Identification of sequence-structure RNA binding motifs for SELEX-derived aptamers. - Jan Hoinka; Elena Zotenko; Adam Friedman; Zuben E. Sauna; Teresa M. Przytycka (Bioinform., 2012)

AptaCluster - A Method to Cluster HT-SELEX Aptamer Pools and Lessons from Its Application. - Jan Hoinka; Alexey Berezhnoy; Zuben E. Sauna; Eli Gilboa; Teresa M. Przytycka (RECOMB, 2014)

AptaTRACE: Elucidating Sequence-Structure Binding Motifs by Uncovering Selection Trends in HT-SELEX Experiments. - Phuong Dao; Jan Hoinka; Yijie Wang 004; Mayumi Takahashi; Jiehua Zhou; Fabrizio Costa; John Rossi; John Burnett; Rolf Backofen; Teresa M. Przytycka (RECOMB, 2016)

Aptamers in the age of big data: development and application of algorithmic solutions in the field of high-throughput systematic evolution of ligands by exponental enrichment - Jan Hoinka (2016)

AptaBlocks: Accelerating the Design of RNA-Based Drug Delivery Systems. - Yijie Wang 004; Jan Hoinka; Piotr Swiderski; Teresa M. Przytycka (RECOMB, 2018)

Accurate Sub-population Detection and Mapping Across Single Cell Experiments with PopCorn. - Yijie Wang 004; Jan Hoinka; Teresa M. Przytycka (RECOMB, 2019)

AptaBlocks Online: A Web-Based Toolkit for the In Silico Design of Oligonucleotide Sticky Bridges. - Jan Hoinka; Yijie Wang 004; Teresa M. Przytycka (J. Comput. Biol., 2020)

Embedding gene sets in low-dimensional space. - Jan Hoinka; Teresa M. Przytycka (Nat. Mach. Intell., 2020)

Improved Algorithms for Bi-Partition Function Computation. - John D. Bridgers; Jan Hoinka; S. Cenk Sahinalp; Salem Malikic; Teresa M. Przytycka; Funda Ergün (WABI, 2025)