2021

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

uPIC-M: efficient and scalable preparation of clonal single mutant libraries for high-throughput protein biochemistry.

Appel, M.J., Longwell, S.A., Morri, M., Neff, N., Herschlag, D., & Fordyce, P.M. bioRXiv (2021).

(web) (pdf)

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Revealing enzyme functional architecture via high-throughput microfluidic enzyme kinetics. 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.

Markin, C.J.*, Mokhtari, D.A.*, Sunden, F., Appel, M.J., Akiva, E., Longwell, S.A., Sabatti, C., Herschlag, D.‡, & Fordyce, P.M.‡, Science (2021). (web) (pdf)

• Science Perspective by Baumer & Whitehead.
• Discussion in Nature.
• Stanford News article.
• Chemical & Engineering News article.

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Structure-activity mapping of the peptide- and force-dependent landscape of T-cell activation Feng, Y. , Zhao, X., White, A.K., Garcia, K.C., & Fordyce, P.M. , bioRxiv (2021). ( web ) (pdf)

Structure-activity mapping of the peptide- and force-dependent landscape of T-cell activation

Feng, Y., Zhao, X., White, A.K., Garcia, K.C., & Fordyce, P.M., bioRxiv (2021).

(web) (pdf)

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

Fundamentals to function: quantitative and scalable approaches for measuring protein stability.

Atsavapranee, B.*, Stark, C.D.*, Sunden, S., Thompson, S.‡, & Fordyce, P.M.‡. Cell Systems (2021).

(web) (pdf)

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

MRBLE-pep measurements reveal accurate binding affinities for B56, a PP2A regulatory subunit.

Hein, J.B., Cyert, M.S., & Fordyce, P.M. ACS Measurement Science (in press).

(web) (pdf)

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2020

Featured
MRBLES 2.0: High-throughput generation of chemically functionalized spectrally and magnetically-encoded hydrogel beads using a simple single-layer microfluidic device. 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.

Feng, Y., White, A.K., Hein, J.B., Appel, E.A., & Fordyce, P.M., Microsystems & Nanoengineering (2020).

(web) (pdf) (OSF repository with all data and design files)

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High-throughput binding affinity measurements for mutations spanning a transcription factor-DNA interface reveal affinity and specificity determinants Aditham, A.K. , Markin, C.J.*, Mokhtari, D.A.*, DelRosso, N.V., & Fordyce, P.M. Cell Sy

High-throughput binding affinity measurements for mutations spanning a transcription factor-DNA interface reveal affinity and specificity determinants

Aditham, A.K., Markin, C.J.*, Mokhtari, D.A.*, DelRosso, N.V., & Fordyce, P.M. Cell Systems (2020).

(pdf) (web)

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Double emulsion picoreactors for high-throughput single-cell encapsulation and phenotyping via FACS. Brower, K.B.*, Khariton, M.* , Suzuki, P.H., Still, C. , Kim, G., Calhoun, S.G.K., Qi, L.S., Wang, B.*, & Fordyce, P.M.* Analytical C

Double emulsion picoreactors for high-throughput single-cell encapsulation and phenotyping via FACS.

Brower, K.B.*, Khariton, M.*, Suzuki, P.H., Still, C., Kim, G., Calhoun, S.G.K., Qi, L.S., Wang, B.*, & Fordyce, P.M.* Analytical Chemistry (2020).

(web) (pdf) (OSF repository with all data and design files)

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

Protocol for peptide synthesis on spectrally encoded beads for MRBLE-pep assays.

Hein, J.B., Nguyen, H.Q., Cyert, M., & Fordyce, P.M. Bio-protocols (2020).

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

Optimized double emulsion flow cytometry with high-throughput single-droplet isolation.

Brower, K.B., Carswell-Crumpton, C., Klemm, S., Cruz, B., Kim, G., Calhoun, S.G.K., Nichols, L, & Fordyce, P.M. Lab on a Chip (2020).

(PDF) (web) (OSF repository with all data and design files)

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

DeCoDe: degenerate codon design for complete protein-coding DNA libraries.

Shimko, T.C., Fordyce, P.M., & Orenstein, Y. Bioinformatics (2020).

(PDF) (web)

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2019

Featured
micrIO: An open-source autosampler and fraction collector for automated microfluidic input-output. Longwell, S.A., & Fordyce, P.M. Lab on a Chip (2019). ( PDF ) ( web )

micrIO: An open-source autosampler and fraction collector for automated microfluidic input-output.

Longwell, S.A., & Fordyce, P.M. Lab on a Chip (2019).

(PDF) (web)

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Why do long zinc finger proteins have short motifs? Zuo, Z., Billings, T., Walker, M., Petkov, P., Fordyce, P., & Stormo, G.D. bioRXiv (2019). ( PDF ) ( web )

Why do long zinc finger proteins have short motifs?

Zuo, Z., Billings, T., Walker, M., Petkov, P., Fordyce, P., & Stormo, G.D. bioRXiv (2019).

(PDF) (web)

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Quantitative mapping of protein-peptide affinity landscapes using spectrally encoded beads. Nguyen, H. Q., Roy, J., Harink, B., Damle, N. P., Latorraca, N. R., Baxter, B. C., Brower, K., Longwell, S., Kortemme, T., Thorn, K. S., Cyert, M. S.

Quantitative mapping of protein-peptide affinity landscapes using spectrally encoded beads.

Nguyen, H. Q., Roy, J., Harink, B., Damle, N. P., Latorraca, N. R., Baxter, B. C., Brower, K., Longwell, S., Kortemme, T., Thorn, K. S., Cyert, M. S., Fordyce, P.M eLife 8 (2019): e40499

(PDF) (Web) (OSF repository with all data)

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Live imaging of Aiptasia larvae, a model system for coral and anemone bleaching, using a simple microfluidic device Treuren, W. V.*, Brower, K. K*. , Labanieh, L., Hunt, D., Lensch, S., Cruz, B ., Cartwright, H. N., Tran, C., Fordyce, P. M.

Live imaging of Aiptasia larvae, a model system for coral and anemone bleaching, using a simple microfluidic device

Treuren, W. V.*, Brower, K. K*., Labanieh, L., Hunt, D., Lensch, S., Cruz, B., Cartwright, H. N., Tran, C., Fordyce, P. M. Scientific reports 9 (2019).

(PDF) (Web)

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An open-source software analysis package for Microspheres with Ratiometric Barcode Lanthanide Encoding (MRBLEs) Harink, B., Nguyen, H., Thorn, K., Fordyce, P. M. PLOS/ONE (PDF) (Web) ( OSF Repository ).

An open-source software analysis package for Microspheres with Ratiometric Barcode Lanthanide Encoding (MRBLEs)

Harink, B., Nguyen, H., Thorn, K., Fordyce, P. M. PLOS/ONE

(PDF) (Web) (OSF Repository).

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2018

Featured
Diversification of DNA binding specificities enabled SREBP transcription regulators to expand the repertoire of cellular functions that they govern in fungi. Toledo, V. D. O., Puccinelli, R., Fordyce, P.M., and Perez, J.C. PLoS Genetics ( in

Diversification of DNA binding specificities enabled SREBP transcription regulators to expand the repertoire of cellular functions that they govern in fungi.

Toledo, V. D. O., Puccinelli, R., Fordyce, P.M., and Perez, J.C. PLoS Genetics (in press).

(PDF) (Web)

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

BET-seq: Binding energy topographies revealed by microfluidics and high-throughput sequencing.

Aditham, A.K., Shimko, T.C., and Fordyce, P.M. Methods in Cell Biology - Microfluidics on a Molecular Scale (2018).

(PDF) (web).

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Satb1 integrates DNA sequence, shape, motif density and torsional stress to differentially bind targets in nucleosome-dense regions. Ghosh, R.P., Shi, Q., Yang, L., Reddick, M.P., Nikitina, T., Zhurkin, V.B., Fordyce, P. , Stasevich, T.J., Chan

Satb1 integrates DNA sequence, shape, motif density and torsional stress to differentially bind targets in nucleosome-dense regions.

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., preprint on bioRXiv 10/2018; doi:10.1101/450262. (web)

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High-throughput chromatin accessibility profiling at single-cell resolution. Mezger, A., Klemm, S., Mann, I., Brower, K. , Mir, A., Bostick, M., Farmer, A., Fordyce, P. , Linnarsson, S., & Greenleaf, W.; Nat. Comm. (2018) ( pdf ) ( web

High-throughput chromatin accessibility profiling at single-cell resolution. Mezger, A., Klemm, S., Mann, I., Brower, K., Mir, A., Bostick, M., Farmer, A., Fordyce, P., Linnarsson, S., & Greenleaf, W.; Nat. Comm. (2018)

(pdf) (web) (bioRXiv doi: 10.1101/310284)

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Discovering epistatic feature interactions from neural network models of regulatory DNA sequences. Greenside, P.G., Shimko, T. , Fordyce, P. , & Kundaje, A.; preprint on bioRXiv (04/17/2018); doi: 10.1101/302711 ( web )

Discovering epistatic feature interactions from neural network models of regulatory DNA sequences. Greenside, P.G., Shimko, T., Fordyce, P., & Kundaje, A.; preprint on bioRXiv (04/17/2018); doi: 10.1101/302711 (web)

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Comprehensive, high-resolution binding energy landscapes reveal context dependencies of transcription factor binding. Le, D.D., Shimko, T.C., Aditham, A.K., Keys, A.M. , Orenstein, Y., and Fordyce, P.M . PNAS (3/27,8) ( web ) ( pdf ) (preprin

Comprehensive, high-resolution binding energy landscapes reveal context dependencies of transcription factor binding. Le, D.D., Shimko, T.C., Aditham, A.K., Keys, A.M., Orenstein, Y., and Fordyce, P.M. PNAS (3/27,8)

(web) (pdf) (preprint in bioRXiv (9/26/17)

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2017

Featured
An open-Source, programmable pneumatic setup for operation and automated control of single-and multi-Layer microfluidic devices. Brower, K., Puccinelli, R., Markin, C., Shimko, T., Longwell, S., Cruz, B. , Gomez-Sjoberg, R, Fordyce, P. ; Hardware

An open-Source, programmable pneumatic setup for operation and automated control of single-and multi-Layer microfluidic devices. Brower, K., Puccinelli, R., Markin, C., Shimko, T., Longwell, S., Cruz, B., Gomez-Sjoberg, R, Fordyce, P.; HardwareX (2017) (web); preprint on bioRXiv (2017) (web).
OSF repository available here.

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Peptide library synthesis on spectrally encoded beads for multiplexed protein/peptide bioassays. Nguyen, H.Q., Brower, K., Harink, B. , Baxter, B, Thorn, K., Fordyce, P. Proc. SPIE 10061, Microfluidics, BioMEMS, and Medical Microsystems XV, 1

Peptide library synthesis on spectrally encoded beads for multiplexed protein/peptide bioassays. Nguyen, H.Q., Brower, K., Harink, B., Baxter, B, Thorn, K., Fordyce, P. Proc. SPIE 10061, Microfluidics, BioMEMS, and Medical Microsystems XV, 100610Z (2017) (web).

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Joker de Bruijn: Sequence libraries to cover all k-mers using joker characters. Ornenstein, Y., Puccinelli, R. , Kim, R., Fordyce, P. , and Berger, B.; Cell Systems (2017) ( web ).

Joker de Bruijn: Sequence libraries to cover all k-mers using joker characters. Ornenstein, Y., Puccinelli, R., Kim, R., Fordyce, P., and Berger, B.; Cell Systems (2017) (web).

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2016

Featured
Multi-step variable height photolithography for valved multilayer microfluidic devices.  Brower, K.*, White, A.K.*, & Fordyce, P.M.   Journal of Visualized Experiments ( in press ). (* denotes equal authorship).

Multi-step variable height photolithography for valved multilayer microfluidic devices. Brower, K.*, White, A.K.*, & Fordyce, P.M. Journal of Visualized Experiments (in press). (* denotes equal authorship).

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Programmable microfluidic synthesis of over one thousand uniquely identifiable spectral codes. Nguyen, H.Q., Baxter, B.C., Brower, K., Diaz-Botia, C.A., DeRisi, J.L, Fordyce, P.M.* , and Thorn., K.S.*  Advanced Optical Materials (2016). (*

Programmable microfluidic synthesis of over one thousand uniquely identifiable spectral codes. Nguyen, H.Q., Baxter, B.C., Brower, K., Diaz-Botia, C.A., DeRisi, J.L, Fordyce, P.M.*, and Thorn., K.S.* Advanced Optical Materials (2016). (* denotes co-corresponding authors).

(pdf) (web)

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2014

Featured
How duplicated transcription regulators can diversify to govern the expression of non overlapping sets of genes. Perez, J.C., Fordyce, P.M. , Lohse, M.B., Hanson-Smith, V., DeRisi, J.L., & Johnson, A.D.  Genes & Development (2014).

How duplicated transcription regulators can diversify to govern the expression of non overlapping sets of genes. Perez, J.C., Fordyce, P.M., Lohse, M.B., Hanson-Smith, V., DeRisi, J.L., & Johnson, A.D. Genes & Development (2014).

(pdf) (web)

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Hydraulic expulsion of tumbu fly larvae. Dybbro, E., Fordyce, P. , Ponte, M., & Arron, S.T.  JAMA Derm.  (2014). ( pdf ) ( web )

Hydraulic expulsion of tumbu fly larvae. Dybbro, E., Fordyce, P., Ponte, M., & Arron, S.T. JAMA Derm. (2014).

(pdf) (web)

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2013

Featured
Structure of the transcriptional network controlling white-opaque switching in Candida albicans . Hernday, A.D., Lohse, M.B.*, Fordyce, P.M.* , Nobile, C.J., DeRisi, J.L., & Johnson, A.D.  Molecular Microbiology (2013). (* denotes equa

Structure of the transcriptional network controlling white-opaque switching in Candida albicans. Hernday, A.D., Lohse, M.B.*, Fordyce, P.M.*, Nobile, C.J., DeRisi, J.L., & Johnson, A.D. Molecular Microbiology (2013). (* denotes equal authorship).

(pdf) (web)

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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.  Nelson, C.S., Fuller, C.K.,  Fordyce, P.M.,  Greninger, A.L.,

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.  Nelson, C.S., Fuller, C.K., Fordyce, P.M., Greninger, A.L., Li, H., & DeRisi, J.L. Nucleic Acids Research (2013).

(pdf) (web)

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Identification and characterization of a previously undescribed family of sequence-specific DNA-binding domains. Lohse, M.B., Hernday, A.D., Fordyce, P.M. , Noiman, L., Sorrells, T.R., Hanson-Smith, V., Nobile, C., DeRisi, J.L., & Johnson, A.

Identification and characterization of a previously undescribed family of sequence-specific DNA-binding domains. Lohse, M.B., Hernday, A.D., Fordyce, P.M., Noiman, L., Sorrells, T.R., Hanson-Smith, V., Nobile, C., DeRisi, J.L., & Johnson, A.D. PNAS (2013).

(pdf) (web)

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2012

Featured
Basic leucine zipper transcription factor Hac1 binds DNA in two distinct modes as revealed by microfluidic analyses.   Fordyce, P.M.,  Pincus, D., Kimmig, P., Nelson, C.S., El-Samad, H., Walter, P., & DeRisi, J.L.  PNAS (2012).

Basic leucine zipper transcription factor Hac1 binds DNA in two distinct modes as revealed by microfluidic analyses. Fordyce, P.M., Pincus, D., Kimmig, P., Nelson, C.S., El-Samad, H., Walter, P., & DeRisi, J.L. PNAS (2012).

(pdf) (web)

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Programmable microfluidic synthesis of spectrally encoded microspheres.  Gerver, R.E.*, Gomez-Sjoberg, R.*, Baxter, B.C.*, Thorn, K.S.*, Fordyce, P.M.* , Diaz-Botia, C.A., Helms, B.A., & DeRisi, J.L.  Lab on a Chip (2012). (* denote

Programmable microfluidic synthesis of spectrally encoded microspheres. Gerver, R.E.*, Gomez-Sjoberg, R.*, Baxter, B.C.*, Thorn, K.S.*, Fordyce, P.M.*, Diaz-Botia, C.A., Helms, B.A., & DeRisi, J.L. Lab on a Chip (2012). (* denotes equal authorship, author order was determined by random draw).

(pdf) (web)

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

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

(pdf) (web)

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2011

Featured
Integrating systems biology data to yield functional genomics insights. Fordyce, P. , & Ingolia, N.  Genome Biology (2011). ( pdf ) ( web )

Integrating systems biology data to yield functional genomics insights. Fordyce, P., & Ingolia, N. Genome Biology (2011).

(pdf) (web)

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2010

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De novo identification and biophysical characterization of transcription factor binding with microfluidic affinity analysis. Fordyce, P.M.* , Gerber, D.*, Tran, D., Zheng, J., Li, H., DeRisi, J.L., & Quake, S.R.  Nature Biotechnolog

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

(pdf) (web)

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2008

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Advances in surface-based assays for single molecules.  Fordyce, P.M.*,  Valentine, M.T.*, & Block, S.M. in " ingle-Molecule Techniques: A Laboratory Manual"  (Cold Spring Harbor Monograph Series) (2008). (* denotes equal author

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

(pdf) (web)

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2006

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Eg5 steps it up!  Valentine, M.T., Fordyce, P.M. , & Block, S.M.  Cell Division (2006). ( pdf ) ( web )

Eg5 steps it up! Valentine, M.T., Fordyce, P.M., & Block, S.M. Cell Division (2006).

(pdf) (web)

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Individual dimers of the mitotic kinetin Eg5 step processively and support substantial loads in vitro .  Valentine, M.T.*, Fordyce, P.M.* , Krzysiak, T.C., Gilbert, S.P., & Block, S.M.  Nature Cell Biology (2006). (* denotes equal

Individual dimers of the mitotic kinetin Eg5 step processively and support substantial loads in vitro. Valentine, M.T.*, Fordyce, P.M.*, Krzysiak, T.C., Gilbert, S.P., & Block, S.M. Nature Cell Biology (2006). (* denotes equal authorship)

(pdf) (web)

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2004

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

Simultaneous, coincident optical trapping and single-molecule fluorescence. Lang, M.J.*, Fordyce, P.M.*, Engh, A.M., Neuman, K.C., & Block, S.M. Nature Methods (2004). (* denotes equal authorship).

(pdf) (web)

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2003

Featured
Combined optical trapping and single-molecule fluorescence.  Lang, M.J., Fordyce, P.M. , & Block, S.M.  Journal of Biology (2003). ( pdf ) ( web )

Combined optical trapping and single-molecule fluorescence. Lang, M.J., Fordyce, P.M., & Block, S.M. Journal of Biology (2003).

(pdf) (web)

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Stepping and stretching: how kinesis uses external strain to step processively.  Rosenfeld, S.S., Fordyce, P.M. , Jefferson, G.M., King, P.H., & Block, S.M.  Journal of Biological Chemistry (2003). ( pdf ) ( web )

Stepping and stretching: how kinesis uses external strain to step processively. Rosenfeld, S.S., Fordyce, P.M., Jefferson, G.M., King, P.H., & Block, S.M. Journal of Biological Chemistry (2003).

(pdf) (web)

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2001

Featured
Search for the decay KL -> pi(0)e+e-.  Alavi-Harati, A.,  et al. Physical Review Letters (2001). ( web )

Search for the decay KL -> pi(0)e+e-. Alavi-Harati, A., et al. Physical Review Letters (2001).

(web)

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Measurement of the branching ratio of the decay KL -> e+e-gammagamma.  Alavi-Harati,  et al.   Physical Review D (2001). ( web )

Measurement of the branching ratio of the decay KL -> e+e-gammagamma. Alavi-Harati, et al. Physical Review D (2001).

(web)

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