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Polly Fordyce, Ph.D. - Publications

Affiliations: 
Stanford University, Palo Alto, CA 
Area:
biophysics, single molecules, motor proteins, transcription
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44 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Sockell A, Wong W, Longwell S, Vu T, Karlsson K, Mokhtari D, Schaepe J, Lo YH, Cornelius V, Kuo C, Van Valen D, Curtis C, Fordyce PM. A microwell platform for high-throughput longitudinal phenotyping and selective retrieval of organoids. Cell Systems. 14: 764-776.e6. PMID 37734323 DOI: 10.1016/j.cels.2023.08.002  0.732
2023 Horton CA, Alexandari AM, Hayes MGB, Marklund E, Schaepe JM, Aditham AK, Shah N, Suzuki PH, Shrikumar A, Afek A, Greenleaf WJ, Gordân R, Zeitlinger J, Kundaje A, Fordyce PM. Short tandem repeats bind transcription factors to tune eukaryotic gene expression. Science (New York, N.Y.). 381: eadd1250. PMID 37733848 DOI: 10.1126/science.add1250  0.805
2023 Alexandari AM, Horton CA, Shrikumar A, Shah N, Li E, Weilert M, Pufall MA, Zeitlinger J, Fordyce PM, Kundaje A. distillation of thermodynamic affinity from deep learning regulatory sequence models of protein-DNA binding. Biorxiv : the Preprint Server For Biology. PMID 37214836 DOI: 10.1101/2023.05.11.540401  0.348
2023 Zuo Z, Billings T, Walker M, Petkov PM, Fordyce PM, Stormo GD. On the dependent recognition of some long zinc finger proteins. Nucleic Acids Research. PMID 36951113 DOI: 10.1093/nar/gkad207  0.3
2022 Li Q, van de Groep J, White AK, Song JH, Longwell SA, Fordyce PM, Quake SR, Kik PG, Brongersma ML. Metasurface optofluidics for dynamic control of light fields. Nature Nanotechnology. PMID 36163507 DOI: 10.1038/s41565-022-01197-y  0.744
2022 Feng Y, Zhao X, White AK, Garcia KC, Fordyce PM. A bead-based method for high-throughput mapping of the sequence- and force-dependence of T cell activation. Nature Methods. PMID 36064771 DOI: 10.1038/s41592-022-01592-2  0.649
2021 Appel MJ, Longwell SA, Morri M, Neff N, Herschlag D, Fordyce PM. uPIC-M: Efficient and Scalable Preparation of Clonal Single Mutant Libraries for High-Throughput Protein Biochemistry. Acs Omega. 6: 30542-30554. PMID 34805683 DOI: 10.1021/acsomega.1c04180  0.765
2020 Aditham AK, Markin CJ, Mokhtari DA, DelRosso N, Fordyce PM. High-Throughput Affinity Measurements of Transcription Factor and DNA Mutations Reveal Affinity and Specificity Determinants. Cell Systems. PMID 33340452 DOI: 10.1016/j.cels.2020.11.012  0.816
2020 Feng Y, White AK, Hein JB, Appel EA, Fordyce PM. MRBLES 2.0: High-throughput generation of chemically functionalized spectrally and magnetically encoded hydrogel beads using a simple single-layer microfluidic device. Microsystems & Nanoengineering. 6: 109. PMID 33299601 DOI: 10.1038/s41378-020-00220-3  0.681
2020 Shimko TC, Fordyce PM, Orenstein Y. DeCoDe: degenerate codon design for complete protein-coding DNA libraries. Bioinformatics (Oxford, England). PMID 32176271 DOI: 10.1093/Bioinformatics/Btaa162  0.78
2020 Fordyce P, Aditham A, Horton C, DelRosso N, Mokhtari D, Markin C. Leveraging Microfluidics for High‐Throughput Studies of Transcription Factor/DNA Binding The Faseb Journal. 34: 1-1. DOI: 10.1096/Fasebj.2020.34.S1.00183  0.808
2020 Aditham AK, DelRosso NV, Fordyce P. A High-Throughput Platform Characterizes Functional Effects of Transcription Factor Mutations Biophysical Journal. 118: 74a-75a. DOI: 10.1016/J.Bpj.2019.11.581  0.77
2020 Markin CJ, Mokhtari DA, Sunden F, Appel MJ, Herschlag DM, Fordyce P. A High-Throughput Assay Platform for Next-Generation Mechanistic Enzymology and Applications Biophysical Journal. 118: 535a. DOI: 10.1016/J.Bpj.2019.11.2935  0.311
2019 Longwell SA, Fordyce PM. micrIO: an open-source autosampler and fraction collector for automated microfluidic input-output. Lab On a Chip. PMID 31701110 DOI: 10.1039/C9Lc00512A  0.77
2019 Ghosh RP, Shi Q, Yang L, Reddick MP, Nikitina T, Zhurkin VB, Fordyce P, Stasevich TJ, Chang HY, Greenleaf WJ, Liphardt JT. Satb1 integrates DNA binding site geometry and torsional stress to differentially target nucleosome-dense regions. Nature Communications. 10: 3221. PMID 31324780 DOI: 10.1038/S41467-019-11118-8  0.655
2019 Nguyen HQ, Roy J, Harink B, Damle NP, Latorraca NR, Baxter BC, Brower K, Longwell SA, Kortemme T, Thorn KS, Cyert MS, Fordyce PM. Quantitative mapping of protein-peptide affinity landscapes using spectrally encoded beads. Elife. 8. PMID 31282865 DOI: 10.7554/Elife.40499  0.774
2019 Harink B, Nguyen H, Thorn K, Fordyce P. An open-source software analysis package for Microspheres with Ratiometric Barcode Lanthanide Encoding (MRBLEs). Plos One. 14: e0203725. PMID 30901328 DOI: 10.1371/Journal.Pone.0203725  0.719
2019 Shimko TC, Fordyce PM. Deep Learning Models Explore the Structural Effects of Transcription Factor-DNA Complexes on Binding Specificity Biophysical Journal. 116: 503a. DOI: 10.1016/J.Bpj.2018.11.2714  0.787
2019 Aditham A, Fordyce PM. A High-Throughput Platform for Probing Mechanisms of Transcription Factor-DNA Binding Biophysical Journal. 116: 502a. DOI: 10.1016/J.Bpj.2018.11.2708  0.81
2018 Del Olmo Toledo V, Puccinelli R, Fordyce PM, Pérez JC. Diversification of DNA binding specificities enabled SREBP transcription regulators to expand the repertoire of cellular functions that they govern in fungi. Plos Genetics. 14: e1007884. PMID 30596634 DOI: 10.1371/journal.pgen.1007884  0.352
2018 Aditham AK, Shimko TC, Fordyce PM. BET-seq: Binding energy topographies revealed by microfluidics and high-throughput sequencing. Methods in Cell Biology. 148: 229-250. PMID 30473071 DOI: 10.1016/Bs.Mcb.2018.09.011  0.787
2018 Greenside P, Shimko T, Fordyce P, Kundaje A. Discovering epistatic feature interactions from neural network models of regulatory DNA sequences. Bioinformatics (Oxford, England). 34: i629-i637. PMID 30423062 DOI: 10.1093/Bioinformatics/Bty575  0.792
2018 Brower K, Puccinelli R, Markin CJ, Shimko TC, Longwell SA, Cruz B, Gomez-Sjoberg R, Fordyce PM. An Open-Source, Programmable Pneumatic Setup for Operation and Automated Control of Single- and Multi-Layer Microfluidic Devices. Hardwarex. 3: 117-134. PMID 30221210 DOI: 10.1016/J.Ohx.2017.10.001  0.732
2018 Mezger A, Klemm S, Mann I, Brower K, Mir A, Bostick M, Farmer A, Fordyce P, Linnarsson S, Greenleaf W. High-throughput chromatin accessibility profiling at single-cell resolution. Nature Communications. 9: 3647. PMID 30194434 DOI: 10.1038/S41467-018-05887-X  0.573
2018 Le DD, Shimko TC, Aditham AK, Keys AM, Longwell SA, Orenstein Y, Fordyce PM. Comprehensive, high-resolution binding energy landscapes reveal context dependencies of transcription factor binding. Proceedings of the National Academy of Sciences of the United States of America. PMID 29588420 DOI: 10.1073/Pnas.1715888115  0.752
2017 Orenstein Y, Puccinelli R, Kim R, Fordyce P, Berger B. Optimized Sequence Library Design for Efficient In Vitro Interaction Mapping. Cell Systems. 5: 230-236.e5. PMID 28957657 DOI: 10.1016/J.Cels.2017.07.006  0.317
2017 Nguyen HQ, Baxter BC, Brower K, Diaz-Botia CA, DeRisi JL, Fordyce PM, Thorn KS. Programmable Microfluidic Synthesis of Over One Thousand Uniquely Identifiable Spectral Codes. Advanced Optical Materials. 5. PMID 28936383 DOI: 10.1002/Adom.201600548  0.649
2017 Brower K, White AK, Fordyce PM. Multi-step Variable Height Photolithography for Valved Multilayer Microfluidic Devices. Journal of Visualized Experiments : Jove. PMID 28190039 DOI: 10.3791/55276  0.676
2015 Gerver RE, Gómez-Sjöberg R, Baxter BC, Thorn KS, Fordyce PM, Diaz-Botia CA, Helms BA, DeRisi JL. Correction: Programmable microfluidic synthesis of spectrally encoded microspheres. Lab On a Chip. 15: 1213. PMID 26038840 DOI: 10.1039/c5lc90018b  0.695
2015 Gerver RE, Gómez-Sjöberg R, Baxter BC, Thorn KS, Fordyce PM, Diaz-Botia CA, Helms BA, DeRisi JL. Correction: Programmable microfluidic synthesis of spectrally encoded microspheres. Lab On a Chip. 15: 1213. PMID 25619960 DOI: 10.1039/C5Lc90018B  0.688
2014 Pérez JC, Fordyce PM, Lohse MB, Hanson-Smith V, DeRisi JL, Johnson AD. How duplicated transcription regulators can diversify to govern the expression of nonoverlapping sets of genes. Genes & Development. 28: 1272-7. PMID 24874988 DOI: 10.1101/Gad.242271.114  0.495
2013 Hernday AD, Lohse MB, Fordyce PM, Nobile CJ, DeRisi JL, Johnson AD. Structure of the transcriptional network controlling white-opaque switching in Candida albicans. Molecular Microbiology. 90: 22-35. PMID 23855748 DOI: 10.1111/Mmi.12329  0.473
2013 Nelson CS, Fuller CK, Fordyce PM, Greninger AL, Li H, DeRisi JL. Microfluidic affinity and ChIP-seq analyses converge on a conserved FOXP2-binding motif in chimp and human, which enables the detection of evolutionarily novel targets. Nucleic Acids Research. 41: 5991-6004. PMID 23625967 DOI: 10.1093/Nar/Gkt259  0.665
2013 Lohse MB, Hernday AD, Fordyce PM, Noiman L, Sorrells TR, Hanson-Smith V, Nobile CJ, DeRisi JL, Johnson AD. Identification and characterization of a previously undescribed family of sequence-specific DNA-binding domains. Proceedings of the National Academy of Sciences of the United States of America. 110: 7660-5. PMID 23610392 DOI: 10.1073/Pnas.1221734110  0.58
2012 Fordyce PM, Pincus D, Kimmig P, Nelson CS, El-Samad H, Walter P, DeRisi JL. Basic leucine zipper transcription factor Hac1 binds DNA in two distinct modes as revealed by microfluidic analyses. Proceedings of the National Academy of Sciences of the United States of America. 109: E3084-93. PMID 23054834 DOI: 10.1073/Pnas.1212457109  0.56
2012 Gerver RE, Gómez-Sjöberg R, Baxter BC, Thorn KS, Fordyce PM, Diaz-Botia CA, Helms BA, DeRisi JL. Programmable microfluidic synthesis of spectrally encoded microspheres. Lab On a Chip. 12: 4716-23. PMID 23042484 DOI: 10.1039/C2Lc40699C  0.72
2012 Fordyce PM, Diaz-Botia CA, DeRisi JL, Gomez-Sjoberg R. Systematic characterization of feature dimensions and closing pressures for microfluidic valves produced via photoresist reflow. Lab On a Chip. 12: 4287-95. PMID 22930180 DOI: 10.1039/c2lc40414a  0.426
2010 Fordyce PM, Gerber D, Tran D, Zheng J, Li H, DeRisi JL, Quake SR. De novo identification and biophysical characterization of transcription-factor binding sites with microfluidic affinity analysis. Nature Biotechnology. 28: 970-5. PMID 20802496 DOI: 10.1038/Nbt.1675  0.586
2010 Fordyce PM, Gerber D, Tran D, Zheng J, Li H, Quake SR, DeRisi JL. A Microfluidics-Based Platform For Identification and Detailed Characterization of Transcription Factor Binding Sites Biophysical Journal. 98: 70a. DOI: 10.1016/j.bpj.2009.12.396  0.547
2006 Valentine MT, Fordyce PM, Block SM. Eg5 steps it up! Cell Division. 1: 31. PMID 17173688 DOI: 10.1186/1747-1028-1-31  0.472
2006 Valentine MT, Fordyce PM, Krzysiak TC, Gilbert SP, Block SM. Individual dimers of the mitotic kinesin motor Eg5 step processively and support substantial loads in vitro. Nature Cell Biology. 8: 470-6. PMID 16604065 DOI: 10.1038/Ncb1394  0.499
2004 Lang MJ, Fordyce PM, Engh AM, Neuman KC, Block SM. Simultaneous, coincident optical trapping and single-molecule fluorescence. Nature Methods. 1: 133-9. PMID 15782176 DOI: 10.1038/Nmeth714  0.734
2003 Lang MJ, Fordyce PM, Block SM. Combined optical trapping and single-molecule fluorescence. Journal of Biology. 2: 6. PMID 12733997 DOI: 10.1186/1475-4924-2-6  0.672
2003 Rosenfeld SS, Fordyce PM, Jefferson GM, King PH, Block SM. Stepping and stretching. How kinesin uses internal strain to walk processively. The Journal of Biological Chemistry. 278: 18550-6. PMID 12626516 DOI: 10.1074/Jbc.M300849200  0.485
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