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1

Automated gating of flow cytometry data via robust model-based clustering

Kenneth Lo, Ryan Remy Brinkman, Raphael Gottardo

Journal:

Cytometry Part A

Year:

2008

Language:

english

File:

PDF, 574 KB

english, 2008

2

The occurrence of Psittacosaurus xinjiangensis Sereno and Chow, 1988 in the Urho area, Junggar Basin, Xinjiang, People's Republic of China

Brinkman, Donald B, Eberth, David A, Ryan, M J, Chen, Pei-ji

Journal:

Canadian Journal of Earth Sciences

Year:

2001

Language:

english

File:

PDF, 1.36 MB

english, 2001

3

Flow cytometry data analysis: Recent tools and algorithms

Montante, Sebastiano, Brinkman, Ryan R.

Journal:

International Journal of Laboratory Hematology (Blackwell)

Year:

2019

Language:

english

File:

PDF, 826 KB

english, 2019

4

Outcomes of Isolated Tricuspid Valve Surgery Have Improved in the Modern Era

Hamandi, Mohanad, Smith, Robert L., Ryan, William H., Grayburn, Paul A., Vasudevan, Anupama, George, Timothy J., DiMaio, J. Michael, Hutcheson, Kelley A., Brinkman, William, Szerlip, Molly, Moore, Dav

Journal:

The Annals of Thoracic Surgery

Year:

2019

Language:

english

File:

PDF, 201 KB

english, 2019

5

Gating-ML: XML-based gating descriptions in flow cytometry

Josef Spidlen, Robert C. Leif, Wayne Moore, Mario Roederer, Ryan R. Brinkman

Journal:

Cytometry Part A

Year:

2008

Language:

english

File:

PDF, 285 KB

english, 2008

6

Aortic Valve Replacement Surgery: Comparison of Outcomes in Matched Sternotomy and PORT ACCESS Groups

William T. Brinkman, William Hoffman, Todd M. Dewey, Dan Culica, Syma L. Prince, Morley A. Herbert, Michael J. Mack, William H. Ryan

Journal:

The Annals of Thoracic Surgery

Year:

2010

Language:

english

File:

PDF, 262 KB

english, 2010

7

New leptoceratopsids from the Upper Cretaceous of Alberta, Canada

Michael J. Ryan, David C. Evans, Philip J. Currie, Caleb M. Brown, Don Brinkman

Journal:

Cretaceous Research

Year:

2012

Language:

english

File:

PDF, 2.08 MB

english, 2012

8

High-Content Flow Cytometry and Temporal Data Analysis for Defining a Cellular Signature of Graft-Versus-Host Disease

Ryan Remy Brinkman, Maura Gasparetto, Shang-Jung Jessica Lee, Albert J. Ribickas, Janelle Perkins, William Janssen, Renee Smiley, Clay Smith

Journal:

Biology of Blood and Marrow Transplantation

Year:

2007

Language:

english

File:

PDF, 2.33 MB

english, 2007

9

Renewable Electricity Futures for the United States

Mai, Trieu, Hand, M. Maureen, Baldwin, Samuel F., Wiser, Ryan H., Brinkman, Greg L., Denholm, Paul, Arent, Doug J., Porro, Gian, Sandor, Debra, Hostick, Donna J., Milligan, Michael, DeMeo, Edgar A., B

Journal:

IEEE Transactions on Sustainable Energy

Year:

2014

Language:

english

File:

PDF, 825 KB

english, 2014

10

Repair of Prestressed-Concrete Girders Combining Internal Strand Splicing and Externally Bonded CFRP Techniques

Kasan, Jarret L., Harries, Kent A., Miller, Richard, Brinkman, Ryan J.

Journal:

Journal of Bridge Engineering

Year:

2014

Language:

english

File:

PDF, 1.02 MB

english, 2014

11

Evaluating flow cytometer performance with weighted quadratic least squares analysis of LED and multi-level bead data

Parks, David R., El Khettabi, Faysal, Chase, Eric, Hoffman, Robert A., Perfetto, Stephen P., Spidlen, Josef, Wood, James C.S., Moore, Wayne A., Brinkman, Ryan R.

Journal:

Cytometry Part A

Year:

2017

Language:

english

File:

PDF, 1.34 MB

english, 2017

12

High Throughput Automated Analysis of Big Flow Cytometry Data

Rahim, Albina, Meskas, Justin, Drissler, Sibyl, Yue, Alice, Lorenc, Anna, Laing, Adam, Saran, Namita, White, Jacqui, Abeler-Dörner, Lucie, Hayday, Adrian, Brinkman, Ryan R.

Journal:

Year:

2017

Language:

english

File:

PDF, 5.50 MB

english, 2017

13

flowLearn: Fast and precise identification and quality checking of cell populations in flow cytometry

Lux, Markus, Brinkman, Ryan Remy, Chauve, Cedric, Laing, Adam, Lorenc, Anna, Abeler-Dörner, Lucie, Hammer, Barbara, Wren, Jonathan

Journal:

Year:

2018

Language:

english

File:

PDF, 1.42 MB

english, 2018

14

Methodology for evaluating and comparing flow cytometers: A multisite study of 23 instruments

Parks, David R., Moore, Wayne A., Brinkman, Ryan R., Chen, Yong, Condello, Danilo, El Khettabi, Faysal, Nolan, John P., Perfetto, Stephen P., Redelman, Doug, Spidlen, Josef, Van Dyke, Jonathan, Wang,

Journal:

Cytometry Part A

Year:

2018

Language:

english

File:

PDF, 537 KB

english, 2018

15

Improving the Rigor and Reproducibility of Flow Cytometry‐Based Clinical Research and Trials Through Automated Data Analysis

Brinkman, Ryan R.

Journal:

Cytometry Part A

Year:

2019

Language:

english

File:

PDF, 1.53 MB

english, 2019

16

Occurrence of T-cell and NK-cell subsets with less well-recognized phenotypes in peripheral blood submitted for routine flow cytometry analysis

Hill, Ainsleigh J., Zhang, Chaoran, Kusakabe, Manabu, Gowing, Kevin, Wang, Xuehai, Brinkman, Ryan R., Weng, Andrew P., Craig, Jeffrey W.

Journal:

Cytometry Part B: Clinical Cytometry

Year:

2020

File:

PDF, 1.39 MB

2020

17

Data File Standard for Flow Cytometry, Version FCS 3.2

Spidlen, Josef, Moore, Wayne, Parks, David, Goldberg, Michael, Blenman, Kim, Cavenaugh, James S., Brinkman, Ryan

Journal:

Cytometry Part A

Year:

2020

File:

PDF, 1.30 MB

2020

18

Data quality assessment of ungated flow cytometry data in high throughput experiments

Nolwenn Le Meur, Anthony Rossini, Maura Gasparetto, Clay Smith, Ryan R. Brinkman, Robert Gentleman

Journal:

Cytometry Part A

Year:

2007

Language:

english

File:

PDF, 1.20 MB

english, 2007

19

Correlation analysis of intracellular and secreted cytokines via the generalized integrated mean fluorescence intensity

Parisa Shooshtari, Edgardo S. Fortuno III, Darren Blimkie, Miao Yu, Arvind Gupta, Tobias R. Kollmann, Ryan R. Brinkman

Journal:

Cytometry Part A

Year:

2010

Language:

english

File:

PDF, 678 KB

english, 2010

20

Rapid cell population identification in flow cytometry data

Nima Aghaeepour, Radina Nikolic, Holger H. Hoos, Ryan R. Brinkman

Journal:

Cytometry Part A

Year:

2011

Language:

english

File:

PDF, 1.00 MB

english, 2011

21

Cytogenetic and molecular responses to standard-dose imatinib in chronic myeloid leukemia are correlated with Sokal risk scores and duration of therapy but not trough imatinib plasma levels

Donna L. Forrest, Shannon Trainor, Ryan R. Brinkman, Michael J. Barnett, Donna E. Hogge, Thomas J. Nevill, John D. Shepherd, Stephen H. Nantel, Cynthia L. Toze, Heather J. Sutherland, Kevin W. Song, J

Journal:

Leukemia Research

Year:

2009

Language:

english

File:

PDF, 162 KB

english, 2009

22

Correlation between trough imatinib plasma concentration and clinical response in chronic myeloid leukemia

Donna L. Forrest, Shannon Trainor, Ryan R. Brinkman, Michael J. Barnett, Donna E. Hogge, Thomas J. Nevill, John D. Shepherd, Stephen H. Nantel, Cynthia L. Toze, Heather J. Sutherland, Kevin W. Song, J

Journal:

Leukemia Research

Year:

2009

Language:

english

File:

PDF, 92 KB

english, 2009

23

Reduction in multi-lineage and erythroid progenitors distinguishes myelodysplastic syndromes from non-malignant cytopenias

Suzanne M. Vercauteren, Ali Bashashati, Donghong Wu, Ryan R. Brinkman, Connie Eaves, Allen Eaves, Aly Karsan

Journal:

Leukemia Research

Year:

2009

Language:

english

File:

PDF, 1.01 MB

english, 2009

24

Lyoplate-based multiparameter flow cytometry for the analysis of T cell subsets in human immuno-monitoring studies

Federica Villanova, Paola Di Meglio, Susanne Heck, Margaret Inokuma, Ryan Brinkman, Esperanza Perucha, Maria Hernandez Fuentes, Graham Lord, Skip Maino, Frank O Nestle

Journal:

Journal of Translational Medicine

Year:

2011

Language:

english

File:

PDF, 82 KB

english, 2011

25

Flow cytometry data standards

Josef Spidlen, Parisa Shooshtari, Tobias R Kollmann, Ryan R Brinkman

Journal:

BMC Research Notes

Year:

2011

Language:

english

File:

PDF, 283 KB

english, 2011

26

Toward Understanding the Molecular Pathology of Huntington's Disease

Cheryl L. Wellington, Ryan R. Brinkman, John R. O'Kusky, Michael R. Hayden

Journal:

Brain Pathology

Year:

1997

Language:

english

File:

PDF, 2.44 MB

english, 1997

27

Wrestling with SUMO and bio-ontologies

Stoeckert, Christian, Ball, Catherine, Brazma, Alvis, Brinkman, Ryan, Causton, Helen, Fan, Liju, Fostel, Jennifer, Fragoso, Gilberto, Heiskanen, Mervi, Holstege, Frank

Journal:

Nature Biotechnology

Year:

2006

Language:

english

File:

PDF, 146 KB

english, 2006

28

Reply to 'Reassessing the human mammary stem cell concept by modeling limiting dilution transplantation assays'

Eirew, Peter, Yu, Miao, Brinkman, Ryan, Eaves, Connie J

Journal:

Nature Medicine

Year:

2009

Language:

english

File:

PDF, 140 KB

english, 2009

29

Human monogenic disorders — a source of novel drug targets

Brinkman, Ryan R., Dubé, Marie-Pierre, Rouleau, Guy A., Orr, Andrew C., Samuels, Mark E.

Journal:

Nature Reviews Genetics

Year:

2006

Language:

english

File:

PDF, 467 KB

english, 2006

30

VO: Vaccine Ontology

He, Yongqun, Chen, Fang, Scheuermann, Richard, Todd, Thomas, Brinkman, Ryan, Colby, Lesley, Courtot, Melanie, Rush, Howard, Mungall, Chris, Whetzel, Trish, Musen, Mark, Athey, Brian, Cowell, Lindsay,

Journal:

Bioentrepreneur

Year:

2009

File:

PDF, 273 KB

2009

31

FCS 3.1 Implementation Guidance

Chris Bray, Josef Spidlen, Ryan R. Brinkman

Journal:

Cytometry Part A

Year:

2012

Language:

english

File:

PDF, 342 KB

english, 2012

32

Preoperative Beta-Blocker Usage: Is It Really Worthy of Being a Quality Indicator?

William T. Brinkman, Morley A. Herbert, Syma L. Prince, Mitchell J. Magee, Todd M. Dewey, Robert L. Smith, James R. Edgerton, Stuart J. Head, William H. Ryan, Michael J. Mack

Journal:

The Annals of Thoracic Surgery

Year:

2011

Language:

english

File:

PDF, 440 KB

english, 2011

33

Influence of Surgeon Volume on Outcomes With Aortic Valve Replacement

Todd M. Dewey, Morley A. Herbert, William H. Ryan, William T. Brinkman, Robert Smith, Syma L. Prince, Michael J. Mack

Journal:

The Annals of Thoracic Surgery

Year:

2012

Language:

english

File:

PDF, 374 KB

english, 2012

34

Does Body Mass Index Affect Outcomes for Aortic Valve Replacement Surgery for Aortic Stenosis?

Robert L. Smith II, Morley A. Herbert, Todd M. Dewey, William T. Brinkman, Syma L. Prince, William H. Ryan, Michael J. Mack

Journal:

The Annals of Thoracic Surgery

Year:

2012

Language:

english

File:

PDF, 303 KB

english, 2012

35

Redo Autograft Operations After the Ross Procedure

William T. Brinkman, Morley A. Herbert, Syma L. Prince, Connor Ryan, William H. Ryan

Journal:

The Annals of Thoracic Surgery

Year:

2012

Language:

english

File:

PDF, 243 KB

english, 2012

36

flowCore: a Bioconductor package for high throughput flow cytometry

Florian Hahne, Nolwenn LeMeur, Ryan R Brinkman, Byron Ellis, Perry Haaland, Deepayan Sarkar, Josef Spidlen, Errol Strain, Robert Gentleman

Journal:

BMC Bioinformatics

Year:

2009

Language:

english

File:

PDF, 2.57 MB

english, 2009

37

flowClust: a Bioconductor package for automated gating of flow cytometry data

Kenneth Lo, Florian Hahne, Ryan R Brinkman, Raphael Gottardo

Journal:

BMC Bioinformatics

Year:

2009

Language:

english

File:

PDF, 495 KB

english, 2009

38

FuGEFlow: data model and markup language for flow cytometry

Yu Qian, Olga Tchuvatkina, Josef Spidlen, Peter Wilkinson, Maura Gasparetto, Andrew R Jones, Frank J Manion, Richard H Scheuermann, Rafick-Pierre Sekaly, Ryan R Brinkman

Journal:

BMC Bioinformatics

Year:

2009

Language:

english

File:

PDF, 457 KB

english, 2009

39

Data reduction for spectral clustering to analyze high throughput flow cytometry data

Habil Zare, Parisa Shooshtari, Arvind Gupta, Ryan R Brinkman

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 2.70 MB

english, 2010

40

OntoFox: web-based support for ontology reuse

Zuoshuang Xiang, Mélanie Courtot, Ryan R Brinkman, Alan Ruttenberg, Yongqun He

Journal:

BMC Research Notes

Year:

2010

Language:

english

File:

PDF, 995 KB

english, 2010

41

Modeling biomedical experimental processes with OBI

Ryan R Brinkman, Mélanie Courtot, Dirk Derom, Jennifer M Fostel, Yongqun He, Phillip Lord, James Malone, Helen Parkinson, Bjoern Peters, Philippe Rocca-Serra, Alan Ruttenberg, Susanna-Assunta Sansone,

Journal:

Journal of Biomedical Semantics

Year:

2010

Language:

english

File:

PDF, 1.02 MB

english, 2010

42

Multi-institutional analysis of pancreatic adenocarcinoma demonstrating the effect of diabetes status on survival after resection

Robert M. Cannon, Ryan LeGrand, Ryaz B. Chagpar, Syed A. Ahmad, Rebecca McClaine, Hong Jin Kim, Christopher Rupp, Cliff S. Cho, Adam Brinkman, Sharon Weber, Emily R. Winslow, David A. Kooby, Carrie K.

Journal:

Year:

2012

Language:

english

File:

PDF, 186 KB

english, 2012

43

The phenotypic distribution and functional profile of tuberculin-specific CD4 T-cells characterizes different stages of TB infection

Mathias Streitz, Stephan Fuhrmann, David Thomas, Elizabeth Cheek, Laurel Nomura, Holden Maecker, Peter Martus, Nima Aghaeepour, Ryan R Brinkman, Hans-Dieter Volk, Florian Kern

Journal:

Cytometry Part B: Clinical Cytometry

Year:

2012

Language:

english

File:

PDF, 640 KB

english, 2012

44

FlowRepository: A resource of annotated flow cytometry datasets associated with peer-reviewed publications

Josef Spidlen, Karin Breuer, Chad Rosenberg, Nikesh Kotecha, Ryan R. Brinkman

Journal:

Cytometry Part A

Year:

2012

Language:

english

File:

PDF, 665 KB

english, 2012

45

A Yeast Artificial Chromosome-Based Physical Map of the Juvenile Amyotrophic Lateral Sclerosis (ALS2) Critical Region on Human Chromosome 2q33–q34

Shinji Hadano, Kerrie Nichol, Ryan R. Brinkman, Jamal Nasir, Duane Martindale, Ben F. Koop, Donald W. Nicholson, Stephen W. Scherer, Joh-E Ikeda, Michael R. Hayden

Journal:

Year:

1999

Language:

english

File:

PDF, 138 KB

english, 1999

46

Long-Term Propagation of Distinct Hematopoietic Differentiation Programs In Vivo

Brad Dykstra, David Kent, Michelle Bowie, Lindsay McCaffrey, Melisa Hamilton, Kristin Lyons, Shang-Jung Lee, Ryan Brinkman, Connie Eaves

Journal:

Year:

2007

Language:

english

File:

PDF, 1.49 MB

english, 2007

47

Hematopoietic Stem Cell Subtypes Expand Differentially during Development and Display Distinct Lymphopoietic Programs

Claudia Benz, Michael R. Copley, David G. Kent, Stefan Wohrer, Adrian Cortes, Nima Aghaeepour, Elaine Ma, Heidi Mader, Keegan Rowe, Christopher Day, David Treloar, Ryan R. Brinkman, Connie J. Eaves

Journal:

Year:

2012

Language:

english

File:

PDF, 1.31 MB

english, 2012

48

A Worldwide Assessment of the Frequency of Suicide, Suicide Attempts, or Psychiatric Hospitalization after Predictive Testing for Huntington Disease

Elisabeth W. Almqvist, Maurice Bloch, Ryan Brinkman, David Craufurd, Michael R. Hayden

Journal:

The American Journal of Human Genetics

Year:

1999

Language:

english

File:

PDF, 186 KB

english, 1999

49

A Genome Scan for Modifiers of Age at Onset in Huntington Disease: The HD MAPS Study

Jian-Liang Li, Michael R. Hayden, Elisabeth W. Almqvist, Ryan R. Brinkman, Alexandra Durr, Catherine Dodé, Patrick J. Morrison, Oksana Suchowersky, Christopher A. Ross, Russell L. Margolis, Adam Rosen

Journal:

The American Journal of Human Genetics

Year:

2003

Language:

english

File:

PDF, 593 KB

english, 2003

50

Identification of a Novel Gene (HSN2) Causing Hereditary Sensory and Autonomic Neuropathy Type II through the Study of Canadian Genetic Isolates

Ronald G. Lafrenière, Marcia L.E. MacDonald, Marie-Pierre Dubé, Julie MacFarlane, Mary O’Driscoll, Bernard Brais, Sébastien Meilleur, Ryan R. Brinkman, Owen Dadivas, Terry Pape, Christèle Platon, Chri

Journal:

The American Journal of Human Genetics

Year:

2004

Language:

english

File:

PDF, 674 KB

english, 2004