Dr. Ryan Brinkman’s Publications  

Hahne F*, Khodabakhshi AH*,  Bashashati A, Wong C-J, Gascoyne RD, . Weng AP, Seifert-Margolis S, Bourcier K, Asare A, Lumley T, Gentleman R, Brinkman RR. Per-channel basis normalization methods for flow cytometry data. Cytometry A. [Epub ahead of print Nov 6], 2009. View Abstract

Qian Y*, Tchuvatkina O*, Spidlen J, Wilkinson P, Gasparetto M, Jones AR, Manion FJ, Scheuermann RH,  Sekaly R-P,  Brinkman RR. FuGEFlow: data model and markup language for flow cytometry. BMC Bioinformatics 10:184. 2009. View Abstract

Vercauteren S, Bashashati A; Wu D; Brinkman R; Eaves C, Eaves A, Karsten A. Reduction in multilineage and erythroid progenitors distinguishes myelodysplastic syndromes from non-malignant cytopenias Leukemia Research 33 (12):1636-42 2009. View Abstract

Lo K, Hahne F, Brinkman RR, Gottardo R. flowClust: a Bioconductor package for automated gating of flow cytometry data. BMC Bioinformatics 10(1): 145 2009. View Abstract

Forrest DL, Trainor S, Brinkman RR, Barnett MJ, Hogge DE, Nevill TJ, Shepherd JD, Nantel SH, Toze CL, Sutherland HJ, Song KW, Lavoie JC, Power MM, Abou-Mourad Y, & Smith CA. 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. Leuk Res 33(2):271-5, 2009. View Abstract

Forrest Dl, Trainor S, Brinkman RR, Barnett MJ, Hogge DE, Nevill TJ, Shepherd JD, Nantel SH, Toze CL, Sutherland HJ, Song KW, Lavoie JC, Power MM, Abou-Mourad Y, Smith CA.  Correlation between trough imatinib plasma concentration and clinical response in chronic myeloid leukemia.  Leukemia Research 33(8):1149-50, 2009.

Hahne F, Le Meur N, Brinkman RR, Ellis B, Haaland P, Sarkar D, Spidlen J, Strain E, Gentleman R.  flowCore: a Bioconductor package for high throughput flow cytometry.  BMC Bioinformatics 10(1): 106, 2009. View Abstract

Johnson NA, Boyle M, Bashashati A, Leach S, Brooks-Wilson A, Sehn LH, Chhanabhai M, Brinkman RR, Connors JM, Weng AP, Gascoyne. Diffuse large B cell lymphoma: reduced CD20 expression is associated with an inferior survival. Blood 113(16): 3773-3780 2008.  View Abstract 

Lee JA, Spidlen J, Boyce K, Cai J, Crosbie N, Dalphin M, Furlong J, Gasparetto M, Goldberg M, Goralczyk EM, Hyun B, Jansen K, Kollmann T, Kong M, Leif R, McWeeney S, Moloshok TD, Moore W, Nolan G, Nolan J, Nikolich-Zugich J, Parrish D, Purcell B, Qian Y, Selvaraj B, Smith C, Tchuvatkina O, Wertheimer A, Wilkinson P, Wilson C, Wood J, Zigon R, Scheuermann RH, & Brinkman RR. MIFlowCyt: the minimum information about a Flow Cytometry Experiment. Cytometry A 73 (10): 926-30, 2008.View Abstract

Lo K, Brinkman RR, & Gottardo R. Automated gating of flow cytometry data via robust model-based clustering. Cytometry A 73 (4): 321-32, 2008. View Abstract

Ramadan KM, Connors JM, Al-Tourah AJ, Song KW, Gascoyne RD, Barnett MJ, Nevill TJ, Shepherd JD, Nantel SH, Sutherland HJ, Forrest DL, Hogge DE, Lavoie JC, Abou-Mourad YR, Chhanabhai M, Voss NJ, Brinkman RR, Smith CA, & Toze CL. Allogeneic SCT for relapsed composite and transformed lymphoma using related and unrelated donors: long-term results. Bone Marrow Transplant, 2008. View Abstract

Spidlen J, Leif RC, Moore W, Roederer M, & Brinkman RR. Gating-ML: XML-based gating descriptions in flow cytometry. Cytometry A, 2008. View Abstract

Taylor CF, Field D, Sansone SA, Aerts J, Apweiler R, Ashburner M, Ball CA, Binz PA, Bogue M, Booth T, Brazma A, Brinkman RR, Michael Clark A, Deutsch EW, Fiehn O, Fostel J, Ghazal P, Gibson F, Gray T, Grimes G, Hancock JM, Hardy NW, Hermjakob H, Julian RK, Jr., Kane M, Kettner C, Kinsinger C, Kolker E, Kuiper M, Novere NL, Leebens-Mack J, Lewis SE, Lord P, Mallon AM, Marthandan N, Masuya H, McNally R, Mehrle A, Morrison N, Orchard S, Quackenbush J, Reecy JM, Robertson DG, Rocca-Serra P, Rodriguez H, Rosenfelder H, Santoyo-Lopez J, Scheuermann RH, Schober D, Smith B, Snape J, Stoeckert CJ, Jr., Tipton K, Sterk P, Untergasser A, Vandesompele J, & Wiemann S. Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nat Biotechnol 26 (8): 889-96, 2008. View Abstract

Brinkman RR, Gasparetto M, Lee SJ, Ribickas AJ, Perkins J, Janssen W, Smiley R, & Smith C. High-content flow cytometry and temporal data analysis for defining a cellular signature of graft-versus-host disease. Biol Blood Marrow Transplant 13 (6): 691-700, 2007. View Abstract

Dykstra B, Kent D, Bowie M, McCaffrey L, Hamilton M, Lyons K, Lee SJ, Brinkman R, & Eaves C. Long-term propagation of distinct hematopoietic differentiation programs in vivo. Cell Stem Cell 1 (2): 218-29, 2007. View Abstract

Le Meur N, Rossini A, Gasparetto M, Smith C, Brinkman RR, & Gentleman R. Data quality assessment of ungated flow cytometry data in high throughput experiments. Cytometry A 71 (6): 393-403, 2007. View Abstract

Brinkman RR, Dube MP, Rouleau GA, Orr AC, & Samuels ME. Human monogenic disorders - a source of novel drug targets. Nat Rev Genet 7 (4): 249-60, 2006. View Abstract

Spidlen J, Gentleman RC, Haaland PD, Langille M, Le Meur N, Ochs MF, Schmitt C, Smith CA, Treister AS, & Brinkman RR. Data standards for flow cytometry. Omics 10 (2): 209-14, 2006. View Abstract

Stoeckert C, Ball C, Brazma A, Brinkman R, Causton H, Fan L, Fostel J, Fragoso G, Heiskanen M, Holstege F, Morrison N, Parkinson H, Quackenbush J, Rocca-Serra P, Sansone SA, Sarkans U, Sherlock G, Stevens R, Taylor C, Taylor R, Whetzel P, & White J. Wrestling with SUMO and bio-ontologies. Nat Biotechnol 24 (1): 21-2; author reply 23, 2006. View Abstract

Whetzel PL, Brinkman RR, Causton HC, Fan L, Fostel J, Fragoso G, Heiskanen M, Hernandez-Boussard T, Morrison N, Parkinson H, Rocco-Serra P, Sansone SA, Schober D, Smith B, Stevens R, Stoeckert CJ, Jr., Taylor C, White J, & Wood A. Development of FuGO: an ontology for functional genomics investigations. Omics 10 (2): 199-204, 2006. View Abstract

Whetzel PL, Brinkman RR, Causton HC, Fan L, Field D, Fostel J, Fragoso G, Gray T, Heiskanen M, Hernandez-Boussard T, Morrison N, Parkinson H, Rocca-Serra P, Djousse L, Knowlton B, Hayden MR, Almqvist EW, Brinkman RR, Ross CA, Margolis RL, Rosenblatt A, Durr A, Dode C, Morrison PJ, Novelletto A, Frontali M, Trent RJ, McCusker E, Gomez-Tortosa E, Mayo Cabrero D, Jones R, Zanko A, Nance M, Abramson RK, Suchowersky O, Paulsen JS, Harrison MB, Yang Q, Cupples LA, Mysore J, Gusella JF, MacDonald ME, & Myers RH. Evidence for a modifier of onset age in Huntington disease linked to the HD gene in 4p16. Neurogenetics 5 (2): 109-14, 2004. View Abstract

Djousse L, Knowlton B, Hayden M, Almqvist EW, Brinkman R, Ross CA, Margolis R, Rosenblatt A, Durr A, Dode C, Morrison PJ, Novelletto A, Frontali M, Trent RJA, McCusker E, Gomez-Tortosa E, Mayo D, Jones R, Zanko A, Nance M, Abramson R, Suchowersky O, Paulsen J, Harrison M, Yang Q, Cupples LA, Mysore J, Gusella JF, MacDonald ME, and Nyers RH.  Evidence for a Modifier of Onset Age in Huntington’s Disease Linked to the HD Gene in 4p16.  Neurogenetics 5(2): 109-14 (2004).

Lafreniere RG, MacDonald ML, Dube MP, MacFarlane J, O’Driscoll M, Brais B, Meilleur S, Brinkman RR, Dadivas O, Pape T, Platon C, Radomski C, Risler J, Thompson J, Guerra-Escobio AM, Davar G, Breakefield XO, Pimstone SN, Green R, Pryse-Phillips W, Goldberg YP, Younghusband HB, Hayden MR, Sherrington R, Rouleau GA, & Samuels ME. Identification of a novel gene (HSN2) causing hereditary sensory and autonomic neuropathy type II through the Study of Canadian Genetic Isolates. Am J Hum Genet 74 (5): 1064-73, 2004. View Abstract

Langbehn DR, Brinkman RR, Falush D, Paulsen JS, & Hayden MR. A new model for prediction of the age of onset and penetrance for Huntington’s disease based on CAG length. Clin Genet 65 (4): 267-77, 2004. View Abstract

Almqvist EW, Brinkman RR, Wiggins S, & Hayden MR. Psychological consequences and predictors of adverse events in the first 5 years after predictive testing for Huntington’s disease. Clin Genet 64 (4): 300-9, 2003. View Abstract

 Djousse L, Knowlton B, Hayden M, Almqvist EW, Brinkman R, Ross C, Margolis R, Rosenblatt A, Durr A, Dode C, Morrison PJ, Novelletto A, Frontali M, Trent RJ, McCusker E, Gomez-Tortosa E, Mayo D, Jones R, Zanko A, Nance M, Abramson R, Suchowersky O, Paulsen J, Harrison M, Yang Q, Cupples LA, Gusella JF, MacDonald ME, & Myers RH. Interaction of normal and expanded CAG repeat sizes influences age at onset of Huntington disease. Am J Med Genet A 119A (3): 279-82, 2003. View Abstract

 Li JL, Hayden MR, Almqvist EW, Brinkman RR, Durr A, Dode C, Morrison PJ, Suchowersky O, Ross CA, Margolis RL, Rosenblatt A, Gomez-Tortosa E, Cabrero DM, Novelletto A, Frontali M, Nance M, Trent RJ, McCusker E, Jones R, Paulsen JS, Harrison M, Zanko A, Abramson RK, Russ AL, Knowlton B, Djousse L, Mysore JS, Tariot S, Gusella MF, Wheeler VC, Atwood LD, Cupples LA, Saint-Hilaire M, Cha JH, Hersch SM, Koroshetz WJ, Gusella JF, MacDonald ME, & Myers RH. A genome scan for modifiers of age at onset in Huntington disease: The HD MAPS study. Am J Hum Genet 73 (3): 682-7, 2003. View Abstract

Paulsen JS, Zhao H, Stout JC, Brinkman RR, Guttman M, Ross CA, Como P, Manning C, Hayden MR, & Shoulson I. Clinical markers of early disease in persons near onset of Huntington’s disease. Neurology 57 (4): 658-62, 2001. View Abstract

Rosenblatt A, Brinkman RR, Liang KY, Almqvist EW, Margolis RL, Huang CY, Sherr M, Franz ML, Abbott MH, Hayden MR, & Ross CA. Familial influence on age of onset among siblings with Huntington disease. Am J Med Genet 105 (5): 399-403, 2001. View Abstract

Almqvist EW, Bloch M, Brinkman R, Craufurd D, & Hayden MR. A worldwide assessment of the frequency of suicide, suicide attempts, or psychiatric hospitalization after predictive testing for Huntington disease. Am J Hum Genet 64 (5): 1293-304, 1999. View Abstract

Hadano S, Nichol K, Brinkman RR, Nasir J, Martindale D, Koop BF, Nicholson DW, Scherer SW, Ikeda JE, & Hayden MR. A yeast artificial chromosome-based physical map of the juvenile amyotrophic lateral sclerosis (ALS2) critical region on human chromosome 2q33-q34. Genomics 55 (1): 106-12, 1999. View Abstract

Brinkman RR, Mezei MM, Theilmann J, Almqvist E, & Hayden MR. The likelihood of being affected with Huntington disease by a particular age, for a specific CAG size. Am J Hum Genet 60 (5): 1202-10, 1997. View Abstract

Chissoe SL, Marra MA, Hillier L, Brinkman R, Wilson RK, & Waterston RH. Representation of cloned genomic sequences in two sequencing vectors: correlation of DNA sequence and subclone distribution. Nucleic Acids Res 25 (15): 2960-6, 1997. View Abstract

Wellington CL, Brinkman RR, O’Kusky JR, & Hayden MR. Toward understanding the molecular pathology of Huntington’s disease. Brain Pathol 7 (3): 979-1002, 1997. View Abstact

Vaudin M, Roopra A, Hillier L, Brinkman R, Sulston J, Wilson RK, and Waterson RH.  The Construction and Analysis of M13 Libraries prepared from YAC DNA.  Nucleic Acids Research, 23: 670-674, 1995.

Johnston M, Andrews S, Brinkman R, Cooper J, Ding H, Dover J, Du Z, Favello A, Fulton L, Gattung SC,     Giesel C, Kirsten J, Kucuba T, Hillier L, Jier M, Johnston L, Langston Y, Latreille P, Louis EJ, Macri C, Mardis E, Menezes S, Mouser L, Hnan M, Rifkin L, Riles L, St. Peter H, Trevaskis E, Vaughan K, Vignati D, Wilcos L, Wohldman P, Waterston R, Wilson R, and Vaudin M, Complte Nucleotide Sequence of Saccharomyces cervisiae Chromosome VIII.  Science 265: 2077-2082, 1994.