Deep learning-based cross-classifications reveal conserved spatial behaviors within tumor histological images J Noorbakhsh, S Farahmand, A Foroughi Pour, S Namburi, D Caruana, ... Nature communications 11 (1), 6367, 2020 | 133 | 2020 |
Integrating chemical footprinting data into RNA secondary structure prediction K Zarringhalam, MM Meyer, I Dotu, JH Chuang, P Clote Public Library of Science 7 (10), e45160, 2012 | 103 | 2012 |
Deep learning trained on hematoxylin and eosin tumor region of Interest predicts HER2 status and trastuzumab treatment response in HER2+ breast cancer S Farahmand, AI Fernandez, FS Ahmed, DL Rimm, JH Chuang, ... Modern Pathology 35 (1), 44-51, 2022 | 70 | 2022 |
Interpreting transcriptional changes using causal graphs: new methods and their practical utility on public networks CT Fakhry, P Choudhary, A Gutteridge, B Sidders, P Chen, D Ziemek, ... BMC bioinformatics 17, 1-15, 2016 | 50 | 2016 |
A biological network-based regularized artificial neural network model for robust phenotype prediction from gene expression data T Kang, W Ding, L Zhang, D Ziemek, K Zarringhalam BMC bioinformatics 18, 1-11, 2017 | 39 | 2017 |
An open system for automatic home-cage behavioral analysis and its application to male and female mouse models of Huntington's disease K Zarringhalam, M Ka, YH Kook, JI Terranova, Y Suh, OD King, M Um Behavioural brain research 229 (1), 216-225, 2012 | 31 | 2012 |
The modular circuitry of apicomplexan cell division plasticity MJ Gubbels, I Coppens, K Zarringhalam, MT Duraisingh, K Engelberg Frontiers in Cellular and Infection Microbiology 11, 670049, 2021 | 30 | 2021 |
Robust clinical outcome prediction based on Bayesian analysis of transcriptional profiles and prior causal networks K Zarringhalam, A Enayetallah, P Reddy, D Ziemek Bioinformatics 30 (12), i69-i77, 2014 | 29 | 2014 |
Robust phenotype prediction from gene expression data using differential shrinkage of co-regulated genes K Zarringhalam, D Degras, C Brockel, D Ziemek Scientific reports 8 (1), 1237, 2018 | 26 | 2018 |
Statistical analysis of the processes controlling choline and ethanolamine glycerophospholipid molecular species composition K Zarringhalam, L Zhang, MA Kiebish, K Yang, X Han, RW Gross, ... PLoS One 7 (5), e37293, 2012 | 26 | 2012 |
Nonlinear Least Squares in ℝ N A Aldroubi, K Zaringhalam Acta applicandae mathematicae 107, 325-337, 2009 | 26 | 2009 |
Identification of competing endogenous RNAs of the tumor suppressor gene PTEN: a probabilistic approach K Zarringhalam, Y Tay, P Kulkarni, AC Bester, PP Pandolfi, RV Kulkarni Scientific reports 7 (1), 7755, 2017 | 19 | 2017 |
Pressure dependency of localization degree in heavy fermion CeIn3: A density functional theory analysis M Yazdani-Kachoei, S Jalali-Asadabadi, I Ahmad, K Zarringhalam Scientific reports 6 (1), 31734, 2016 | 18 | 2016 |
Sequential adaptive compressed sampling via huffman codes A Aldroubi, H Wang, K Zarringhalam Sampling Theory in Signal and Image Processing 10, 231-254, 2011 | 18 | 2011 |
Molecular causes of transcriptional response: a Bayesian prior knowledge approach K Zarringhalam, A Enayetallah, A Gutteridge, B Sidders, D Ziemek Bioinformatics 29 (24), 3167-3173, 2013 | 16 | 2013 |
The Extracellular Milieu of Toxoplasma's Lytic Cycle Drives Lab Adaptation, Primarily by Transcriptional Reprogramming VA Primo Jr, Y Rezvani, A Farrell, CQ Murphy, J Lou, A Vajdi, GT Marth, ... Msystems 6 (6), e01196-21, 2021 | 15 | 2021 |
Causal Inference Engine: a platform for directional gene set enrichment analysis and inference of active transcriptional regulators S Farahmand, C O’Connor, JA Macoska, K Zarringhalam Nucleic acids research 47 (22), 11563-11573, 2019 | 15 | 2019 |
Dynamics of the ethanolamine glycerophospholipid remodeling network L Zhang, N Díaz–Díaz, K Zarringhalam, M Hermansson, P Somerharju, ... PLoS One 7 (12), e50858, 2012 | 15 | 2012 |
Pan-cancer classifications of tumor histological images using deep learning J Noorbakhsh, S Farahmand, M Soltanieh-ha, S Namburi, K Zarringhalam, ... Preprint at https://www. biorxiv. org/content/10.1101/715656v1, 2019 | 14 | 2019 |
Generating an adaptive multiresolution image analysis with compact cupolets K Zarringhalam, KM Short Nonlinear Dynamics 52, 51-70, 2008 | 13 | 2008 |