The threading approach to the inverse protein folding problem. - Temple F. Smith; Loredana Lo Conte; Jadwiga R. Bienkowska; Robert G. Rogers; Chrysanthe Gaitatzes; Richard H. Lathrop (RECOMB, 1997)

Current Limitations to Protein Threading Approaches. - Temple F. Smith; Loredana Lo Conte; Jadwiga R. Bienkowska; Chrysanthe Gaitatzes; Robert G. Rogers; Richard H. Lathrop (J. Comput. Biol., 1997)

A method for optimal design of a threading scoring function. - Jadwiga R. Bienkowska; Robert G. Rogers; Temple F. Smith (RECOMB, 1999)

Performance of Threading Scoring Functions Designed Using New Optimization Method. - Jadwiga R. Bienkowska; Robert G. Rogers; Temple F. Smith (J. Comput. Biol., 1999)

Comprehensive statistical method for protein fold recognition. - Jadwiga R. Bienkowska; Lihua Yu; Sophia Zarakhovich; Robert G. Rogers; Temple F. Smith (RECOMB, 2000)

Automatic Pattern Embedding in Protein Structure Models. - Jadwiga R. Bienkowska; Hongxian He; Temple F. Smith (IEEE Intell. Syst., 2001)

Using fold recognition to search for useful proteins: Bayesian approach to fold recognition. - Jadwiga R. Bienkowska (Briefings Bioinform., 2002)

GOTrees: Predicting GO Associations from Protein Domain Composition Using Decision Trees. - Boris Hayete; Jadwiga R. Bienkowska (Pacific Symposium on Biocomputing, 2005)

PANP - a New Method of Gene Detection on Oligonucleotide Expression Arrays. - Peter Warren; Deanne M. Taylor; Paolo G. V. Martini; Jennifer Jackson; Jadwiga R. Bienkowska (BIBE, 2007)

Lthreader: Prediction of Ligand-Receptor Interactions Using Localized Threading. - Vinay Pulim; Jadwiga R. Bienkowska; Bonnie Berger (Pacific Symposium on Biocomputing, 2007)

Optimal contact map alignment of protein-protein interfaces. - Vinay Pulim; Bonnie Berger; Jadwiga R. Bienkowska (Bioinform., 2008)

Causal Modeling Using Network Ensemble Simulations of Genetic and Gene Expression Data Predicts Genes Involved in Rheumatoid Arthritis. - Heming Xing; Paul D. McDonagh; Jadwiga R. Bienkowska; Tanya Cashorali; Karl Runge; Robert E. Miller; Dave DeCaprio; Bruce Church; Ronenn Roubenoff; Iya G. Khalil; John Carulli (PLoS Comput. Biol., 2011)

ProbeSelect: selecting differentially expressed probes in transcriptional profile data. - Raghavendra Hosur; Suzanne Szak; Alice Thai; Norm Allaire; Jadwiga R. Bienkowska (Bioinform., 2014)

Discovering What Dimensionality Reduction Really Tells Us About RNA-Seq Data. - Sean Simmons 001; Jian Peng 001; Jadwiga R. Bienkowska; Bonnie Berger (J. Comput. Biol., 2015)

TNER: a novel background error suppression method for mutation detection in circulating tumor DNA. - Shibing Deng; Maruja Lira; Donghui Huang; Kai Wang 045; Crystal Valdez; Jennifer Kinong; Paul A. Rejto; Jadwiga R. Bienkowska; James Hardwick; Tao Xie 002 (BMC Bioinform., 2018)

Detecting somatic mutations with high accuracy in plasma cell-free DNA with TNER2. - Shibing Deng; Joy Hsu; Jadwiga R. Bienkowska; Paul A. Rejto; Tao Xie 002 (BIBM, 2019)

Single-cell gene expression prediction using H&E images based on spatial transcriptomics. - Chao-Hui Huang; Yoson Park; Jincheng Pang; Jadwiga R. Bienkowska (Digital and Computational Pathology, 2023)