jfr's library 2831 articles Export

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	A gene expression predictor of response to EGFR-targeted therapy stratifies progression-free survival to cetuximab in KRAS wild-type metastatic colorectal cancer. [My Copy] BMC cancer, Vol. 9, No. 1. (13 May 2009), 145. by Justin M. Balko, Esther P. Black posted to therapy gene_expression egfr colon_cancer classification cetuximab by jfr on 2009-11-15 14:27:04 as along with 1 person frohike
	Association of survival and disease progression with chromosomal instability: A genomic exploration of colorectal cancer [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 17. (28 April 2009), pp. 7131-7136. by Michal Sheffer, Manny D. Bacolod, Or Zuk, et al.Sarah F. Giardina, Hanna Pincas, Francis Barany, Philip B. Paty, William L. Gerald, Daniel A. Notterman, Eytan Domany posted to survival copy-number colon_cancer by jfr on 2009-11-08 23:03:53 as along with 2 people kdpreter rdiaz
	The breast cancer somatic 'muta-ome': tackling the complexity. [My Copy] Breast cancer research : BCR, Vol. 11, No. 2. (30 March 2009), 301. by Andrew E. Teschendorff, Carlos Caldas posted to sequencing mutations copy-number comment breast_cancer by jfr on 2009-11-08 22:45:12 as
	Molecular classification of solid tumours: towards pathway-driven therapeutics. [My Copy] British journal of cancer, Vol. 100, No. 10. (19 May 2009), pp. 1517-1522. by C. Swanton, C. Caldas posted to subtypes review personalized_medicine breast_cancer by jfr on 2009-11-08 22:22:43 as along with 5 people rdiaz tonamswish guhjy xtizon giovenko
	A genomic strategy to elucidate modules of oncogenic pathway signaling networks. [My Copy] Molecular cell, Vol. 34, No. 1. (10 April 2009), pp. 104-114. by Jeffrey T. Chang, Carlos Carvalho, Seiichi Mori, et al.Andrea H. Bild, Michael L. Gatza, Quanli Wang, Joseph E. Lucas, Anil Potti, Phillip G. Febbo, Mike West, Joseph R. Nevins posted to pathway_analysis network modules gene_lists by jfr on 2009-11-02 15:54:31 as along with 8 people and 1 group bertelsen jmstat guhjy mspivako renatomilani fenghezi shikin roys Journal picks
	Cross-Study Projections of Genomic Biomarkers: An Evaluation in Cancer Genomics [My Copy] PLoS ONE, Vol. 4, No. 2. (19 February 2009), e4523. by Joseph E. Lucas, Carlos M. Carvalho, Julia L. Chen, Jen-Tsan Chi, Mike West posted to projection gene_lists cross-study cross-platform by jfr on 2009-09-30 10:11:25 as along with 4 people zufar frohike jmstat bertelsen
	Molecular characterization of breast cancer with high-resolution oligonucleotide comparative genomic hybridization array. [My Copy] Clinical cancer research : an official journal of the American Association for Cancer Research, Vol. 15, No. 2. (15 January 2009), pp. 441-451. by F. Andre, B. Job, P. Dessen, et al.A. Tordai, S. Michiels, C. Liedtke, C. Richon, K. Yan, B. Wang, G. Vassal, S. Delaloge, G. N. Hortobagyi, W. F. Symmans, V. Lazar, L. Pusztai posted to array-cgh breast_cancer copy-number gene_expression integration by jfr on 2009-07-06 12:41:41 as
	Dynamic modularity in protein interaction networks predicts breast cancer outcome. [My Copy] Nature biotechnology, Vol. 27, No. 2. (1 February 2009), pp. 199-204. by Ian W. Taylor, Rune Linding, David Warde-Farley, et al.Yongmei Liu, Catia Pesquita, Daniel Faria, Shelley Bull, Tony Pawson, Quaid Morris, Jeffrey L. Wrana posted to breast_cancer network prognosis by jfr on 2009-04-28 13:55:26 as along with 14 people and 1 group ukhan zufar guhjy frohike fenghezi ptrobajo jaimie nedwards dakelley absterga phoenixzxl grahamc provero brianb cube_and_beyond
	Exploring the human genome with functional maps [My Copy] Genome Research, Vol. 19, No. 6. (1 June 2009), pp. 1093-1106. by Curtis Huttenhower, Erin M. Haley, Matthew A. Hibbs, et al.Vanessa Dumeaux, Daniel R. Barrett, Hilary A. Coller, Olga G. Troyanskaya posted to visualization software integration functional_genomics by jfr on 2009-11-19 11:25:00 as along with 9 people ptrobajo daforerog fenghezi shikin idoerg guhjy pinney grahamc pkonings
	Probabilistic retrieval and visualization of biologically relevant microarray experiments [My Copy] Bioinformatics, Vol. 25, No. 12. (15 June 2009), pp. i145-153. by Jose Caldas, Nils Gehlenborg, Ali Faisal, Alvis Brazma, Samuel Kaski posted to meta-analysis gene_expression database by jfr on 2009-11-18 14:48:03 as along with 6 people ngehlenborg greg ptrobajo bertelsen guhjy shikin
	Fewer permutations, more accurate P-values [My Copy] Bioinformatics, Vol. 25, No. 12. (15 June 2009), pp. i161-168. by Theo A. Knijnenburg, Lodewyk F. A. Wessels, Marcel J. T. Reinders, Ilya Shmulevich posted to permutations by jfr on 2009-11-18 14:45:58 as along with 10 people and 1 group heliopais rdiaz Ayest farhat AlexBateman bmajoros idonaldson TRHvidsten djkt sameersoi Journal picks
	Application and evaluation of automated semantic annotation of gene expression experiments. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 12. (15 June 2009), pp. 1543-1549. by Leon French, Suzanne Lane, Tamryn Law, Lydia Xu, Paul Pavlidis posted to semantic_web gene_expression annotation by jfr on 2009-11-18 14:42:06 as along with 3 people mitko shikin guhjy
	Chromosomal instability determines taxane response. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 106, No. 21. (26 May 2009), pp. 8671-8676. by Charles Swanton, Barbara Nicke, Marion Schuett, et al.Aron C. Eklund, Charlotte Ng, Qiyuan Li, Thomas Hardcastle, Alvin Lee, Rajat Roy, Philip East, Maik Kschischo, David Endesfelder, Paul Wylie, Se Nyun N. Kim, Jie-Guang G. Chen, Michael Howell, Thomas Ried, Jens K. Habermann, Gert Auer, James D. Brenton, Zoltan Szallasi, Julian Downward posted to taxane classification cin breast_cancer by jfr on 2009-11-18 14:23:36 as
	Data driven derivation of cutoffs from a pool of 3,030 Affymetrix arrays to stratify distinct clinical types of breast cancer. [My Copy] Breast cancer research and treatment (20 May 2009) by Thomas Karn, Dirk Metzler, Eugen Ruckhäberle, et al.Lars Hanker, Regine Gätje, Christine Solbach, Andre Ahr, Marcus Schmidt, Uwe Holtrich, Manfred Kaufmann, Achim Rody posted to subtypes proliferation pr meta-analysis her2 er breast_cancer by jfr on 2009-11-18 13:14:00 as
	MicroRNAs: Novel regulators in the hallmarks of human cancer [My Copy] Cancer Letters (22 May 2009) by Kai Ruan, Xiaoguang Fang, Gaoliang Ouyang posted to review mirna cancer_hallmarks by jfr on 2009-11-17 14:42:12 as along with 2 people and 1 group zufar guhjy microRNA
	Data structures and algorithms for analysis of genetics of gene expression with Bioconductor: GGtools 3.x [My Copy] Bioinformatics, Vol. 25, No. 11. (1 June 2009), pp. 1447-1448. by Vincent J. Carey, Adam R. Davis, Michael F. Lawrence, Robert Gentleman, Benjamin A. Raby posted to software snp gene_expression bioconductor by jfr on 2009-11-15 16:09:51 as along with 6 people guhjy druvus nuin rdiaz djkt giovanni
	Ki67 index, HER2 status, and prognosis of patients with luminal B breast cancer. [My Copy] Journal of the National Cancer Institute, Vol. 101, No. 10. (20 May 2009), pp. 736-750. by Maggie C. Cheang, Stephen K. Chia, David Voduc, et al.Dongxia Gao, Samuel Leung, Jacqueline Snider, Mark Watson, Sherri Davies, Philip S. Bernard, Joel S. Parker, Charles M. Perou, Matthew J. Ellis, Torsten O. Nielsen posted to subtypes rt-pcr proliferation pr luminal_subtype immunohistochemistry her2 er breast_cancer by jfr on 2009-11-15 14:43:06 as along with 1 person zufar
	Mining metastasis related genes by primary-secondary tumor comparisons from large-scale databases. [My Copy] BMC bioinformatics, Vol. 10 Suppl 3 (2009) by Sangwoo Kim, Doheon Lee posted to public_data metastasis meta-analysis colon_cancer by jfr on 2009-11-15 14:22:31 as
	MicroRNA signatures predict oestrogen receptor, progesterone receptor and HER2/neu receptor status in breast cancer. [My Copy] Breast cancer research : BCR, Vol. 11, No. 3. (11 May 2009), R27. by Aoife J. Lowery, Nicola Miller, Amanda Devaney, et al.Roisin E. McNeill, Pamela A. Davoren, Christophe Lemetre, Vladimir Benes, Sabine Schmidt, Jonathon Blake, Graham Ball, Michael J. Kerin posted to pr mirna her2 er breast_cancer by jfr on 2009-11-13 11:46:37 as along with 2 people and 1 group tonamswish giovenko microRNA
	The apoptotic machinery as a biological complex system: analysis of its omics and evolution, identification of candidate genes for fourteen major types of cancer, and experimental validation in CML and neuroblastoma [My Copy] BMC Medical Genomics, Vol. 2, No. 1. (2009), 20. by Cinzia Di Pietro, Marco Ragusa, Davide Barbagallo, et al.Laura Duro, Maria Guglielmino, Alessandra Majorana, Rosario Angelica, Marina Scalia, Luisa Statello, Loredana Salito, Luisa Tomasello, Salvo Pernagallo, Salvo Valenti, Vito D'Agostino, Patrizio Triberio, Igor Tandurella, Giuseppe Palumbo, Piera La Cava, Viviana Cafiso, Taschia Bertuccio, Maria Santagati, Giovanni L. Destri, Salvatore Lanzafame, Francesco Di Raimondo, Stefania Stefani, Bud Mishra, Michele Purrello posted to network apoptosis by jfr on 2009-11-10 17:15:49 as along with 1 person shikin
	Aneuploidy prediction and tumor classification with heterogeneous hidden conditional random fields [My Copy] Bioinformatics, Vol. 25, No. 10. (15 May 2009), pp. 1307-1313. by Zafer Barutcuoglu, Edoardo M. Airoldi, Vanessa Dumeaux, Robert E. Schapire, Olga G. Troyanskaya posted to copy-number by jfr on 2009-11-09 14:36:20 as along with 3 people rdiaz pkonings Zephyrus
	Statistical comparison framework and visualization scheme for ranking-based algorithms in high-throughput genome-wide studies. [My Copy] Journal of computational biology : a journal of computational molecular cell biology, Vol. 16, No. 4. (April 2009), pp. 565-577. by Waibhav D. Tembe, John V. Pearson, Nils Homer, James Lowey, Edward Suh, David W. Craig posted to ranked_lists gene_set_analysis by jfr on 2009-11-09 13:42:57 as along with 1 person guhjy
	Target discovery from data mining approaches. [My Copy] Drug discovery today, Vol. 14, No. 3-4. (7 February 2009), pp. 147-154. by Yongliang Yang, S. James Adelstein, Amin I. Kassis posted to target_discovery review by jfr on 2009-11-09 13:38:08 as along with 8 people and 1 group agomez eesruiz tonamswish mitko nicklynch sschurer guhjy zimbo1 ImagCom - Biomedical Text Computing
	Allelic imbalance sequencing reveals that single-nucleotide polymorphisms frequently alter microRNA-directed repression [My Copy] Nature Biotechnology, Vol. 27, No. 5. (26 April 2009), pp. 472-477. by Jinkuk Kim, David P. Bartel posted to snp mirna_regulation mirna by jfr on 2009-11-08 23:34:07 as along with 7 people and 1 group guhjy fenghezi giovanni jbhiatt daforerog samgj valeriehilgers microRNA
	Genomic Grade Index Is Associated With Response to Chemotherapy in Patients With Breast Cancer [My Copy] J Clin Oncol, Vol. 27, No. 19. (1 July 2009), pp. 3185-3191. by Cornelia Liedtke, Christos Hatzis, William F. Symmans, et al.Christine Desmedt, Benjamin Haibe-Kains, Vicente Valero, Henry Kuerer, Gabriel N. Hortobagyi, Martine Piccart-Gebhart, Christos Sotiriou, Lajos Pusztai posted to gene_expression chemotherapy breast_cancer by jfr on 2009-11-08 22:33:09 as
	The use of gene ontology evidence codes in preventing classifier assessment bias [My Copy] Bioinformatics, Vol. 25, No. 9. (1 May 2009), pp. 1173-1177. by Mark F. Rogers, Asa Ben-Hur posted to gene_ontology classification by jfr on 2009-11-03 17:15:49 as along with 4 people kshameer vkwn rdiaz dullhunk
	Ultrasome: efficient aberration caller for copy number studies of ultra-high resolution. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 8. (15 April 2009), pp. 1078-1079. by Björn Nilsson, Mikael Johansson, Fatima Al-Shahrour, Anne E. Carpenter, Benjamin L. Ebert posted to software segmentation copy-number by jfr on 2009-11-02 17:27:22 as along with 3 people daed rdiaz pkonings
	Human microRNAs co-silence in well-separated groups and have different predicted essentialities. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 8. (15 April 2009), pp. 1063-1069. by Gábor Boross, Katalin Orosz, Illés J. Farkas posted to mirna by jfr on 2009-11-02 17:23:03 as along with 6 people and 2 groups heliopais samgj shikin ealloza daforerog valeriehilgers microRNA BenosLab
	Personalizing medicine: a systems biology perspective. [My Copy] Molecular systems biology, Vol. 5 (17 March 2009) by Thomas S. Deisboeck posted to systems_biology personalized_medicine editorial by jfr on 2009-11-02 17:13:21 as along with 2 people phoenixzxl allysonlister
	New class of microRNA targets containing simultaneous 5'-UTR and 3'-UTR interaction sites. [My Copy] Genome research, Vol. 19, No. 7. (31 July 2009), pp. 1175-1183. by Inhan Lee, Subramanian S. Ajay, Jong In I. Yook, et al.Hyun Sil S. Kim, Su Hyung H. Hong, Nam Hee H. Kim, Saravana M. Dhanasekaran, Arul M. Chinnaiyan, Brian D. Athey posted to mirna_target mirna by jfr on 2009-11-02 17:01:43 as along with 15 people and 5 groups hzoltan ebcgantman ashkelon13 heliopais megraw fenghezi fpattyn tmmurali ppgardne tonamswish stajich Einat daforerog valeriehilgers ealloza Neuroblastoma Journal picks microRNA Mycology cube_and_beyond
	MicroRNAs preferentially target the genes with high transcriptional regulation complexity. [My Copy] Biochemical and biophysical research communications, Vol. 352, No. 3. (19 January 2007), pp. 733-738. by Qinghua Cui, Zhenbao Yu, Youlian Pan, Enrico O. Purisima, Edwin Wang posted to mirna_target mirna by jfr on 2009-11-02 15:56:44 as along with 12 people and 6 groups danaiancu epinatel mtagaya daforerog eckart_bindewald tardigrade dchughes cdawson cursonivel1 heliopais maralena natstreet cube_and_beyond microRNA G4ID GIG Genetics-of-Gambling cursonivel1
	Combinatorial microRNAs: working together to make a difference. [My Copy] Cell cycle (Georgetown, Tex.), Vol. 7, No. 20. (4 October 2008), pp. 3137-3142. by Irena Ivanovska, Michele A. Cleary posted to review mirna by jfr on 2009-11-02 15:51:56 as along with 2 people samgj pengchy
	A computational screen for mouse signaling pathways targeted by microRNA clusters. [My Copy] RNA (New York, N.Y.), Vol. 14, No. 7. (29 July 2008), pp. 1276-1283. by Jianzhen Xu, Chiwai Wong posted to mirna_target mirna_cluster mirna by jfr on 2009-11-02 15:12:20 as along with 7 people and 1 group heliopais coela guhjy bootsy mtagaya maralena daforerog microRNA
	Analysis of Gene Sets Based on the Underlying Regulatory Network [My Copy] Journal of Computational Biology, Vol. 16, No. 3. (March 2009), pp. 407-426. by Ali Shojaie, George Michailidis posted to gene_set_analysis network by jfr on 2009-07-23 16:00:07 as along with 4 people and 1 group zufar shikin guhjy rdiaz Bioinformatics
	Correlation signature of the macroscopic states of the gene regulatory network in cancer. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 106, No. 11. (17 March 2009), pp. 4079-4084. by Nikolai Slavov, Kenneth A. Dawson posted to cancer gene_expression meta-analysis network prioritization by jfr on 2009-07-22 12:52:06 as along with 5 people and 1 group zufar fpattyn vertikalist rdiaz provero BTS-PT-AS-CS
	MicroRNAs--the micro steering wheel of tumour metastases. [My Copy] Nature reviews. Cancer, Vol. 9, No. 4. (5 April 2009), pp. 293-302. by Milena S. Nicoloso, Riccardo Spizzo, Masayoshi Shimizu, Simona Rossi, George A. Calin posted to metastasis mirna review by jfr on 2009-07-17 15:44:51 as along with 6 people and 1 group guhjy reyez tonamswish giovenko provero valeriehilgers microRNA
	Emerging biomarkers and new understanding of traditional markers in personalized therapy for breast cancer. [My Copy] Clinical cancer research : an official journal of the American Association for Cancer Research, Vol. 14, No. 24. (15 December 2008), pp. 8019-8026. by Mitch Dowsett, Anita K. Dunbier posted to biomarker breast_cancer personalized_medicine review by jfr on 2009-07-09 13:58:00 as along with 2 people Zephyrus misonneh
	Triple-Negative Breast Cancer: Risk Factors to Potential Targets [My Copy] Clin Cancer Res, Vol. 14, No. 24. (15 December 2008), pp. 8010-8018. by Bryan P. Schneider, Eric P. Winer, William D. Foulkes, et al.Judy Garber, Charles M. Perou, Andrea Richardson, George W. Sledge, Lisa A. Carey posted to breast_cancer review subtypes target triple_negative by jfr on 2009-07-09 13:56:12 as along with 3 people and 1 group Zephyrus NaliniChilkov misonneh Breast Cancer Reading Club
	Reduced expression of a gene proliferation signature is associated with enhanced malignancy in colon cancer. [My Copy] British journal of cancer, Vol. 99, No. 6. (16 September 2008), pp. 966-973. by A. Anjomshoaa, Y. H. Lin, M. A. Black, et al.J. L. McCall, B. Humar, S. Song, R. Fukuzawa, H. S. Yoon, B. Holzmann, J. Friederichs, A. van Rij, M. Thompson-Fawcett, A. E. Reeve posted to classification colon_cancer proliferation by jfr on 2009-07-01 14:47:34 as
	Genomic copy number determination in cancer cells from single nucleotide polymorphism microarrays based on quantitative genotyping corrected for aneuploidy. [My Copy] Genome research, Vol. 19, No. 2. (February 2009), pp. 276-283. by E. F. Attiyeh, S. J. Diskin, M. A. Attiyeh, et al.Y. P. Mossé, C. Hou, E. M. Jackson, C. Kim, J. Glessner, H. Hakonarson, J. A. Biegel, J. M. Maris posted to copy-number snp-arrays by jfr on 2009-04-28 13:35:14 as along with 3 people and 1 group absterga rdiaz skoch3 Koch_Lab
	The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores [My Copy] Nat Genet, Vol. 41, No. 2. (18 February 2009), pp. 178-186. by Rafael A. Irizarry, Christine Ladd-Acosta, Bo Wen, et al.Zhijin Wu, Carolina Montano, Patrick Onyango, Hengmi Cui, Kevin Gabo, Michael Rongione, Maree Webster, Hong Ji, James B. Potash, Sarven Sabunciyan, Andrew P. Feinberg posted to colon_cancer methylation by jfr on 2009-04-15 14:03:54 as along with 5 people saravana suizifish felsani wpuszyk misonneh
	Assessing the quality of hybridized RNA in Affymetrix GeneChips using linear regression. [My Copy] Journal of biomolecular techniques : JBT, Vol. 19, No. 2. (April 2008), pp. 122-128. by Meijuan Li, Cavan Reilly posted to affy quality_control rna_quality by jfr on 2009-04-14 11:29:44 as along with 1 person shikin
	GeneChaser: identifying all biological and clinical conditions in which genes of interest are differentially expressed. [My Copy] BMC bioinformatics, Vol. 9, No. 1. (2008) by R. Chen, R. Mallelwar, A. Thosar, S. Venkatasubrahmanyam, A. J. Butte posted to database meta-analysis by jfr on 2009-03-23 14:48:52 as along with 13 people and 2 groups rcr1991 zufar daforerog TRHvidsten ilyashl dswan renatomilani Zephyrus tny guhjy cgaugain barriot GeeSharpMinor Bioinformatics Roswell Cancer Crosstalk
	An empirical framework for binary interactome mapping. [My Copy] Nature methods, Vol. 6, No. 1. (07 January 2009), pp. 83-90. by Kavitha Venkatesan, Jean-François F. Rual, Alexei Vazquez, et al.Ulrich Stelzl, Irma Lemmens, Tomoko Hirozane-Kishikawa, Tong Hao, Martina Zenkner, Xiaofeng Xin, Kwang-Il I. Goh, Muhammed A. Yildirim, Nicolas Simonis, Kathrin Heinzmann, Fana Gebreab, Julie M. Sahalie, Sebiha Cevik, Christophe Simon, Anne-Sophie S. de Smet, Elizabeth Dann, Alex Smolyar, Arunachalam Vinayagam, Haiyuan Yu, David Szeto, Heather Borick, Amélie Dricot, Niels Klitgord, Ryan R. Murray, Chenwei Lin, Maciej Lalowski, Jan Timm, Kirstin Rau, Charles Boone, Pascal Braun, Michael E. Cusick, Frederick P. Roth, David E. Hill, Jan Tavernier, Erich E. Wanker, Albert-László L. Barabási, Marc Vidal posted to network protein_interaction by jfr on 2009-03-18 15:30:17 as along with 4 people chica lawraga lp2 guhjy
	Sparse combinatorial inference with an application in cancer biology [My Copy] Bioinformatics, Vol. 25, No. 2. (15 January 2009), pp. 265-271. by Sach Mukherjee, Steven Pelech, Richard M. Neve, et al.Wen-Lin Kuo, Safiyyah Ziyad, Paul T. Spellman, Joe W. Gray, Terence P. Speed posted to no-tag by jfr on 2009-03-18 14:22:02 as along with 3 people ipark-kaist mstumpf imina
	Microarray-based gene set analysis: a comparison of current methods [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (2008), 502. by Sarah Song, Michael Black posted to comparison gene_set_analysis by jfr on 2009-03-13 14:36:53 as along with 26 people and 1 group bertelsen giovenko dipenps holecm lwaldron ptrobajo ekotelnikova zufar buyske guhjy heliopais fhalbrit lptolik balicea daforerog Zephyrus irinamohorianu dswan shikin nuin hersh006 behindtherabbit colinDotAIBN druvus barriot GeeSharpMinor Roswell Cancer Crosstalk
	Inferring Pathway Activity toward Precise Disease Classification [My Copy] PLoS Comput Biol, Vol. 4, No. 11. (7 November 2008), e1000217. by Eunjung Lee, Han-Yu Chuang, Jong-Won Kim, Trey Ideker, Doheon Lee posted to classification methodology pathway_analysis by jfr on 2009-03-13 11:29:35 as along with 13 people rschulz isimpson yaredo frohike ipark-kaist aviad_work ajbattle zufar carlk renatomilani dragonrez tmmurali ptrobajo
	A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 52. (30 December 2008), pp. 20870-20875. by Kasper Lage, Niclas T. Hansen, Olof E. Karlberg, et al.Aron C. Eklund, Francisco S. Roque, Patricia K. Donahoe, Zoltan Szallasi, Thomas S. Jensen, Søren Brunak posted to disease_genes tissue_specificity by jfr on 2009-03-02 14:19:04 as along with 4 people grahamc bertelsen brianb nedwards
	Genome-wide functional synergy between amplified and mutated genes in human breast cancer. [My Copy] Cancer research, Vol. 68, No. 22. (15 November 2008), pp. 9532-9540. by Y. Nikolsky, E. Sviridov, J. Yao, et al.D. Dosymbekov, V. Ustyansky, V. Kaznacheev, Z. Dezso, L. Mulvey, L. E. Macconaill, W. Winckler, T. Serebryiskaya, T. Nikolskaya, K. Polyak posted to breast_cancer copy-number gene_expression integration mutation by jfr on 2009-02-25 17:59:21 as along with 4 people and 2 groups shikin ipark-kaist chrisamiller Zephyrus GeneGo Breast Cancer Reading Club
	DNA Copy-Number Alterations Underlie Gene Expression Differences between Microsatellite Stable and Unstable Colorectal Cancers. [My Copy] Clinical cancer research : an official journal of the American Association for Cancer Research, Vol. 14, No. 24. (15 December 2008), pp. 8061-8069. by R. N. Jorissen, L. Lipton, P. Gibbs, et al.M. Chapman, J. Desai, I. T. Jones, T. J. Yeatman, P. East, I. P. Tomlinson, H. W. Verspaget, L. A. Aaltonen, M. Kruhøffer, T. F. Orntoft, C. L. Andersen, O. M. Sieber posted to cin colon_cancer copy-number gene_expression msi by jfr on 2009-02-25 17:58:09 as along with 1 person Terkko

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breast_cancer	468
review	336
mirna	333
classification	268
software	268
colon_cancer	227
gene_expression	169
methodology	168
copy-number	153
network	148
microarray_technology	133
integration	132
bioinformatics	121
clustering	119
feature_selection	105
meta-analysis	94
affy	83
database	81
therapy	80
mirna_target	74
array-cgh	69
crc_bib	69
gene_set_analysis	67
low_level	66
regulation	63
systems_biology	62
pathway_analysis	60
rt-pcr	60
genomics	58
subtypes	57
annotation	56
snp-arrays	56
comment	51
quality_control	48
normalization	44
mutations	43
metastasis	42
ffpe	41
prognosis	41
deep_sequencing	40
estrogen	40
microarray_analysis	40
proteomics	38
bioconductor	37
cancer	37
statistics	36
alternative_splicing	35
progression	35
protein_interaction	35
fdr	34
markers	34
methylation	32
snp	32
class_discovery	28
r	28
tamoxifen	28
mutation	27
standards	26
exon_arrays	25
jfrbib	24
microarray_protocol	23
mir17-92	23
two-color	23
experiment_design	22
pathway	22
brca	21
co-expression	21
comparison	21
ovarian_cancer	21
model	20
survival_analysis	20
tfbs	20
treatment	19
functional_analysis	18
kras	18
p53	18
platform_comparison	18
chip-chip	16
evaluation	16
illumina	16
jfrbib04-09	16
multiple_testing	16
stem_cell	16
technology	16
antisense	15
biomarker	15
module_detection	15
nmf	15
text-mining	15
basal_subtype	14
erbb	14
sequencing	14
bio_signature	13
reproducible_research	13
rna_quality	13
stageii	13
staging	13
tma	13
cnv	12
egfr	12
gene_ontology	12
genotyping	12
lung_cancer	12
maqc	12
marker	12
cell_line	11
drug_discovery	11
missing_values	11
proliferation	11
protocol	11
control_genes	10
disease_genes	10
gene_lists	10
genome_browser	10
loh	10
pten	10
semantic_web	10
tissue_specificity	10
visualization	10
immunohistochemistry	9
msi	9
probe_design	9
segmentation	9
boutique_arrays	8
can_genes	8
chip-seq	8
consensus_clustering	8
e2f1	8
inter-laboratory	8
mirna_regulation	8
personalized_medicine	8
sample_size	8
tgfb	8
time-course	8
18q_loh	7
lymphoma	7
myc	7
tiling_array	7
validation	7
community	6
editorial	6
gene_interaction	6
graphs	6
hpc	6
leukemia	6
motif	6
nci60	6
non-coding	6
ontology	6
plos_rules	6
promoters	6
read_mapping	6
serum	6
stem	6
chemotherapy	5
cin	5
correlation	5
cross-platform	5
gene_pairs	5
grid_computing	5
gwas	5
her2	5
machine_learning	5
mir21	5
plos_primer	5
plos_start	5
radiation	5
trial	5
biobank	4
data_curation	4
er	4
go	4
grading	4
image_analysis	4
lims	4
mir34	4
mirna_cluster	4
pooling	4
prioritization	4
prostate_cancer	4
public_data	4
resource	4
web_services	4
agilent	3
apc	3
bim	3
biomarkers	3
chromatin	3
confounders	3
copa	3
evolution	3
functional_classification	3
functional_genomics	3
hapmap	3
interaction	3
loops	3
mass_spec	3
micro_environment	3
mir192	3
ontologies	3
open-source	3
outlier	3
pca	3
pik3ca	3
pr	3
primer	3
roc	3
sage	3
small_molecule	3
sop	3
stability	3
stroma	3
survival	3
triple_negative	3
tutorial	3
wnt	3
20q	2
8q24	2
alignment	2
batch-effect	2
bcatenin	2
caching	2
cdk8	2
cetuximab	2
chemo	2
diagnostic	2
dna_damage	2
ephb	2
epigenetics	2
er-positive	2
filtering	2
flow_cytometry	2
gene_fusion	2
glioblastoma	2
guidelines	2
in-situ	2
letter	2
local_recurrence	2
luminal_subtype	2
lymphocytes	2
mage	2
meeting_report	2
mir20a	2
mir215	2
mutual_information	2
oncomine	2
permutations	2
priors	2
projection	2
protein_microarray	2
protein_networks	2
qtl	2
recommendation	2
rin	2
semi-supervised	2
serm	2
smad	2
snp_arrays	2
svm	2
sweave	2
target	2
tbfs	2
thyroid	2
translational	2
upd	2
web_server	2
3utr	1
454	1
aging	1
akt	1
apoptosis	1
aroma	1
asco	1
association_studies	1
au-rich	1
aurora_kinase	1
bayesian	1
beads	1
biclustering	1
bmp	1
braf	1
brain_cancer	1
cables1	1
cancer_hallmarks	1
cell_cycle	1
cervical_cancer	1
circulating_tumor_cells	1
cloud_computing	1
clusterin	1
compression	1
concordance	1
cross-species	1
cross-study	1
dasl	1
dcc	1
dimension_reduction	1
disease	1
distance	1
driver_genes	1
dye_bias	1
early-stage	1
ecm	1
eno1	1
ensemble	1
ependymoma	1
erg	1
er-negative	1
est_analysis	1
estradiol	1
fgfr2	1
fish	1
formalization	1
formats	1
funding	1
gastric_cancer	1
gene_clusters	1
gene_function_prediction	1
genetics	1
genoty	1
graph_approach	1
hypoxia	1
il8	1
in_situ_hybridization	1
invasion	1
latent	1
latex	1
markup	1
mcm7	1
melanoma	1
met	1
meta_analysis	1
metagene	1
microrna	1
mir101	1
mir-106b-25	1
mir126	1
mir135	1
mir143	1
mir145	1
mir155	1
mir15a	1
mir16-1	1
mir199	1
mir203	1
mir449	1
mirna221	1
mirna222	1
mirna_discovery	1
mixture_models	1
model-based	1
modules	1
mrna-seq	1
myb	1
neural_networks	1
news	1
ngs	1
nomogram	1
oncogene	1
oncogene_addiction	1
p21	1
pancreatic_cancer	1
passenger_genes	1
pbc	1
perturbation	1
pilot_study	1
plasma	1
power_analysis	1
prb	1
pre-post	1
python	1
randomization	1
ranked_lists	1
rb	1
ret	1
rnai	1
rna-interference	1
sampling	1
selection_bias	1
shrna	1
signaling	1
simulation	1
single_cell	1
smad7	1
stageiii	1
stem_cells	1
study_design	1
target_discovery	1
taxane	1
tissue_origin	1
translocation	1
ucs	1
wiki	1

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