Polly Fordyce, Ph.D. - Publications

Stanford University, Palo Alto, CA 
biophysics, single molecules, motor proteins, transcription

34 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
2020 Hein JB, Nguyen HQ, Cyert M, Fordyce PM. Protocol for Peptide Synthesis on Spectrally Encoded Beads for MRBLE-pep Assays. Bio-Protocol. 10: e3669. PMID 33659339 DOI: 10.21769/BioProtoc.3669  0.52
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  1
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  0.32
2020 Brower KK, Carswell-Crumpton C, Klemm S, Cruz B, Kim G, Calhoun SGK, Nichols L, Fordyce PM. Double emulsion flow cytometry with high-throughput single droplet isolation and nucleic acid recovery. Lab On a Chip. PMID 32417874 DOI: 10.1039/d0lc00261e  0.32
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  1
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  0.8
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  0.8
2019 Van Treuren W, Brower KK, Labanieh L, Hunt D, Lensch S, Cruz B, Cartwright HN, Tran C, Fordyce PM. Live imaging of Aiptasia larvae, a model system for coral and anemone bleaching, using a simple microfluidic device. Scientific Reports. 9: 9275. PMID 31239506 DOI: 10.1038/S41598-019-45167-2  0.32
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  0.32
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  1
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  1
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  0.52
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  1
2017 Orenstein Y, Kim R, Fordyce P, Berger B. Joker de Bruijn: Sequence Libraries to Cover All -mers Using Joker Characters. Research in Computational Molecular Biology : ... Annual International Conference, Recomb ... : Proceedings. Recomb (Conference : 2005-). 10229: 389-390. PMID 29707702 DOI: 10.1007/978-3-319-56970-3  0.72
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  0.72
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  0.56
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  0.52
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  0.6
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  0.56
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  0.6
2014 Dybbro E, Fordyce P, Ponte M, Arron ST. Hydraulic expulsion of tumbu fly larvae. Jama Dermatology. 150: 791-2. PMID 24647598 DOI: 10.1001/Jamadermatol.2013.9571  0.6
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  0.6
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  0.6
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  0.6
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  0.6
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  0.6
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  0.6
2011 Fordyce P, Ingolia N. Integrating systems biology data to yield functional genomics insights. Genome Biology. 12: 302. PMID 21247510 DOI: 10.1186/Gb-2011-12-1-302  0.6
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  0.6
2006 Valentine MT, Fordyce PM, Block SM. Eg5 steps it up! Cell Division. 1: 31. PMID 17173688 DOI: 10.1186/1747-1028-1-31  0.6
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  0.6
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  0.6
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  0.6
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  0.6
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