A framework for organizing cancer-related variations from existing databases, publications and NGS data using a High-performance Integrated Virtual Environment …

TJ Wu, A Shamsaddini, Y Pan, K Smith, DJ Crichton… - Database, 2014 - academic.oup.com
Years of sequence feature curation by UniProtKB/Swiss-Prot, PIR-PSD, NCBI-CDD, RefSeq
and other database biocurators has led to a rich repository of information on functional sites …

HIVE-hexagon: high-performance, parallelized sequence alignment for next-generation sequencing data analysis

L Santana-Quintero, H Dingerdissen, J Thierry-Mieg… - PloS one, 2014 - journals.plos.org
Due to the size of Next-Generation Sequencing data, the computational challenge of
sequence alignment has been vast. Inexact alignments can take up to 90% of total CPU time …

Proteomic studies related to genetic determinants of variability in protein concentrations

P Horvatovich, L Franke, R Bischoff - Journal of proteome research, 2014 - ACS Publications
Genetic variation has multiple effects on the proteome. It may influence the expression level
of proteins, modify their sequences through single nucleotide polymorphisms, the …

Structural and energetic analyses of SNPs in drug targets and implications for drug therapy

HY Sun, FQ Ji, LY Fu, ZY Wang… - Journal of chemical …, 2013 - ACS Publications
Mutations in drug targets can alter the therapeutic effects of drugs. Therefore, evaluating the
effects of single-nucleotide polymorphisms (SNPs) on drug-target binding is of significant …

Human germline and pan-cancer variomes and their distinct functional profiles

Y Pan, K Karagiannis, H Zhang… - Nucleic acids …, 2014 - academic.oup.com
Identification of non-synonymous single nucleotide variations (nsSNVs) has exponentially
increased due to advances in Next-Generation Sequencing technologies. The functional …

Non-synonymous variations in cancer and their effects on the human proteome: workflow for NGS data biocuration and proteome-wide analysis of TCGA data

C Cole, K Krampis, K Karagiannis, JS Almeida… - BMC …, 2014 - Springer
Background Next-generation sequencing (NGS) technologies have resulted in petabytes of
scattered data, decentralized in archives, databases and sometimes in isolated hard-disks …

Differential expression of glycosyltransferases identified through comprehensive pan-cancer analysis

HM Dingerdissen, J Vora, E Cauley, A Bell, CH King… - bioRxiv, 2021 - biorxiv.org
Despite accumulating evidence supporting a role for glycosylation in cancer progression
and prognosis, the complexity of the human glycome and glycoproteome poses many …

Predikce efektu bodových mutací na interakci proteinu s nukleovými kyselinami

VT Štěpánková - 2024 - dspace.cuni.cz
Bodové mutace jsou nejčastějším typem mutací a mnohé z nich mohou mít patogenní efekt,
je proto užitečné umět kvalitně a efektivně predikovat jejich vliv na daný protein, a právě …

[图书][B] Comprehensive Analysis of Glycosyltransferases in Cancer Identified from a Multifaceted Genomics Approach

HM Dingerdissen - 2021 - search.proquest.com
Despite accumulating evidence supporting a role for glycosylation in cancer progression
and prognosis, the complexity of the human glycome and study thereof poses many …

A framework for application of metabolic modeling in yeast to predict the effects of nsSNV in human orthologs

H Dingerdissen, DS Weaver, PD Karp, Y Pan… - Biology Direct, 2014 - Springer
Background We have previously suggested a method for proteome wide analysis of
variation at functional residues wherein we identified the set of all human genes with …