相关论文: CplexA: a Mathematica package to study macromolecu…

The AGP format is a tab-separated table format describing how components of a genome assembly fit together. A standard submission format for genome assemblies is a fasta file giving the sequence of contigs along with an AGP file showing how…

Biology stores information and computes at the molecular scale, yet the ways in which it does so are often distinct from human-engineered computers. Mapping biological computation onto architectures familiar to computer science remains an…

Biomolecular condensates are essential for cellular organization and result from phase separation in systems far from thermodynamic equilibrium. Among various models, chemically active droplets play a significant role, consisting of…

The use of reduced models for investigating the self-assembly dynamics underlying protein shell formation in spherical viruses is described. The spontaneous self-assembly of these polyhedral, supramolecular structures, in which icosahedral…

In biomolecular systems (especially all-atom models) with many degrees of freedom such as proteins and nucleic acids, there exist an astronomically large number of local-minimum-energy states. Conventional simulations in the canonical…

Cytoplasmic streaming, the coherent flow of cytoplasm, plays a critical role in transport and mixing over large scales in eukaryotic cells. In many large cells, this process is driven by active forces at the cell boundary, such as cortical…

Modern computing workloads commonly involve matrix-matrix multiplication (mmul) as a core computing pattern. Coarse-Grained Reconfigurable Arrays (CGRAs) can flexibly and efficiently support it, since they combine operation-level…

Recent experiments at the level of a single cell have shown that gene expression occurs in abrupt stochastic bursts. Further, in an ensemble of cells, the levels of proteins produced have a bimodal distribution. In a large fraction of…

Modeling to generate alternatives (MGA) is an increasingly popular method in energy system optimization. MGA explores the near-optimal space, namely, system alternatives whose costs are within a certain fraction of the globally optimal…

The recently introduced method of excess collisions (MEC) is modified to estimate diffusion-controlled reaction times inside systems of arbitrary size. The resulting MEC-E equations contain a set of empirical parameters, which have to be…

We propose `Dracula', a new framework for unsupervised feature selection from sequential data such as text. Dracula learns a dictionary of $n$-grams that efficiently compresses a given corpus and recursively compresses its own dictionary;…

Molecular representation learning is pivotal for various molecular property prediction tasks related to drug discovery. Robust and accurate benchmarks are essential for refining and validating current methods. Existing molecular property…

We provide a probabilistic and infinitesimal view of how the principal component analysis procedure (PCA) can be generalized to analysis of nonlinear manifold valued data. Starting with the probabilistic PCA interpretation of the Euclidean…

By integrating heterogeneous functional genomic datasets, we have developed a new framework for detecting combinatorial control of gene expression, which includes estimating transcription factor activities using a singular value…

Gene assembly in ciliates is one of the most involved DNA processings going on in any organism. This process transforms one nucleus (the micronucleus) into another functionally different nucleus (the macronucleus). We continue the…

Biomolecular condensates are liquid- or gel-like droplets of proteins and nucleic acids formed at least in part through liquid-liquid phase separation. Condensates enable diverse functions of cells and the pathogens that infect them,…

We investigate the ability of a genetic algorithm to design cellular automata that perform computations. The computational strategies of the resulting cellular automata can be understood using a framework in which ``particles'' embedded in…

There are a number of well-established methods such as principal components analysis (PCA) for automatically capturing systematic variation due to latent variables in large-scale genomic data. PCA and related methods may directly provide a…

A method for studying the qualitative dynamical properties of abstract computing machines based on the approximation of their program-size complexity using a general lossless compression algorithm is presented. It is shown that the…

Background: Duplication of genes is important for evolution of molecular networks. Many authors have therefore considered gene duplication as a driving force in shaping the topology of molecular networks. In particular it has been noted…