The Fordyce Lab is committed to providing full access to all data, design files, software, and protocols associated with an experiment. These are available at the OSF repository link after each citation.

2024

DelRosso, N.*, Suzuki, P.H.*, Griffith, D., Lotthammer, J.M., Novak, B., Kocalar, S., Sheth, M.U., Holehouse, A.S., Bintu, L.‡, Fordyce, P.M.‡, “High-throughput affinity measurements of direct interactions between activation domains and co-activators”, bioRXiv (2024).

Lee, B., Sunden, F., Miller, M., Pak, B., Krebber, A., Lutz, S., & Fordyce, P.M., “Hydrophilic/omniphobic droplet arrays for high-throughput and quantitative enzymology”, bioRXiv (2024).

Thompson, S.*, Zhang, Y., Yang, Z., Nichols, L.A., & Fordyce, P.M.*, “FACS-Sortable Picoreactors for Ultra High-throughput Screening of Catalysts in Biphasic Environments”, bioRXiv (2024). (pdf) (web) (OSF repository) .

Lashkaripour, A.*, McIntyre, D.P., Calhoun, S.G.K., Krauth, K., Densmore, D.M., & Fordyce, P.M.*, “Design automation of microfluidic single and double emulsion droplets with machine learning”, Nature Communications (2024). (pdf) (web) (OSF repository) (bioRXiv).

Hastings, R.*, Aditham, A.*, DelRosso, N., Suzuki, P., & Fordyce, P.M., “High-throughput thermodynamic and kinetic measurements of transcription factor/DNA mutations reveal how conformational heterogeneity can shape motif selectivity”, bioRXiv (2024).

2023

McIntyre, D., Lashkaripour, A., Arguijo, D., Fordyce, P.M., & Densmore, D., “Versatility and stability optimization of flow-focusing droplet generators via quality metric-driven design automation”, Lab on a Chip (in press). (pdf) (web).

Hein, J.B., Nguyen, H.T., Garvanska, D., Nasa, I., Feng, Y., Lopez-Mendez, B., Davey, N.E., Kettenbach, A., Fordyce, P.M.*, Nilsson, J., “Global substrate identification and high throughput in vitro dephosphorylation reactions uncover PP1 and PP2A-B55 specificity principles”, bioRXiv (2023). (pdf) (web) (OSF repository).

Alexandari, A.M., Horton, C.A., Shrikumar, A., Shah, N., Li, E., Weilert, M., Pufall, M.A., Zeitlinger, J., Fordyce, P.M.*, & Kundaje, A.*, “De novo distillation of thermodynamic affinity from deep learning regulatory sequence models of in vivo protein-DNA binding”, bioRXiv (2023). (pdf) (web).

Horton, C.A., Alexandari, A.M., Hayes, M.G.B., Marklund, E., Schaepe, J.M., Aditham, A.K., Shah, N., Suzuki, P., Shrikumar, A., Afek, A., Greenleaf, W.J., Gordan, R., Zeitlinger, J., Kundaje, A., & Fordyce, P.M., “Short tandem repeats bind transcription factors to tune eukaryotic gene expression”, Science (2023). (pdf) (web) (zenodo) (OSF repository) (bioRXiv).

Sockell, A., Wong, W., Longwell, S., Vu, T., Karlsson, K., Mokhtari, D., Schaepe, J., Lo, Y.-H., Cornelius, V., Kuo, C., Van Valen, D., Curtis, C.*, & Fordyce, P.M.*, “A microwell platform for high-throughput longitudinal phenotyping and selective retrieval of organoids”, Cell Systems (2023). (pdf) (web) (OSF repository) (bioRXiv).

McCully, A.L., Yao, M.L., Brower, K.K., Fordyce, P.M., & Spormann, A.M., “Double emulsions as a high-throughput enrichment and isolation platform for slower-growing microbes”, ISME communications (2023). (pdf) (web) (bioRXiv).

DelRosso, N., Tycko, J., Suzuki, P., Andrews, C., Aradhana, Mukund, A., Liongson, I., Ludwig, C., Spees, K., Fordyce, P.M., Bassik, M.C., & Bintu, L. “Large-scale mapping and systematic mutagenesis of human transcriptional effector domains”, Nature (2023). (pdf) (web) (bioRXiv).

Zuo, Z., Billings, T., Walker, M., Petkov, P., Fordyce, P.M., & Stormo, G. “On the dependent recognition of some zinc finger proteins”, Nuc. Acids Res. (2023). (pdf) (web) (bioRXiv).

Stapleton, L.M., Farry, J.M., Lucian, H.J., Wang, H., Paulson, M.J., Totherow, K.P., Roth, G.A., Brower, K.K., Fordyce, P.M., Appel, E.A.*, & Woo, Y.J.* “Microfluidic encapsulation of photosynthetic cyanobacteria in hydrogel microparticles augments oxygen delivery to rescue ischemic myocardium”, J. Biosci. Bioeng. (2023). (pdf) (web).

Khariton, M.*, McClune, C.J.*, Brower, K.K., Klemm, S., Sattely, E., Fordyce, P.M.‡, & Wang, B.‡, “Alleviating cell lysate-induced inhibition to enable RT-PCR from single cells in picoliter volume double emulsion droplets”, Anal. Chem. (2023). (pdf) (web) (bioRXiv).

2022

Li, Q., van de Groep, J., White, A.K., Song, J.-H., Longwell, S., Fordyce, P.M., Quake, S.R., Kik, P., & Brongersma, M. “Metasurface optofluidics for dynamic control of light fields”, Nature Nanotechnol. (2022). (pdf) (web).

McIntyre, D., Lashkaripour, A., Fordyce, P.M., & Densmore, D. “Machine learning for microfluidic design and control”, Lab on a Chip (2022). (pdf) (web).

Feng, Y., Zhao, X., White, A.K., Garcia, K.C., & Fordyce, P.M., “Structure-activity mapping of the peptide- and force-dependent landscape of T-cell activation”, Nature Methods (2022). (pdf) (web) (OSF repository) (bioRXiv).

Calhoun, S.G.K., Brower, K.K., Suja, V.C., Kim, G., Wang, N., McCully, A.L., Kusumaatmaja, H., Fuller, G.G., & Fordyce, P.M. “Systematic characterization of double emulsion droplets for biological applications”, Lab on a Chip (2022). (pdf) (web) (OSF repository) (bioRXiv).

Zhao, X., Kolawole, E., Chan, W., Feng, Y., Yang, X., Jude, K., Sibener, L., Fordyce, P.M., Germain, R., Evavold, B., & Garcia, K.C. “Engineering high-sensitivity T cell receptors with physiological affinities through catch bond recruitment”, Science (2022). (pdf) (web).

Fannjiang, C., Olivas, M., Greene, E.R., Markin, C.J., Wallace, B., Krause, B., Pinney, M., Fraser, J., Fordyce, P., Madani, A., & Naik, N. “Designing active and thermostable enzymes with sequence-only predictive models”, NeurIPs (2022). (web).

2021

Appel, M.J., Longwell, S.A., Morri, M., Neff, N., Herschlag, D., & Fordyce, P.M. “uPIC-M: efficient and scalable preparation of clonal single mutant libraries for high-throughput protein biochemistry”, ACS Omega (2021). (pdf) (web) (OSF repository) (bioRXiv).

Markin, C.J.*, Mokhtari, D.A.*, Sunden, F., Appel, M.J., Akiva, E., Longwell, S.A., Sabatti, C., Herschlag, D.*, & Fordyce, P.M.*. “Revealing enzyme functional architecture via high-throughput microfluidic enzyme kinetics”, Science (2021). (pdf) (web) (OSF repository) (bioRXiv).

Hein, J.B., Cyert, M.S., & Fordyce, P.M. “MRBLE-pep measurements reveal accurate binding affinities for B56, a PP2A regulatory subunit”, ACS Measurement Science (2021). (pdf) (web) (raw data) (bioRXiv).

Aditham, A.K., Markin, C.J., Mokhtari, D.A., DelRosso, N.V., & Fordyce, P.M. “High-throughput binding affinity measurements for mutations spanning a transcription factor-DNA interface reveal affinity and specificity determinants”, Cell Systems (2021). (pdf) (web) (OSF repository) (bioRXiv).

Mokhtari, D.A.*, Appel, M.J.*, Fordyce, P.M., & Herschlag, D. “High-throughput and quantitative enzymology in the genomic era”, Curr. Op. Struct. Biol. (2021). (pdf) (web).

Atsavapranee, B., Stark, C.D., Sunden, F., Thompson, S., and Fordyce, P.M. “Fundamentals to function: quantitative and scalable approaches for measuring protein stability”, Cell Systems (2021). (pdf) (web).

2020

Feng, Y., White, A.K., Hein, J.B., Appel, E.A., & Fordyce, P.M “MRBLES 2.0: High-throughput generation of chemically functionalized spectrally and magnetically encoded hydrogel beads using a simple single-layer microfluidic device”, Microsystems & Nanoengineering (2020). (pdf) (web) (OSF repository) (bioRXiv).

Brower, K.K.*, Khariton, M.*, Suzuki, P., Still, C., Kim, G., Calhoun, S., Qi, S., Wang, B.*, & Fordyce, P.M.*. “Double emulsion picoreactors for high-throughput single-cell encapsulation and phenotyping via FACS”, Analytical Chemistry (2020). (pdf) (web) (OSF repository) (bioRXiv version) .

Hein, J.B., Nguyen, H.Q., Cyert, M., & Fordyce, P.M. “Protocol for peptide synthesis on spectrally encoded beads for MRBLE-pep assays”. Bio-protocols (2020). (pdf) (web).

Brower, K.K., Carswell-Crumpton, C., Klemm, S., Cruz, B., Kim, G., Calhoun, S., Nichols, L., & Fordyce, P.M. “Optimized double emulsion flow cytometry with high-throughput single droplet isolation”. Lab on a Chip (2020). (pdf) (web) (OSF repository) (bioRXiv).

Shimko, T., Fordyce, P.M., & Orenstein, Y. “DeCoDe: degenerate codon design for complete protein-coding DNA libraries”, Bioinformatics (2020). (pdf) (web) (bioRXiv).

2019

Longwell, S., & Fordyce, P.M. “micrIO: An open-source autosampler and fraction collector for automated microfluidic IO”, Lab on a Chip (2019). (pdf) (web) (github) (bioRXiv).

Nguyen, H.Q., Roy, J., Harink, B., Damle, N., Baxter, B., Brower, K., Kortemme, T., Thorn, K., Cyert, M., & Fordyce, P.M. “High-throughput, quantitative mapping of protein-peptide affinity landscapes using spectrally encoded beads”, eLife (2019). (pdf) (web) (OSF repository) (bioRXiv).

Treuren, W.V.*, Brower, K.*, Labanieh, L., Hunt, D., Lensch, S., Cruz, B., Cartwright, H.N., Tran, C., and Fordyce, P. “Live imaging of Aiptasia larvae, a model system for studying coral bleaching, using a simple microfluidic device”, Scientific Reports (2019). (pdf) (web) (OSF repository) (bioRXiv) (device design files)

Ghosh, R.P., Shi, Q., Yang, L., Reddick, M.P., Nikitina, T., Zhurkin, V.B., Fordyce, P., Stasevich, T.J., Chang, H.Y., Greenleaf, W.J., and Liphardt, J.T. “Satb1 integrates DNA sequence, shape, motif density, and torsional stress to differentially bind targets in nucleosome-dense regions”, Nature Communications (2019). (pdf) (web) (bioRXiv).

Harink, B., Nguyen, H.Q., Thorn, K., and Fordyce, P.M. “An open-source software package for Microspheres with Ratiometric Barcode Lanthanide Encoding (MRBLEs)”, PLoS ONE (2019). (pdf) (web) (OSF repository) (github) (bioRXiv).

2018

del Olmo Toledo, V., Puccinelli, R., Fordyce, P.M., & Perez, J.C. “Diversification of DNA binding specificities enabled SREBP transcription regulators to expand the repertoire of cellular functions that they govern in fungi”, PLoS Genetics (2018). (pdf) (web).

Greenside, P.G., Shimko, T., Fordyce, P.M., & Kundaje, A. “Discovering epistatic feature interactions from neural network models of regulatory DNA sequences”, Bioinformatics (2018). (pdf) (web).

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”, Nat. Comm. (2018). (pdf) (web).

Le, D.D., Shimko, T.C., Aditham, A.K., Keys, A.M., Orenstein, Y., and Fordyce, P.M. “Comprehensive, high-resolution binding energy landscapes reveal context dependencies of transcription factor binding”, PNAS (2018). (pdf) (web) (figshare) (github) (bioRXiv).

Brower, K., Puccinelli, R., Markin, C.J., Shimko, T.C., Longwell, S.A., Cruz, B., Gomez-Sjoberg, R., and Fordyce, P.M. “An open-source, programmable pneumatic setup for operation and automated control of single- and multi-layer microfluidic devices”, HardwareX (2018). (pdf) (web) (OSF repository) (bioRXiv).

Aditham, A.K., Shimko, T.C., and Fordyce, P.M., “BET-seq: Binding energy topographies revealed by microfluidics and high-throughput sequencing”, Methods in Cell Biology – Microfluidics on a Molecular Scale (2018). (pdf) (web).

2017

Orenstein, Y., Puccinelli, R., Kim, R., Fordyce, P.M., & Berger, B. “Optimized sequence library design for efficient in vitro interaction mapping”, Cell Systems 5:230-236 (2017). (pdf) (web).

Brower, K.*, White, A.K., and Fordyce, P.M. “Multi-step variable height photolithography for valved multilayer microfluidic devices”, Journal of Visualized Experiments 119, e55276 (2017). (* denotes equal authorship). (pdf) (web).

Nguyen, H.Q., Baxter, B.C., Brower, K., Diaz-Botia, C.A., DeRisi, J.L, Fordyce, P.M.*, and Thorn, K.S.*. “Programmable microfluidic synthesis of over one thousand uniquely identifiable spectral codes”, Advanced Optical Materials 5(3), 1600548 (2017). (* denotes co-corresponding authors). (pdf) (web).

Doudna, J., Bar-Ziv, R., Elf, J., Noireaux, V., Berro, J., Saiz, L., Vavylonis, D., Faulon, J.L., and Fordyce, P. “How will kinetics and thermodynamics inform our future efforts to understand and build biological systems?”, Cell Systems 4:144-146 (2017). (pdf) (web).

Nguyen, H.Q, Brower. K., Harink, B., Baxter, B., Thorn, K.S., & Fordyce, P.M. “Peptide library synthesis on spectrally encoded beads for multiplexed protein/peptide bioassays”, Progress in Biomedical Optics and Imaging – Proceedings of SPIE 10061, 100610Z (2017). (pdf) (web).

2014

Perez, J.C., Fordyce, P.M., Lohse, M.B., Hanson-Smith, V., DeRisi, J.L., and Johnson, A.J. “How duplicated transcription regulators can diversify to govern the expression of non-overlapping sets of genes”, Genes & Development 28:1272-7 (2014). (pdf) (web).

Dybbro, E., Fordyce, P.M., Ponte, M., and Arron, S.T. “Hydraulic expulsion of Tumbu fly larvae”, JAMA Derm. 150:791-2 (2014). (pdf) (web).

2013

Lohse, M.B., Hernday, A.D., Fordyce, P.M., Noiman, L., Sorrells, T.R., Hanson-Smith, V., Nobile, C.J., DeRisi, J.L. and Johnson, A.D. “Identification and characterization of a recently evolved, novel class of sequence-specific DNA binding domains”, PNAS 110:7660-5 (2013). (pdf) (web).

Hernday, A.D., Lohse, M.B.*, Fordyce, P.M.*, Nobile, C.J., DeRisi, J.L., and Johnson, A.D. “Structure of the transcriptional network controlling white-opaque switching in Candida albicans”, Molecular Microbiology [Epub ahead of print] (2013).  (* denotes equal authorship). (pdf) (web).

Nelson, C.S., Fuller, C.K., Fordyce, P.M., Greninger, A.L., Li, H., and DeRisi, J.L. “Microfluidic affinity and ChIP-seq analyses converge on a conserved FOXP2 binding motif that enables the detection of evolutionarily novel regulatory targets”, Nucleic Acids Research, 41:5991-6004 (2013). (pdf) (web).

2012

Fordyce, P.M., Pincus, D., Kimmig, P., Nelson, C., El-Samad, H., Walter, P., and DeRisi, J.L. “Basic leucine zipper transcription factor Hac1 binds DNA in two distinct modes as revealed by microfluidic analyses”, PNAS 109:E3084-93 (2012). (pdf) (web).

Gerver, R.E.*, Gomez-Sjoberg, R.*, Baxter, B.C.*, Thorn, K.S.*, Fordyce, P.M.*, Diaz-Botia, C.A., Helms, B.A., and DeRisi, J.L. “Programmable microfluidic synthesis of spectrally encoded microspheres”, Lab on a Chip 12:4716-23 (2012). (* denotes equal authorship; author order was chosen by random draw). (pdf) (web).

Fordyce, P.M., Diaz-Botia, C.A., Gomez-Sjoberg, R., and DeRisi, J.L. “Systematic characterization of feature dimensions and closing pressures for microfluidic valves produced via photoresist reflow”,  Lab on a Chip 12:4287-95 (2012). (pdf) (web).

2011

Fordyce, P., and Ingolia, N. “Integrating systems biology data to yield functional genomics insights”, Genome Biology 12:302 (2011). (pdf) (web).

2010

Fordyce, P.M.*, Gerber, D.*, Tran, D., Zheng, J., Li, H., DeRisi, J.L., and Quake, S.R., “De novo identification and biophysical characterization of transcription factor binding with microfluidic affinity analysis”, Nature Biotechnology 28:970-5 (2010). (* denotes equal authorship). (pdf) (web).

2008

Fordyce, P.M.*, Valentine, M.T.*, and Block, S.M., “Advances in surface-based assays for single molecules”, in “Single-Molecule Techniques: A Laboratory Manual” (Cold Spring Harbor Monograph Series, 2008).  (* denotes equal authorship). (pdf)

2006

Valentine, M.T.*, Fordyce, P.M.*, Krzysiak, T.C., Gilbert, S.P., and Block, S.M., “Individual dimers of the mitotic kinesin motor Eg5 step processively and support substantial loads in vitro”, Nature Cell Biology 8:470-476 (2006). (* denotes equal authorship). (pdf) (web).

Valentine, M.T., Fordyce, P.M., and Block, S.M., “Eg5 steps it up!”, Cell Division 1:31-39 (2006). (pdf) (web).

2004

Lang, M.J.*, Fordyce, P.M.*, Engh, A.M., Neuman, K.C., and Block, S.M., “Simultaneous, coincident optical trapping and single-molecule fluorescence”, Nature Methods 1:133-139 (2004). (* denotes equal authorship). (pdf) (web).

2003

Rosenfeld, S.S., Fordyce, P.M., Jefferson, G.M., King, P.H., and Block, S.M., “Stepping and stretching – how kinesin uses internal strain to walk processively”, Journal of Biological Chemistry 278:18550-18556 (2003). (pdf) (web).

Lang, M.J., Fordyce, P.M., and Block, S.M., “Combined optical trapping and single-molecule fluorescence”, Journal of Biology 2:6-10 (2003). (pdf) (web).

2001

Alavi-Harati, A. et al., “Search for the decay KL®p0e+e-“, Physical Review Letters 86:397-401 (2001).

Alavi-Harati, A., et al., “Measurement of the branching ratio of KL®e+e-gg”, Physical Review D 64:1-4 (2001).