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\textit{Drosophila melanogaster} has been established as a model organism for investigating the fundamental principles of developmental gene interactions. The gene expression patterns of \textit{Drosophila melanogaster} can be documented as…
The classic algorithms of Needleman--Wunsch and Smith--Waterman find a maximum a posteriori probability alignment for a pair hidden Markov model (PHMM). In order to process large genomes that have undergone complex genome rearrangements,…
Multiply inverted balancer chromosomes that suppress exchange with their homologs are an essential part of the genetic toolkit in Drosophila melanogaster. Despite their widespread use, the organization of balancer chromosomes has not been…
Natural selection at one site shapes patterns of genetic variation at linked sites. Quantifying the effects of 'linked selection' on levels of genetic diversity is key to making reliable inference about demography, building a null model in…
Drosophila melanogaster, a small dipteran of African origin, represents one of the best-studied model organisms. Early work in this system has uniquely shed light on the basic principles of genetics and resulted in a versatile collection of…
Non-coding RNA are functional molecules that are not translated into proteins. Their function comes as important regulators of biological function. Because they are not translated, they need not be as stable as other types of RNA. The TKF91…
Complex spatial and temporal patterns of gene expression underlie embryo differentiation, yet methods do not yet exist for the efficient genome-wide determination of spatial expression patterns during development. In situ imaging of…
The origins of new genes are among the most fundamental questions in evolutionary biology. Our understanding of the ways that new genetic material appears and how that genetic material shapes population variation remains incomplete. De novo…
Genes are frequently regulated in complex manners, necessitating modelling approaches which go beyond simple (linear) gene-to-gene interactions and address the modularity of cis-regulatory regions and alternate transcription initiation…
Convolutional neural networks are powerful tools for image segmentation and classification. Here, we use this method to identify and mark the heart region of Drosophila at different developmental stages in the cross-sectional images…
The alignment of biological sequences such as DNA, RNA, and proteins, is one of the basic tools that allow to detect evolutionary patterns, as well as functional/structural characterizations between homologous sequences in different…
Histone modification is a vital epigenetic mechanism for transcriptional control in eukaryotes. High-throughput techniques have enabled whole-genome analysis of histone modifications in recent years. However, most studies assume one…
Sequences of nucleotides (for DNA and RNA) or amino acids (for proteins) are central objects in biology. Among the most important computational problems is that of sequence alignment, i.e. arranging sequences from different organisms in…
Genetic information is stored in a linear sequence of base-pairs; however, thermal fluctuations and complex DNA conformations such as folds and loops make it challenging to order genomic material for in vitro analysis. In this work, we…
Non protein coding regions of the human genome contain many complex patterns which regulate the cellular activity. Studying the human genome is limited by the lack of understanding of its features and their complex interactions. However,…
A fundamental goal in neuroscience is to understand the relationship between neural activity and behavior. For example, the ability to extract behavioral intentions from neural data, or neural decoding, is critical for developing effective…
(ABRIDGED) We report the genome sequencing of 139 wild-derived strains of D. melanogaster, representing 22 population samples from the sub-Saharan ancestral range of this species, along with one European population. Most genomes were…
Due to the dynamic nature of biological systems, biological networks underlying temporal process such as the development of {\it Drosophila melanogaster} can exhibit significant topological changes to facilitate dynamic regulatory…
Recent studies have consistently inferred high rates of adaptive molecular evolution between Drosophila species. At the same time, the Drosophila genome evolves under different rates of recombination, which results in partial genetic…
In this paper, we present an optical computing method for string data alignment applicable to genome information analysis. By applying moire technique to spatial encoding patterns of deoxyribonucleic acid (DNA) sequences, association…