Literature DB >> 27683602

Integration of complex data sources to provide biologic insight into pulmonary vascular disease (2015 Grover Conference Series).

Evan L Brittain1, Stephen Y Chan2.   

Abstract

The application of complex data sources to pulmonary vascular diseases is an emerging and promising area of investigation. The use of -omics platforms, in silico modeling of gene networks, and linkage of large human cohorts with DNA biobanks are beginning to bear biologic insight into pulmonary hypertension. These approaches to high-throughput molecular phenotyping offer the possibility of discovering new therapeutic targets and identifying variability in response to therapy that can be leveraged to improve clinical care. Optimizing the methods for analyzing complex data sources and accruing large, well-phenotyped human cohorts linked to biologic data remain significant challenges. Here, we discuss two specific types of complex data sources-gene regulatory networks and DNA-linked electronic medical record cohorts-that illustrate the promise, challenges, and current limitations of these approaches to understanding and managing pulmonary vascular disease.

Entities:  

Keywords:  biorepository; computational network modeling; electronic medical record; genomics; pulmonary vascular disease; systems biology

Year:  2016        PMID: 27683602      PMCID: PMC5019078          DOI: 10.1086/686995

Source DB:  PubMed          Journal:  Pulm Circ        ISSN: 2045-8932            Impact factor:   3.017


  41 in total

1.  Critical Genomic Networks and Vasoreactive Variants in Idiopathic Pulmonary Arterial Hypertension.

Authors:  Anna R Hemnes; Min Zhao; James West; John H Newman; Stuart Rich; Stephen L Archer; Ivan M Robbins; Timothy S Blackwell; Joy Cogan; James E Loyd; Zhongming Zhao; Christa Gaskill; Christopher Jetter; Jonathan A Kropski; Susan M Majka; Eric D Austin
Journal:  Am J Respir Crit Care Med       Date:  2016-08-15       Impact factor: 21.405

2.  Association of Borderline Pulmonary Hypertension With Mortality and Hospitalization in a Large Patient Cohort: Insights From the Veterans Affairs Clinical Assessment, Reporting, and Tracking Program.

Authors:  Bradley A Maron; Edward Hess; Thomas M Maddox; Alexander R Opotowsky; Ryan J Tedford; Tim Lahm; Karen E Joynt; Daniel J Kass; Thomas Stephens; Maggie A Stanislawski; Erik R Swenson; Ronald H Goldstein; Jane A Leopold; Roham T Zamanian; Jean M Elwing; Mary E Plomondon; Gary K Grunwald; Anna E Barón; John S Rumsfeld; Gaurav Choudhary
Journal:  Circulation       Date:  2016-02-12       Impact factor: 29.690

3.  Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

Authors:  Ewan Birney; John A Stamatoyannopoulos; Anindya Dutta; Roderic Guigó; Thomas R Gingeras; Elliott H Margulies; Zhiping Weng; Michael Snyder; Emmanouil T Dermitzakis; Robert E Thurman; Michael S Kuehn; Christopher M Taylor; Shane Neph; Christoph M Koch; Saurabh Asthana; Ankit Malhotra; Ivan Adzhubei; Jason A Greenbaum; Robert M Andrews; Paul Flicek; Patrick J Boyle; Hua Cao; Nigel P Carter; Gayle K Clelland; Sean Davis; Nathan Day; Pawandeep Dhami; Shane C Dillon; Michael O Dorschner; Heike Fiegler; Paul G Giresi; Jeff Goldy; Michael Hawrylycz; Andrew Haydock; Richard Humbert; Keith D James; Brett E Johnson; Ericka M Johnson; Tristan T Frum; Elizabeth R Rosenzweig; Neerja Karnani; Kirsten Lee; Gregory C Lefebvre; Patrick A Navas; Fidencio Neri; Stephen C J Parker; Peter J Sabo; Richard Sandstrom; Anthony Shafer; David Vetrie; Molly Weaver; Sarah Wilcox; Man Yu; Francis S Collins; Job Dekker; Jason D Lieb; Thomas D Tullius; Gregory E Crawford; Shamil Sunyaev; William S Noble; Ian Dunham; France Denoeud; Alexandre Reymond; Philipp Kapranov; Joel Rozowsky; Deyou Zheng; Robert Castelo; Adam Frankish; Jennifer Harrow; Srinka Ghosh; Albin Sandelin; Ivo L Hofacker; Robert Baertsch; Damian Keefe; Sujit Dike; Jill Cheng; Heather A Hirsch; Edward A Sekinger; Julien Lagarde; Josep F Abril; Atif Shahab; Christoph Flamm; Claudia Fried; Jörg Hackermüller; Jana Hertel; Manja Lindemeyer; Kristin Missal; Andrea Tanzer; Stefan Washietl; Jan Korbel; Olof Emanuelsson; Jakob S Pedersen; Nancy Holroyd; Ruth Taylor; David Swarbreck; Nicholas Matthews; Mark C Dickson; Daryl J Thomas; Matthew T Weirauch; James Gilbert; Jorg Drenkow; Ian Bell; XiaoDong Zhao; K G Srinivasan; Wing-Kin Sung; Hong Sain Ooi; Kuo Ping Chiu; Sylvain Foissac; Tyler Alioto; Michael Brent; Lior Pachter; Michael L Tress; Alfonso Valencia; Siew Woh Choo; Chiou Yu Choo; Catherine Ucla; Caroline Manzano; Carine Wyss; Evelyn Cheung; Taane G Clark; James B Brown; Madhavan Ganesh; Sandeep Patel; Hari Tammana; Jacqueline Chrast; Charlotte N Henrichsen; Chikatoshi Kai; Jun Kawai; Ugrappa Nagalakshmi; Jiaqian Wu; Zheng Lian; Jin Lian; Peter Newburger; Xueqing Zhang; Peter Bickel; John S Mattick; Piero Carninci; Yoshihide Hayashizaki; Sherman Weissman; Tim Hubbard; Richard M Myers; Jane Rogers; Peter F Stadler; Todd M Lowe; Chia-Lin Wei; Yijun Ruan; Kevin Struhl; Mark Gerstein; Stylianos E Antonarakis; Yutao Fu; Eric D Green; Ulaş Karaöz; Adam Siepel; James Taylor; Laura A Liefer; Kris A Wetterstrand; Peter J Good; Elise A Feingold; Mark S Guyer; Gregory M Cooper; George Asimenos; Colin N Dewey; Minmei Hou; Sergey Nikolaev; Juan I Montoya-Burgos; Ari Löytynoja; Simon Whelan; Fabio Pardi; Tim Massingham; Haiyan Huang; Nancy R Zhang; Ian Holmes; James C Mullikin; Abel Ureta-Vidal; Benedict Paten; Michael Seringhaus; Deanna Church; Kate Rosenbloom; W James Kent; Eric A Stone; Serafim Batzoglou; Nick Goldman; Ross C Hardison; David Haussler; Webb Miller; Arend Sidow; Nathan D Trinklein; Zhengdong D Zhang; Leah Barrera; Rhona Stuart; David C King; Adam Ameur; Stefan Enroth; Mark C Bieda; Jonghwan Kim; Akshay A Bhinge; Nan Jiang; Jun Liu; Fei Yao; Vinsensius B Vega; Charlie W H Lee; Patrick Ng; Atif Shahab; Annie Yang; Zarmik Moqtaderi; Zhou Zhu; Xiaoqin Xu; Sharon Squazzo; Matthew J Oberley; David Inman; Michael A Singer; Todd A Richmond; Kyle J Munn; Alvaro Rada-Iglesias; Ola Wallerman; Jan Komorowski; Joanna C Fowler; Phillippe Couttet; Alexander W Bruce; Oliver M Dovey; Peter D Ellis; Cordelia F Langford; David A Nix; Ghia Euskirchen; Stephen Hartman; Alexander E Urban; Peter Kraus; Sara Van Calcar; Nate Heintzman; Tae Hoon Kim; Kun Wang; Chunxu Qu; Gary Hon; Rosa Luna; Christopher K Glass; M Geoff Rosenfeld; Shelley Force Aldred; Sara J Cooper; Anason Halees; Jane M Lin; Hennady P Shulha; Xiaoling Zhang; Mousheng Xu; Jaafar N S Haidar; Yong Yu; Yijun Ruan; Vishwanath R Iyer; Roland D Green; Claes Wadelius; Peggy J Farnham; Bing Ren; Rachel A Harte; Angie S Hinrichs; Heather Trumbower; Hiram Clawson; Jennifer Hillman-Jackson; Ann S Zweig; Kayla Smith; Archana Thakkapallayil; Galt Barber; Robert M Kuhn; Donna Karolchik; Lluis Armengol; Christine P Bird; Paul I W de Bakker; Andrew D Kern; Nuria Lopez-Bigas; Joel D Martin; Barbara E Stranger; Abigail Woodroffe; Eugene Davydov; Antigone Dimas; Eduardo Eyras; Ingileif B Hallgrímsdóttir; Julian Huppert; Michael C Zody; Gonçalo R Abecasis; Xavier Estivill; Gerard G Bouffard; Xiaobin Guan; Nancy F Hansen; Jacquelyn R Idol; Valerie V B Maduro; Baishali Maskeri; Jennifer C McDowell; Morgan Park; Pamela J Thomas; Alice C Young; Robert W Blakesley; Donna M Muzny; Erica Sodergren; David A Wheeler; Kim C Worley; Huaiyang Jiang; George M Weinstock; Richard A Gibbs; Tina Graves; Robert Fulton; Elaine R Mardis; Richard K Wilson; Michele Clamp; James Cuff; Sante Gnerre; David B Jaffe; Jean L Chang; Kerstin Lindblad-Toh; Eric S Lander; Maxim Koriabine; Mikhail Nefedov; Kazutoyo Osoegawa; Yuko Yoshinaga; Baoli Zhu; Pieter J de Jong
Journal:  Nature       Date:  2007-06-14       Impact factor: 49.962

4.  Iron homeostasis and pulmonary hypertension: iron deficiency leads to pulmonary vascular remodeling in the rat.

Authors:  Emanuele Cotroneo; Ali Ashek; Lei Wang; John Wharton; Olivier Dubois; Sophie Bozorgi; Mark Busbridge; Kambiz N Alavian; Martin R Wilkins; Lan Zhao
Journal:  Circ Res       Date:  2015-03-12       Impact factor: 17.367

5.  Network analysis of temporal effects of intermittent and sustained hypoxia on rat lungs.

Authors:  Wei Wu; Nilesh B Dave; Guoying Yu; Patrick J Strollo; Elizabeta Kovkarova-Naumovski; Stefan W Ryter; Stephen R Reeves; Ehab Dayyat; Yang Wang; Augustine M K Choi; David Gozal; Naftali Kaminski
Journal:  Physiol Genomics       Date:  2008-09-30       Impact factor: 3.107

6.  PheWAS: demonstrating the feasibility of a phenome-wide scan to discover gene-disease associations.

Authors:  Joshua C Denny; Marylyn D Ritchie; Melissa A Basford; Jill M Pulley; Lisa Bastarache; Kristin Brown-Gentry; Deede Wang; Dan R Masys; Dan M Roden; Dana C Crawford
Journal:  Bioinformatics       Date:  2010-03-24       Impact factor: 6.937

7.  Architecture of the human regulatory network derived from ENCODE data.

Authors:  Mark B Gerstein; Anshul Kundaje; Manoj Hariharan; Stephen G Landt; Koon-Kiu Yan; Chao Cheng; Xinmeng Jasmine Mu; Ekta Khurana; Joel Rozowsky; Roger Alexander; Renqiang Min; Pedro Alves; Alexej Abyzov; Nick Addleman; Nitin Bhardwaj; Alan P Boyle; Philip Cayting; Alexandra Charos; David Z Chen; Yong Cheng; Declan Clarke; Catharine Eastman; Ghia Euskirchen; Seth Frietze; Yao Fu; Jason Gertz; Fabian Grubert; Arif Harmanci; Preti Jain; Maya Kasowski; Phil Lacroute; Jing Jane Leng; Jin Lian; Hannah Monahan; Henriette O'Geen; Zhengqing Ouyang; E Christopher Partridge; Dorrelyn Patacsil; Florencia Pauli; Debasish Raha; Lucia Ramirez; Timothy E Reddy; Brian Reed; Minyi Shi; Teri Slifer; Jing Wang; Linfeng Wu; Xinqiong Yang; Kevin Y Yip; Gili Zilberman-Schapira; Serafim Batzoglou; Arend Sidow; Peggy J Farnham; Richard M Myers; Sherman M Weissman; Michael Snyder
Journal:  Nature       Date:  2012-09-06       Impact factor: 49.962

Review 8.  Genetics and genomics of pulmonary arterial hypertension.

Authors:  Florent Soubrier; Wendy K Chung; Rajiv Machado; Ekkehard Grünig; Micheala Aldred; Mark Geraci; James E Loyd; C Gregory Elliott; Richard C Trembath; John H Newman; Marc Humbert
Journal:  J Am Coll Cardiol       Date:  2013-12-24       Impact factor: 24.094

9.  Biobanks and electronic medical records: enabling cost-effective research.

Authors:  Erica Bowton; Julie R Field; Sunny Wang; Jonathan S Schildcrout; Sara L Van Driest; Jessica T Delaney; James Cowan; Peter Weeke; Jonathan D Mosley; Quinn S Wells; Jason H Karnes; Christian Shaffer; Josh F Peterson; Joshua C Denny; Dan M Roden; Jill M Pulley
Journal:  Sci Transl Med       Date:  2014-04-30       Impact factor: 17.956

10.  Letter by Mosley Regarding Article, "Iron Homeostasis and Pulmonary Hypertension: Iron Deficiency Leads to Pulmonary Vascular Remodeling in the Rat".

Authors:  Jonathan D Mosley; Evan L Brittain; James E Loyd; Joshua C Denny; Eric D Austin; Emma K Larkin
Journal:  Circ Res       Date:  2015-08-28       Impact factor: 17.367

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  8 in total

1.  Evolving Schema for Employing Network Biology Approaches to Understand Pulmonary Hypertension.

Authors:  Shohini Ghosh-Choudhary; Stephen Y Chan
Journal:  Adv Exp Med Biol       Date:  2021       Impact factor: 2.622

Review 2.  Translational Advances in the Field of Pulmonary Hypertension. Focusing on Developmental Origins and Disease Inception for the Prevention of Pulmonary Hypertension.

Authors:  Bradley A Maron; Steven H Abman
Journal:  Am J Respir Crit Care Med       Date:  2017-02-01       Impact factor: 21.405

3.  Evolving systems biology approaches to understanding non-coding RNAs in pulmonary hypertension.

Authors:  Lloyd D Harvey; Stephen Y Chan
Journal:  J Physiol       Date:  2018-09-02       Impact factor: 5.182

4.  Thermodilution vs Estimated Fick Cardiac Output Measurement in Clinical Practice: An Analysis of Mortality From the Veterans Affairs Clinical Assessment, Reporting, and Tracking (VA CART) Program and Vanderbilt University.

Authors:  Alexander R Opotowsky; Edward Hess; Bradley A Maron; Evan L Brittain; Anna E Barón; Thomas M Maddox; Laith I Alshawabkeh; Bradley M Wertheim; Meng Xu; Tufik R Assad; Jonathan D Rich; Gaurav Choudhary; Ryan J Tedford
Journal:  JAMA Cardiol       Date:  2017-10-01       Impact factor: 14.676

5.  Hemodynamic evidence of vascular remodeling in combined post- and precapillary pulmonary hypertension.

Authors:  Tufik R Assad; Evan L Brittain; Quinn S Wells; Eric H Farber-Eger; Stephen J Halliday; Laura N Doss; Meng Xu; Li Wang; Frank E Harrell; Chang Yu; Ivan M Robbins; John H Newman; Anna R Hemnes
Journal:  Pulm Circ       Date:  2016-09       Impact factor: 3.017

6.  Pulmonary hypertension in patients with chronic kidney disease: invasive hemodynamic etiology and outcomes.

Authors:  Jared M O'Leary; Tufik R Assad; Meng Xu; Kelly A Birdwell; Eric Farber-Eger; Quinn S Wells; Anna R Hemnes; Evan L Brittain
Journal:  Pulm Circ       Date:  2017-06-29       Impact factor: 3.017

7.  Lack of a Tricuspid Regurgitation Doppler Signal and Pulmonary Hypertension by Invasive Measurement.

Authors:  Jared M O'Leary; Tufik R Assad; Meng Xu; Eric Farber-Eger; Quinn S Wells; Anna R Hemnes; Evan L Brittain
Journal:  J Am Heart Assoc       Date:  2018-06-30       Impact factor: 5.501

8.  Racial differences in patients referred for right heart catheterization and risk of pulmonary hypertension.

Authors:  Bin Q Yang; Tufik R Assad; Jared M O'Leary; Meng Xu; Stephen J Halliday; Reid W D'Amico; Eric H Farber-Eger; Quinn S Wells; Anna R Hemnes; Evan L Brittain
Journal:  Pulm Circ       Date:  2018-02-26       Impact factor: 3.017

  8 in total

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