Related papers: Nucleosome positioning: resources and tools online
As computer scientists working in bioinformatics/computational biology, we often face the challenge of coming up with an algorithm to answer a biological question. This occurs in many areas, such as variant calling, alignment, and assembly.…
Along with recent progress in structural biology and genome biology, structural dynamics of molecular systems including nucleic acids has attracted attention in the context of gene regulation. Structure-function relationship is an important…
This work proposes a unified framework to leverage biological information in network propagation-based gene prioritization algorithms. Preliminary results on breast cancer data show significant improvements over state-of-the-art baselines,…
We present Glioma C6, a new open dataset for instance segmentation of glioma C6 cells, designed as both a benchmark and a training resource for deep learning models. The dataset comprises 75 high-resolution phase-contrast microscopy images…
The human-associated microbiome is closely tied to human health and is of substantial clinical interest. Metagenomics-based tools are emerging for clinical diagnostics, tracking the spread of diseases, and surveillance of potential…
Computational pathology is part of precision oncology medicine. The integration of high-throughput data including genomics, transcriptomics, proteomics, metabolomics, pathomics, and radiomics into clinical practice improves cancer treatment…
Genetic regulatory networks enable cells to respond to the changes in internal and external conditions by dynamically coordinating their gene expression profiles. Our ability to make quantitative measurements in these biochemical circuits…
We describe a software toolbox for the configuration of deep neural networks in the domain of skin cancer classification. The implemented software architecture allows developers to quickly set up new convolutional neural network (CNN)…
Inspired by biology's most sophisticated computer, the brain, neural networks constitute a profound reformulation of computational principles. Remarkably, analogous high-dimensional, highly-interconnected computational architectures also…
The three dimensional structure of DNA in the nucleus (chromatin) plays an important role in many cellular processes. Recent experimental advances have led to high-throughput methods of capturing information about chromatin conformation on…
DNA is subject to large deformations in a wide range of biological processes. Two key examples illustrate how such deformations influence the readout of the genetic information: the sequestering of eukaryotic genes by nucleosomes, and DNA…
Transcription is one of the essential processes for cells to read genetic information encoded in genes, which is initiated by the binding of RNA polymerase to related promoter. Experiments have found that the nucleotide sequence of promoter…
Throughout the evolution of biological species on Earth, cells and organs have developed many complex structures and processes to ensure their interactions with individual chemical molecules (small and macromolecular) and nanoscale objects…
The process of polymerizing a protein by a ribosome, using a messenger RNA (mRNA) as the corresponding template, is called {\it translation}. Ribosome may be regarded as a molecular motor for which the mRNA template serves also as the…
Genetic information is encoded in a linear sequence of nucleotides, represented by letters ranging from thousands to billions. Mutations refer to changes in the DNA or RNA nucleotide sequence. Thus, mutation detection is vital in all areas…
Cells regulate themselves via dizzyingly complex biochemical processes called signaling pathways. These are usually depicted as a network, where nodes represent proteins and edges indicate their influence on each other. In order to…
Gene sequences in the vicinity of splice sites are found to possess dinucleotide periodicities, especially RR and YY, with the period close to the pitch of nucleosome DNA. This confirms previously reported finding about preferential…
Over the past decade there has been a significant growth in bioinformatics databases, tools and resources. Although, bioinformatics is becoming more specific, increasing the number of bioinformatics-wares has made it difficult for…
Alignment of large genomic sequences is a fundamental task in computational genome analysis. Most methods for genomic alignment use high-scoring local alignments as {\em anchor points} to reduce the search space of the alignment procedure.…
Molecular docking is a critical computational strategy in drug design and discovery, but the complex diversity of biomolecular structures and flexible binding conformations create an enormous search space that challenges conventional…