Related papers: MotifbreakR v2: extended capability and database i…
Breeding by introgressive hybridization is a pivotal strategy to broaden the genetic basis of crops. Usually, the desired traits are monitored in consecutive crossing generations by marker-assisted selection, but their analyses fail in…
Molecular docking that predicts the bound structures of small molecules (ligands) to their protein targets, plays a vital role in drug discovery. However, existing docking methods often face limitations: they either overlook crucial…
Recent experiments show that transcription factors (TFs) indeed use the facilitated diffusion mechanism to locate their target sequences on DNA in living bacteria cells: TFs alternate between sliding motion along DNA and relocation events…
The search for patterns or motifs in data represents an area of key interest to many researchers. In this paper we present the Motif Tracking Algorithm, a novel immune inspired pattern identification tool that is able to identify unknown…
Progress in hardware, algorithms, and force fields are pushing the scope of molecular dynamics (MD) simulations towards the length- and time scales of complex biochemical processes. This creates a need for developing advanced analysis…
Computational approaches to transcription factor binding site identification have been actively researched for the past decade. Negative examples have long been utilized in de novo motif discovery and have been shown useful in transcription…
Gene-regulatory enhancers have been identified by many lines of evidence, including evolutionary conservation, regulatory protein binding, chromatin modifications, and DNA sequence motifs. To integrate these different approaches, we…
Despite the rapid adoption of text-to-image (T2I) diffusion models, causal and representation-level analysis remains fragmented and largely limited to isolated probing techniques. To address this gap, we introduce DreamReader: a unified…
Quality traits are some of the most important and time-consuming phenotypes to evaluate in plant breeding programs. These traits are often evaluated late in the breeding pipeline due to their cost, resulting in the potential advancement of…
SweepFinder is a popular program that implements a powerful likelihood-based method for detecting recent positive selection, or selective sweeps. Here, we present SweepFinder2, an extension of SweepFinder with increased sensitivity and…
TraitLab is a software package for simulating, fitting and analysing tree-like binary data under a stochastic Dollo model of evolution. The model also allows for rate heterogeneity through catastrophes, evolutionary events where many traits…
We introduce the software tool NTRFinder to find the complex repetitive structure in DNA we call a nested tandem repeat (NTR). An NTR is a recurrence of two or more distinct tandem motifs interspersed with each other. We propose that nested…
Many fault diagnosis methods of rotating machines are based on discriminative features extracted from signals collected from the key components such as bearings. However, under complex operating conditions, periodic impulsive…
Distinguishing the rare "driver" mutations that fuel cancer progression from the vast background of "passenger" mutations in the non-coding genome is a fundamental challenge in cancer biology. A primary mechanism that non-coding driver…
We discuss a simple and powerful approach for the ab initio identification of cis-regulatory motifs involved in transcriptional regulation. The method we present integrates several elements: human-mouse comparison, statistical analysis of…
The binding of a transcription factor (TF) to a DNA operator site can initiate or repress the expression of a gene. Computational prediction of sites recognized by a TF has traditionally relied upon knowledge of several cognate sites,…
While accurate protein structure predictions are now available for nearly every observed protein sequence, predicted structures lack much of the functional context offered by experimental structure determination. We address this gap with…
Protein Fragment Motif Finder (PFMFind) is a system that enables efficient discovery of relationships between short fragments of protein sequences using similarity search. It supports queries based on score matrices and PSSMs obtained…
Modeling the effects of mutations on the binding affinity plays a crucial role in protein engineering and drug design. In this study, we develop a novel deep learning based framework, named GraphPPI, to predict the binding affinity changes…
Breakage-Fusion-Bridge (BFB) is a mechanism of genomic instability characterized by the joining and subsequent tearing apart of sister chromatids. When this process is repeated during multiple rounds of cell division, it leads to patterns…