Revealing the vectors of cellular identity with single-cell genomics
Single-cell genomics has now made it possible to create a comprehensive atlas of human
cells. At the same time, it has reopened definitions of a cell's identity and of the ways in …
cells. At the same time, it has reopened definitions of a cell's identity and of the ways in …
DOCKSTRING: easy molecular docking yields better benchmarks for ligand design
The field of machine learning for drug discovery is witnessing an explosion of novel
methods. These methods are often benchmarked on simple physicochemical properties …
methods. These methods are often benchmarked on simple physicochemical properties …
BioSeq-BLM: a platform for analyzing DNA, RNA and protein sequences based on biological language models
In order to uncover the meanings of 'book of life', 155 different biological language models
(BLMs) for DNA, RNA and protein sequence analysis are discussed in this study, which are …
(BLMs) for DNA, RNA and protein sequence analysis are discussed in this study, which are …
Development and benchmarking of open force field 2.0. 0: the Sage small molecule force field
We introduce the Open Force Field (OpenFF) 2.0. 0 small molecule force field for drug-like
molecules, code-named Sage, which builds upon our previous iteration, Parsley. OpenFF …
molecules, code-named Sage, which builds upon our previous iteration, Parsley. OpenFF …
Clustering trees: a visualization for evaluating clusterings at multiple resolutions
Clustering techniques are widely used in the analysis of large datasets to group together
samples with similar properties. For example, clustering is often used in the field of single …
samples with similar properties. For example, clustering is often used in the field of single …
iLearnPlus: a comprehensive and automated machine-learning platform for nucleic acid and protein sequence analysis, prediction and visualization
Sequence-based analysis and prediction are fundamental bioinformatic tasks that facilitate
understanding of the sequence (-structure)-function paradigm for DNAs, RNAs and proteins …
understanding of the sequence (-structure)-function paradigm for DNAs, RNAs and proteins …
SUPPA2: fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions
Despite the many approaches to study differential splicing from RNA-seq, many challenges
remain unsolved, including computing capacity and sequencing depth requirements. Here …
remain unsolved, including computing capacity and sequencing depth requirements. Here …
CHIME/FRB discovery of 25 repeating fast radio burst sources
BC Andersen, K Bandura, M Bhardwaj… - The Astrophysical …, 2023 - iopscience.iop.org
We present the discovery of 25 new repeating fast radio burst (FRB) sources found among
CHIME/FRB events detected between 2019 September 30 and 2021 May 1. The sources …
CHIME/FRB events detected between 2019 September 30 and 2021 May 1. The sources …
Unsupervised learning of phase transitions: From principal component analysis to variational autoencoders
SJ Wetzel - Physical Review E, 2017 - APS
We examine unsupervised machine learning techniques to learn features that best describe
configurations of the two-dimensional Ising model and the three-dimensional XY model. The …
configurations of the two-dimensional Ising model and the three-dimensional XY model. The …
Defining a new nomenclature for the structures of active and inactive kinases
V Modi, RL Dunbrack Jr - Proceedings of the National …, 2019 - National Acad Sciences
Targeting protein kinases is an important strategy for intervention in cancer. Inhibitors are
directed at the active conformation or a variety of inactive conformations. While attempts …
directed at the active conformation or a variety of inactive conformations. While attempts …