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Analysis of substructural variation in families of enzymatic proteins with applications to protein function prediction

Drew H Bryant, Mark Moll, Brian Y Chen, Viacheslav Y Fofanov, Lydia E Kavraki
2010 BMC Bioinformatics  
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]

Sebastian Virreira Winter, Ozge Karayel, Maximilian T Strauss, Shalini Padmanabhan, Matthew Surface, Kalpana Merchant, Roy N Alcalay, Matthias Mann
2020 bioRxiv   pre-print
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 .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

Paolo Nuciforo, Nina Radosevic-Robin, Tony Ng, Maurizio Scaltriti
2015 Breast Cancer Research  
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

Ivette Cruz-Bautista, Alicia Huerta-Chagoya, Hortensia Moreno-Macías, Rosario Rodríguez-Guillén, María Luisa Ordóñez-Sánchez, Yayoi Segura-Kato, Roopa Mehta, Paloma Almeda-Valdés, Lizeth Gómez-Munguía, Ximena Ruiz-De Chávez, Ximena Rosas-Flota, Arali Andrade-Amado (+14 others)
2021 Lipids in Health and Disease  
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

Anne Jamet, Marie Touchon, Bruno Ribeiro-Gonçalves, João André Carriço, Alain Charbit, Xavier Nassif, Mario Ramirez, Eduardo P. C. Rocha
2017 BMC Biology  
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

Ming Kei Chung, Matthew Ryan Smith, Yufei Lin, Douglas I Walker, Dean Jones, Chirag J Patel, Sek Won Kong
2021 Exposome  
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

François Fauteux, Jennifer J. Hill, Maria L. Jaramillo, Youlian Pan, Sieu Phan, Fazel Famili, Maureen O'Connor-McCourt
2015 OncoTarget  
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

Johanna Zoppi, Jean-François Guillaume, Michel Neunlist, Samuel Chaffron
2021 BMC Bioinformatics  
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  
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

Rajneesh Malhotra, Nisha Kurian, Xiao-Hong Zhou, Fanyi Jiang, Susan Monkley, Amy DeMicco, Ib G. Clausen, Göran Delgren, Goran Edenro, Miika J. Ahdesmäki, Maryam Clausen, Lisa Öberg (+4 others)
2017 PLoS ONE  
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

Adriana Tomic, Ivan Tomic, Yael Rosenberg-Hasson, Cornelia L. Dekker, Holden T. Maecker, Mark M. Davis
2019 Journal of Immunology  
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

John Smestad, Oksana Hamidi, Lin Wang, Molly Nelson Holte, Fatimah Al Khazal, Luke Erber, Yue Chen, L. James Maher
2017 OncoTarget  
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

Ying Yan, Xyrus X. Maurer-Alcalá, Rob Knight, Sergei L. Kosakovsky Pond, Laura A. Katz, Colleen M. Cavanaugh
2019 mBio  
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

J. H. Phan, C. F. Quo, M. D. Wang
2012 IEEE Transactions on Information Technology in Biomedicine  
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

Marta Costa, James D. Manton, Aaron D. Ostrovsky, Steffen Prohaska, Gregory S.X.E. Jefferis
2016 Neuron  
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
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