jfr's Quackenbush:J [20 articles] Export

Recent papers posted to jfr's library by the author Quackenbush:J. You can also see everyone's Quackenbush:J.

	Data-driven normalization strategies for high-throughput quantitative RT-PCR. [My Copy] BMC bioinformatics, Vol. 10, No. 1. (19 April 2009), 110. by Jessica C. Mar, Yasumasa Kimura, Kate Schroder, et al.Katharine M. Irvine, Yoshihide Hayashizaki, Harukazu Suzuki, David Hume, John Quackenbush posted to rt-pcr r normalization bioconductor by jfr on 2009-11-15 14:37:52 as along with 7 people and 1 group guhjy lwaldron renatomilani trfield shikin druvus natstreet Bioinformatics
	Proliferative genes dominate malignancy-risk gene signature in histologically-normal breast tissue. [My Copy] Breast cancer research and treatment (6 March 2009) by Dung-Tsa T. Chen, Aejaz Nasir, Aedin Culhane, et al.Chinnambally Venkataramu, William Fulp, Renee Rubio, Tao Wang, Deepak Agrawal, Susan M. McCarthy, Mike Gruidl, Gregory Bloom, Tove Anderson, Joe White, John Quackenbush, Timothy Yeatman posted to proliferation gene_expression breast_cancer by jfr on 2009-09-30 10:05:01 as along with 1 person and 1 group Zephyrus Breast Cancer Reading Club
	Functional classification analysis of somatically mutated genes in human breast and colorectal cancers. [My Copy] Genomics, Vol. 91, No. 6. (21 June 2008), pp. 508-511. by T. W. Chittenden, E. A. Howe, A. C. Culhane, et al.R. Sultana, J. M. Taylor, C. Holmes, J. Quackenbush posted to breast_cancer can_genes colon_cancer functional_analysis by jfr on 2009-07-22 13:57:06 as along with 2 people fpattyn capitall
	Supervised risk predictor of breast cancer based on intrinsic subtypes. [My Copy] Journal of clinical oncology : official journal of the American Society of Clinical Oncology, Vol. 27, No. 8. (10 March 2009), pp. 1160-1167. by Joel S. Parker, Michael Mullins, Maggie C. Cheang, et al.Samuel Leung, David Voduc, Tammi Vickery, Sherri Davies, Christiane Fauron, Xiaping He, Zhiyuan Hu, John F. Quackenbush, Inge J. Stijleman, Juan Palazzo, J. S. Marron, Andrew B. Nobel, Elaine Mardis, Torsten O. Nielsen, Matthew J. Ellis, Charles M. Perou, Philip S. Bernard posted to breast_cancer classification subtypes by jfr on 2009-07-22 11:45:47 as along with 3 people Zephyrus misonneh ptrobajo
	What would you do if you could sequence everything? [My Copy] Nature Biotechnology, Vol. 26, No. 10. (01 October 2008), pp. 1125-1133. by Avak Kahvejian, John Quackenbush, John F. Thompson posted to comment deep_sequencing genomics integration by jfr on 2009-06-11 11:26:31 as along with 19 people n00c hzoltan seb1 inesdesantiago heliopais stubrown installe Annab Borelli jbhiatt Pascalichouchou bertelsen frohike natstreet druvus reyez alexknight psique GeeSharpMinor
	Comprehensive biostatistical analysis of CpG island methylator phenotype in colorectal cancer using a large population-based sample. [My Copy] PLoS ONE, Vol. 3, No. 11. (2008) by K. Nosho, N. Irahara, K. Shima, et al.S. Kure, G. J. Kirkner, E. S. Schernhammer, A. Hazra, D. J. Hunter, J. Quackenbush, D. Spiegelman, E. L. Giovannucci, C. S. Fuchs, S. Ogino posted to colon_cancer methylation by jfr on 2009-03-13 10:40:48 as
	Agreement in breast cancer classification between microarray and quantitative reverse transcription PCR from fresh-frozen and formalin-fixed, paraffin-embedded tissues. [My Copy] Clinical chemistry, Vol. 53, No. 7. (July 2007), pp. 1273-1279. by Michael Mullins, Laurent Perreard, John F. Quackenbush, et al.Nicholas Gauthier, Steven Bayer, Matthew Ellis, Joel Parker, Charles M. Perou, Aniko Szabo, Philip S. Bernard posted to breast_cancer ffpe microarray_technology rt-pcr by jfr on 2008-11-26 17:54:32 as along with 1 person and 1 group Zephyrus Breast Cancer Reading Club
	Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project [My Copy] Nat Biotech, Vol. 26, No. 8. (August 2008), pp. 889-896. by Chris F. Taylor, Dawn Field, Susanna-Assunta Sansone, et al.Jan Aerts, Rolf Apweiler, Michael Ashburner, Catherine A. Ball, Pierre-Alain Binz, Molly Bogue, Tim Booth, Alvis Brazma, Ryan R. Brinkman, Adam Michael Clark, Eric W. Deutsch, Oliver Fiehn, Jennifer Fostel, Peter Ghazal, Frank Gibson, Tanya Gray, Graeme Grimes, John M. Hancock, Nigel W. Hardy, Henning Hermjakob, Randall K. Julian, Matthew Kane, Carsten Kettner, Christopher Kinsinger, Eugene Kolker, Martin Kuiper, Nicolas L. Novere, Jim Leebens-Mack, Suzanna E. Lewis, Phillip Lord, Ann-Marie Mallon, Nishanth Marthandan, Hiroshi Masuya, Ruth Mcnally, Alexander Mehrle, Norman Morrison, Sandra Orchard, John Quackenbush, James M. Reecy, Donald G. Robertson, Philippe Rocca-Serra, Henry Rodriguez, Heiko Rosenfelder, Javier Santoyo-Lopez, Richard H. Scheuermann, Daniel Schober, Barry Smith, Jason Snape, Christian J. Stoeckert, Keith Tipton, Peter Sterk, Andreas Untergasser, Jo Vandesompele, Stefan Wiemann posted to reproducible_research standards by jfr on 2008-10-08 14:49:47 as along with 13 people and 1 group Zephyrus plosmedicine CameronNeylon allysonlister shikin guhjy jandot dullhunk GeeSharpMinor ChrisEvelo lenov fgibson renatomilani GelML
	Sources of variation in baseline gene expression levels from toxicogenomics study control animals across multiple laboratories [My Copy] BMC Genomics, Vol. 9 (12 June 2008), 285. by Michael J. Boedigheimer, Russell D. Wolfinger, Michael B. Bass, et al.Pierre R. Bushel, Jeff W. Chou, Matthew Cooper, Christopher J. Corton, Jennifer Fostel, Susan Hester, Janice S. Lee, Fenglong Liu, Jie Liu, Hui-Rong Qian, John Quackenbush, Syril Pettit, Karol L. Thompson posted to maqc quality_control by jfr on 2008-10-07 16:37:24 as
	Seeded Bayesian Networks: Constructing genetic networks from microarray data [My Copy] BMC Systems Biology, Vol. 2, No. 1. (2008), 57. by Amira Djebbari, John Quackenbush posted to network by jfr on 2008-09-26 11:39:48 as along with 7 people meanerelk ptrobajo frohike renatomilani beete phoenixzxl guhjy
	Standardizing the standards [My Copy] Molecular Systems Biology, Vol. 2 (21 February 2006) by John Quackenbush posted to comment standards by jfr on 2008-07-25 16:51:57 as along with 7 people seb1 brianb allysonlister neils fgibson dullhunk mhucka
	Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE) [My Copy] Nature Biotechnology, Vol. 26, No. 3. (07 March 2008), pp. 305-312. by Eric W. Deutsch, Catherine A. Ball, Jules J. Berman, et al.G. Steven Bova, Alvis Brazma, Roger E. Bumgarner, David Campbell, Helen C. Causton, Jeffrey H. Christiansen, Fabrice Daian, Delphine Dauga, Duncan R. Davidson, Gregory Gimenez, Young A. Goo, Sean Grimmond, Thorsten Henrich, Bernhard G. Herrmann, Michael H. Johnson, Martin Korb, Jason C. Mills, Asa J. Oudes, Helen E. Parkinson, Laura E. Pascal, Nicolas Pollet, John Quackenbush, Mirana Ramialison, Martin Ringwald, David Salgado, Susanna-Assunta Sansone, Gavin Sherlock, Christian J. Stoeckert, Jason Swedlow, Ronald C. Taylor, Laura Walashek, Anthony Warford, David G. Wilkinson, Yi Zhou, Leonard I. Zon, Alvin Y. Liu, Lawrence D. True posted to immunohistochemistry in_situ_hybridization standards by jfr on 2008-05-05 11:12:40 as along with 6 people and 1 group aaltenburger mordiano zwang katerinakal guhjy psique parkinson's disease references
	Extracting biology from high-dimensional biological data [My Copy] J Exp Biol, Vol. 210, No. 9. (1 May 2007), pp. 1507-1517. by John Quackenbush posted to review by jfr on 2008-04-30 18:22:56 as along with 8 people operon fgibson guhjy frohike balicea Sharpshoot jo_davies AlexanderPico
	The Transcriptional Landscape of the Mammalian Genome [My Copy] Science, Vol. 309, No. 5740. (2 September 2005), pp. 1559-1563. by The FANTOM Consortium, P. Carninci, T. Kasukawa, et al.S. Katayama, J. Gough, M. C. Frith, N. Maeda, R. Oyama, T. Ravasi, B. Lenhard, C. Wells, R. Kodzius, K. Shimokawa, V. B. Bajic, S. E. Brenner, S. Batalov, A. R. R. Forrest, M. Zavolan, M. J. Davis, L. G. Wilming, V. Aidinis, J. E. Allen, A. Ambesi-Impiombato, R. Apweiler, R. N. Aturaliya, T. L. Bailey, M. Bansal, L. Baxter, K. W. Beisel, T. Bersano, H. Bono, A. M. Chalk, K. P. Chiu, V. Choudhary, A. Christoffels, D. R. Clutterbuck, M. L. Crowe, E. Dalla, B. P. Dalrymple, B. de Bono, G. Della Gatta, D. di Bernardo, T. Down, P. Engstrom, M. Fagiolini, G. Faulkner, C. F. Fletcher, T. Fukushima, M. Furuno, S. Futaki, M. Gariboldi, P. Georgii-Hemming, T. R. Gingeras, T. Gojobori, R. E. Green, S. Gustincich, M. Harbers, Y. Hayashi, T. K. Hensch, N. Hirokawa, D. Hill, L. Huminiecki, M. Iacono, K. Ikeo, A. Iwama, T. Ishikawa, M. Jakt, A. Kanapin, M. Katoh, Y. Kawasawa, J. Kelso, H. Kitamura, H. Kitano, G. Kollias, S. P. T. Krishnan, A. Kruger, S. K. Kummerfeld, I. V. Kurochkin, L. F. Lareau, D. Lazarevic, L. Lipovich, J. Liu, S. Liuni, S. McWilliam, Madan M. Babu, M. Madera, L. Marchionni, H. Matsuda, S. Matsuzawa, H. Miki, F. Mignone, S. Miyake, K. Morris, S. Mottagui-Tabar, N. Mulder, N. Nakano, H. Nakauchi, P. Ng, R. Nilsson, S. Nishiguchi, S. Nishikawa, F. Nori, O. Ohara, Y. Okazaki, V. Orlando, K. C. Pang, W. J. Pavan, G. Pavesi, G. Pesole, N. Petrovsky, S. Piazza, J. Reed, J. F. Reid, B. Z. Ring, M. Ringwald, B. Rost, Y. Ruan, S. L. Salzberg, A. Sandelin, C. Schneider, C. Schonbach, K. Sekiguchi, C. A. M. Semple, S. Seno, L. Sessa, Y. Sheng, Y. Shibata, H. Shimada, K. Shimada, D. Silva, B. Sinclair, S. Sperling, E. Stupka, K. Sugiura, R. Sultana, Y. Takenaka, K. Taki, K. Tammoja, S. L. Tan, S. Tang, M. S. Taylor, J. Tegner, S. A. Teichmann, H. R. Ueda, E. van Nimwegen, R. Verardo, C. L. Wei, K. Yagi, H. Yamanishi, E. Zabarovsky, S. Zhu, A. Zimmer, W. Hide, C. Bult, S. M. Grimmond, R. D. Teasdale, E. T. Liu, V. Brusic, J. Quackenbush, C. Wahlestedt, J. S. Mattick, D. A. Hume, RIKEN Genome Exploration Research Group and Genome Science Group Genome Network Project Core Group, C. Kai, D. Sasaki, Y. Tomaru, S. Fukuda, M. Kanamori-Katayama, M. Suzuki, J. Aoki, T. Arakawa, J. Iida, K. Imamura, M. Itoh, T. Kato, H. Kawaji, N. Kawagashira, T. Kawashima, M. Kojima, S. Kondo, H. Konno, K. Nakano, N. Ninomiya, T. Nishio, M. Okada, C. Plessy, K. Shibata, T. Shiraki, S. Suzuki, M. Tagami, K. Waki, A. Watahiki, Y. Okamura-Oho, H. Suzuki, J. Kawai, Y. Hayashizaki posted to jfrbib jfrbib04-09 by jfr on 2008-03-30 21:04:02 as along with 20 people and 1 group rsaito hagechouchin443 daforerog guhjy myrtilus setar miguel Cortel jwortman tuck lyongu eckart_bindewald troels_marstrand kaspermunch balicea forbiddenfaith99 mtagaya olympos raylim gjuggler Bioinformatics
	Molecular staging for survival prediction of colorectal cancer patients. [My Copy] J Clin Oncol, Vol. 23, No. 15. (20 May 2005), pp. 3526-3535. by S. Eschrich, I. Yang, G. Bloom, et al.K. Y. Kwong, D. Boulware, A. Cantor, D. Coppola, M. Kruhøffer, L. Aaltonen, T. F. Orntoft, J. Quackenbush, T. J. Yeatman posted to classification colon_cancer gene_expression staging by jfr on 2008-02-29 10:52:18 as along with 1 person frohike
	Microarray Blob-Defect Removal Improves Array Analysis. [My Copy] Bioinformatics (1 March 2007) by Jun S S. Song, Kaveh Maghsoudi, Wei Li, Edward Fox, John Quackenbush, X Shirley Liu posted to affy low_level microarray_technology by jfr on 2007-07-31 17:12:32 as along with 5 people and 1 group kengg shigepong ghattem caseybrown waszak Plantandetc
	The molecular portraits of breast tumors are conserved across microarray platforms. [My Copy] BMC genomics, Vol. 7, No. 1. (2006), 96. by Zhiyuan Hu, Cheng Fan, Daniel S. Oh, et al.J. S. Marron, Xiaping He, Bahjat F. Qaqish, Chad Livasy, Lisa A. Carey, Evangeline Reynolds, Lynn Dressler, Andrew Nobel, Joel Parker, Matthew G. Ewend, Lynda R. Sawyer, Junyuan Wu, Yudong Liu, Rita Nanda, Maria Tretiakova, Alejandra Ruiz Orrico, Donna Dreher, Juan P. Palazzo, Laurent Perreard, Edward Nelson, Mary Mone, Heidi Hansen, Michael Mullins, John F. Quackenbush, Matthew J. Ellis, Olufunmilayo I. Olopade, Philip S. Bernard, Charles M. Perou posted to subtypes class_discovery breast_cancer by jfr on 2007-01-19 15:13:29 as along with 4 people ptrobajo giovenko frohike macavity1g
	Classification and risk stratification of invasive breast carcinomas using a real-time quantitative RT-PCR assay [My Copy] Breast Cancer Research, Vol. 8 (20 April 2006), R23. by Laurent Perreard, Cheng Fan, John F. Quackenbush, et al.Michael Mullins, Nicholas P. Gauthier, Edward Nelson, Mary Mone, Heidi Hansen, Saundra S. Buys, Karen Rasmussen, Alejandra R. Orrico, Donna Dreher, Rhonda Walters, Joel Parker, Zhiyuan Hu, Xiaping He, Juan P. Palazzo, Olufunmilayo I. Olopade, Aniko Szabo, Charles M. Perou, Philip S. Bernard posted to rt-pcr classification breast_cancer by jfr on 2007-01-19 14:57:09 as
	A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB [My Copy] BMC Bioinformatics, Vol. 7 (06 November 2006), 489. by Tim F. Rayner, Philippe Rocca-Serra, Paul T. Spellman, et al.Helen C. Causton, Anna Farne, Ele Holloway, Rafael A. Irizarry, Junmin Liu, Donald S. Maier, Michael Miller, Kjell Petersen, John Quackenbush, Gavin Sherlock, Christian J. Stoeckert, Joseph White, Patricia L. Whetzel, Farrell Wymore, Helen Parkinson, Ugis Sarkans, Catherine A. Ball, Alvis Brazma posted to standards software by jfr on 2007-01-11 13:52:57 as along with 4 people bertelsen shikin zakmck dansullivanblk
	Statistical modeling for selecting housekeeper genes. [My Copy] Genome Biol, Vol. 5, No. 8. (2004) by A. Szabo, C. M. Perou, M. Karaca, L. Perreard, J. F. Quackenbush, P. S. Bernard posted to rt-pcr normalization by jfr on 2007-01-09 12:05:33 as along with 1 person brutledge

Note: You may cite this page as: http://www.citeulike.org/user/jfr/author/Quackenbush:J

breast_cancer	477
mirna	348
review	345
software	275
classification	272
colon_cancer	234
gene_expression	176
methodology	169
copy-number	161
network	148
integration	138
microarray_technology	133
bioinformatics	122
clustering	121
feature_selection	106
meta-analysis	97
affy	86
database	82
therapy	80
mirna_target	77
gene_set_analysis	69
array-cgh	69
crc_bib	69
regulation	67
low_level	66
rt-pcr	64
systems_biology	63
genomics	60
pathway_analysis	60
subtypes	58
snp-arrays	57
annotation	57
comment	53
quality_control	49
metastasis	47
normalization	46
mutations	43
deep_sequencing	42
ffpe	41
prognosis	41
microarray_analysis	40
estrogen	40
proteomics	39
cancer	38
bioconductor	37
statistics	37
protein_interaction	35
alternative_splicing	35
progression	35
markers	35
fdr	34
snp	33
methylation	32
r	31
standards	29
mutation	28
tamoxifen	28
class_discovery	28
exon_arrays	25
jfrbib	24
two-color	24
ovarian_cancer	23
mir17-92	23
microarray_protocol	23
pathway	22
experiment_design	22
comparison	21
brca	21
co-expression	21
tfbs	20
survival_analysis	20
model	20
kras	20
p53	19
treatment	19
functional_analysis	19
platform_comparison	18
technology	17
multiple_testing	17
biomarker	16
stem_cell	16
jfrbib04-09	16
module_detection	16
evaluation	16
illumina	16
chip-chip	16
text-mining	15
antisense	15
reproducible_research	15
nmf	15
sequencing	14
bio_signature	14
erbb	14
basal_subtype	14
lung_cancer	13
staging	13
rna_quality	13
stageii	13
egfr	13
tma	13
cell_line	12
cnv	12
marker	12
gene_ontology	12
maqc	12
genotyping	12
loh	11
drug_discovery	11
gene_lists	11
pten	11
missing_values	11
proliferation	11
protocol	11
semantic_web	11
immunohistochemistry	10
disease_genes	10
visualization	10
genome_browser	10
tissue_specificity	10
control_genes	10
tgfb	10
mirna_regulation	10
msi	9
inter-laboratory	9
probe_design	9
segmentation	9
e2f1	8
can_genes	8
chemotherapy	8
sample_size	8
consensus_clustering	8
chip-seq	8
boutique_arrays	8
personalized_medicine	8
myc	8
time-course	8
editorial	8
plos_start	7
18q_loh	7
tiling_array	7
validation	7
mir21	7
lymphoma	7
plos_rules	7
hpc	6
serum	6
er	6
read_mapping	6
promoters	6
stem	6
motif	6
correlation	6
gene_interaction	6
non-coding	6
leukemia	6
community	6
ontology	6
nci60	6
graphs	6
plos_primer	5
radiation	5
cross-platform	5
grid_computing	5
gene_pairs	5
her2	5
trial	5
gwas	5
prostate_cancer	5
functional_genomics	5
survival	5
machine_learning	5
cin	5
prioritization	5
mir34	4
public_data	4
pooling	4
data_curation	4
resource	4
mirna_cluster	4
biobank	4
image_analysis	4
open-source	4
pr	4
web_services	4
lims	4
mir192	4
grading	4
functional_classification	4
go	4
micro_environment	3
primer	3
bim	3
confounders	3
tutorial	3
mass_spec	3
interaction	3
small_molecule	3
outlier	3
apc	3
low-level	3
wnt	3
svm	3
stroma	3
sop	3
epigenetics	3
chromatin	3
er-positive	3
copa	3
mage	3
sage	3
ngs	3
in-situ	3
roc	3
letter	3
pik3ca	3
evolution	3
hapmap	3
loops	3
cross-study	3
agilent	3
stability	3
glioblastoma	3
triple_negative	3
ontologies	3
biomarkers	3
pca	3
web_server	3
estradiol	2
guidelines	2
lymphocytes	2
ephb	2
ranked_lists	2
luminal_subtype	2
batch-effect	2
filtering	2
cloud_computing	2
serm	2
permutations	2
8q24	2
recommendation	2
protein_networks	2
sweave	2
mir20a	2
20q	2
diagnostic	2
akt	2
thyroid	2
chemo	2
qtl	2
compression	2
oncomine	2
caching	2
bcatenin	2
flow_cytometry	2
projection	2
tbfs	2
upd	2
mir215	2
translational	2
alignment	2
dna_damage	2
semi-supervised	2
cell_cycle	2
stageiii	2
dfs	2
smad	2
snp_arrays	2
target	2
web_resource	2
differential_expression	2
mutual_information	2
protein_microarray	2
meeting_report	2
priors	2
rin	2
cetuximab	2
gene_fusion	2
local_recurrence	2
cdk8	2
bayesian	1
invasion	1
assembly	1
oncogene	1
mirna222	1
mir16-1	1
model-based	1
mir199	1
mir135	1
single_cell	1
smad7	1
xml	1
randomization	1
mir449	1
target_discovery	1
est_analysis	1
funding	1
mir126	1
pre-post	1
circulating_tumor_cells	1
braf	1
neural_networks	1
au-rich	1
wiki	1
apoptosis	1
aroma	1
module	1
biclustering	1
beads	1
bmp	1
pancreatic_cancer	1
dcc	1
brain_cancer	1
cross-species	1
association_studies	1
rna-interference	1
taxane	1
er-negative	1
distance	1
melanoma	1
ccnd1	1
nomogram	1
gene_clusters	1
formats	1
454	1
dasl	1
gene_function_prediction	1
python	1
cervical_cancer	1
shrna	1
reproducibility	1
perturbation	1
stem_cells	1
mir31	1
dye_bias	1
p21	1
meta_analysis	1
plasma	1
in_situ_hybridization	1
formalization	1
metastatis	1
passenger_genes	1
met	1
mirna_discovery	1
cancer_hallmarks	1
tissue_origin	1
mir145	1
modules	1
aurora_kinase	1
selection_bias	1
erg	1
3utr	1
power_analysis	1
markup	1
pilot_study	1
ret	1
gene_networks	1
driver_genes	1
metagene	1
cables1	1
mixture_models	1
prb	1
data_mining	1
fgfr2	1
fantom	1
signaling	1
ecm	1
translocation	1
il8	1
mir217	1
concordance	1
simulation	1
mir101	1
graph_approach	1
peripheral_blood	1
news	1
mir203	1
mir15a	1
mcm7	1
genome_assembly	1
resampling	1
transfection	1
tcga	1
mir-106b-25	1
rnai	1
ndrg4	1
ependymoma	1
oncogene_addiction	1
hypoxia	1
mirna221	1
microrna	1
ucs	1
mir155	1
gastric_cancer	1
mir143	1
bambi	1
latex	1
genoty	1
fish	1
disease	1
ensemble	1
dimension_reduction	1
asco	1
genetics	1
mrna-seq	1
rb	1
myb	1
mir216a	1
aging	1
latent	1
translation	1
pattern_discovery	1
pbc	1
early-stage	1
eno1	1
study_design	1
clusterin	1
sampling	1

jfr's Quackenbush:J [20 articles] Export

jfr's tags