A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2011; you can also visit the original URL.
The file type is application/pdf.
Filters
Analysis of substructural variation in families of enzymatic proteins with applications to protein function prediction
2010
BMC Bioinformatics
Preserved Fulltext
Our work provides an unbiased, automated assessment of the structural variability of identified binding site substructures among protein structure families and a technique for exploring the relation of ...
As available proteomic data continues to expand, the techniques proposed will be indispensable for the large-scale analysis and interpretation of structural data. ...
This work was supported in part by National Science Foundation grant DBI-0547695 under a subcontract to Rice University, National Science Foundation Graduate Research Fellowship grant DGE-0237081 to DHB ...
doi:10.1186/1471-2105-11-242
pmid:20459833
pmcid:PMC2885373
fatcat:s2icxjkgazdqnmslb4c4zwipre
Urinary proteome profiling for stratifying patients with familial Parkinsons disease
[article]
2020
bioRxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
other PD-associated proteins as the most discriminating features. ...
Our workflow enabled the reproducible quantification of more than 2,000 proteins in more than 200 urine samples using minimal volumes from two independent patient cohorts. ...
For up-to-date information on the study, visit www.michaeljfox.org/lcc .We thank all members of the Proteomics and Signal Transduction Group at the Max Planck Institute of Biochemistry and the Clinical ...
doi:10.1101/2020.08.09.243584
fatcat:6ihlsylsvvdj7ln3k33unh56du
Quantification of HER family receptors in breast cancer
2015
Breast Cancer Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
Although HER2 protein expression by immunohistochemistry (IHC) and gene amplification by fluorescence in situ hybridization (FISH) assays are routinely used to select patients to receive trastuzumab, both ...
Even less is known for HER3 and HER4, mainly due to lack of robust and validated assays detecting these proteins. ...
Acknowledgments We want to acknowledge the support from the Tumor Biomarkers Research Program funded by the Banco Bilbao Vizcaya Argentaria (BBVA) Foundation.
Author details ...
doi:10.1186/s13058-015-0561-8
pmid:25887735
pmcid:PMC4389676
fatcat:zfvmuol7szho7bc22yebodg5hu
Familial hypertriglyceridemia: an entity with distinguishable features from other causes of hypertriglyceridemia
2021
Lipids in Health and Disease
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
The aim of this work is to search for specific features that can help physicians recognize this disease. ...
Apolipoprotein B, fibroblast growth factor 21(FGF-21), angiopoietin-like proteins 3 (ANGPTL3) and apolipoprotein A-II concentrations, were independent components of a model to detect FHTG compared with ...
We want to express our gratitude to the patients enrolled in this study. ...
doi:10.1186/s12944-021-01436-6
pmid:33588820
fatcat:aflse7iri5fujmawqwwyjokkcy
A widespread family of polymorphic toxins encoded by temperate phages
2017
BMC Biology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
Polymorphic toxins (PTs) are multi-domain bacterial exotoxins belonging to distinct families that share common features in terms of domain organization. ...
The MuF toxin family is likely to play an important role in the ecology of the human microbiota where pathogens and commensal species belonging to the Firmicutes are abundant. ...
Acknowledgements The authors are grateful to Paulo Tavares for his comments on the manuscript and thank Ogün Adebali for helping with the use of the CDvist tool and Kan Nishida for helping with the Exploratory ...
doi:10.1186/s12915-017-0415-1
pmid:28851366
pmcid:PMC5576092
fatcat:uscpmh5n5rahxkymq44narmy6e
Plasma metabolomics of autism spectrum disorder and influence of shared components in proband families
2021
Exposome
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
Then we leveraged a family-based design (31 families) to investigate the influence of shared genetic and environmental components on the autism-associated features. ...
We hypothesize that, without feature identification, family-based correlation analysis of autism-associated features can be an alternative way to assist the prioritization of potentially diagnostic features ...
The study was funded by research grants from the National Institute of Mental Health (R01MH107205) and National Institute of Allergy and Infectious Diseases (R01AI127250). ...
doi:10.1093/exposome/osab004
pmid:35028569
pmcid:PMC8739333
fatcat:nrqrpeshcrgohbpskgifnruac4
Computational selection of antibody-drug conjugate targets for breast cancer
2015
OncoTarget
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
Microarray data corresponding to over 8,000 tissue samples were collected from the public domain. ...
This feature selection method was used in conjunction with differential expression and subcellular localization information to assemble a primary list of targets. ...
CONFLICTS OF INTEREST The authors declare that there are no conflicts of interest. ...
doi:10.18632/oncotarget.6679
pmid:26700623
pmcid:PMC4823055
fatcat:ocatr2x66je4rj62sya7hlifjy
MiBiOmics: an interactive web application for multi-omics data exploration and integration
2021
BMC Bioinformatics
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
The integrative analysis of heterogeneous datasets generally allows to acquire additional insights and generate novel hypotheses about a given biological system. ...
Results Here, we present MiBiOmics, a web-based and standalone application that facilitates multi-omics data visualization, exploration, integration, and analysis by providing easy access to dedicated ...
We also thank the bioinformatics core facility of Nantes (BiRD-Biogenouest) for providing computing resources and support. ...
doi:10.1186/s12859-020-03921-8
pmid:33407076
fatcat:pmemua4jhbc5zchcmjuvrsmayu
Ossified blood vessels in primary familial brain calcification elicit a neurotoxic astrocyte response
2019
Brain
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
in a subset of patients. ...
is a diagnostic criterion. ...
Imaging was performed with equipment maintained by the Center for Microscopy and Image Analysis, University of Zurich. ...
doi:10.1093/brain/awz032
pmid:30805583
pmcid:PMC6439320
fatcat:6w57hqa3ufbqxe4ifb6shtrsca
Altered regulation and expression of genes by BET family of proteins in COPD patients
2017
PLoS ONE
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
BET proteins (BRD2, BRD3, BRDT and BRD4) belong to the family of bromodomain containing proteins, which form a class of transcriptional co-regulators. ...
Using the BET regulated gene signature, we identified a subset of COPD patients, which we propose to benefit from BET inhibition. ...
Acknowledgments We thank the department of thorax surgery in the Sahlgrenska university hospital for the excellent collaboration on the tissue acquisition. ...
doi:10.1371/journal.pone.0173115
pmid:28248992
pmcid:PMC5332090
fatcat:uizgfqhbx5amfan3xrxymokg3e
SIMON, an Automated Machine Learning System, Reveals Immune Signatures of Influenza Vaccine Responses
2019
Journal of Immunology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
We applied SIMON to data from five clinical studies of seasonal influenza vaccination. ...
Hence, it is a highly useful approach for data-driven hypothesis generation from disparate clinical datasets. ...
Special acknowledgment goes to Dr. Purvesh Khatri for critical reading of the manuscript. We appreciate helpful discussions and support from all members of the Davis and Y. ...
doi:10.4049/jimmunol.1900033
pmid:31201239
pmcid:PMC6643048
fatcat:dszre7ycv5b4zdevmcphtqexyi
Characterization and metabolic synthetic lethal testing in a new model of SDH-loss familial pheochromocytoma and paraganglioma
2017
OncoTarget
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
Finally, we perform analysis of SDHC synthetic lethality with lactate dehydrogenase A (LDHA) and pyruvate carboxylase (PCX), which are important for regeneration of NAD+ and aspartate biosynthesis, respectively ...
Our data show that SDH-loss cells are selectively vulnerable to LDH genetic knock-down or chemical inhibition, suggesting that LDH inhibition may be an effective therapeutic strategy for SDH-loss PPGL. ...
CONFLICTS OF INTEREST None declared. ...
doi:10.18632/oncotarget.23639
pmid:29464059
pmcid:PMC5814199
fatcat:q6orgzndrfbg5pqznoxnnzon7q
Single-Cell Transcriptomics Reveal a Correlation between Genome Architecture and Gene Family Evolution in Ciliates
2019
mBio
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
IMPORTANCE To further our understanding of genome evolution in eukaryotes, we assess the relationship between patterns of molecular evolution within gene families and variable genome structures found among ...
We combine single-cell transcriptomics with bioinformatic tools, focusing on understudied and uncultivable lineages selected from across the ciliate tree of life. ...
S.L.K.P. developed analytical tools, analyzed data, and contributed to the paper. R.K. provided advice on methods and supported the first round of data collection. ...
doi:10.1128/mbio.02524-19
pmid:31874915
pmcid:PMC6935857
fatcat:detk54pqfrg3pdwp4nvxjpkcfi
Cardiovascular Genomics: A Biomarker Identification Pipeline
2012
IEEE Transactions on Information Technology in Biomedicine
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
Classification Exploratory analysis and feature selection ultimately lead to predictive analysis, an important aspect of diagnostic and prognostic bioinformatics. ...
Because of the small-sample size compared to the large feature size, feature selection often suffers from lack of statistical power. ...
doi:10.1109/titb.2012.2199570
pmid:22614726
pmcid:PMC5003026
fatcat:zkre2bctmjhj5mxecz2l4i7azm
NBLAST: Rapid, Sensitive Comparison of Neuronal Structure and Construction of Neuron Family Databases
2016
Neuron
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
We thank A. Cardona, H. Cuntz, and members of the G.S.X.E.J. lab for comments on the manuscript; J. Grimmett and T. Darling for their vital assistance with the LMB compute cluster; and T. ...
We thank A. Cardona and M. Zlatic for larval Drosophila EM skeleton data. We thank N. Miyasaka, Y. Yoshihara, I. Arganda-Carreras, U. Sü mbü l, and S. ...
database queries as well as hierarchically organized protein family databases. ...
doi:10.1016/j.neuron.2016.06.012
pmid:27373836
pmcid:PMC4961245
fatcat:scjmtlm2inco5dpdps2fmzhui4
« Previous
Showing results 1 — 15 out of 6,426 results