R. Machiraju

Most-cited papers

Canonical and Atypical E2Fs Regulate the Mammalian Endocycle
Hui-Zi Chen, Madhu M Ouseph, Jing Li, T. Pécot +28 more
2012Nature Cell Biology164 citations Open access
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Metabolomics and Multi-Omics Integration: A Survey of Computational Methods and Resources
T. Eicher, G. Kinnebrew, Andrew C. Patt, Kyle Spencer +4 more
2020Metabolites144 citations Open access
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Atypical E2F Repressors and Activators Coordinate Placental Development
Madhu M Ouseph, Jing Li, Hui-Zi Chen, T. Pécot +11 more
2012Developmental Cell117 citations Open access
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E2f8 mediates tumor suppression in postnatal liver development.
Lindsey N. Kent, Jessica B. Rakijas, Shusil K. Pandit, B. Westendorp +29 more
2016Journal of Clinical Investigation90 citations Open access
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Predictive models for pressure ulcers from intensive care unit electronic health records using Bayesian networks
Pacharmon Kaewprag, Cheryl Newton, B. Vermillion, S. Hyun +2 more
2017BMC Medical Informatics and Decision Making79 citations Open access
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Redeployment of Myc and E2f1-3 drives Rb deficient cell cycles
Huayang Liu, Xing Tang, Arunima Srivastava, T. Pécot +15 more
2015Nature Cell Biology74 citations Open access
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An Annotated Corpus for Machine Reading of Instructions in Wet Lab Protocols
Chaitanya Kulkarni, Wei Xu, Alan Ritter, R. Machiraju
2018North American Chapter of the Association for Computational Linguistics67 citations Open access
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Analysis of live cell images: Methods, tools and opportunities.
Thomas A. Nketia, Heba Sailem, G. Rohde, R. Machiraju +1 more
2017Methods64 citations Open access
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GEMS: GPU-Enabled Memory-Aware Model-Parallelism System for Distributed DNN Training
Arpan Jain, A. Awan, Asmaa Aljuhani, J. Hashmi +5 more
2020International Conference for High Performance Computing, Networking, Storage and Analysis56 citations
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Breast Cancer Patient Stratification using a Molecular Regularized Consensus Clustering Method
Chao Wang, R. Machiraju, Kun Huang
2014Methods54 citations Open access
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Tocotrienol Vitamin E Protects against Preclinical Canine Ischemic Stroke by Inducing Arteriogenesis
Cameron Rink, G. Christoforidis, S. Khanna, Laura Peterson +7 more
2011Journal of Cerebral Blood Flow and Metabolism53 citations Open access
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Visual Exploration of Neural Document Embedding in Information Retrieval: Semantics and Feature Selection
Xiao-Nan Ji, Han-Wei Shen, Alan Ritter, R. Machiraju +1 more
2019IEEE Transactions on Visualization and Computer Graphics48 citations
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Examining the Distribution, Modularity, and Community Structure in Article Networks for Systematic Reviews
Xiao-Nan Ji, R. Machiraju, Alan Ritter, Po-Yin Yen
2015American Medical Informatics Association Annual Symposium38 citations
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Visualizing Multidimensional Data with Glyph SPLOMs
A. Yates, A. Webb, Michael F. Sharpnack, H. Chamberlin +2 more
2014Computer graphics forum (Print)35 citations
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Single-Cell Co-expression Analysis Reveals Distinct Functional Modules, Co-regulation Mechanisms and Clinical Outcomes
Jie Wang, S. Xia, Brian Arand, Heng Zhu +4 more
2016PLoS Comput. Biol.32 citations Open access
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Boosting Techniques for Physics‐Based Vortex Detection
L. Zhang, Qi Deng, R. Machiraju, Anand Rangarajan +3 more
2014Computer graphics forum (Print)31 citations Open access
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Integrative cancer patient stratification via subspace merging
Hao Ding, Michael F. Sharpnack, Chao Wang, Kun Huang +1 more
2018Bioinform.28 citations Open access
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Spatio-temporal models of mental processes from fMRI
F. Janoos, R. Machiraju, Shantanu Singh, I. Mórocz
2011NeuroImage26 citations
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Autonomous Computing Materials.
M. Bathe, R. Hernandez, T. Komiyama, R. Machiraju +1 more
2021ACS Nano25 citations Open access
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iGPSe: A visual analytic system for integrative genomic based cancer patient stratification
Hao Ding, Chao Wang, Kun Huang, R. Machiraju
2014BMC Bioinformatics25 citations Open access
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Identifying survival associated morphological features of triple negative breast cancer using multiple datasets
Chao Wang, Thierry Pécot, Debra L. Zynger, R. Machiraju +2 more
2013JAMIA Journal of the American Medical Informatics Association25 citations Open access
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Proteogenomic Analysis of Surgically Resected Lung Adenocarcinoma
Michael F. Sharpnack, Nilini Ranbaduge, Arunima Srivastava, F. Cerciello +16 more
2018Journal of Thoracic Oncology23 citations Open access
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Research and applications: Identifying survival associated morphological features of triple negative breast cancer using multiple datasets
Chao Wang, T. Pécot, D. Zynger, R. Machiraju +2 more
2013J. Am. Medical Informatics Assoc.23 citations
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Susceptibility Distortion Correction for Echo Planar Images with Non-uniform B-Spline Grid Sampling: A Diffusion Tensor Image Study
M. Irfanoglu, L. Walker, Steffen Sammet, C. Pierpaoli +1 more
2011International Conference on Medical Image Computing and Computer-Assisted Intervention23 citations Open access
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An uncertainty-driven approach to vortex analysis using oracle consensus and spatial proximity
Ayan Biswas, D. Thompson, Wenbin He, Qi Deng +4 more
2015IEEE Pacific Visualization Symposium19 citations
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Predictive Modeling for Pressure Ulcers from Intensive Care Unit Electronic Health Records
Pacharmon Kaewprag, Cheryl Newton, B. Vermillion, S. Hyun +2 more
2015AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science18 citations
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AZGP1 deficiency promotes angiogenesis in prostate cancer
Ru M. Wen, Zhengyuan Qiu, G. E. Marti, Eric E. Peterson +21 more
2024Journal of Translational Medicine17 citations Open access
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An integrative analysis of regional gene expression profiles in the human brain.
Emma M. Myers, Christopher W. Bartlett, R. Machiraju, J. Bohland
2015Methods17 citations
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Feature‐based adaptive mesh refinement for wingtip vortices
N. Kasmai, D. Thompson, E. Luke, Monika Jankun-Kelly +1 more
201117 citations Open access
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Spatial cell type composition in normal and Alzheimers human brains is revealed using integrated mouse and human single cell RNA sequencing
T. Johnson, Shunian Xiang, Bryan R Helm, Zachary B. Abrams +5 more
2020Scientific Reports15 citations Open access
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Imitating Pathologist Based Assessment With Interpretable and Context Based Neural Network Modeling of Histology Images
Arunima Srivastava, Chaitanya Kulkarni, Kun Huang, A. Parwani +2 more
2018Biomedical Informatics Insights15 citations Open access
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Effectively processing medical term queries on the UMLS Metathesaurus by layered dynamic programming
Kaiyu Ren, Albert M. Lai, Aveek Mukhopadhyay, R. Machiraju +2 more
2014BMC Medical Genomics15 citations Open access
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Cyberinfrastructure for machine learning applications in agriculture: experiences, analysis, and vision
Lucas Waltz, Sushma Katari, Chaeun Hong, A. Anup +13 more
2025Frontiers Artif. Intell.14 citations
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Gene × smoking interactions on human brain gene expression: Finding common mechanisms in adolescents and adults
Samuel L. Wolock, A. Yates, S. Petrill, J. Bohland +5 more
2013Journal of Child Psychology and Psychiatry and Allied Disciplines14 citations Open access
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Identifying Nuclear Phenotypes Using Semi-supervised Metric Learning
Shantanu Singh, F. Janoos, T. Pécot, Enrico Caserta +3 more
2011Information Processing in Medical Imaging14 citations Open access
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Actin Grips: Circular Actin-Rich Cytoskeletal Structures that Mediate the Wrapping of Polymeric Microfibers by Endothelial Cells
Desiree Jones, Doyoung Park, M. Anghelina, T. Pécot +7 more
2015Biomaterials13 citations Open access
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GRAPHIE: graph based histology image explorer
Hao Ding, Chao Wang, Kun Huang, R. Machiraju
2015BMC Bioinformatics13 citations Open access
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Deep learning-based automated pipeline for blood vessel detection and distribution analysis in multiplexed prostate cancer images
G. Karageorgos, Sanghee Cho, E. McDonough, Chrystal Chadwick +8 more
2024Frontiers Bioinform.11 citations Open access
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Challenges in proteogenomics: a comparison of analysis methods with the case study of the DREAM proteogenomics sub-challenge
T. Eicher, Andrew C. Patt, Esko A Kautto, R. Machiraju +2 more
2019BMC Bioinformatics11 citations Open access
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A signal processing approach for enriched region detection in RNA polymerase II ChIP-seq data
Zhi Han, Lu Tian, T. Pécot, T. Huang +2 more
2012BMC Bioinformatics11 citations Open access
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Non-parametric Population Analysis of Cellular Phenotypes
Shantanu Singh, F. Janoos, T. Pécot, Enrico Caserta +4 more
2011International Conference on Medical Image Computing and Computer-Assisted Intervention11 citations Open access
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State–Space Models of Mental Processes from fMRI
F. Janoos, Shantanu Singh, R. Machiraju, W. Wells +1 more
2011Information Processing in Medical Imaging11 citations Open access
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Non parametric cell nuclei segmentation based on a tracking over depth from 3D fluorescence confocal images
T. Pécot, Shantanu Singh, Enrico Caserta, Kun Huang +2 more
2012IEEE International Symposium on Biomedical Imaging9 citations
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Creating intelligent cyberinfrastructure for democratizing AI
Dhabaleswar K. Panda, Vipin Chaudhary, Eric Fosler‐Lussier, R. Machiraju +6 more
2024The AI Magazine8 citations Open access
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Uncertainty Aware Sampling Framework of Weak-Label Learning for Histology Image Classification
Asmaa Aljuhani, Ishya Casukhela, Jany Chan, D. Liebner +1 more
2022International Conference on Medical Image Computing and Computer-Assisted Intervention7 citations
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Semantic workflows for benchmark challenges: Enhancing comparability, reusability and reproducibility
Arunima Srivastava, Ravali Adusumilli, Hunter Boyce, D. Garijo +6 more
2018Pacific Symposium on Biocomputing7 citations Open access
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Building trans-omics evidence: using imaging and 'omics' to characterize cancer profiles
Arunima Srivastava, Chaitanya Kulkarni, P. Mallick, Kun Huang +1 more
2018Pacific Symposium on Biocomputing7 citations Open access
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Improving Compound Activity Classification via Deep Transfer and Representation Learning
Vishal Dey, R. Machiraju, Xia Ning
2021ACS Omega6 citations Open access
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Visualizing Article Similarities via Sparsified Article Network and Map Projection for Systematic Reviews
Xiao-Nan Ji, R. Machiraju, Alan Ritter, Po-Yin Yen
2017Medinfo6 citations
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annoPeak: a web application to annotate and visualize peaks from ChIP‐seq/ChIP‐exo‐seq
Xing Tang, Arunima Srivastava, Huayang Liu, R. Machiraju +2 more
2017Bioinform.5 citations Open access
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