Anja Baresic

Anja Baresic
Ruđer Bošković Institute | RBI · Division of Electronics

PhD

About

24
Publications
4,419
Reads
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520
Citations
Additional affiliations
June 2012 - July 2018
Imperial College London
Position
  • PostDoc Position
September 2007 - November 2011
University College London
Position
  • PhD Student
Description
  • MPhil/PhD studies

Publications

Publications (24)
Article
Full-text available
The knowledge on how gut microbes contribute to the inflammatory bowel disease (IBD) at the onset of disease is still scarce. We compared gut microbiota in newly diagnosed, treatment-naïve adult IBD (Crohn's disease (CD) and ulcerative colitis (UC)) to irritable bowel syndrome (IBS) patients and healthy group. Mucosal and fecal microbiota of 49 pat...
Article
Full-text available
The current paradigm of urinary tract infection (UTI) pathogenesis takes into account the contamination of the periurethral space by specific uropathogens residing in the gut, which is followed by urethral colonization and pathogen ascension to the urinary bladder. Consequently, studying the relationship between gut microbiota and the subsequent de...
Article
Full-text available
The human microbiota is a diverse microbial ecosystem associated with many beneficial physiological functions as well as numerous disease etiologies. Dominated by bacteria, the microbiota also includes commensal populations of fungi, viruses, archaea, and protists. Unlike bacterial microbiota, which was extensively studied in the past two decades,...
Article
Full-text available
Recent genome-wide association studies have identified numerous loci associated with neuropsychiatric disorders. The majority of these are in non-coding regions, and are commonly assigned to the nearest gene along the genome. However, this approach neglects the three-dimensional organisation of the genome, and the fact that the genome contains arra...
Article
Full-text available
Inflammatory bowel diseases are a group of chronic inflammatory conditions that affect gastrointestinal tract due to inapt and continuous immune activation in response to a myriad of predisposing factors (most notably genetics, environmental impact and gut microbiota composition). It has been shown that vitamin D status can also play a role in the...
Article
Full-text available
The transcription factor BCL11B is essential for development of the nervous and the immune system, and Bcl11b deficiency results in structural brain defects, reduced learning capacity, and impaired immune cell development in mice. However, the precise role of BCL11B in humans is largely unexplored, except for a single patient with a BCL11B missense...
Article
Full-text available
The information on microbiota composition in the human gastrointestinal tract predominantly originates from the analyses of human faeces by application of next generation sequencing (NGS). However, the detected composition of the faecal bacterial community can be affected by various factors including experimental design and procedures. This study e...
Article
Background The intestine represents an interface where host tissues come in contact with microbiota in a balanced state of homeostasis. Mounting knowledge on gut microbiota led to many important findings associating the composition of bacterial taxa in the human gastrointestinal tract with many human disorders including the inflammatory bowel disea...
Article
Full-text available
Motivation: Protein-protein interactions are vital for protein function with the average protein having between three and ten interacting partners. Knowledge of precise protein-protein interfaces comes from crystal structures deposited in the Protein Data Bank (PDB), but only 50% of structures in the PDB are complexes. There is therefore a need to...
Article
Full-text available
Background: Precise quantitative and spatiotemporal control of gene expression is necessary to ensure proper cellular differentiation and the maintenance of homeostasis. The relationship between gene expression and the spatial organisation of chromatin is highly complex, interdependent and not completely understood. The development of experimental...
Article
[ Phil. Trans. R. Soc. B 368 , 20130021 (2013; Published 11 November 2013) ([doi:10.1098/rstb.2013.0021][2])][2] At the end of the second paragraph in §3b of the manuscript, entitled ‘Emergence and recruitment of conserved non-coding elements', there is a typo. The authors refer to the MER21
Article
Full-text available
Regions of several dozen to several hundred base pairs of extreme conservation have been found in non-coding regions in all metazoan genomes. The distribution of these elements within and across genomes has suggested that many have roles as transcriptional regulatory elements in multi-cellular organization, differentiation and development. Currentl...
Chapter
Full-text available
The simplest form of mutation is a single DNA base change, frequently referred to as a “single nucleotide polymorphism” (SNP). Strictly, this term should only be applied to single base changes that are observed in at least 1% of a “normal” population. However, it is frequently used to refer to any single base mutation and is used in that context he...
Thesis
Understanding genetic variation is the basis for prevention and diagnosis of inherited disease. In the `next generation sequencing' era with rapidly accumulating variation data, the focus has shifted from population-level analyses to individuals. This thesis is centred on the problem of gathering, storing and analysing mutation data to understand a...
Article
Full-text available
Deleterious or 'Disease-Associated Mutations' (DAMs) are mutations that lead to disease with high phenotype penetrance: they are inherited in a simple Mendelian manner, or, in the case of cancer, accumulate in somatic cells leading directly to disease. However, in some cases, the amino acid that is substituted resulting in disease, is the wild-type...
Article
Full-text available
Protein Kinases are a superfamily of proteins involved in crucial cellular processes such as cell cycle regulation and signal transduction. Accordingly, they play an important role in cancer biology. To contribute to the study of the relation between kinases and disease we compared pathogenic mutations to neutral mutations as an extension to our pr...
Article
Pathogenic deviations (PDs) in humans are disease-causing missense mutations. However, in some cases, these disease-associated residues occur as the wild-type residues in functionally equivalent proteins in other species and these cases are termed ‘compensated pathogenic deviations’ (CPDs). The lack of pathogenicity in a non-human protein is presum...
Article
Full-text available
The phenotypic effects of sequence variations in protein-coding regions come about primarily via their effects on the resulting structures, for example by disrupting active sites or affecting structural stability. In order better to understand the mechanisms behind known mutant phenotypes, and predict the effects of novel variations, biologists nee...

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