850 citations · 1.9k across the 15 of their papers we have counts for
16 papers
On learning functions over biological sequence space: relating Gaussian process priors, regularization, and gauge fixing
Samantha Petti, Carlos Martí-Gómez, Justin B. Kinney +2
Mappings from biological sequences (DNA, RNA, protein) to quantitative measures of sequence functionality play an important role in contemporary biology. We are interested in the r…
A Method for Fabricating CMOS Back-End-of-Line-Compatible Solid-State Nanopore Devices
Mohamed Yassine Bouhamidi, Chunhui Dai, Michel Stephan +8
Solid-state nanopores, nm-sized holes in thin, freestanding membranes, are powerful single-molecule sensors capable of interrogating a wide range of target analytes, from small mol…
Algebraic and diagrammatic methods for the rule-based modeling of multi-particle complexes
Rebecca J. Rousseau, Justin B. Kinney
The formation, dissolution, and dynamics of multi-particle complexes is of fundamental interest in the study of stochastic chemical systems. In 1976, Masao Doi introduced a Fock sp…
Biophysical models of cis-regulation as interpretable neural networks
Ammar Tareen, Justin B. Kinney
The adoption of deep learning techniques in genomics has been hindered by the difficulty of mechanistically interpreting the models that these techniques produce. In recent years,…
Deciphering the regulatory genome of , one hundred promoters at a time
William T. Ireland, Suzannah M. Beeler, Emanuel Flores-Bautista +5
Advances in DNA sequencing have revolutionized our ability to read genomes. However, even in the most well-studied of organisms, the bacterium , for $\appro…
Density estimation on small datasets
Wei-Chia Chen, Ammar Tareen, Justin B. Kinney
How might a smooth probability distribution be estimated, with accurately quantified uncertainty, from a limited amount of sampled data? Here we describe a field-theoretic approach…