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To understand the particular evolutionary patterns of plant genomes, there is a need to systematically survey the fate of the subgenomes of polyploids fixed as whole genome duplicates, including patterns of re...
We study the problem of mapping proteins between two protein families in the presence of paralogs. This problem occurs as a difficult subproblem in coevolution-based computational approaches for protein-protei...
Among challenges that hamper reaping the benefits of genome assembly are both unfinished assemblies and the ensuing experimental costs. First, numerous software solutions for genome de novo assembly are available...
Comparative genomics has revealed that some species have exceptional genomes, compared to their closest relatives. For instance, some species have undergone a strong reduction of their genome with a drastic re...
Gene duplication is considered to be a major driving force in evolution that enables the genome of a species to acquire new functions. A reconciliation - a mapping of gene tree vertices to the edges or vertice...
Phylogenomic analyses involving whole-genome or multi-locus data often entail dealing with incongruent gene trees. In this paper, we consider two causes of such incongruence, namely, incomplete lineage sorting...
Reconciled gene trees yield orthology and paralogy relationships between genes. This information may however contradict other information on orthology and paralogy provided by other footprints of evolution, su...
The inversion distance, that is the distance between two unichromosomal genomes with the same content allowing only inversions of DNA segments, can be computed thanks to a pioneering approach of Hannenhalli an...
The role of epistatic interactions among loci is a central question in evolutionary biology and is increasingly relevant in the genomic age. While the population genetics of compensatory substitution have rece...
Gene expression is a central process in all living organisms. Central questions in the field are related to the way the expression levels of genes are encoded in the transcripts and affect their evolution, and...
A key goal of systems biology and translational genomics is to utilize high-throughput measurements of cellular states to develop expression-based classifiers for discriminating among different phenotypes. Rec...
Boolean networks capture switching behavior of many naturally occurring regulatory networks. For semi-quantitative modeling, interpolation between ON and OFF states is necessary. The high degree polynomial int...
Modern cancer research often involves large datasets and the use of sophisticated statistical techniques. Together these add a heavy computational load to the analysis, which is often coupled with issues surro...
Since membrane protein structures are challenging to crystallize, computational approaches are essential for elucidating the sequence-to-structure relationships. Structural modeling of membrane proteins requir...
Experimentally validated co-expression correlations between miRNAs and genes are a valuable resource to corroborate observations about miRNA/mRNA changes after experimental perturbations, as well as compare mi...
In drug discovery and development, it is crucial to determine which conformers (instances) of a given molecule are responsible for its observed biological activity and at the same time to recognize the most re...
Pulsed field gel electrophoresis (PFGE) is currently the most widely and routinely used method by the Centers for Disease Control and Prevention (CDC) and state health labs in the United States for Salmonella sur...
Reversible posttranslational protein modifications such as phosphorylation of Ser/Thr/Tyr and Met oxidation are critical for both metabolic regulation and cellular signalling. Although these modifications are ...
Alternative splicing is an important and widespread mechanism for generating protein diversity and regulating protein expression. High-throughput identification and analysis of alternative splicing in the prot...
In recent years, the use and importance of predicted protein residue-residue contacts has grown considerably with demonstrated applications such as drug design, protein tertiary structure prediction and model ...
High Content Screening (HCS) has become an important tool for toxicity assessment, partly due to its advantage of handling multiple measurements simultaneously. This approach has provided insight and contribut...
Advances in technology have led to the generation of massive amounts of complex and multifarious biological data in areas ranging from genomics to structural biology. The volume and complexity of such data lea...
Dicer, an RNase III enzyme, plays a vital role in the processing of pre-miRNAs for generating the miRNAs. The structural and sequence features on pre-miRNA which can facilitate position and efficiency of cleav...
The advances in high throughput omics technologies have made it possible to characterize molecular interactions within and across various species. Alignments and comparison of molecular networks across species...
Plastids are an important component of plant cells, being the site of manufacture and storage of chemical compounds used by the cell, and contain pigments such as those used in photosynthesis, starch synthesis...
An important mechanism of endocrine activity is chemicals entering target cells via transport proteins and then interacting with hormone receptors such as the estrogen receptor (ER). α-Fetoprotein (AFP) is a m...
The dynamic, decentralized world-wide-web has become an essential part of scientific research and communication. Researchers create thousands of web sites every year to share software, data and services. These...
Transcriptome analysis by microarrays has produced important advances in biomedicine. For instance in multiple myeloma (MM), microarray approaches led to the development of an effective disease subtyping via c...
Pathway alterations reflected as changes in gene expression regulation and gene interaction can result from cellular exposure to toxicants. Such information is often used to elucidate toxicological modes of ac...
Even though only 1.5% of the human genome is translated into proteins, recent reports indicate that most of it is transcribed into non-coding RNAs (ncRNAs), which are becoming the subject of increased scientif...
Knowledge of which genes are essential to the survival of an organism is critical to understanding the function of genes, and for the identification of potential drug targets for antimicrobial treatment. Previ...
Residual Dipolar Couplings (RDCs) have emerged in the past two decades as an informative source of experimental restraints for the study of structure and dynamics of biological macromolecules and complexes. Th...
Next-generation DNA sequencing technologies have made it possible to generate transcriptome data for novel organisms quickly and cheaply, to the extent that the effort required to annotate and publish a new tr...
Molecular recognition features (MoRFs) are short binding regions located in longer intrinsically disordered protein regions. Although these short regions lack a stable structure in the natural state, they read...
Comprehensive protein-protein interaction (PPI) maps are a powerful resource for uncovering the molecular basis of genetic interactions and providing mechanistic insights. Over the past decade, high-throughput...
Gene expression in the Drosophila embryo is controlled by functional interactions between a large network of protein transcription factors (TFs) and specific sequences in DNA cis-regulatory modules (CRMs). The bi...
In recent years, high-throughput microscopy has emerged as a powerful tool to analyze cellular dynamics in an unprecedentedly high resolved manner. The amount of data that is generated, for example in long-ter...
Fundamental cellular processes such as cell movement, division or food uptake critically depend on cells being able to change shape. Fast acquisition of three-dimensional image time series has now become possi...
For the analysis of spatio-temporal dynamics, various automated processing methods have been developed for nuclei segmentation. These methods tend to be complex for segmentation of images with crowded nuclei, ...
Segmenting electron microscopy (EM) images of cellular and subcellular processes in the nervous system is a key step in many bioimaging pipelines involving classification and labeling of ultrastructures. Howev...
We briefly identify several critical issues in current computational neuroscience, and present our opinions on potential solutions based on bioimage informatics, especially automated image computing.
Gene perturbation experiments in combination with fluorescence time-lapse cell imaging are a powerful tool in reverse genetics. High content applications require tools for the automated processing of the large...
Pattern recognition algorithms are useful in bioimage informatics applications such as quantifying cellular and subcellular objects, annotating gene expressions, and classifying phenotypes. To provide effectiv...
RNAi screening is a powerful method to study the genetics of intracellular processes in metazoans. Technically, the approach has been largely inspired by techniques and tools developed for compound screening, ...
A number of different statistics are used for detecting natural selection using DNA sequencing data, including statistics that are summaries of the frequency spectrum, such as Tajima’s D. These statistics are now...
The development of new therapies for orphan genetic diseases represents an extremely important medical and social challenge. Drug repositioning, i.e. finding new indications for approved drugs, could be one of...
Dendritic spines serve as key computational structures in brain plasticity. Much remains to be learned about their spatial and temporal distribution among neurons. Our aim in this study was to perform explorat...
Since the advent of microarray technology, numerous methods have been devised to infer gene regulatory relationships from gene expression data. Many approaches that infer entire regulatory networks. This produ...
Identification of the genetic alterations responsible for human disease is a central challenge facing medical genetics. While many algorithms have been developed to predict the degree of damage caused by a giv...
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Citation Impact 2023
Journal Impact Factor: 2.9
5-year Journal Impact Factor: 3.6
Source Normalized Impact per Paper (SNIP): 0.821
SCImago Journal Rank (SJR): 1.005
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