Katerina Michalickova

Katerina Michalickova
Imperial College London | Imperial · Information and Communication Technologies

Doctor of Philosophy

About

25
Publications
2,493
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4,038
Citations
Citations since 2016
0 Research Items
486 Citations
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2016201720182019202020212022020406080
2016201720182019202020212022020406080
2016201720182019202020212022020406080

Publications

Publications (25)
Data
Table S1. Information about the single-gene alignments used in the test case. Table S2. Sequences randomly extracted from the singlegene alignments. Table S3. Results from COCO-CL.
Article
Full-text available
We present a pipeline named BIR (Blast, Identify and Realign) developed for phylogenomic analyses. BIR is intended for the identification of gene sequences applicable for phylogenomic inference. The pipeline allows users to apply their own manually curated sequence alignments (seed) in search for homologous genes in sequence databases and available...
Article
Full-text available
Background Multigenic diseases are often associated with protein complexes or interactions involved in the same pathway. We wanted to estimate to what extent this is true given a consolidated protein interaction data set. The study stresses data integration and data representation issues. Results We constructed 497 multigenic disease groups from O...
Data
Significance of overlaps between disease groups and binary data was calculated as described in the text. Number of interaction edges for each disease group is listed. Only those disease group overlaps with raw p-values less than 0.0004 are considered statistically significant.
Data
Mapping of OMIM titles to disease groups and Entrez Gene identifiers.
Data
The file can be opened in Cytoscape ( http://cytoscape.org ) to reproduce Figure 3 and explore disease groups and their overlaps with n-ary data in iRefIndex.
Data
Overlaps between disease groups and regenerated complex data showing best overlaps and number of overlaps (complex span) before and after correction for multiple hypothesis testing. Example regenerated complexes have regular names that can be used to retrieve the binary interactions that make up the regenerated complex. For example: in the name “MI...
Data
The file can be opened in Cytoscape ( http://cytoscape.org ) to reproduce Figure 1 and explore disease groups and their overlaps.
Data
Overlaps between disease groups and n-ary records showing best overlaps (icrigid) and number of overlaps (complex span) before and after correction for multiple hypothesis testing. Additional information on n-ary records with the best overlap with a disease group can be found at http://wodaklab.org/iRefWeb/interaction/show/xxx where xxx is the icri...
Data
Summary of disease groups in terms of both genes and proteins.
Article
Full-text available
The iRefIndex consolidates protein interaction data from ten databases in a rigorous manner using sequence-based hash keys. Working with consolidated interaction data comes with distinct challenges: data are redundant, overlapping, highly interconnected and may be collected and represented using different curation practices. These phenomena were qu...
Article
Base excision repair (BER) is a major mode of repair of DNA base damage. BER is required for maintenance of genetic stability, which is important in the prevention of cancer. However, direct genetic associations between BER deficiency and human cancer have been difficult to firmly establish, and the first-generation mouse models deficient in indivi...
Article
In this work we describe the implementation of a 216- processor Beowulf cluster with switched gigabit Ethernet networking. This design includes the use of a 8-CPU high performance midrange computer with 8 gigabit ports as a cluster head, a design that limits I/O contention. We have been developing applications software for bioinformatics research i...
Article
Full-text available
The majority of experimentally verified molecular interaction and biological pathway data are present in the unstructured text of biomedical journal articles where they are inaccessible to computational methods. The Biomolecular interaction network database (BIND) seeks to capture these data in a machine-readable format. We hypothesized that the fo...
Article
Full-text available
An organism's ability to adapt to its particular environmental niche is of fundamental importance to its survival and proliferation. In the largest study of its kind, we sought to identify and exploit the amino-acid signatures that make species-specific protein adaptation possible across 100 complete genomes. Environmental niche was determined to b...
Data
Species-specific fold composition (CF) scoring functions
Article
Full-text available
SeqHound has been developed as an integrated biological sequence, taxonomy, annotation and 3-D structure database system. It provides a high-performance server platform for bioinformatics research in a locally-hosted environment. SeqHound is based on the National Center for Biotechnology Information data model and programming tools. It offers daily...
Article
Human colorectal, endometrial, and gastric cancers with defective DNA mismatch repair (MMR) have microsatellite instability, a unique molecular alteration characterized by widespread frameshift mutations of repetitive DNA sequences. We developed "Kangaroo," a bioinformatics program for searches in nucleotide and protein sequence databases, and perf...
Article
Full-text available
The recent abundance of genome sequence data has brought an urgent need for systematic proteomics to decipher the encoded protein networks that dictate cellular function. To date, generation of large-scale protein-protein interaction maps has relied on the yeast two-hybrid system, which detects binary interactions through activation of reporter gen...
Article
Ehlers-Danlos syndrome (EDS) is a heterogeneous connective tissue disorder that severely impairs the structure and function of the skin, joints, eyes and blood vessels. We have identified mutations of the COL5A2 gene, which encodes the alpha2(V) chain of type V collagen, in two unrelated patients with the severe type I form of EDS. The first proban...
Article
A girl with severe Hunter disease was found to have a submicroscopic deletion distrupting the IDS locus in the region Xq27.3-q28 together with non-random inactivation of the non-mutant X chromosome. Southern analysis of DNA from the parents and from hamster-patient somatic cell hybrids containing only the mutant X chromosome revealed that the delet...

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