Genome sequence of the palaeopolyploid soybean J Schmutz, SB Cannon, J Schlueter, J Ma, T Mitros, W Nelson, DL Hyten, ... Nature 463 (7278), 178-183, 2010 | 4629 | 2010 |
SCRATCH: a protein structure and structural feature prediction server J Cheng, AZ Randall, MJ Sweredoski, P Baldi Nucleic acids research 33 (suppl_2), W72-W76, 2005 | 1160 | 2005 |
Prediction of protein stability changes for single‐site mutations using support vector machines J Cheng, A Randall, P Baldi Proteins: Structure, Function, and Bioinformatics 62 (4), 1125-1132, 2006 | 1063 | 2006 |
A large-scale evaluation of computational protein function prediction P Radivojac, WT Clark, TR Oron, AM Schnoes, T Wittkop, A Sokolov, ... Nature methods 10 (3), 221-227, 2013 | 1048 | 2013 |
An expanded evaluation of protein function prediction methods shows an improvement in accuracy Y Jiang, TR Oron, WT Clark, AR Bankapur, D D’Andrea, R Lepore, ... Genome biology 17, 1-19, 2016 | 414 | 2016 |
3Drefine: an interactive web server for efficient protein structure refinement D Bhattacharya, J Nowotny, R Cao, J Cheng Nucleic acids research 44 (W1), W406-W409, 2016 | 400 | 2016 |
A Deep Learning Network Approach to ab initio Protein Secondary Structure Prediction M Spencer, J Eickholt, J Cheng IEEE/ACM Transactions on Computational Biology and Bioinformatics, 1, 2014 | 369 | 2014 |
The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens N Zhou, Y Jiang, TR Bergquist, AJ Lee, BZ Kacsoh, AW Crocker, ... Genome biology 20 (1), 1-23, 2019 | 359 | 2019 |
Improved residue contact prediction using support vector machines and a large feature set J Cheng, P Baldi BMC bioinformatics 8 (1), 113, 2007 | 312 | 2007 |
Accurate prediction of protein disordered regions by mining protein structure data J Cheng, MJ Sweredoski, P Baldi Data Mining and Knowledge Discovery 11 (3), 213-222, 2005 | 267 | 2005 |
A neural network approach to ordinal regression J Cheng, Z Wang, G Pollastri 2008 IEEE International Joint Conference on Neural Networks (IEEE World …, 2008 | 266 | 2008 |
A machine learning information retrieval approach to protein fold recognition J Cheng, P Baldi Bioinformatics 22 (12), 1456-1463, 2006 | 261 | 2006 |
3Drefine: Consistent protein structure refinement by optimizing hydrogen bonding network and atomic‐level energy minimization D Bhattacharya, J Cheng Proteins: Structure, Function, and Bioinformatics, 2012 | 225 | 2012 |
DeepSF: deep convolutional neural network for mapping protein sequences to folds J Hou, B Adhikari, J Cheng Bioinformatics 34 (8), 1295-1303, 2018 | 208 | 2018 |
Bioinformatics Methods for Mass Spectrometry-Based Proteomics Data Analysis C Chen, J Hou, JJ Tanner, J Cheng International Journal of Molecular Sciences 21 (8), 2873, 2020 | 204 | 2020 |
NNcon: improved protein contact map prediction using 2D-recursive neural networks AN Tegge, Z Wang, J Eickholt, J Cheng Nucleic acids research 37 (suppl 2), W515-W518, 2009 | 201 | 2009 |
Predicting protein residue-residue contacts using deep networks and boosting J Eickholt, J Cheng Bioinformatics, 2012 | 189 | 2012 |
CONFOLD: Residue‐residue contact‐guided ab initio protein folding B Adhikari, D Bhattacharya, R Cao, J Cheng Proteins: Structure, Function, and Bioinformatics 83 (8), 1436-1449, 2015 | 184 | 2015 |
DNCON2: Improved protein contact prediction using two-level deep convolutional neural networks B Adhikari, J Hou, J Cheng Bioinformatics, 2017 | 179 | 2017 |
DeepQA: improving the estimation of single protein model quality with deep belief networks R Cao, D Bhattacharya, J Hou, J Cheng BMC Bioinformatics 17 (1), 495, 2016 | 171 | 2016 |