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). ( 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.;  preprint on bioRXiv (7/18/2018) ;  doi:    10.1101/370478  ( web )
  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) ( 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 ); preprint in  b ioRXiv (9/26/17) ( web ) ( pdf )

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). (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.; preprint on bioRXiv (7/18/2018); doi: 10.1101/370478 (web)

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