(3).  

Stochastic scheduling of active support vector learning algorithms. Pandey, Gaurav; Gupta, Himanshu; Mitra, Pabitra. Proceedings of the 2005 ACM Symposium on Applied computing. 2005.  

EUCLID: A System for the Exploratory Discovery of Geometrical Properties of Triangles. Pandey, Gaurav; Anand, Ankit; Karnick, Harish. IICAI. 2005.  

On Local Pruning of Association Rules Using Directed Hypergraphs. Chawla, Sanjay; Davis, Joseph G; Pandey, Gaurav. ICDE. 2004. 4  

TANSEN: A System for Automatic Raga Identification. Pandey, Gaurav; Mishra, Chaitanya; Ipe, Paul. IICAI. 2003.  

By topics:

Multimodal/Ensemble Learning:

Integrating multimodal data through interpretable heterogeneous ensemblesLi, Yan Chak; Wang, Linhua; Law, Jeffrey; Murali, TM; Pandey, Gaurav. Bioinformatics Advances, Volume 2, Issue 1, vbac065.

Developing parsimonious ensembles using predictor diversity within a reinforcement learning framework. Stanescu, Ana; Pandey, Gaurav. arXiv preprint arXiv:2102.07344. 2021.  

Developing better digital health measures of Parkinson’s disease using free living data and a crowdsourced data analysis challenge. Sieberts, Solveig K; Borzymowski, Henryk; Guan, Yuanfang; Huang, Yidi; Matzner, Ayala; Page, Alex; … Li, Yan-Chak; … ; Stanescu, Ana; … ; Pandey, Gaurav; Shawen, Nicholas; Synder, Phil; Omberg, Larsson. medRxiv. 2021.  

Computational performance of heterogeneous ensemble frameworks on high-performance computing platforms. Wang, Linhua; Timsina, Prem; Pandey, Gaurav. 2020 IEEE International Conference on Big Data (Big Data). 2020.  

Data integration through heterogeneous ensembles for protein function prediction. Wang, Linhua; Law, Jeffrey; Murali, TM; Pandey, Gaurav. bioRxiv. 2020.

Large-scale protein function prediction using heterogeneous ensembles. Wang, Linhua; Law, Jeffrey; Kale, Shiv D; Murali, TM; Pandey, Gaurav. F1000Research. 2018. 7  

Learning parsimonious ensembles for unbalanced computational genomics problems. Stanescu, Ana; Pandey, Gaurav. PACIFIC SYMPOSIUM ON BIOCOMPUTING 2017. 2017.  

Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis. Sieberts, Solveig K; Zhu, Fan; García-García, Javier; Stahl, Eli; Pratap, Abhishek; Pandey, Gaurav; Pappas, Dimitrios; Aguilar, Daniel; Anton, Bernat; Bonet, Jaume. Nature communications. 2016. 7(1).  

Predicting protein function and other biomedical characteristics with heterogeneous ensembles. Whalen, Sean; Pandey, Om Prakash; Pandey, Gaurav. Methods. 2016. 93  

A comparative analysis of ensemble classifiers: case studies in genomics. Whalen, Sean; Pandey, Gaurav. 2013 IEEE 13th International Conference on Data Mining. 2013.  

Improving breast cancer survival analysis through competition-based multidimensional modeling. Bilal, Erhan; Dutkowski, Janusz; Guinney, Justin; Jang, In Sock; Logsdon, Benjamin A; Pandey, Gaurav; Sauerwine, Benjamin A; Shimoni, Yishai; Moen Vollan, Hans Kristian; Mecham, Brigham H. PLoS computational biology. 2013. 9(5).  

An integrative multi-network and multi-classifier approach to predict genetic interactions. Pandey, Gaurav; Zhang, Bin; Chang, Aaron N; Myers, Chad L; Zhu, Jun; Kumar, Vipin; Schadt, Eric E. PLoS computational biology. 2010. 6(9).  

Disease/Translational Studies:

Signal from Noise: Using Machine Learning to Distil Knowledge from Data in Biological Psychiatry, Quinn, Thomas P.; Hess,Jonathan L.; Marshe, Victoria S.;Barnett, Michelle M.;Hauschild, Anne-Christin;Maciukiewicz, Malgorzata; Elsheikh, Samar S.M.; Men, Xiaoyu; Trakadis, Yannis J.; Breen, Michael S.; Barnett, Eric J.; Zhang-James, Yanli; Ahsen, Mehmet Eren;Cao, Han; Chen, Junfang; Asif, Salekin ; Hou, Jiahui; Lin, Ping-I; Nicodemus, Kristin K.; Meyer-Lindenberg, Andreas; Bichindaritz, Isabelle; Faraone, Stephen V.; Cairns, Murray J.; Pandey, Gaurav; Muller, Daniel J.; Glatt, Stephen J.. PsyArXiv. 

l applications of audio recordings, Kumar, Anish; Jaquenoud, Theo; Becker, Jacqueline Helcer; Cho, Dayeon; Mindt, Monica Rivera; Federman, Alex; Pandey, Gaurav. medRxiv. 2022.

Machine learning-driven identification of early-life air toxic combinations associated with childhood asthma outcomes. Li, Yan-Chak; Hsu, Hsiao-Hsien Leon; Chun, Yoojin; Chiu, Po-Hsiang; Arditi, Zoe; Claudio, Luz; Pandey, Gaurav; Bunyavanich, Supinda. The Journal of Clinical Investigation. 2021. 131(22).  

Predicting youth diabetes risk using NHANES data and machine learning. Vangeepuram, Nita; Liu, Bian; Chiu, Po-hsiang; Wang, Linhua; Pandey, Gaurav. Scientific reports. 2021. 11(1).  

Developing better digital health measures of Parkinson’s disease using free living data and a crowdsourced data analysis challenge. Sieberts, Solveig K; Borzymowski, Henryk; Guan, Yuanfang; Huang, Yidi; Matzner, Ayala; Page, Alex; … Li, Yan-Chak; … ; Stanescu, Ana; … ; Pandey, Gaurav; Shawen, Nicholas; Synder, Phil; Omberg, Larsson. medRxiv. 2021.  

Clinical features of COVID-19 mortality: development and validation of a clinical prediction model. Yadaw, Arjun S; Li, Yan-chak; Bose, Sonali; Iyengar, Ravi; Bunyavanich, Supinda; Pandey, Gaurav. The Lancet Digital Health. 2020. 2(10).  

Clinical predictors of COVID-19 mortality. Yadaw, Arjun S; Li, Yan-chak; Bose, Sonali; Iyengar, Ravi; Bunyavanich, Supinda; Pandey, Gaurav. medRxiv. 2020.  

Evaluation of combined artificial intelligence and radiologist assessment to interpret screening mammograms. Schaffter, Thomas; Buist, Diana SM; Lee, Christoph I; Nikulin, Yaroslav; Ribli, Dezső; Guan, Yuanfang; Lotter, William; Jie, Zequn; Du, Hao; Wang, Sijia; … ; Pandey, Gaurav (the DM DREAM Consortium) . JAMA network open. 2020. 3(3).

Pharmacological Silencing of MicroRNA-152 Prevents Pressure Overload-Induced Heart Failure. LaRocca, Thomas J; Seeger, Timon; Prado, Maricela; Perea-Gil, Isaac; Neofytou, Evgenios; Mecham, Brigham H; Ameen, Mohamed; Chang, Alex Chia Yu; Pandey, Gaurav; Wu, Joseph C. Circulation: Heart Failure. 2020. 13(3).  

NeTFactor, a framework for identifying transcriptional regulators of gene expression-based biomarkers. Ahsen, Mehmet Eren; Chun, Yoojin; Grishin, Alexander; Grishina, Galina; Stolovitzky, Gustavo; Pandey, Gaurav; Bunyavanich, Supinda. Scientific Reports. 2019. 9(12970).

Objective risk stratification of prostate cancer using machine learning and radiomics applied to multiparametric magnetic resonance images. Varghese, Bino; Chen, Frank; Hwang, Darryl; Palmer, Suzanne L; De Castro Abreu, Andre Luis; Ukimura, Osamu; Aron, Monish; Aron, Manju; Gill, Inderbir; Duddalwar, Vinay; Pandey, Gaurav. Scientific Reports. 2019. 9(1570).  

Assessing computational predictions of the phenotypic effect of cystathionine-beta-synthase variants. Kasak, Laura; Bakolitsa, Constantina; Hu, Zhiqiang; Yu, Changhua; Rine, Jasper; Dimster-Denk, Dago F; Pandey, Gaurav; De Baets, Greet; Bromberg, Yana; Cao, Chen. Human mutation. 2019. 40(9).  

A crowdsourced analysis to identify ab initio molecular signatures predictive of susceptibility to viral infection. Fourati, Slim; Talla, Aarthi; Mahmoudian, Mehrad; Burkhart, Joshua G; Klén, Riku; Henao, Ricardo; Yu, Thomas; Aydın, Zafer; Yeung, Ka Yee; Ahsen, Mehmet Eren; … ; Ana Stanescu; … ; Pandey, Gaurav. Nature communications. 2018. 9(1).  

A nasal brush-based classifier of asthma identified by machine learning analysis of nasal RNA sequence data. Pandey, Gaurav; Pandey, Om P; Rogers, Angela J; Ahsen, Mehmet E; Hoffman, Gabriel E; Raby, Benjamin A; Weiss, Scott T; Schadt, Eric E; Bunyavanich, Supinda. Scientific reports. 2018. 8(1).  

Radiogenomics. Rosenstein, Barry S; Pandey, Gaurav; Speers, Corey W; Oh, Jung Hun; West, Catharine ML; Mayo, Charles S. Big Data in Radiation Oncology. 2019.

A machine learning approach predicts essential genes and pharmacological targets in cancer. Gilvary, Coryandar; Madhukar, Neel S; Gayvert, Kaitlyn; Foronda, Miguel; Perez, Alexendar; Leslie, Christina S; Dow, Lukas; Pandey, Gaurav; Elemento, Olivier. bioRxiv. 2019.  

Analysis of transcriptional variability in a large human iPSC library reveals genetic and non-genetic determinants of heterogeneity. Carcamo-Orive, Ivan; Hoffman, Gabriel E; Cundiff, Paige; Beckmann, Noam D; D’Souza, Sunita L; Knowles, Joshua W; Patel, Achchhe; Papatsenko, Dimitri; Abbasi, Fahim; Reaven, Gerald M; Whalen, Sean; … ; Pandey, Gaurav. Cell stem cell. 2017. 20(4).  

Endothelial to mesenchymal transition is common in atherosclerotic lesions and is associated with plaque instability. Evrard, Solene M; Lecce, Laura; Michelis, Katherine C; Nomura-Kitabayashi, Aya; Pandey, Gaurav; Purushothaman, K-Raman; d’Escamard, Valentina; Li, Jennifer R; Hadri, Lahouaria; Fujitani, Kenji. Nature communications. 2016. 7(1).  

Microbiota regulate the ability of lung dendritic cells to induce IgA class-switch recombination and generate protective gastrointestinal immune responses. Ruane, Darren; Chorny, Alejo; Lee, Haekyung; Faith, Jeremiah; Pandey, Gaurav; Shan, Meimei; Simchoni, Noa; Rahman, Adeeb; Garg, Aakash; Weinstein, Erica G. Journal of Experimental Medicine. 2016. 213(1).  

Protein Function Prediction:

Integrating multimodal data through interpretable heterogeneous ensemblesLi, Yan Chak; Wang, Linhua; Law, Jeffrey; Murali, TM; Pandey, Gaurav. Bioinformatics Advances, Volume 2, Issue 1, vbac065.

Developing parsimonious ensembles using predictor diversity within a reinforcement learning framework. Stanescu, Ana; Pandey, Gaurav. arXiv preprint arXiv:2102.07344. 2021.  

Data integration through heterogeneous ensembles for protein function prediction. Wang, Linhua; Law, Jeffrey; Murali, TM; Pandey, Gaurav. bioRxiv. 2020.

Large-scale protein function prediction using heterogeneous ensembles. Wang, Linhua; Law, Jeffrey; Kale, Shiv D; Murali, TM; Pandey, Gaurav. F1000Research. 2018. 7  

Learning parsimonious ensembles for unbalanced computational genomics problems. Stanescu, Ana; Pandey, Gaurav. PACIFIC SYMPOSIUM ON BIOCOMPUTING 2017. 2017.  

Predicting protein function and other biomedical characteristics with heterogeneous ensembles. Whalen, Sean; Pandey, Om Prakash; Pandey, Gaurav. Methods. 2016. 93  

A comparative analysis of ensemble classifiers: case studies in genomics. Whalen, Sean; Pandey, Gaurav. 2013 IEEE 13th International Conference on Data Mining. 2013.  

A large-scale evaluation of computational protein function prediction. Radivojac, Predrag; Clark, Wyatt T; Oron, Tal Ronnen; Schnoes, Alexandra M; Wittkop, Tobias; Sokolov, Artem; Graim, Kiley; Funk, Christopher; Verspoor, Karin; Ben-Hur, Asa; … ; Pandey, Gaurav; …; Friedberg Iddo. Nature methods. 2013. 10(3).  

Data mining techniques for enhancing protein function prediction. Pandey, Gaurav. PhD thesis, University of Minnesota. 2010.  

Association analysis-based transformations for protein interaction networks: a function prediction case study. Pandey, Gaurav; Steinbach, Michael; Gupta, Rohit; Garg, Tushar; Kumar, Vipin. Proceedings of the 13th ACM SIGKDD international conference on Knowledge discovery and data mining. 2007.  

Comparative study of various genomic data sets for protein function prediction and enhancements using association analysis. Gupta, Rohit; Garg, Tushar; Pandey, Gaurav; Steinbach, Michael; Kumar, Vipin. SIAM Workshop on Data Mining for Biomedical Informatics. 2007.  

Incorporating functional inter-relationships into algorithms for protein function prediction. Pandey, Gaurav; Kumar, Vipin. ISMB/ECCB Special Interest Group meeting on Automated Function Prediction. 2007.  

Computational approaches for protein function prediction: A survey. Pandey, Gaurav; Kumar, Vipin; Steinbach, Michael. 2006.  

Medical Imaging/Radiomics/Radiogenomics:

An interpretable connectivity-based decoding model for classification of chronic marijuana use. Kulkarni, Kaustubh R; Schafer, Matthew; Berner, Laura; Fiore, Vincenzo G; Heflin, Matt; Hutchison, Kent; Calhoun, Vince; Filbey, Francesca; Pandey, Gaurav; Schiller, Daniela. bioRxiv. 2021.

Objective risk stratification of prostate cancer using machine learning and radiomics applied to multiparametric magnetic resonance images. Varghese, Bino; Chen, Frank; Hwang, Darryl; Palmer, Suzanne L; De Castro Abreu, Andre Luis; Ukimura, Osamu; Aron, Monish; Aron, Manju; Gill, Inderbir; Duddalwar, Vinay; Pandey, Gaurav. Scientific Reports. 2019. 9(1570).  

Radiogenomics consortium genome-wide association study meta-analysis of late toxicity after prostate cancer radiotherapy. Kerns, Sarah L; Fachal, Laura; Dorling, Leila; Barnett, Gillian C; Baran, Andrea; Peterson, Derick R; Hollenberg, Michelle; Hao, Ke; Narzo, Antonio Di; Ahsen, Mehmet Eren; Pandey, Gaurav; … ;. JNCI: Journal of the National Cancer Institute. 2020. 112(2).  

Radiation therapy outcomes models in the era of radiomics and radiogenomics: uncertainties and validation. El Naqa, Issam; Pandey, Gaurav; Aerts, Hugo; Chien, Jen-Tzung; Andreassen, Christian Nicolaj; Niemierko, Andrzej; Ten Haken, Randall K. International journal of radiation oncology, biology, physics. 2018. 102(4).  

Breast imaging in the era of big data: structured reporting and data mining. Margolies, Laurie R; Pandey, Gaurav; Horowitz, Eliot R; Mendelson, David S. AJR. American journal of roentgenology. 2016. 206(2).  

Environmental Health:

Machine learning-driven identification of early-life air toxic combinations associated with childhood asthma outcomes. Li, Yan-Chak; Hsu, Hsiao-Hsien Leon; Chun, Yoojin; Chiu, Po-Hsiang; Arditi, Zoe; Claudio, Luz; Pandey, Gaurav; Bunyavanich, Supinda. The Journal of Clinical Investigation. 2021. 131(22).  

MetaClean: a machine learning-based classifier for reduced false positive peak detection in untargeted LC-MS metabolomics data. Chetnik, Kelsey; Petrick, Lauren; Pandey, Gaurav. Metabolomics. 2020. 16(11).  

Using machine learning to identify air pollution exposure profiles associated with early cognitive skills among us children. Stingone, Jeanette A; Pandey, Om P; Claudio, Luz; Pandey, Gaurav. Environmental Pollution. 2017. 230  

Predicting submicron air pollution indicators: a machine learning approach. Pandey, Gaurav; Zhang, Bin; Jian, Le. Environmental Science: Processes & Impacts. 2013. 15(5).  

Systems Biology:

Predicting Individual Cell Division Events from Single-Cell ERK and Akt Dynamics. Stern, Alan D; Smith, Gregory R; Santos, Luis C; Sarmah, Deepraj; Zhang, Xiang; Lu, Xiaoming; Iuricich, Federico; Pandey, Gaurav; Iyengar, Ravi; Birtwistle, Marc R. bioRxiv. 2021.  

Tissue-resident PDGFRα+ progenitor cells contribute to fibrosis versus healing in a context-and spatiotemporally dependent manner. Santini, Maria Paola; Malide, Daniela; Hoffman, Gabriel; Pandey, Gaurav; D’Escamard, Valentina; Nomura-Kitabayashi, Aya; Rovira, Ilsa; Kataoka, Hiroshi; Ochando, Jordi; Harvey, Richard P. Cell reports. 2020. 30(2).  

Enhancing the functional content of eukaryotic protein interaction networks. Pandey, Gaurav; Arora, Sonali; Manocha, Sahil; Whalen, Sean. PloS one. 2014. 9(10). 

Decoding dendritic cell function through module and network analysis. Pandey, Gaurav; Cohain, Ariella; Miller, Jennifer; Merad, Miriam. Journal of immunological methods. 2013. 387(01-Feb).  

Deciphering the transcriptional network of the dendritic cell lineage. Miller, Jennifer C; Brown, Brian D; Shay, Tal; Gautier, Emmanuel L; Jojic, Vladimir; Cohain, Ariella; Pandey, Gaurav; Leboeuf, Marylene; Elpek, Kutlu G; Helft, Julie. Nature immunology. 2012. 13(9).  

Enhancing the functional content of protein interaction networks. Pandey, Gaurav; Manocha, Sahil; Atluri, Gowtham; Kumar, Vipin. arXiv preprint arXiv:1210.6912. 2012.  

Putting genetic interactions in context through a global modular decomposition. Bellay, Jeremy; Atluri, Gowtham; Sing, Tina L; Toufighi, Kiana; Costanzo, Michael; Ribeiro, Philippe Souza Moraes; Pandey, Gaurav; Baller, Joshua; VanderSluis, Benjamin; Michaut, Magali. Genome research. 2011. 21(8).  

Subspace differential coexpression analysis: problem definition and a general approach. Fang, Gang; Kuang, Rui; Pandey, Gaurav; Steinbach, Michael; Myers, Chad L; Kumar, Vipin. Biocomputing 2010. 2010.  

Discovering coherent value bicliques in genetic interaction data. Atluri, Gowtham; Bellay, Jeremy; Pandey, Gaurav; Myers, Chad; Kumar, Vipin. Proceedings of 9th International Workshop on Data Mining in Bioinformatics (BIOKDD10). 2010.

Incorporating functional inter-relationships into protein function prediction algorithms. Pandey, Gaurav; Myers, Chad L; Kumar, Vipin. BMC bioinformatics. 2009. 10(1).  

Association analysis techniques for analyzing complex biological data sets. Pandey, Gaurav; Atluri, Gowtham; Fang, Gang; Gupta, Rohit; Steinbach, Michael; Kumar, Vipin. 2009 IEEE International Workshop on Genomic Signal Processing and Statistics. 2009.  

Association analysis techniques for bioinformatics problems. Atluri, Gowtham; Gupta, Rohit; Fang, Gang; Pandey, Gaurav; Steinbach, Michael; Kumar, Vipin. International Conference on Bioinformatics and Computational Biology. 2009.  

Systematic evaluation of scaling methods for gene expression data. Pandey, Gaurav; Ramakrishnan, Lakshmi Naarayanan; Steinbach, Michael; Kumar, Vipin. 2008 IEEE International Conference on Bioinformatics and Biomedicine. 2008.  

Association analysis techniques for discovering functional modules from microarray data. Pandey, Gaurav; Atluri, Gowtham; Steinbach, Michael; Kumar, Vipin. Nature Precedings. 2008.  

Systematic evaluation of normalization methods for gene expression data. Pandey, Gaurav; Ramakrishnan, Lakshmi Naarayanan; Steinbach, Michael; Kumar, Vipin. 2007.  

Others:

Mining low-support discriminative patterns from dense and high-dimensional data. Fang, Gang; Pandey, Gaurav; Wang, Wen; Gupta, Manish; Steinbach, Michael; Kumar, Vipin. IEEE Transactions on Knowledge and Data Engineering. 2010. 24(2).  

Scientific Data Analysis. Kamath, Chandrika; Wale, Nikil; Karypis, George; Pandey, Gaurav; Kumar, Vipin; Rajan, Krishna; Samatova, Nagiza F; Breimyer, Paul; Kora, Guruprasad; Pan, Chongle. Scientific Data Management. 2009.  

Structure extraction from unstructured documents. Daga, Rakshit; Pandey, Gaurav. 2009.  

Two-Dimensional Association Analysis For Finding Constant Value Biclusters In Real-Valued Data. Atluri, Gowtham; Bellay, Jeremy; Pandey, Gaurav; Myers, Chad L; Kumar, Vipin. 2009.  

An association analysis approach to biclustering. Pandey, Gaurav; Atluri, Gowtham; Steinbach, Michael; Myers, Chad L; Kumar, Vipin. Proceedings of the 15th ACM SIGKDD international conference on Knowledge discovery and data mining. 2009.  

Determination of document similarity. Daga, Rakshit; Pandey, Gaurav. 2008.  

On extracting structured knowledge from unstructured business documents. Pandey, Gaurav; Daga, Rakshit. Proc IJCAI Workshop on Analytics for Noisy Unstructured Text Data. 2007.  

Enhancing data analysis with noise removal. Xiong, Hui; Pandey, Gaurav; Steinbach, Michael; Kumar, Vipin. IEEE Transactions on Knowledge and Data Engineering. 2006. 18(3).  

Stochastic scheduling of active support vector learning algorithms. Pandey, Gaurav; Gupta, Himanshu; Mitra, Pabitra. Proceedings of the 2005 ACM Symposium on Applied computing. 2005.  

EUCLID: A System for the Exploratory Discovery of Geometrical Properties of Triangles. Pandey, Gaurav; Anand, Ankit; Karnick, Harish. IICAI. 2005.  

On Local Pruning of Association Rules Using Directed Hypergraphs. Chawla, Sanjay; Davis, Joseph G; Pandey, Gaurav. ICDE. 2004. 4  

TANSEN: A System for Automatic Raga Identification. Pandey, Gaurav; Mishra, Chaitanya; Ipe, Paul. IICAI. 2003.