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)
  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 ).
  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 )
  An open-source software analysis package for Microspheres with Ratiometric Barcode Lanthanide Encoding (MRBLEs).     Harink, B. ,  Nguyen, H. , Thorn, K., and  Fordyce, P.M. , preprint on bioRXiv 08/27/18; doi: 10.1101/402560; ( web ).
  Live imaging of Aiptasia larvae, a model system for studying coral bleaching, using a simple microfluidic device.  Treuren, W.V.* , Brower, K. *, Labanieh, L., Hunt D., Lensch, S,  Cruz., B ., Cartwright, H.N., Tran, C., &  Fordyce, P.;   BioRXiv  (2018)   (*denotes equal authorship)    ( pdf ) ( web ) (bioRXiv (7/18/2018) ;  doi:    10.1101/370478 )
  Discovering novel calcineurin inhibitors through quantitative mapping of protein-peptide affinity landscapes. Nguyen, H.Q ., Roy, J.*, Harink, B.*, Damle, N.*, Baxter, B., Brower, K., Kortemme, T., Thorn, K., Cyert, M., and  Fordyce, P.M;  preprint in  BioRxiv.  (4/23/18); doi:  10.1101/306779  ( 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 )
  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 )
  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  b ioRXiv (9/26/17)

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)

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).

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)

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

Harink, B., Nguyen, H., Thorn, K., and Fordyce, P.M., preprint on bioRXiv 08/27/18; doi: 10.1101/402560; (web).

Live imaging of Aiptasia larvae, a model system for studying coral bleaching, using a simple microfluidic device. Treuren, W.V.*, Brower, K.*, Labanieh, L., Hunt D., Lensch, S, Cruz., B., Cartwright, H.N., Tran, C., & Fordyce, P.; BioRXiv (2018) (*denotes equal authorship)

(pdf) (web) (bioRXiv (7/18/2018); doi: 10.1101/370478)

Discovering novel calcineurin inhibitors through quantitative mapping of protein-peptide affinity landscapes. Nguyen, H.Q., Roy, J.*, Harink, B.*, Damle, N.*, Baxter, B., Brower, K., Kortemme, T., Thorn, K., Cyert, M., and Fordyce, P.M; preprint in BioRxiv. (4/23/18); doi: 10.1101/306779 (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)

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)

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)