Large-scale model quality assessment for improving protein tertiary structure prediction. - Renzhi Cao; Debswapna Bhattacharya; Badri Adhikari; Jilong Li; Jianlin Cheng (Bioinform., 2015)

FRAGSION: ultra-fast protein fragment library generation by IOHMM sampling. - Debswapna Bhattacharya; Badri Adhikari; Jilong Li; Jianlin Cheng (Bioinform., 2016)

ConEVA: a toolbox for comprehensive assessment of protein contacts. - Badri Adhikari; Jackson Nowotny; Debswapna Bhattacharya; Jie Hou 001; Jianlin Cheng (BMC Bioinform., 2016)

QAcon: single model quality assessment using protein structural and contact information with machine learning techniques. - Renzhi Cao; Badri Adhikari; Debswapna Bhattacharya; Miao Sun; Jie Hou 001; Jianlin Cheng (Bioinform., 2017)

Improved protein structure reconstruction using secondary structures, contacts at higher distance thresholds, and non-contacts. - Badri Adhikari; Jianlin Cheng (BMC Bioinform., 2017)

Deep learning methods for protein torsion angle prediction. - Haiou Li; Jie Hou 001; Badri Adhikari; Qiang Lyu; Jianlin Cheng (BMC Bioinform., 2017)

DNCON2: improved protein contact prediction using two-level deep convolutional neural networks. - Badri Adhikari; Jie Hou 001; Jianlin Cheng (Bioinform., 2018)

DeepSF: deep convolutional neural network for mapping protein sequences to folds. - Jie Hou 001; Badri Adhikari; Jianlin Cheng (Bioinform., 2018)

CONFOLD2: improved contact-driven ab initio protein structure modeling. - Badri Adhikari; Jianlin Cheng (BMC Bioinform., 2018)

DEEPCON: protein contact prediction using dilated convolutional neural networks with dropout. - Badri Adhikari (Bioinform., 2020)

Analysis of several key factors influencing deep learning-based inter-residue contact prediction. - Tianqi Wu; Jie Hou 001; Badri Adhikari; Jianlin Cheng (Bioinform., 2020)

DISTEVAL: a web server for evaluating predicted protein distances. - Badri Adhikari; Bikash Shrestha; Matthew Bernardini; Jie Hou 001; Jamie Lea (BMC Bioinform., 2021)

Scoring protein sequence alignments using deep learning. - Bikash Shrestha; Badri Adhikari (Bioinform., 2022)

New Labeling Methods for Deep Learning Real-Valued Inter-Residue Distance Prediction. - Jacob Barger; Badri Adhikari (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

Thinking beyond chatbots' threat to education: Visualizations to elucidate the writing and coding process. - Badri Adhikari (CoRR, 2023)

Adversarial sample generation and training using geometric masks for accurate and resilient license plate character recognition. - Bishal Shrestha; Griwan Khakurel; Kritika Simkhada; Badri Adhikari (CoRR, 2023)

Maximizing Student Engagement in Coding Education with Explanatory AI. - Badri Adhikari; Sameep Dhakal; Aadya Jha (FIE, 2024)

Teaching Coding in the Age of AI: A Hands-on Tutorial on Process Feedback. - Badri Adhikari; Jie Hou 001 (SIGCSE (2), 2025)