| Genetic effects on gene expression across human tissues GTEx Consortium Lead analysts: Aguet François 1 Brown Andrew A. 2 3 4 Castel ... Nature 550 (7675), 204-213, 2017 | 3644 | 2017 |
| A Powerful New Quantitative Genetics Platform, Combining Caenorhabditis elegans High-Throughput Fitness Assays with a Large Collection of Recombinant Strains EC Andersen, TC Shimko, JR Crissman, R Ghosh, JS Bloom, HS Seidel, ... G3: Genes, Genomes, Genetics 5 (5), 911-920, 2015 | 119 | 2015 |
| Discovering epistatic feature interactions from neural network models of regulatory DNA sequences P Greenside, T Shimko, P Fordyce, A Kundaje Bioinformatics 34 (17), i629-i637, 2018 | 93 | 2018 |
| Comprehensive, high-resolution binding energy landscapes reveal context dependencies of transcription factor binding DD Le, TC Shimko, AK Aditham, AM Keys, SA Longwell, Y Orenstein, ... Proceedings of the National Academy of Sciences 115 (16), E3702-E3711, 2018 | 89 | 2018 |
| COPASutils: an R package for reading, processing, and visualizing data from COPAS large-particle flow cytometers TC Shimko, EC Andersen PloS one 9 (10), e111090, 2014 | 58 | 2014 |
| An open-source, programmable pneumatic setup for operation and automated control of single-and multi-layer microfluidic devices K Brower, RR Puccinelli, CJ Markin, TC Shimko, SA Longwell, B Cruz, ... HardwareX 3, 117-134, 2018 | 57 | 2018 |
| Genetic effects on gene expression across human tissues DA Laboratory, NIHC Fund, BCS Site—NDRI, BCS Site—RPCI, ... Nature 550 (7675), 204-213, 2017 | 13 | 2017 |
| DeCoDe: degenerate codon design for complete protein-coding DNA libraries TC Shimko, PM Fordyce, Y Orenstein Bioinformatics 36 (11), 3357-3364, 2020 | 12 | 2020 |
| A multi-modal neural network for learning cis and trans regulation of stress response in yeast B Liu, N Hussami, A Shrikumar, T Shimko, S Bhate, S Longwell, ... arXiv preprint arXiv:1908.09426, 2019 | 7 | 2019 |
| BET-seq: Binding energy topographies revealed by microfluidics and high-throughput sequencing AK Aditham, TC Shimko, PM Fordyce Methods in cell biology 148, 229-250, 2018 | 6 | 2018 |
| A powerful new quantitative genetics platform, combining Caenorhabditis elegans high-throughput fitness assays with a large collection of recombinant strains. G3 (Bethesda) 5 … EC Andersen, TC Shimko, JR Crissman, R Ghosh, JS Bloom, HS Seidel, ... | 6 | 2015 |
| Comprehensive, high-resolution binding energy landscapes reveal context dependencies of transcription factor binding DD Le, TC Shimko, AK Aditham, AM Keys, Y Orenstein, PM Fordyce BioRxiv, 193904, 2017 | 3 | 2017 |
| Res2vec: Amino acid vector embeddings from 3d-protein structure S Longwell, T Shimko THRESHOLD 30 (22,344), 22,344, 2022 | 2 | 2022 |
| Method for multiplexed detection of nucleic acids using spectrally encoded beads AK White, HQ Nguyen, FB Yu, T Shimko, PM Fordyce, N Andini, S Yang, ... US Patent App. 17/613,676, 2022 | | 2022 |
| High-Throughput Biophysical Assays and Models to Link Molecular Sequence Variation to Structural and Functional Consequences TC Shimko Stanford University, 2020 | | 2020 |
| Deep Learning Models Explore the Structural Effects of Transcription Factor-DNA Complexes on Binding Specificity TC Shimko, PM Fordyce Biophysical Journal 116 (3), 503a, 2019 | | 2019 |
| Mapping Suppressors of Premature Sperm Activation in C. Elegans T Shimko Department of Biology, University of Utah, 2015 | | 2015 |
| A Powerful New Quantitative Genetics Platform, Combining Caenorhabditis elegans High E Andersen, T Shimko, J Crissman G3: Genes, Genomes, Genetics, 5 (5), 2015 | | 2015 |