Literature DB >> 27516611

Navigating the Phenotype Frontier: The Monarch Initiative.

Julie A McMurry1, Sebastian Köhler2, Nicole L Washington3, James P Balhoff4, Charles Borromeo5, Matthew Brush1, Seth Carbon3, Tom Conlin1, Nathan Dunn3, Mark Engelstad1, Erin Foster1, Jean-Philippe Gourdine1, Julius O B Jacobsen6, Daniel Keith1, Bryan Laraway1, Jeremy Nguyen Xuan3, Kent Shefchek1, Nicole A Vasilevsky1, Zhou Yuan5, Suzanna E Lewis3, Harry Hochheiser5, Tudor Groza7, Damian Smedley8, Peter N Robinson2, Christopher J Mungall3, Melissa A Haendel9.   

Abstract

The principles of genetics apply across the entire tree of life. At the cellular level we share biological mechanisms with species from which we diverged millions, even billions of years ago. We can exploit this common ancestry to learn about health and disease, by analyzing DNA and protein sequences, but also through the observable outcomes of genetic differences, i.e. phenotypes. To solve challenging disease problems we need to unify the heterogeneous data that relates genomics to disease traits. Without a big-picture view of phenotypic data, many questions in genetics are difficult or impossible to answer. The Monarch Initiative (https://monarchinitiative.org) provides tools for genotype-phenotype analysis, genomic diagnostics, and precision medicine across broad areas of disease.
Copyright © 2016 by the Genetics Society of America.

Keywords:  comparative medicine; data integration; disease diagnosis; disease discovery; phenotype ontologies

Mesh:

Year:  2016        PMID: 27516611      PMCID: PMC4981258          DOI: 10.1534/genetics.116.188870

Source DB:  PubMed          Journal:  Genetics        ISSN: 0016-6731            Impact factor:   4.562


  15 in total

1.  Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.

Authors:  M Ashburner; C A Ball; J A Blake; D Botstein; H Butler; J M Cherry; A P Davis; K Dolinski; S S Dwight; J T Eppig; M A Harris; D P Hill; L Issel-Tarver; A Kasarskis; S Lewis; J C Matese; J E Richardson; M Ringwald; G M Rubin; G Sherlock
Journal:  Nat Genet       Date:  2000-05       Impact factor: 38.330

2.  Clinical utility gene card for: Hereditary thoracic aortic aneurysm and dissection including next-generation sequencing-based approaches.

Authors:  Mine Arslan-Kirchner; Eloisa Arbustini; Catherine Boileau; Philippe Charron; Anne H Child; Gwenaelle Collod-Beroud; Julie De Backer; Anne De Paepe; Anna Dierking; Laurence Faivre; Sabine Hoffjan; Guillaume Jondeau; Britta Keyser; Bart Loeys; Karin Mayer; Peter N Robinson; Jörg Schmidtke
Journal:  Eur J Hum Genet       Date:  2015-10-28       Impact factor: 4.246

3.  Data sharing in the undiagnosed diseases network.

Authors:  Catherine A Brownstein; Ingrid A Holm; Rachel Ramoni; David B Goldstein
Journal:  Hum Mutat       Date:  2015-08-27       Impact factor: 4.878

4.  Mutations in the TGF-β repressor SKI cause Shprintzen-Goldberg syndrome with aortic aneurysm.

Authors:  Alexander J Doyle; Jefferson J Doyle; Seneca L Bessling; Samantha Maragh; Mark E Lindsay; Dorien Schepers; Elisabeth Gillis; Geert Mortier; Tessa Homfray; Kimberly Sauls; Russell A Norris; Nicholas D Huso; Dan Leahy; David W Mohr; Mark J Caulfield; Alan F Scott; Anne Destrée; Raoul C Hennekam; Pamela H Arn; Cynthia J Curry; Lut Van Laer; Andrew S McCallion; Bart L Loeys; Harry C Dietz
Journal:  Nat Genet       Date:  2012-09-30       Impact factor: 38.330

5.  Inparanoid: a comprehensive database of eukaryotic orthologs.

Authors:  Kevin P O'Brien; Maido Remm; Erik L L Sonnhammer
Journal:  Nucleic Acids Res       Date:  2005-01-01       Impact factor: 16.971

6.  Mouse anatomy ontologies: enhancements and tools for exploring and integrating biomedical data.

Authors:  Terry F Hayamizu; Richard A Baldock; Martin Ringwald
Journal:  Mamm Genome       Date:  2015-07-25       Impact factor: 2.957

7.  On the reproducibility of science: unique identification of research resources in the biomedical literature.

Authors:  Nicole A Vasilevsky; Matthew H Brush; Holly Paddock; Laura Ponting; Shreejoy J Tripathy; Gregory M Larocca; Melissa A Haendel
Journal:  PeerJ       Date:  2013-09-05       Impact factor: 2.984

8.  The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data.

Authors:  Sebastian Köhler; Sandra C Doelken; Christopher J Mungall; Sebastian Bauer; Helen V Firth; Isabelle Bailleul-Forestier; Graeme C M Black; Danielle L Brown; Michael Brudno; Jennifer Campbell; David R FitzPatrick; Janan T Eppig; Andrew P Jackson; Kathleen Freson; Marta Girdea; Ingo Helbig; Jane A Hurst; Johanna Jähn; Laird G Jackson; Anne M Kelly; David H Ledbetter; Sahar Mansour; Christa L Martin; Celia Moss; Andrew Mumford; Willem H Ouwehand; Soo-Mi Park; Erin Rooney Riggs; Richard H Scott; Sanjay Sisodiya; Steven Van Vooren; Ronald J Wapner; Andrew O M Wilkie; Caroline F Wright; Anneke T Vulto-van Silfhout; Nicole de Leeuw; Bert B A de Vries; Nicole L Washingthon; Cynthia L Smith; Monte Westerfield; Paul Schofield; Barbara J Ruef; Georgios V Gkoutos; Melissa Haendel; Damian Smedley; Suzanna E Lewis; Peter N Robinson
Journal:  Nucleic Acids Res       Date:  2013-11-11       Impact factor: 16.971

9.  Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon.

Authors:  Melissa A Haendel; James P Balhoff; Frederic B Bastian; David C Blackburn; Judith A Blake; Yvonne Bradford; Aurelie Comte; Wasila M Dahdul; Thomas A Dececchi; Robert E Druzinsky; Terry F Hayamizu; Nizar Ibrahim; Suzanna E Lewis; Paula M Mabee; Anne Niknejad; Marc Robinson-Rechavi; Paul C Sereno; Christopher J Mungall
Journal:  J Biomed Semantics       Date:  2014-05-19

10.  Standardized benchmarking in the quest for orthologs.

Authors:  Adrian M Altenhoff; Brigitte Boeckmann; Salvador Capella-Gutierrez; Daniel A Dalquen; Todd DeLuca; Kristoffer Forslund; Jaime Huerta-Cepas; Benjamin Linard; Cécile Pereira; Leszek P Pryszcz; Fabian Schreiber; Alan Sousa da Silva; Damian Szklarczyk; Clément-Marie Train; Peer Bork; Odile Lecompte; Christian von Mering; Ioannis Xenarios; Kimmen Sjölander; Lars Juhl Jensen; Maria J Martin; Matthieu Muffato; Toni Gabaldón; Suzanna E Lewis; Paul D Thomas; Erik Sonnhammer; Christophe Dessimoz
Journal:  Nat Methods       Date:  2016-04-04       Impact factor: 28.547

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  30 in total

Review 1.  Exploring the dark genome: implications for precision medicine.

Authors:  Tudor I Oprea
Journal:  Mamm Genome       Date:  2019-07-04       Impact factor: 2.957

2.  PubCaseFinder: A Case-Report-Based, Phenotype-Driven Differential-Diagnosis System for Rare Diseases.

Authors:  Toyofumi Fujiwara; Yasunori Yamamoto; Jin-Dong Kim; Orion Buske; Toshihisa Takagi
Journal:  Am J Hum Genet       Date:  2018-08-30       Impact factor: 11.025

3.  Encoding Clinical Data with the Human Phenotype Ontology for Computational Differential Diagnostics.

Authors:  Sebastian Köhler; N Christine Øien; Orion J Buske; Tudor Groza; Julius O B Jacobsen; Craig McNamara; Nicole Vasilevsky; Leigh C Carmody; J P Gourdine; Michael Gargano; Julie A McMurry; Daniel Danis; Christopher J Mungall; Damian Smedley; Melissa Haendel; Peter N Robinson
Journal:  Curr Protoc Hum Genet       Date:  2019-09

4.  "Matching" consent to purpose: The example of the Matchmaker Exchange.

Authors:  Stephanie O M Dyke; Bartha M Knoppers; Ada Hamosh; Helen V Firth; Matthew Hurles; Michael Brudno; Kym M Boycott; Anthony A Philippakis; Heidi L Rehm
Journal:  Hum Mutat       Date:  2017-07-12       Impact factor: 4.878

5.  Ontology-based semantic mapping of chemical toxicities.

Authors:  Rong-Lin Wang; Stephen Edwards; Cataia Ives
Journal:  Toxicology       Date:  2018-11-20       Impact factor: 4.221

6.  OMAMO: orthology-based alternative model organism selection.

Authors:  Alina Nicheperovich; Adrian M Altenhoff; Christophe Dessimoz; Sina Majidian
Journal:  Bioinformatics       Date:  2022-03-18       Impact factor: 6.931

Review 7.  The case for open science: rare diseases.

Authors:  Yaffa R Rubinstein; Peter N Robinson; William A Gahl; Paul Avillach; Gareth Baynam; Helene Cederroth; Rebecca M Goodwin; Stephen C Groft; Mats G Hansson; Nomi L Harris; Vojtech Huser; Deborah Mascalzoni; Julie A McMurry; Matthew Might; Christoffer Nellaker; Barend Mons; Dina N Paltoo; Jonathan Pevsner; Manuel Posada; Alison P Rockett-Frase; Marco Roos; Tamar B Rubinstein; Domenica Taruscio; Esther van Enckevort; Melissa A Haendel
Journal:  JAMIA Open       Date:  2020-09-11

8.  KBG syndrome involving a single-nucleotide duplication in ANKRD11.

Authors:  Robert Kleyner; Janet Malcolmson; David Tegay; Kenneth Ward; Annette Maughan; Glenn Maughan; Lesa Nelson; Kai Wang; Reid Robison; Gholson J Lyon
Journal:  Cold Spring Harb Mol Case Stud       Date:  2016-11

9.  Creating a Structured AOP Knowledgebase via Ontology-Based Annotations.

Authors:  Cataia Ives; Ivana Campia; Rong-Lin Wang; Clemens Wittwehr; Stephen Edwards
Journal:  Appl In Vitro Toxicol       Date:  2017-12-01

Review 10.  Clinical Metabolomics: The New Metabolic Window for Inborn Errors of Metabolism Investigations in the Post-Genomic Era.

Authors:  Abdellah Tebani; Lenaig Abily-Donval; Carlos Afonso; Stéphane Marret; Soumeya Bekri
Journal:  Int J Mol Sci       Date:  2016-07-20       Impact factor: 5.923

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