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ORCIDBibTeX records: Richard H. Scheuermann
@article{DBLP:journals/bioinformatics/RoblesJSSBWOQ23,
author = {Edgar E. Robles and
Ye Jin and
Padhraic Smyth and
Richard H. Scheuermann and
Jack D. Bui and
Huan{-}You Wang and
Jean Oak and
Yu Qian},
title = {A cell-level discriminative neural network model for diagnosis of
blood cancers},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad585},
doi = {10.1093/BIOINFORMATICS/BTAD585},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/RoblesJSSBWOQ23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/OlsonABCCDDDDKKLLMMMNNOOPPPPSSSTTVV23,
author = {Robert D. Olson and
Rida Assaf and
Thomas S. Brettin and
Neal Conrad and
Clark Cucinell and
James J. Davis and
Donald M. Dempsey and
Allan Dickerman and
Emily M. Dietrich and
Ronald W. Kenyon and
Mehmet Kuscuoglu and
Elliot J. Lefkowitz and
Jian Lu and
Dustin Machi and
Catherine Macken and
Chunhong Mao and
Anna Maria Niewiadomska and
Marcus Nguyen and
Gary J. Olsen and
Jamie C. Overbeek and
Bruce D. Parrello and
Victoria Parrello and
Jacob s Porter and
Gordon D. Pusch and
Maulik Shukla and
Indresh Singh and
Lucy Stewart and
Gene Tan and
Chris Thomas and
Margo VanOeffelen and
Veronika Vonstein and
Zachary S. Wallace and
Andrew S. Warren and
Alice R. Wattam and
Fangfang Xia and
Hyun Seung Yoo and
Yun Zhang and
Christian M. Zmasek and
Richard H. Scheuermann and
Rick L. Stevens},
title = {Introducing the Bacterial and Viral Bioinformatics Resource Center
{(BV-BRC):} a resource combining PATRIC, {IRD} and ViPR},
journal = {Nucleic Acids Res.},
volume = {51},
number = {{D1}},
pages = {678--689},
year = {2023},
url = {https://doi.org/10.1093/nar/gkac1003},
doi = {10.1093/NAR/GKAC1003},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/OlsonABCCDDDDKKLLMMMNNOOPPPPSSSTTVV23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhangSMAKSQQ22,
author = {Yun Zhang and
Hao Sun and
Aishwarya Mandava and
Brian D. Aevermann and
Tobias R. Kollmann and
Richard H. Scheuermann and
Xing Qiu and
Yu Qian},
title = {FastMix: a versatile data integration pipeline for cell type-specific
biomarker inference},
journal = {Bioinform.},
volume = {38},
number = {20},
pages = {4735--4744},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac585},
doi = {10.1093/BIOINFORMATICS/BTAC585},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhangSMAKSQQ22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/fbinf/WallaceDNOSSZZS22,
author = {Zachary S. Wallace and
James J. Davis and
Anna Maria Niewiadomska and
Robert D. Olson and
Maulik Shukla and
Rick Stevens and
Yun Zhang and
Christian M. Zmasek and
Richard H. Scheuermann},
title = {Early detection of emerging SARS-CoV-2 variants of interest for experimental
evaluation},
journal = {Frontiers Bioinform.},
volume = {2},
year = {2022},
url = {https://doi.org/10.3389/fbinf.2022.1020189},
doi = {10.3389/FBINF.2022.1020189},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/fbinf/WallaceDNOSSZZS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhangABMHLS21,
author = {Yun Zhang and
Brian D. Aevermann and
Trygve E. Bakken and
Jeremy A. Miller and
Rebecca D. Hodge and
Ed S. Lein and
Richard H. Scheuermann},
title = {FR-Match: robust matching of cell type clusters from single cell {RNA}
sequencing data using the Friedman-Rafsky non-parametric test},
journal = {Briefings Bioinform.},
volume = {22},
number = {4},
year = {2021},
url = {https://doi.org/10.1093/bib/bbaa339},
doi = {10.1093/BIB/BBAA339},
timestamp = {Mon, 08 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/ZhangABMHLS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/VitaZJDOMBSHKBL21,
author = {Randi Vita and
Jie Zheng and
Rebecca C. Jackson and
Damion M. Dooley and
James A. Overton and
Mark A. Miller and
Daniel C. Berrios and
Richard H. Scheuermann and
Yongqun He and
Hande K{\"{u}}{\c{c}}{\"{u}}k{-}McGinty and
Mathias Brochhausen and
Aisyah Yu Lin and
Sagar B. Jain and
Marcus C. Chibucos and
John Judkins and
Michelle G. Giglio and
Irene Y. Feng and
Gully Burns and
Matthew H. Brush and
Bjoern Peters and
Christian J. Stoeckert Jr.},
title = {Standardization of assay representation in the Ontology for Biomedical
Investigations},
journal = {Database J. Biol. Databases Curation},
volume = {2021},
year = {2021},
url = {https://doi.org/10.1093/database/baab040},
doi = {10.1093/DATABASE/BAAB040},
timestamp = {Tue, 16 Aug 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/VitaZJDOMBSHKBL21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bibm/Scheuermann21,
author = {Richard H. Scheuermann},
editor = {Yufei Huang and
Lukasz A. Kurgan and
Feng Luo and
Xiaohua Hu and
Yidong Chen and
Edward R. Dougherty and
Andrzej Kloczkowski and
Yaohang Li},
title = {Abstract: Explainable artificial intelligence and single cell genomics
to understand the cellular complexity of human brain},
booktitle = {{IEEE} International Conference on Bioinformatics and Biomedicine,
{BIBM} 2021, Houston, TX, USA, December 9-12, 2021},
pages = {4},
publisher = {{IEEE}},
year = {2021},
url = {https://doi.org/10.1109/BIBM52615.2021.9669451},
doi = {10.1109/BIBM52615.2021.9669451},
timestamp = {Tue, 18 Jan 2022 09:39:01 +0100},
biburl = {https://dblp.org/rec/conf/bibm/Scheuermann21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/mlhc/JiNQSS18,
author = {Disi Ji and
Eric T. Nalisnick and
Yu Qian and
Richard H. Scheuermann and
Padhraic Smyth},
editor = {Finale Doshi{-}Velez and
Jim Fackler and
Ken Jung and
David C. Kale and
Rajesh Ranganath and
Byron C. Wallace and
Jenna Wiens},
title = {Bayesian Trees for Automated Cytometry Data Analysis},
booktitle = {Proceedings of the Machine Learning for Healthcare Conference, {MLHC}
2018, 17-18 August 2018, Palo Alto, California},
series = {Proceedings of Machine Learning Research},
volume = {85},
pages = {465--483},
publisher = {{PMLR}},
year = {2018},
url = {http://proceedings.mlr.press/v85/ji18a.html},
timestamp = {Wed, 03 Apr 2019 18:17:31 +0200},
biburl = {https://dblp.org/rec/conf/mlhc/JiNQSS18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ChristleyLTFMRR17,
author = {Scott Christley and
Mikhail K. Levin and
Inimary T. Toby and
John M. Fonner and
Nancy Monson and
William Rounds and
Florian Rubelt and
Walter Scarborough and
Richard H. Scheuermann and
Lindsay G. Cowell},
title = {VDJPipe: a pipelined tool for pre-processing immune repertoire sequencing
data},
journal = {{BMC} Bioinform.},
volume = {18},
number = {1},
pages = {448:1--448:5},
year = {2017},
url = {https://doi.org/10.1186/s12859-017-1853-z},
doi = {10.1186/S12859-017-1853-Z},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ChristleyLTFMRR17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BakkenCANHMLCMP17,
author = {Trygve E. Bakken and
Lindsay G. Cowell and
Brian D. Aevermann and
Mark Novotny and
Rebecca D. Hodge and
Jeremy A. Miller and
Alexandra Lee and
Ivan Chang and
Jamison M. McCorrison and
Bali Pulendran and
Yu Qian and
Nicholas J. Schork and
Roger S. Lasken and
Ed S. Lein and
Richard H. Scheuermann},
title = {Cell type discovery and representation in the era of high-content
single cell phenotyping},
journal = {{BMC} Bioinform.},
volume = {18},
number = {{S-17}},
pages = {7--16},
year = {2017},
url = {https://doi.org/10.1186/s12859-017-1977-1},
doi = {10.1186/S12859-017-1977-1},
timestamp = {Mon, 08 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/BakkenCANHMLCMP17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/ZhangAABDGHKLLL17,
author = {Yun Zhang and
Brian D. Aevermann and
Tavis K. Anderson and
David F. Burke and
Gwenaelle Dauphin and
Zhiping Gu and
Sherry He and
Sanjeev Kumar and
Christopher N. Larsen and
Alexandra J. Lee and
Xiaomei Li and
Catherine Macken and
Colin Mahaffey and
Brett E. Pickett and
Brian Reardon and
Thomas Smith and
Lucy Stewart and
Christian Suloway and
Guangyu Sun and
Lei Tong and
Amy L. Vincent and
Bryan Walters and
Sam Zaremba and
Hongtao Zhao and
Liwei Zhou and
Christian M. Zmasek and
Edward B. Klem and
Richard H. Scheuermann},
title = {Influenza Research Database: An integrated bioinformatics resource
for influenza virus research},
journal = {Nucleic Acids Res.},
volume = {45},
number = {Database-Issue},
pages = {D466--D474},
year = {2017},
url = {https://doi.org/10.1093/nar/gkw857},
doi = {10.1093/NAR/GKW857},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nar/ZhangAABDGHKLLL17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/AevermannMVHBMN17,
author = {Brian D. Aevermann and
Jamison M. McCorrison and
Pratap Venepally and
Rebecca D. Hodge and
Trygve E. Bakken and
Jeremy A. Miller and
Mark Novotny and
Danny N. Tran and
Francisco Diez{-}Fuertes and
Lena Christiansen and
Fan Zhang and
Frank Steemers and
Roger S. Lasken and
Ed S. Lein and
Nicholas J. Schork and
Richard H. Scheuermann},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Marylyn D. Ritchie and
Teri E. Klein},
title = {Production of a Preliminary Quality Control Pipeline for Single Nuclei
RNA-Seq and Its Application in the Analysis of Cell Type Diversity
of Post-Mortem Human Brain Neocortex},
booktitle = {Biocomputing 2017: Proceedings of the Pacific Symposium, Kohala Coast,
Hawaii, USA, January 3-7, 2017},
pages = {564--575},
year = {2017},
url = {http://psb.stanford.edu/psb-online/proceedings/psb17/aevermann.pdf},
timestamp = {Mon, 08 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/psb/AevermannMVHBMN17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/TobyLSCBBBCFGHM16,
author = {Inimary T. Toby and
Mikhail K. Levin and
Edward Salinas and
Scott Christley and
Sanchita Bhattacharya and
Felix Breden and
Adam Buntzman and
Brian Corrie and
John M. Fonner and
Namita T. Gupta and
Uri Hershberg and
Nishanth Marthandan and
Aaron M. Rosenfeld and
William Rounds and
Florian Rubelt and
Walter Scarborough and
Jamie K. Scott and
Mohamed Uduman and
Jason A. Vander Heiden and
Richard H. Scheuermann and
Nancy Monson and
Steven H. Kleinstein and
Lindsay G. Cowell},
title = {{VDJML:} a file format with tools for capturing the results of inferring
immune receptor rearrangements},
journal = {{BMC} Bioinform.},
volume = {17},
number = {{S-13}},
pages = {333},
year = {2016},
url = {https://doi.org/10.1186/s12859-016-1214-3},
doi = {10.1186/S12859-016-1214-3},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/TobyLSCBBBCFGHM16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CourtotMDDGJTMM15,
author = {M{\'{e}}lanie Courtot and
Justin Meskas and
Alexander D. Diehl and
Radina Droumeva and
Raphael Gottardo and
Adrin Jalali and
Mohammad Jafar Taghiyar and
Holden T. Maecker and
J. Philip McCoy and
Alan Ruttenberg and
Richard H. Scheuermann and
Ryan Remy Brinkman},
title = {flowCL: ontology-based cell population labelling in flow cytometry},
journal = {Bioinform.},
volume = {31},
number = {8},
pages = {1337--1339},
year = {2015},
url = {https://doi.org/10.1093/bioinformatics/btu807},
doi = {10.1093/BIOINFORMATICS/BTU807},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/CourtotMDDGJTMM15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/xsede/QianKPWSLXASS15,
author = {Yu Qian and
Hyunsoo Kim and
Shweta Purawat and
Jianwu Wang and
Rick Stanton and
Alexandra Lee and
Weijia Xu and
Ilkay Altintas and
Robert S. Sinkovits and
Richard H. Scheuermann},
editor = {Gregory D. Peterson},
title = {FlowGate: towards extensible and scalable web-based flow cytometry
data analysis},
booktitle = {Proceedings of the 2015 {XSEDE} Conference: Scientific Advancements
Enabled by Enhanced Cyberinfrastructure, St. Louis, MO, USA, July
26 - 30, 2015},
pages = {5:1--5:8},
publisher = {{ACM}},
year = {2015},
url = {https://doi.org/10.1145/2792745.2792750},
doi = {10.1145/2792745.2792750},
timestamp = {Fri, 30 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/xsede/QianKPWSLXASS15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/scfbm/SpidlenBBCNHQLRMWSSB13,
author = {Josef Spidlen and
Aaron Barsky and
Karin Breuer and
Peter Carr and
Marc{-}Danie Nazaire and
Barbara A. Hill and
Yu Qian and
Ted Liefeld and
Michael Reich and
Jill P. Mesirov and
Peter Wilkinson and
Richard H. Scheuermann and
Rafick{-}Pierre Sekaly and
Ryan Remy Brinkman},
title = {GenePattern Flow Cytometry Suite},
journal = {Source Code Biol. Medicine},
volume = {8},
pages = {14},
year = {2013},
url = {https://doi.org/10.1186/1751-0473-8-14},
doi = {10.1186/1751-0473-8-14},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/scfbm/SpidlenBBCNHQLRMWSSB13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/PickettSZNSHLKZGZLDKS12,
author = {Brett E. Pickett and
Eva L. Sadat and
Yun Zhang and
Jyothi Noronha and
R. Burke Squires and
Victoria Hunt and
Mengya Liu and
Sanjeev Kumar and
Sam Zaremba and
Zhiping Gu and
Liwei Zhou and
Christopher N. Larsen and
Jonathan Dietrich and
Edward B. Klem and
Richard H. Scheuermann},
title = {ViPR: an open bioinformatics database and analysis resource for virology
research},
journal = {Nucleic Acids Res.},
volume = {40},
number = {Database-Issue},
pages = {593--598},
year = {2012},
url = {https://doi.org/10.1093/nar/gkr859},
doi = {10.1093/NAR/GKR859},
timestamp = {Sun, 12 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nar/PickettSZNSHLKZGZLDKS12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/amia/RobertsRHSTBBP12,
author = {Kirk Roberts and
Bryan Rink and
Sanda M. Harabagiu and
Richard H. Scheuermann and
Seth M. Toomay and
Travis Browning and
Teresa Bosler and
Ronald M. Peshock},
title = {A Machine Learning Approach for Identifying Anatomical Locations of
Actionable Findings in Radiology Reports},
booktitle = {{AMIA} 2012, American Medical Informatics Association Annual Symposium,
Chicago, Illinois, USA, November 3-7, 2012},
publisher = {{AMIA}},
year = {2012},
url = {https://knowledge.amia.org/amia-55142-a2012a-1.636547/t-003-1.640625/f-001-1.640626/a-090-1.640963/a-091-1.640960},
timestamp = {Wed, 17 Apr 2024 11:48:03 +0200},
biburl = {https://dblp.org/rec/conf/amia/RobertsRHSTBBP12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ao/Rocca-SerraROWSGCBSSP11,
author = {Philippe Rocca{-}Serra and
Alan Ruttenberg and
Martin J. O'Connor and
Patricia L. Whetzel and
Daniel Schober and
Jay Greenbaum and
M{\'{e}}lanie Courtot and
Ryan Remy Brinkman and
Susanna{-}Assunta Sansone and
Richard H. Scheuermann and
Bjoern Peters},
title = {Overcoming the ontology enrichment bottleneck with Quick Term Templates},
journal = {Appl. Ontology},
volume = {6},
number = {1},
pages = {13--22},
year = {2011},
url = {https://doi.org/10.3233/AO-2011-0086},
doi = {10.3233/AO-2011-0086},
timestamp = {Tue, 14 Jul 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ao/Rocca-SerraROWSGCBSSP11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbi/SmithS11,
author = {Barry Smith and
Richard H. Scheuermann},
title = {Ontologies for clinical and translational research: Introduction},
journal = {J. Biomed. Informatics},
volume = {44},
number = {1},
pages = {3--7},
year = {2011},
url = {https://doi.org/10.1016/j.jbi.2011.01.002},
doi = {10.1016/J.JBI.2011.01.002},
timestamp = {Tue, 16 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jbi/SmithS11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbi/KongDXQKS11,
author = {Y. Megan Kong and
Carl Dahlke and
Qun Xiang and
Yu Qian and
David R. Karp and
Richard H. Scheuermann},
title = {Toward an ontology-based framework for clinical research databases},
journal = {J. Biomed. Informatics},
volume = {44},
number = {1},
pages = {48--58},
year = {2011},
url = {https://doi.org/10.1016/j.jbi.2010.05.001},
doi = {10.1016/J.JBI.2010.05.001},
timestamp = {Tue, 16 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jbi/KongDXQKS11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbi/DiehlABCGGMMMNPPSYZM11,
author = {Alexander D. Diehl and
Alison Deckhut Augustine and
Judith A. Blake and
Lindsay G. Cowell and
Elizabeth S. Gold and
Timothy A. Gondr{\'{e}}{-}Lewis and
Anna Maria Masci and
Terrence F. Meehan and
Penelope A. Morel and
Anastasia Nijnik and
Bjoern Peters and
Bali Pulendran and
Richard H. Scheuermann and
Q. Alison Yao and
Martin S. Zand and
Christopher J. Mungall},
title = {Hematopoietic cell types: Prototype for a revised cell ontology},
journal = {J. Biomed. Informatics},
volume = {44},
number = {1},
pages = {75--79},
year = {2011},
url = {https://doi.org/10.1016/j.jbi.2010.01.006},
doi = {10.1016/J.JBI.2010.01.006},
timestamp = {Tue, 16 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jbi/DiehlABCGGMMMNPPSYZM11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhangCKS10,
author = {Song Zhang and
Jing Cao and
Y. Megan Kong and
Richard H. Scheuermann},
title = {GO-Bayes: Gene Ontology-based overrepresentation analysis using a
Bayesian approach},
journal = {Bioinform.},
volume = {26},
number = {7},
pages = {905--911},
year = {2010},
url = {https://doi.org/10.1093/bioinformatics/btq059},
doi = {10.1093/BIOINFORMATICS/BTQ059},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhangCKS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijbra/ChangLJS10,
author = {Roger L. Chang and
Feng Luo and
Stuart Johnson and
Richard H. Scheuermann},
title = {Deterministic graph-theoretic algorithm for detecting modules in biological
interaction networks},
journal = {Int. J. Bioinform. Res. Appl.},
volume = {6},
number = {2},
pages = {101--119},
year = {2010},
url = {https://doi.org/10.1504/IJBRA.2010.032115},
doi = {10.1504/IJBRA.2010.032115},
timestamp = {Fri, 11 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ijbra/ChangLJS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijcbdd/ChenMLKHYS10,
author = {Zhongxue Chen and
Monnie McGee and
Qingzhong Liu and
Y. Megan Kong and
Xudong Huang and
Jack Y. Yang and
Richard H. Scheuermann},
title = {Identifying Differentially Expressed Genes based on probe level data
for GeneChip arrays},
journal = {Int. J. Comput. Biol. Drug Des.},
volume = {3},
number = {3},
pages = {237--257},
year = {2010},
url = {https://doi.org/10.1504/IJCBDD.2010.038028},
doi = {10.1504/IJCBDD.2010.038028},
timestamp = {Sat, 25 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ijcbdd/ChenMLKHYS10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/ThomsonMHMESWMGKSTGH10,
author = {Glenys Thomson and
Nishanth Marthandan and
Jill A. Hollenbach and
Steven J. Mack and
Henry A. Erlich and
Richard M. Single and
Matthew J. Waller and
Steven G. E. Marsh and
Paula A. Guidry and
David R. Karp and
Richard H. Scheuermann and
Susan D. Thompson and
David N. Glass and
Wolfgang Helmberg},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Tiffany Murray and
Teri E. Klein},
title = {Sequence Feature Variant Type {(SFVT)} Analysis of the {HLA} Genetic
Association in Juvenile Idiopathic Arthritis},
booktitle = {Biocomputing 2010: Proceedings of the Pacific Symposium, Kamuela,
Hawaii, USA, 4-8 January 2010},
pages = {359--370},
publisher = {World Scientific Publishing},
year = {2010},
url = {http://psb.stanford.edu/psb-online/proceedings/psb10/thomson.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/ThomsonMHMESWMGKSTGH10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LuoLWS09,
author = {Feng Luo and
Bo Li and
Xiu{-}Feng Wan and
Richard H. Scheuermann},
title = {Core and periphery structures in protein interaction networks},
journal = {{BMC} Bioinform.},
volume = {10},
number = {{S-4}},
year = {2009},
url = {https://doi.org/10.1186/1471-2105-10-S4-S8},
doi = {10.1186/1471-2105-10-S4-S8},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/LuoLWS09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/MasciADLMSSC09,
author = {Anna Maria Masci and
Cecilia N. Arighi and
Alexander D. Diehl and
Anne E. Lieberman and
Chris Mungall and
Richard H. Scheuermann and
Barry Smith and
Lindsay G. Cowell},
title = {An improved ontological representation of dendritic cells as a paradigm
for all cell types},
journal = {{BMC} Bioinform.},
volume = {10},
year = {2009},
url = {https://doi.org/10.1186/1471-2105-10-70},
doi = {10.1186/1471-2105-10-70},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/MasciADLMSSC09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/QianTSWGJMSSB09,
author = {Yu Qian and
Olga Tchuvatkina and
Josef Spidlen and
Peter Wilkinson and
Maura Gasparetto and
Andrew R. Jones and
Frank J. Manion and
Richard H. Scheuermann and
Rafick{-}Pierre Sekaly and
Ryan Remy Brinkman},
title = {FuGEFlow: data model and markup language for flow cytometry},
journal = {{BMC} Bioinform.},
volume = {10},
year = {2009},
url = {https://doi.org/10.1186/1471-2105-10-184},
doi = {10.1186/1471-2105-10-184},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/QianTSWGJMSSB09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/amia/CariniPLBBGHHMNNSS09,
author = {Simona Carini and
Brad Pollock and
Harold P. Lehmann and
Suzanne Bakken and
Edward M. Barbour and
Davera Gabriel and
Herbert K. Hagler and
Caryn R. Harper and
Shamim Mollah and
Meredith Nahm and
Hien H. Nguyen and
Richard H. Scheuermann and
Ida Sim},
title = {Development and Evaluation of a Study Design Typology for Human Research},
booktitle = {{AMIA} 2009, American Medical Informatics Association Annual Symposium,
San Francisco, CA, USA, November 14-18, 2009},
publisher = {{AMIA}},
year = {2009},
url = {https://knowledge.amia.org/amia-55142-a2009a-1.626575/t-001-1.627318/f-001-1.627319/a-016-1.627673/a-017-1.627670},
timestamp = {Wed, 17 Apr 2024 11:48:10 +0200},
biburl = {https://dblp.org/rec/conf/amia/CariniPLBBGHHMNNSS09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/SquiresMGGNHCLKBS08,
author = {R. Burke Squires and
Catherine Macken and
Adolfo Garcia{-}Sastre and
Shubhada Godbole and
Jyothi Noronha and
Victoria Hunt and
Roger L. Chang and
Christopher N. Larsen and
Edward B. Klem and
Kevin Biersack and
Richard H. Scheuermann},
title = {BioHealthBase: informatics support in the elucidation of influenza
virus host-pathogen interactions and virulence},
journal = {Nucleic Acids Res.},
volume = {36},
number = {Database-Issue},
pages = {497--503},
year = {2008},
url = {https://doi.org/10.1093/nar/gkm905},
doi = {10.1093/NAR/GKM905},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/SquiresMGGNHCLKBS08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bibm/GrindingerLWS08,
author = {Thomas Grindinger and
Feng Luo and
Xiu{-}Feng Wan and
Richard H. Scheuermann},
editor = {Xue{-}wen Chen and
Xiaohua Hu and
Sun Kim},
title = {Exploring Core/Periphery Structures in Protein Interaction Networks
Provides Structure-Property Relation Insights},
booktitle = {2008 {IEEE} International Conference on Bioinformatics and Biomedicine,
{BIBM} 2008, Philadephia, Pennsylvania, USA, November 3-5, 2008},
pages = {179--186},
publisher = {{IEEE} Computer Society},
year = {2008},
url = {https://doi.org/10.1109/BIBM.2008.9},
doi = {10.1109/BIBM.2008.9},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/bibm/GrindingerLWS08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LuoYCCZS07,
author = {Feng Luo and
Yunfeng Yang and
Chin{-}Fu Chen and
Roger L. Chang and
Jizhong Zhou and
Richard H. Scheuermann},
title = {Modular organization of protein interaction networks},
journal = {Bioinform.},
volume = {23},
number = {2},
pages = {207--214},
year = {2007},
url = {https://doi.org/10.1093/bioinformatics/btl562},
doi = {10.1093/BIOINFORMATICS/BTL562},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LuoYCCZS07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ChenMLS07,
author = {Zhongxue Chen and
Monnie McGee and
Qingzhong Liu and
Richard H. Scheuermann},
title = {A distribution free summarization method for Affymetrix GeneChip\({}^{\mbox{{\textregistered}}}\)
arrays},
journal = {Bioinform.},
volume = {23},
number = {3},
pages = {321--327},
year = {2007},
url = {https://doi.org/10.1093/bioinformatics/btl609},
doi = {10.1093/BIOINFORMATICS/BTL609},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ChenMLS07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DiehlLSB07,
author = {Alexander D. Diehl and
Jamie A. Lee and
Richard H. Scheuermann and
Judith A. Blake},
title = {Ontology development for biological systems: immunology},
journal = {Bioinform.},
volume = {23},
number = {7},
pages = {913--915},
year = {2007},
url = {https://doi.org/10.1093/bioinformatics/btm029},
doi = {10.1093/BIOINFORMATICS/BTM029},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/DiehlLSB07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LuoYCCZS07a,
author = {Feng Luo and
Yunfeng Yang and
Chin{-}Fu Chen and
Roger L. Chang and
Jizhong Zhou and
Richard H. Scheuermann},
title = {Modular organization of protein interaction networks},
journal = {Bioinform.},
volume = {23},
number = {7},
pages = {916},
year = {2007},
url = {https://doi.org/10.1093/bioinformatics/btm037},
doi = {10.1093/BIOINFORMATICS/BTM037},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LuoYCCZS07a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LeeSMRCYSHCSS06,
author = {Jamie A. Lee and
Robert S. Sinkovits and
Dennis Mock and
Eva L. Rab and
Jennifer Cai and
Peng Yang and
Brian Saunders and
Robert C. Hsueh and
Sangdun Choi and
Shankar Subramaniam and
Richard H. Scheuermann},
title = {Components of the antigen processing and presentation pathway revealed
by gene expression microarray analysis following {B} cell antigen
receptor {(BCR)} stimulation},
journal = {{BMC} Bioinform.},
volume = {7},
pages = {237},
year = {2006},
url = {https://doi.org/10.1186/1471-2105-7-237},
doi = {10.1186/1471-2105-7-237},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/LeeSMRCYSHCSS06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/imsccs/LuoS06,
author = {Feng Luo and
Richard H. Scheuermann},
editor = {Jun Ni and
Jack J. Dongarra},
title = {Detecting Functional Modules from Protein Interaction Networks},
booktitle = {Interdisciplinary and Multidisciplinary Research in Computer Science,
{IEEE} {CS} Proceeding of the First International Multi-Symposium
of Computer and Computational Sciences (IMSCCS{\(\vert\)}06), June
20-24, 2006, Zhejiang University, Hangzhou, China, Vol. 1},
pages = {123--130},
publisher = {{IEEE} Computer Society},
year = {2006},
url = {https://doi.org/10.1109/IMSCCS.2006.55},
doi = {10.1109/IMSCCS.2006.55},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/imsccs/LuoS06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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