Evaluating eukaryotic secreted protein prediction. - Eric W. Klee; Lynda B. M. Ellis (BMC Bioinform., 2005)

AMOD: a morpholino oligonucleotide selection tool. - Eric W. Klee; Kyong Jin Shim; Michael A. Pickart; Stephen C. Ekker; Lynda B. M. Ellis (Nucleic Acids Res., 2005)

Quantitating tissue specificity of human genes to facilitate biomarker discovery. - George Vasmatzis; Eric W. Klee; Dagmar M. Kube; Terry M. Therneau; Farhad Kosari (Bioinform., 2007)

TREAT: a bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data. - Yan W. Asmann; Sumit Middha; Asif Hossain; Saurabh Baheti; Ying Li; High-Seng Chai; Zhifu Sun; Patrick H. Duffy; Ahmed A. Hadad; Asha A. Nair; Xiaoyu Liu; Yuji Zhang 001; et al. (Bioinform., 2012)

SAAP-RRBS: streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing. - Zhifu Sun; Saurabh Baheti; Sumit Middha; Rahul Kanwar; Yuji Zhang 001; Xing Li; Andreas S. Beutler; Eric W. Klee; Yan W. Asmann; E. Aubrey Thompson; Jean-Pierre A. Kocher (Bioinform., 2012)

The Zebrafish GenomeWiki: a crowdsourcing approach to connect the long tail for zebrafish gene annotation. - Meghna Singh; Deeksha Bhartiya; Jayant Maini; Meenakshi Sharma; Angom Ramcharan Singh; Subburaj Kadarkaraisamy; Rajiv Rana; Ankit Sabharwal; Srishti Nanda; Aravindhakshan Ramachandran; Ashish Mittal; Shruti Kapoor; et al. (Database J. Biol. Databases Curation, 2014)

Proceedings of the 15th Annual UT-KBRIN Bioinformatics Summit 2016: Cadiz, KY, USA. 8-10 April 2016. - Eric C. Rouchka; Julia H. Chariker; Benjamin J. Harrison; Juw Won Park; Xueyuan Cao; Stanley Pounds; Susana C. Raimondi; James R. Downing; Raul C. Ribeiro; Jeffrey Rubnitz; Jatinder Lamba; Bernie J. Daigle Jr.; et al. (BMC Bioinform., 2016)

Deep Learning for Better Variant Calling for Cancer Diagnosis and Treatment. - Anand Ramachandran 001; Huiren Li; Eric W. Klee; Steven S. Lumetta; Deming Chen (ASP-DAC, 2018)

Comparative analysis of de novo assemblers for variation discovery in personal genomes. - Shulan Tian; Huihuang Yan; Eric W. Klee; Michael Kalmbach; Susan L. Slager (Briefings Bioinform., 2018)

Improving Single-Nucleotide Polymorphism-Based Fetal Fraction Estimation of Maternal Plasma Circulating Cell-Free DNA Using Bayesian Hierarchical Models. - Nicholas B. Larson; Chen Wang 001; Jie Na; Ross A. Rowsey; William Edward Highsmith; Nicole L. Hoppman; Jean-Pierre A. Kocher; Eric W. Klee (J. Comput. Biol., 2018)

A recurrent Markov state-space generative model for sequences. - Anand Ramachandran 001; Steven S. Lumetta; Eric W. Klee; Deming Chen (AISTATS, 2019)

Recommendations for performance optimizations when using GATK3.8 and GATK4. - Jacob R Heldenbrand; Saurabh Baheti; Matthew A. Bockol; Travis M. Drucker; Steven N. Hart; Matthew E. Hudson; Ravishankar K. Iyer; Michael Kalmbach; Katherine Irene Kendig; Eric W. Klee; Nathan R Mattson; Eric D. Wieben; et al. (BMC Bioinform., 2019)

Correction to: Recommendations for performance optimizations when using GATK3.8 and GATK4. - Jacob R Heldenbrand; Saurabh Baheti; Matthew A. Bockol; Travis M. Drucker; Steven N. Hart; Matthew E. Hudson; Ravishankar K. Iyer; Michael Kalmbach; Katherine Irene Kendig; Eric W. Klee; Nathan R Mattson; Eric D. Wieben; et al. (BMC Bioinform., 2019)

LeafCutterMD: an algorithm for outlier splicing detection in rare diseases. - W. Garrett Jenkinson; Yang I Li; Shubham Basu; Margot A. Cousin; Gavin R. Oliver; Eric W. Klee (Bioinform., 2020)

HELLO: improved neural network architectures and methodologies for small variant calling. - Anand Ramachandran 001; Steven S. Lumetta; Eric W. Klee; Deming Chen (BMC Bioinform., 2021)

Universally Rank Consistent Ordinal Regression in Neural Networks. - W. Garrett Jenkinson; Kia Khezeli; Gavin R. Oliver; John Kalantari; Eric W. Klee (CoRR, 2021)

Enhancing Patient Care in Rare Genetic Diseases: An HPO-based Phenotyping Pipeline. - Yao Xiao; Moein Enayati; Gavin M. Schaeferle; Brendan C. Lanpher; Eric W. Klee; Che Ngufor (BIBM, 2023)

Deep Phenotyping of Non-Alcoholic Fatty Liver Disease Patients with Genetic Factors for Insights into the Complex Disease. - Tahmina Sultana Priya; Fan Leng; Anthony C. Luehrs; Eric W. Klee; Alina M. Allen; Konstantinos N. Lazaridis; Danfeng Yao; Shulan Tian (CoRR, 2023)

A supervised learning method for classifying methylation disorders. - Jesse R. Walsh; Guangchao Sun; Jagadheshwar Balan; Jayson Hardcastle; Jason Vollenweider; Calvin Jerde; Kandelaria Rumilla; Christy Koellner; Alaa Koleilat; Linda Hasadsri; Benjamin Kipp; W. Garrett Jenkinson; et al. (BMC Bioinform., 2024)

Enriched phenotypes in rare variant carriers suggest pathogenic mechanisms in rare disease patients. - Lane Fitzsimmons; Maria T. Acosta; David R. Adams; Ben Afzali; Ali Al-Beshri; Eric Allenspach; Aimee Allworth; Raquel L. Alvarez; Justin Alvey; Ashley Andrews; Euan A. Ashley; Carlos A. Bacino; et al. (BioData Min., 2025)

UNISOM: Unified Somatic Calling and Machine Learning-based Classification Enhance the Discovery of CHIP. - Shulan Tian; W. Garrett Jenkinson; Alejandro Ferrer; Huihuang Yan; Joel A Morales-Rosado; Kevin L. Wang; Terra L. Lasho; Benjamin B. Yan; Saurabh Baheti; Janet E. Olson; Linda B. Baughn; Wei Ding; et al. (Genom. Proteom. Bioinform., 2025)

A clinical knowledge graph-based framework to prioritize candidate genes for facilitating diagnosis of Mendelian diseases and rare genetic conditions. - Rohan Gnanaolivu; Gavin R. Oliver; W. Garrett Jenkinson; Emily Blake; Wenan Chen; Nicholas Chia; Eric W. Klee; Chen Wang (BMC Bioinform., 2025)