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	Patterns and changes in gene expression following neo-adjuvant anti-estrogen treatment in estrogen receptor-positive breast cancer. [My Copy] Endocrine-related cancer, Vol. 15, No. 2. (June 2008), pp. 439-449. by Vera Cappelletti, Manuela Gariboldi, Loris De Cecco, et al.Sara Toffanin, James F F. Reid, Lara Lusa, Emilio Bajetta, Luigi Celio, Marco Greco, Alessandra Fabbri, Marco A A. Pierotti, Maria Grazia G. Daidone posted to breast_cancer jfrbib jfrbib04-09 by jfr on 2008-06-09 13:33:33 as
	Challenges in projecting clustering results across gene expression-profiling datasets. [My Copy] Journal of the National Cancer Institute, Vol. 99, No. 22. (21 November 2007), pp. 1715-1723. by Lara Lusa, Lisa M. McShane, James F. Reid, et al.Loris De Cecco, Federico Ambrogi, Elia Biganzoli, Manuela Gariboldi, Marco A. Pierotti posted to jfrbib jfrbib04-09 by jfr on 2008-03-30 21:15:19 as along with 5 people ptrobajo frohike guhjy giovenko laral
	Identification of tumor-specific molecular signatures in intracranial ependymoma and association with clinical characteristics. [My Copy] J Clin Oncol, Vol. 24, No. 33. (20 November 2006), pp. 5223-5233. by P. Modena, E. Lualdi, F. Facchinetti, et al.J. Veltman, J. F. Reid, S. Minardi, I. Janssen, F. Giangaspero, M. Forni, G. Finocchiaro, L. Genitori, F. Giordano, R. Riccardi, E. F. Schoenmakers, M. Massimino, G. Sozzi posted to jfrbib jfrbib04-09 by jfr on 2008-03-30 21:14:14 as
	New potential ligand-receptor signaling loops in ovarian cancer identified in multiple gene expression studies. [My Copy] Cancer Res, Vol. 66, No. 22. (15 November 2006), pp. 10709-10719. by G. Castellano, J. F. Reid, P. Alberti, M. L. Carcangiu, A. Tomassetti, S. Canevari posted to jfrbib jfrbib04-09 by jfr on 2008-03-30 21:13:34 as
	Questioning the utility of pooling samples in microarray experiments with cell lines. [My Copy] Int J Biol Markers, Vol. 21, No. 2. (n 2006), pp. 67-73. by L. Lusa, V. Cappelletti, M. Gariboldi, et al.C. Ferrario, L. De Cecco, J. F. Reid, S. Toffanin, G. Gallus, L. M. McShane, M. G. Daidone, M. A. Pierotti posted to jfrbib jfrbib04-09 by jfr on 2008-03-30 21:10:48 as
	Molecular predictors of response and outcome in ovarian cancer. [My Copy] Crit Rev Oncol Hematol, Vol. 60, No. 1. (October 2006), pp. 19-37. by S. Canevari, M. Gariboldi, J. F. Reid, I. Bongarzone, M. A. Pierotti posted to jfrbib jfrbib04-09 by jfr on 2008-03-30 21:10:00 as
	Transcriptional network dynamics in macrophage activation [My Copy] Genomics, Vol. 88, No. 2. (August 2006), pp. 133-142. by Roland Nilsson, Vladimir B. Bajic, Harukazu Suzuki, et al.Diego di Bernardo, Johan Björkegren, Shintaro Katayama, James F. Reid, Matthew J. Sweet, Manuela Gariboldi, Piero Carninci posted to jfrbib jfrbib04-09 by jfr on 2008-03-30 21:06:50 as along with 2 people guhjy gespim
	Complex Loci in human and mouse genomes. [My Copy] PLoS genetics, Vol. 2, No. 4. (April 2006) by P. G. Engström, H. Suzuki, N. Ninomiya, et al.A. Akalin, L. Sessa, G. Lavorgna, A. Brozzi, L. Luzi, S. L. Tan, L. Yang, G. Kunarso, E. L. Ng, S. Batalov, C. Wahlestedt, C. Kai, J. Kawai, P. Carninci, Y. Hayashizaki, C. Wells, V. B. Bajic, V. Orlando, J. F. Reid, B. Lenhard, L. Lipovich posted to jfrbib jfrbib04-09 by jfr on 2008-03-30 21:06:21 as along with 4 people guhjy abrozzi balicea tabu
	Regulation of lipocalin-2 gene by the cancer chemopreventive retinoid 4-HPR. [My Copy] Int J Cancer, Vol. 119, No. 7. (1 October 2006), pp. 1599-1606. by S. Caramuta, L. De Cecco, J. F. Reid, et al.L. Zannini, M. Gariboldi, L. Kjeldsen, M. A. Pierotti, D. Delia posted to jfrbib jfrbib04-09 by jfr on 2008-03-30 21:05:33 as
	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
	Limits of predictive models using microarray data for breast cancer clinical treatment outcome. [My Copy] J Natl Cancer Inst, Vol. 97, No. 12. (15 June 2005), pp. 927-930. by J. F. Reid, L. Lusa, L. De Cecco, et al.D. Coradini, S. Veneroni, M. G. Daidone, M. Gariboldi, M. A. Pierotti posted to jfrbib jfrbib04-09 by jfr on 2008-03-30 21:02:41 as
	Discovery of 342 putative new genes from the analysis of 5'-end-sequenced full-length-enriched cDNA human transcripts. [My Copy] Genomics, Vol. 85, No. 6. (June 2005), pp. 739-751. by E. Dalla, F. Mignone, R. Verardo, et al.L. Marchionni, S. Marzinotto, D. Lazarević, J. F. Reid, R. Marzio, E. Klarić, D. Licastro, G. Marcuzzi, R. Gambetta, M. A. Pierotti, G. Pesole, C. Schneider posted to jfrbib jfrbib04-09 by jfr on 2008-03-30 21:01:56 as
	Gene expression profile identifies a rare epithelioid variant case of pleomorphic liposarcoma carrying FUS-CHOP transcript [My Copy] Histopathology, Vol. 46, No. 3. (March 2005), pp. 334-341. by L. D. De Cecco, M. Gariboldi, J. F. Reid, et al.M. S. Lagonigro, E. Tamborini, V. Albertini, S. Staurengo, S. Pilotti, M. A. Pierotti posted to jfrbib jfrbib04-09 by jfr on 2008-03-30 20:59:43 as
	Gene expression profiling of advanced ovarian cancer: characterization of a molecular signature involving fibroblast growth factor 2. [My Copy] Oncogene, Vol. 23, No. 49. (21 October 2004), pp. 8171-8183. by L. De Cecco, L. Marchionni, M. Gariboldi, et al.J. F. Reid, M. S. Lagonigro, S. Caramuta, C. Ferrario, E. Bussani, D. Mezzanzanica, F. Turatti, D. Delia, M. G. Daidone, M. Oggionni, N. Bertuletti, A. Ditto, F. Raspagliesi, S. Pilotti, M. A. Pierotti, S. Canevari, C. Schneider posted to jfrbib jfrbib04-09 by jfr on 2008-03-30 20:58:20 as along with 1 person tonamswish
	Automated DNA chip annotation tables at IFOM: the importance of synchronisation and cross-referencing of sequence databases. [My Copy] Appl Bioinformatics, Vol. 2, No. 4. (2003), pp. 245-249. by A. Guffanti, G. Finocchiaro, J. F. Reid, et al.L. Luzi, M. Alcalay, S. Confalonieri, L. Lassandro, H. Muller posted to jfrbib by jfr on 2008-03-30 20:55:58 as
	LNCIB human full-length cDNAs collection: towards a better comprehension of the human transcriptome. [My Copy] C R Biol, Vol. 326, No. 10-11. (v 2003), pp. 967-970. by E. Dalla, R. Verardo, D. Lazarević, et al.L. Marchionni, J. F. Reid, N. Bahar, E. Klarić, G. Marcuzzi, R. Marzio, A. Belgrano, D. Licastro, C. Schneider posted to jfrbib by jfr on 2008-03-30 20:55:32 as
	The meaning of it all: web-based resources for large-scale functional annotation and visualization of DNA microarray data. [My Copy] Trends Genet, Vol. 18, No. 11. (November 2002), pp. 589-592. by A. Guffanti, J. F. Reid, M. Alcalay, G. Simon posted to jfrbib by jfr on 2008-03-30 20:49:28 as
	A fast and practical bit-vector algorithm for the Longest Common Subsequence problem [My Copy] Information Processing Letters, Vol. 80, No. 6. (31 December 2001), pp. 279-285. by Maxime Crochemore, Costas S. Iliopoulos, Yoan J. Pinzon, James F. Reid posted to jfrbib by jfr on 2008-03-30 20:47:14 as
	Decomposition of partially occluded strings in the presence of errors [My Copy] Int. J. on Pattern Recognition and Artificial Intelligence, Vol. 15, No. 7. (2001), pp. 1129-1142. by C. S. Iliopoulos, J. F. Reid posted to jfrbib by jfr on 2008-03-30 20:46:42 as
	Two-dimensional dictionary prefix-matching [My Copy] Journal of Combinatorial Mathematics and Combinatorial Computing, Vol. 35 (2000), pp. 225-238. by M. Crochemore, C. S. Iliopoulos, M. Korda, J. F. 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	Optimal parallel analysis and decomposition of partially occluded strings [My Copy] Parallel Computing, Vol. 26, No. 4. (March 2000), pp. 483-494. by Costas S. Iliopoulos, James F. Reid posted to jfrbib by jfr on 2008-03-30 20:37:53 as

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breast_cancer	483
mirna	356
review	347
software	279
classification	275
colon_cancer	236
gene_expression	179
methodology	169
copy-number	162
network	148
integration	139
microarray_technology	133
clustering	125
bioinformatics	122
feature_selection	107
meta-analysis	97
affy	86
database	84
therapy	80
mirna_target	79
gene_set_analysis	71
crc_bib	69
array-cgh	69
regulation	67
low_level	66
rt-pcr	64
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pathway_analysis	61
genomics	60
subtypes	58
annotation	57
snp-arrays	57
comment	54
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cancer	38
bioconductor	37
statistics	37
progression	36
alternative_splicing	35
protein_interaction	35
fdr	35
markers	35
snp	34
r	33
methylation	32
standards	30
class_discovery	28
mutation	28
tamoxifen	28
exon_arrays	25
mir17-92	25
jfrbib	24
two-color	24
experiment_design	23
ovarian_cancer	23
microarray_protocol	23
pathway	22
comparison	21
co-expression	21
brca	21
tfbs	20
model	20
kras	20
survival_analysis	20
treatment	19
functional_analysis	19
p53	19
platform_comparison	18
multiple_testing	18
technology	17
illumina	17
module_detection	16
biomarker	16
stem_cell	16
jfrbib04-09	16
evaluation	16
chip-chip	16
text-mining	15
nmf	15
antisense	15
reproducible_research	15
sequencing	14
erbb	14
bio_signature	14
basal_subtype	14
stageii	13
maqc	13
tma	13
staging	13
cell_line	13
rna_quality	13
lung_cancer	13
egfr	13
gene_lists	12
marker	12
gene_ontology	12
cnv	12
genotyping	12
proliferation	11
loh	11
genome_browser	11
drug_discovery	11
semantic_web	11
pten	11
protocol	11
missing_values	11
visualization	10
mirna_regulation	10
tissue_specificity	10
disease_genes	10
immunohistochemistry	10
tgfb	10
control_genes	10
probe_design	9
inter-laboratory	9
segmentation	9
msi	9
myc	9
sample_size	8
can_genes	8
chemotherapy	8
e2f1	8
boutique_arrays	8
consensus_clustering	8
time-course	8
editorial	8
chip-seq	8
personalized_medicine	8
er	7
nci60	7
18q_loh	7
lymphoma	7
plos_rules	7
mir21	7
plos_start	7
go	7
validation	7
tiling_array	7
graphs	6
motif	6
leukemia	6
non-coding	6
promoters	6
ontology	6
serum	6
community	6
hpc	6
stem	6
trial	6
correlation	6
read_mapping	6
gene_interaction	6
cin	5
plos_primer	5
gwas	5
prioritization	5
grid_computing	5
her2	5
prostate_cancer	5
survival	5
radiation	5
functional_genomics	5
machine_learning	5
cross-platform	5
gene_pairs	5
web_services	4
wnt	4
resource	4
public_data	4
lims	4
pr	4
data_curation	4
functional_classification	4
grading	4
image_analysis	4
mirna_cluster	4
mir34	4
pooling	4
biobank	4
open-source	4
mir192	4
stroma	3
primer	3
bim	3
confounders	3
tutorial	3
mass_spec	3
interaction	3
small_molecule	3
outlier	3
apc	3
low-level	3
svm	3
sop	3
epigenetics	3
er-positive	3
mage	3
filtering	3
sage	3
ngs	3
in-situ	3
roc	3
letter	3
pik3ca	3
evolution	3
luminal_subtype	3
8q24	3
micro_environment	3
hapmap	3
loops	3
cross-study	3
projection	3
agilent	3
stability	3
glioblastoma	3
triple_negative	3
ontologies	3
biomarkers	3
pca	3
web_server	3
chromatin	3
copa	3
dna_damage	2
semi-supervised	2
snp_arrays	2
ephb	2
differential_expression	2
caching	2
mir20a	2
stem_cells	2
target	2
compression	2
alignment	2
estradiol	2
serm	2
bcatenin	2
microarray_data	2
permutations	2
diagnostic	2
mir143	2
akt	2
smad	2
guidelines	2
thyroid	2
qtl	2
cloud_computing	2
cell_cycle	2
tbfs	2
recommendation	2
priors	2
mutual_information	2
batch-effect	2
sweave	2
web_resource	2
rin	2
upd	2
cetuximab	2
stageiii	2
protein_microarray	2
lymphocytes	2
dfs	2
20q	2
mir145	2
gene_fusion	2
protein_networks	2
mir215	2
flow_cytometry	2
chemo	2
meeting_report	2
translational	2
local_recurrence	2
fgfr2	2
ranked_lists	2
oncomine	2
cdk8	2
braf	1
wiki	1
aroma	1
rna-interference	1
invasion	1
dcc	1
plasma	1
gene_ranking	1
cross-species	1
dasl	1
python	1
lin28	1
cervical_cancer	1
shrna	1
disease	1
perturbation	1
fgf10	1
network_analysis	1
p21	1
in_situ_hybridization	1
bayesian	1
metastatis	1
xml	1
early-stage	1
tissue_origin	1
selection_bias	1
reproducibility	1
3utr	1
pilot_study	1
13q	1
dye_bias	1
driver_genes	1
metagene	1
meta_analysis	1
passenger_genes	1
prb	1
cancer_hallmarks	1
modules	1
erg	1
nomogram	1
graph_approach	1
peripheral_blood	1
power_analysis	1
ret	1
cables1	1
mixture_models	1
data_mining	1
rb	1
mir216a	1
translation	1
thyroid_cancer	1
assembly	1
smad7	1
pre-post	1
circulating_tumor_cells	1
neural_networks	1
fantom	1
signaling	1
mir-106b-25	1
breas_cancer	1
ndrg4	1
melanoma	1
ccnd1	1
gene_clusters	1
oncogene_addiction	1
454	1
gene_function_prediction	1
mirna221	1
pattern_discovery	1
mirna_discovery	1
taxane	1
stat3	1
mrna-seq	1
latent	1
mir16-1	1
eno1	1
formalization	1
met	1
ecm	1
bmp	1
brain_cancer	1
randomization	1
association_studies	1
mcm7	1
single_cell	1
grade_index	1
markup	1
concordance	1
gene_networks	1
mir101	1
genoty	1
news	1
cross_platform	1
mir15a	1
genome_assembly	1
resampling	1
tcga	1
er-negative	1
rnai	1
aurora_kinase	1
ucs	1
translocation	1
il8	1
mir217	1
mir155	1
gastric_cancer	1
simulation	1
bambi	1
latex	1
mir135	1
fish	1
mapk14	1
ensemble	1
dimension_reduction	1
asco	1
distance	1
mir203	1
mir196a-2	1
formats	1
transfection	1
pbc	1
ependymoma	1
study_design	1
clusterin	1
sampling	1
data_publication	1
hypoxia	1
microrna	1
oncogene	1
mirna222	1
mir31	1
mir199	1
genetics	1
mir449	1
target_discovery	1
myb	1
funding	1
aging	1
model-based	1
au-rich	1
est_analysis	1
apoptosis	1
mir126	1
module	1
biclustering	1
beads	1
pancreatic_cancer	1
mirna_pathway	1

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