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tuck's library [215 articles]

Recent papers added to tuck's library ordered by importance.
  • Oncogenic pathway signatures in human cancers as a guide to targeted therapies
    Nature (06 November 2005)
    by Andrea H Bild, Guang Yao, Jeffrey T Chang, Quanli Wang, Anil Potti, Dawn Chasse, Mary-Beth Joshi, David Harpole, Johnathan M Lancaster, Andrew Berchuck, John A Olson, Jeffrey R Marks, Holly K Dressman, Mike West, Joseph R Nevins
    posted to cancer microarray pathway by tuck on 2005-11-30 02:38:06 as *** along with 11 people srp33 Yanno jyuh kentsis mfenner ajeffs maryee eckart_bindewald frohike Ao_Li2007 waghsk
  • Oct4 pseudogenes are transcribed in cancers
    Biochemical and Biophysical Research Communications, Vol. 337, No. 4. (2 December 2005), pp. 1047-1051.
    by Guangli Suo, Jin Han, Xia Wang, Jingyu Zhang, Yannan Zhao, Yanhong Zhao, Jianwu Dai
    posted to bioinformatics stemcell by tuck on 2005-11-07 11:19:14 as *** along with 1 person xingxu
  • Reconstructing gene-regulatory networks from time series, knock-out data, and prior knowledge
    BMC Systems Biology, Vol. 1, No. 1. (2007)
    by Florian Geier, Jens Timmer, Christian Fleck
    posted to no-tag by tuck on 2007-03-07 18:27:20 as ** along with 3 people jyuh wnpx Ao_Li2007
  • An improved map of conserved regulatory sites for Saccharomyces cerevisiae.
    BMC Bioinformatics, Vol. 7, No. 1. (7 March 2006)
    by Kenzie D Macisaac, Ting Wang, Benjamin D Gordon, David K Gifford, Gary D Stormo, Ernest Fraenkel
    posted to motif transcription_factor yeast by tuck on 2007-01-05 14:23:52 as ** along with 7 people kristallreiner eckart_bindewald cconboy raiyar lusk nklee barwil
  • Changes in gene expression during the development of mammary tumors in MMTV-Wnt-1 transgenic mice.
    Genome Biol, Vol. 6, No. 10. (2005)
    by S Huang, Y Li, Y Chen, K Podsypanina, M Chamorro, AB Olshen, KV Desai, A Tann, D Petersen, JE Green, HE Varmus
    posted to breast cancer her2 wnt by tuck on 2007-01-04 16:16:24 as **
  • Experimental validation of predicted mammalian erythroid cis-regulatory modules
    Genome Res., Vol. 16, No. 12. (1 December 2006), pp. 1480-1492.
    by Hao Wang, Ying Zhang, Yong Cheng, Yuepin Zhou, David C King, James Taylor, Francesca Chiaromonte, Jyotsna Kasturi, Hanna Petrykowska, Brian Gibb, Christine Dorman, Webb Miller, Louis C Dore, John Welch, Mitchell J Weiss, Ross C Hardison
    posted to cis_regulatory_module erythroid by tuck on 2007-01-03 01:17:26 as ** along with 1 person fpattyn
  • Gene expression patterns for doxorubicin (Adriamycin) and cyclophosphamide (Cytoxan) (AC) response and resistance
    Breast Cancer Research and Treatment, Vol. V95, No. 3. (28 February 2006), pp. 229-233.
    by Susan Cleator, Anna Tsimelzon, Alan Ashworth, Mitch Dowsett, Timothy Dexter, Trevor Powles, Susan Hilsenbeck, Helen Wong, Kent C Osborne, Peter Oâconnell, Jenny C Chang
    posted to breast microarray by tuck on 2006-12-29 02:21:11 as **
  • Comprehensive DNA methylation profiling in a human cancer genome identifies novel epigenetic targets
    Carcinogenesis, Vol. 27, No. 12. (December 2006), pp. 2409-2423.
    by Ordway, , Bedell, , Citek, , Nunberg, , Garrido, , Kendall, , Stevens, , Cao, , Doerge, , Korshunova, , Holemon, , Mcpherson, , Lakey, , Leon, , Martienssen, , Jeddeloh,
    posted to cpg_island methylation promoter by tuck on 2006-12-28 11:47:22 as **
  • Identification of alterations in DNA copy number in host stromal cells during tumor progression
    PNAS, Vol. 103, No. 52. (26 December 2006), pp. 19848-19853.
    by Robert J Pelham, Linda Rodgers, Ira Hall, Robert Lucito, Ken C Nguyen, Nicholas Navin, James Hicks, David Mu, Scott Powers, Michael Wigler, David Botstein
    posted to chromosomal_abnormality by tuck on 2006-12-27 03:23:40 as **
  • Short blocks from the noncoding parts of the human genome have instances within nearly all known genes and relate to biological processes.
    Proc Natl Acad Sci U S A (24 April 2006)
    by Isidore Rigoutsos, Tien Huynh, Kevin Miranda, Aristotelis Tsirigos, Alice McHardy, Daniel Platt
    posted to genome pattern pyknon by tuck on 2006-12-24 02:14:01 as ** along with 5 people and 1 group ep161302 imouthesmp andersbj mtagaya ilh microRNA
  • A Pattern-Based Method for the Identification of MicroRNA Binding Sites and Their Corresponding Heteroduplexes
    Cell, Vol. 126, No. 6. (22 September 2006), pp. 1203-1217.
    by Kevin C Miranda, Tien Huynh, Yvonne Tay, Yen-Sin Ang, Wai-Leong Tam, Andrew M Thomson, Bing Lim, Isidore Rigoutsos
    posted to microrna by tuck on 2006-12-24 02:04:58 as ** along with 6 people and 2 groups jfr tardigrade andersbj kengg joshuashen natstreet microRNA Plantandetc
  • Computational analysis of tissue-specific combinatorial gene regulation: predicting interaction between transcription factors in human tissues.
    Nucleic Acids Res (18 September 2006)
    by Xueping Yu, Jimmy Lin, Donald J J Zack, Jiang Qian
    posted to no-tag by tuck on 2006-12-19 04:24:57 as ** along with 2 people and 1 group jfr nickluscombe EBI-regulation
  • Forces shaping the fastest evolving regions in the human genome.
    PLoS Genet, Vol. 2, No. 10. (13 October 2006)
    by KS Pollard, SR Salama, B King, AD Kern, T Dreszer, S Katzman, A Siepel, JS Pedersen, G Bejerano, R Baertsch, KR Rosenbloom, J Kent, D Haussler
    posted to evolution genome by tuck on 2006-12-19 04:19:22 as ** along with 3 people pradiptaray bpb rrhudson
  • An improved distance measure between the expression profiles linking co-expression and co-regulation in mouse.
    BMC Bioinformatics, Vol. 7, No. 1. (26 January 2006)
    by Ryung S Kim, Hongkai Ji, Wing H Wong
    posted to transcription_factor by tuck on 2006-12-19 03:37:15 as ** along with 3 people troels_marstrand gpalidwor minostro
  • Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences
    Journal of Molecular Biology, Vol. 212, No. 4. (20 April 1990), pp. 563-578.
    by Philipp Bucher
    posted to pwm transcription_factor by tuck on 2006-12-19 03:35:40 as **
  • Differential sensitivities of transcription factor target genes underlie cell type-specific gene expression profiles.
    Proc Natl Acad Sci U S A (16 October 2006)
    by Kirby D D Johnson, Shin-Il I Kim, Emery H H Bresnick
    posted to transcription_factor by tuck on 2006-12-14 12:27:27 as ** along with 1 person and 1 group brant EisenLab
  • Quantitative genetic analysis in Saccharomyces cerevisiae using epistatic miniarray profiles (E-MAPs) and its application to chromatin functions
    Methods, Vol. 40, No. 4. (December 2006), pp. 344-352.
    by M Schuldiner, SR Collins, JS Weissman, NJ Krogan
    posted to epistasis genetic interaction by tuck on 2006-12-14 11:04:54 as **
  • Identifying DNA and protein patterns with statistically significant alignments of multiple sequences
    Bioinformatics, Vol. 15, No. 7. (1 July 1999), pp. 563-577.
    by Gz Hertz, Gd Stormo
    posted to regulatory transcription_factor by tuck on 2006-12-14 03:24:18 as ** along with 4 people and 1 group chad_davis indigoviolet dquest lusk EisenLab
  • Array-CGH and breast cancer
    Breast Cancer Research, Vol. 8 (30 June 2006), 210.
    by Erik H van Beers, Petra M Nederlof
    posted to breast cancer cgh by tuck on 2006-12-14 03:08:51 as ** along with 1 person rdiaz
  • Mutations of mitotic checkpoint genes in human cancers
    Nature, Vol. 392, No. 6673. (19 March 1998), pp. 300-303.
    by Daniel P Cahill, Christoph Lengauer, Jian Yu, Gregory J Riggins, James K Willson, Sanford D Markowitz, Kenneth W Kinzler, Bert Vogelstein
    posted to no-tag by tuck on 2006-12-14 03:07:05 as ** along with 1 person jackjackjjj
  • A supervised hidden Markov model framework for efficiently segmenting tiling array data in transcriptional and ChIP-chip experiments: systematically incorporating validated biological knowledge.
    Bioinformatics (12 October 2006)
    by Jiang Du, Joel S S Rozowsky, Jan O O Korbel, Zhengdong D D Zhang, Thomas E E Royce, Martin H H Schultz, Michael Snyder, Mark Gerstein
    posted to chip-chip by tuck on 2006-12-14 03:04:45 as ** along with 7 people and 2 groups xingxu miguel eckart_bindewald djkt SeungjoonOh blobbybirdman inesdesantiago Bioinformatics UH - Computational Biology
  • DNA structures at chromosomal translocation sites
    BioEssays, Vol. 28, No. 5. (2006), pp. 480-494.
    by Sathees C Raghavan, Michael R Lieber
    posted to chromosomal_abnormality fusion lymphoma by tuck on 2006-10-03 16:54:55 as **
  • Decoding the fine-scale structure of a breast cancer genome and transcriptome
    Genome Res., Vol. 16, No. 3. (1 March 2006), pp. 394-404.
    by Stanislav Volik, Benjamin J Raphael, Guiqing Huang, Michael R Stratton, Graham Bignel, John Murnane, John H Brebner, Krystyna Bajsarowicz, Pamela L Paris, Quanzhou Tao, David Kowbel, Anna Lapuk, Dmitri A Shagin, Irina A Shagina, Joe W Gray, Jan-Fang Cheng, Pieter J de Jong, Pavel Pevzner, Colin Collins
    posted to breast genome mcf7 by tuck on 2006-09-26 21:12:39 as ** along with 2 people jfr emb51
  • Epigenetic remodeling in colorectal cancer results in coordinate gene suppression across an entire chromosome band
    Nature Genetics, Vol. 38, No. 5. (23 April 2006), pp. 540-549.
    by Jordi Frigola, Jenny Song, Clare Stirzaker, Rebecca A Hinshelwood, Miguel A Peinado, Susan J Clark
    posted to epigenetics histone by tuck on 2006-09-24 03:43:53 as ** along with 1 person Anders
  • Distribution and dynamics of chromatin modification induced by a defined DNA double-strand break.
    Curr Biol, Vol. 14, No. 19. (5 October 2004), pp. 1703-1711.
    by R Shroff, A Arbel-Eden, D Pilch, G Ira, WM Bonner, JH Petrini, JE Haber, M Lichten
    posted to chromatin dna_damage by tuck on 2006-09-18 14:57:58 as **
  • DNA Damage Regulates Chk2 Association with Chromatin
    J. Biol. Chem., Vol. 280, No. 45. (11 November 2005), pp. 37948-37956.
    by Jia Li, David F Stern
    posted to checkpoint dna_damage rad53 by tuck on 2006-09-15 21:36:48 as **
  • The Consensus Coding Sequences of Human Breast and Colorectal Cancers
    Science (7 September 2006), 1133427.
    by Tobias Sjoblom, Sian Jones, Laura D Wood, Williams D Parsons, Jimmy Lin, Thomas Barber, Diana Mandelker, Rebecca J Leary, Janine Ptak, Natalie Silliman, Steve Szabo, Phillip Buckhaults, Christopher Farrell, Paul Meeh, Sanford D Markowitz, Joseph Willis, Dawn Dawson, James K Willson, Adi F Gazdar, James Hartigan, Leo Wu, Changsheng Liu, Giovanni Parmigiani, Ben H Park, Kurtis E Bachman, Nickolas Papadopoulos, Bert Vogelstein, Kenneth W Kinzler, Victor E Velculescu
    posted to breast mutation by tuck on 2006-09-11 01:35:07 as ** along with 18 people and 1 group frohike chrisamiller mingzhi aalibes bicko jfr balajis nickluscombe rdiaz eisei jackjackjjj vicsta jtaylor emb51 ramensky massivemayhem cerami xingxu EBI-regulation
  • MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model.
    Genome Biol, Vol. 5, No. 12. (2004)
    by AM Moses, DY Chiang, DA Pollard, VN Iyer, MB Eisen
    posted to transcription transcription_factor by tuck on 2006-09-09 03:16:42 as ** along with 5 people and 2 groups ihpark indigoviolet lusk Garamonfok cisevol EisenLab cis-regulatory-evolution
  • The replicator equation on graphs
    Journal of Theoretical Biology, Vol. In Press, Corrected Proof
    by Hisashi Ohtsuki, Martin A Nowak
    posted to game_theory network by tuck on 2006-09-05 21:22:20 as ** along with 2 people jpmague marcusfrean
  • Stochastic dynamics of invasion and fixation
    Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 74, No. 1. (2006)
    by Arne Traulsen, Martin A Nowak, Jorge M Pacheco
    posted to game_theory by tuck on 2006-09-05 21:17:09 as ** along with 1 person Koh
  • A signature of chromosomal instability inferred from gene expression profiles predicts clinical outcome in multiple human cancers
    Nature Genetics, Vol. 38, No. 9. (20 August 2006), pp. 1043-1048.
    by Scott L Carter, Aron C Eklund, Isaac S Kohane, Lyndsay N Harris, Zoltan Szallasi
    posted to aneuploidy cancer chromosomal_instability microarray by tuck on 2006-09-05 19:47:12 as ** along with 3 people and 1 group jfr ealloza cpnP BioinfoCIPF
  • Dynamic model-based clustering for time-course gene expression data.
    J Bioinform Comput Biol, Vol. 3, No. 4. (August 2005), pp. 821-836.
    by FX Wu, WJ Zhang, AJ Kusalik
    posted to microarray time_series by tuck on 2006-07-21 19:21:51 as ** along with 1 person dps
  • Predicting the in vivo signature of human gene regulatory sequences.
    Bioinformatics, Vol. 21 Suppl 1 (1 June 2005)
    by WS Noble, S Kuehn, R Thurman, M Yu, J Stamatoyannopoulos
    posted to algorithm sequence svm by tuck on 2006-07-12 20:44:30 as ** along with 2 people and 1 group royalzhang inesdesantiago Computational-Genomics
  • Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays
    Nature Methods, Vol. 3, No. 7. (21 June 2006), pp. 511-518.
    by Peter J Sabo, Michael S Kuehn, Robert Thurman, Brett E Johnson, Ericka M Johnson, Hua Cao, Man Yu, Elizabeth Rosenzweig, Jeff Goldy, Andrew Haydock, Molly Weaver, Anthony Shafer, Kristin Lee, Fidencio Neri, Richard Humbert, Michael A Singer, Todd A Richmond, Michael O Dorschner, Michael Mcarthur, Michael Hawrylycz, Roland D Green, Patrick A Navas, William S Noble, John A Stamatoyannopoulos
    posted to algorithm tiling_array by tuck on 2006-07-12 20:39:49 as ** along with 1 person olympos
  • Transcriptional regulatory code of a eukaryotic genome
    Nature, Vol. 431, No. 7004. (2004), pp. 99-104.
    by Christopher T Harbison, Benjamin D Gordon, Tong I Lee, Nicola J Rinaldi, Kenzie D Macisaac, Timothy W Danford, Nancy M Hannett, Jean-Bosco Tagne, David B Reynolds, Jane Yoo, Ezra G Jennings, Julia Zeitlinger, Dmitry K Pokholok, Manolis Kellis, Alex P Rolfe, Ken T Takusagawa, Eric S Lander, David K Gifford, Ernest Fraenkel, Richard A Young
    posted to network transcription yeast by tuck on 2006-06-29 17:20:59 as ** along with 22 people and 8 groups kristallreiner mariakmejia brant alokm chad_davis lyongu kaspermunch dpollard balicea kt dchughes nirfriedman cmm nickluscombe kengg gespim koller lusk nklee cisevol njcitulike xili03 Bioinformatics EisenLab FAB-lab G4ID EBI-regulation Plantandetc Genetics-of-Gambling BergmanLab
  • Analysis of weighted networks
    (20 July 2004)
    by MEJ Newman
    posted to network network_analysis by tuck on 2006-06-16 19:38:10 as ** along with 18 people and 5 groups apwesolowski theus camster nettraq korakot devzero ldietz lfriedl balicea kei_s entropy fukken AbnerCYH kubyaddi jaspervoskuilen michaelmampaey gsthakur dpf Philosophy_of_Information dbk-lab Blog_and_Wiki_Research kdl ADMiRes
  • Dissecting self-renewal in stem cells with RNA interference
    Nature, Vol. 442, No. 7102. (11 June 2006), pp. 533-538.
    by Natalia Ivanova, Radu Dobrin, Rong Lu, Iulia Kotenko, John Levorse, Christina Decoste, Xenia Schafer, Yi Lun, Ihor R Lemischka
    posted to microarray microrna mouse stemcell by tuck on 2006-06-16 18:52:48 as ** along with 1 person jsnoddy
  • Systems-level analyses identify extensive coupling among gene expression machines
    Mol Syst Biol, Vol. 2, No. 1. (17 January 2006), pp. msb4100045-E1-msb4100045-E14.
    by Karolina Maciag, Steven J Altschuler, Michael D Slack, Nevan J Krogan, Andrew Emili, Jack F Greenblatt, Tom Maniatis, Lani F Wu
    posted to protein yeast by tuck on 2006-06-15 02:37:44 as ** along with 2 people tmmurali koller
  • Comprehensive Analysis of Combinatorial Regulation using the Transcriptional Regulatory Network of Yeast
    Journal of Molecular Biology, Vol. In Press, Corrected Proof
    by S Balaji, Madan M Babu, Lakshminarayan M Iyer, Nicholas M Luscombe, L Aravind
    posted to network transcription yeast by tuck on 2006-06-15 02:20:07 as ** along with 2 people gespim cjeans
  • A high-resolution map of transcription in the yeast genome
    PNAS, Vol. 103, No. 14. (4 April 2006), pp. 5320-5325.
    by Lior David, Wolfgang Huber, Marina Granovskaia, Joern Toedling, Curtis J Palm, Lee Bofkin, Ted Jones, Ronald W Davis, Lars M Steinmetz
    posted to tiling_array yeast by tuck on 2006-06-14 10:35:24 as ** along with 7 people and 2 groups chasmand alexg eckart_bindewald dpollard entropy raiyar xingxu EisenLab steinmetzlab
  • Transcriptional Maps of 10 Human Chromosomes at 5-Nucleotide Resolution
    Science, Vol. 308, No. 5725. (20 May 2005), pp. 1149-1154.
    by Jill Cheng, Philipp Kapranov, Jorg Drenkow, Sujit Dike, Shane Brubaker, Sandeep Patel, Jeffrey Long, David Stern, Hari Tammana, Gregg Helt, Victor Sementchenko, Antonio Piccolboni, Stefan Bekiranov, Dione K Bailey, Madhavan Ganesh, Srinka Ghosh, Ian Bell, Daniela S Gerhard, Thomas R Gingeras
    posted to chip-chip transcription by tuck on 2006-06-14 10:26:45 as ** along with 4 people jasonflannick karbak tmmurali bertelsen
  • Analysis of computational approaches for motif discovery
    Algorithms for Molecular Biology, Vol. 1, No. 1. (19 May 2006), 8.
    by Nan Li, Martin Tompa
    posted to algorithm motif transcription_factor by tuck on 2006-06-13 12:09:42 as ** along with 9 people and 2 groups ana barry chad_davis dquest lusk nklee maximilianh xi03 csdhwang structural_bioinformatics Bioinformatics
  • Effects of radiotherapy and of differences in the extent of surgery for early breast cancer on local recurrence and 15-year survival: an overview of the randomised trials.
    Lancet, Vol. 366, No. 9503. (17 December 2005), pp. 2087-2106.
    by M Clarke, R Collins, S Darby, C Davies, P Elphinstone, E Evans, J Godwin, R Gray, C Hicks, S James, E MacKinnon, P McGale, T McHugh, R Peto, C Taylor, Y Wang,
    posted to breast cancer radiation by tuck on 2006-06-11 11:41:15 as ** along with 1 person CCCMA
  • Long-term outcome after postmastectomy radiation therapy for the treatment of ductal carcinoma in situ of the breast.
    Am J Clin Oncol, Vol. 22, No. 3. (June 1999), pp. 215-217.
    by JM Metz, LJ Solin
    posted to dcis radiation by tuck on 2006-06-11 11:31:38 as **
  • Translating the histone code into leukemia.
    J Cell Biochem, Vol. 96, No. 5. (1 December 2005), pp. 938-950.
    by BE Linggi, SJ Brandt, ZW Sun, SW Hiebert
    posted to hematopoiesis histone_code leukemia by tuck on 2006-06-07 02:22:32 as **
  • Cellular memory and hematopoietic stem cell aging.
    Stem Cells, Vol. 24, No. 5. (May 2006), pp. 1143-1149.
    by LM Kamminga, G de Haan
    posted to hematopoiesis histone_code polycomb stemcell by tuck on 2006-06-07 02:11:48 as **
  • The necessity of a human epigenome project
    Carcinogenesis, Vol. 27, No. 6. (1 June 2006), pp. 1121-1125.
    by Manel Esteller
    posted to epigenetics by tuck on 2006-06-07 01:32:59 as **
  • Methylation of histone H4 by arginine methyltransferase PRMT1 is essential in vivo for many subsequent histone modifications
    Genes Dev., Vol. 19, No. 16. (15 August 2005), pp. 1885-1893.
    by Suming Huang, Michael Litt, Gary Felsenfeld
    posted to chromatin histone methylation by tuck on 2006-05-28 18:30:53 as **
  • The Conserved Mec1/Rad53 Nuclear Checkpoint Pathway Regulates Mitochondrial DNA Copy Number in Saccharomyces cerevisiae
    Mol. Biol. Cell, Vol. 16, No. 6. (1 June 2005), pp. 3010-3018.
    by Sean D Taylor, Hong Zhang, Jana S Eaton, Matthew S Rodeheffer, Maria A Lebedeva, Thomas W O'Rourke, Wolfram Siede, Gerald S Shadel
    posted to copy_number dna_damage mitochdonria rad53 by tuck on 2006-05-27 12:02:28 as **
  • Geminin's double life: chromatin connections that regulate transcription at the transition from proliferation to differentiation.
    Cell Cycle, Vol. 5, No. 4. (February 2006), pp. 374-379.
    by S Seo, KL Kroll
    posted to chromatin regulation transcription trithorax by tuck on 2006-05-19 10:22:25 as **
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