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eckart_bindewald's library [354 articles]

Recent papers added to eckart_bindewald's library ordered by importance.
  • Predicting Protein Function with Hierarchical Phylogenetic Profiles: The Gene3D Phylo-Tuner Method Applied to Eukaryotic Genomes
    PLoS Computational Biology, Vol. 3, No. 11. (1 November 2007), e237.
    by Juan A Ranea, Corin Yeats, Alastair Grant, Christine A Orengo
  • Predicting expression patterns from regulatory sequence in Drosophila segmentation
    Nature (02 January 2008)
    by Eran Segal, Tali Raveh-Sadka, Mark Schroeder, Ulrich Unnerstall, Ulrike Gaul
  • A skin microRNA promotes differentiation by repressing ‘stemness’
    Nature (02 March 2008)
    by Rui Yi, Matthew N Poy, Markus Stoffel, Elaine Fuchs
  • High-resolution structure prediction and the crystallographic phase problem
    Nature (14 October 2007)
    by Bin Qian, Srivatsan Raman, Rhiju Das, Philip Bradley, Airlie J Mccoy, Randy J Read, David Baker
  • Discovering Motifs in Ranked Lists of DNA Sequences
    PLoS Computational Biology, Vol. 3, No. 3. (1 March 2007), e39.
    by Eran Eden, Doron Lipson, Sivan Yogev, Zohar Yakhini
  • RNA tectonics: towards RNA design.
    Fold Des, Vol. 1, No. 4. (1996)
    posted to tectoshapes rna nanotechnology design by eckart_bindewald on 2007-02-09 12:05:21 as *****
  • Considerations in the identification of functional RNA structural elements in genomic alignments
    BMC Bioinformatics, Vol. 8 (30 January 2007), 33.
    by Tomas Babak, Benjamin J Blencowe, Timothy R Hughes
  • Modelling 'evo-devo' with RNA.
    Bioessays, Vol. 24, No. 12. (December 2002), pp. 1164-1177.
    by W Fontana
  • The population genetic theory of hidden variation and genetic robustness.
    Genetics, Vol. 168, No. 4. (December 2004), pp. 2271-2284.
    by J Hermisson, GP Wagner
    posted to theory robustness polution genetics genetic by eckart_bindewald on 2007-01-23 16:46:27 as *****
  • Viral RNA and evolved mutational robustness.
    J Exp Zool, Vol. 285, No. 2. (15 August 1999), pp. 119-127.
    by A Wagner, PF Stadler
  • The robustness of naturally and artificially selected nucleic acid secondary structures.
    J Mol Evol, Vol. 58, No. 6. (June 2004), pp. 681-691.
    posted to structure secondary robustness rna mutation by eckart_bindewald on 2007-01-23 16:27:10 as *****
  • The transcriptional landscape of the mammalian genome.
    Science, Vol. 309, No. 5740. (2 September 2005), pp. 1559-1563.
    by P Carninci, T Kasukawa, S Katayama, J Gough, MC Frith, N Maeda, R Oyama, T Ravasi, B Lenhard, C Wells, R Kodzius, K Shimokawa, VB Bajic, SE Brenner, S Batalov, AR Forrest, M Zavolan, MJ Davis, LG Wilming, V Aidinis, JE Allen, A Ambesi-Impiombato, R Apweiler, RN Aturaliya, TL Bailey, M Bansal, L Baxter, KW Beisel, T Bersano, H Bono, AM Chalk, KP Chiu, V Choudhary, A Christoffels, DR Clutterbuck, ML Crowe, E Dalla, BP Dalrymple, B de Bono, G Della Gatta, D di Bernardo, T Down, P Engstrom, M Fagiolini, G Faulkner, CF Fletcher, T Fukushima, M Furuno, S Futaki, M Gariboldi, P Georgii-Hemming, TR Gingeras, T Gojobori, RE Green, S Gustincich, M Harbers, Y Hayashi, TK 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, SP Krishnan, A Kruger, SK Kummerfeld, IV Kurochkin, LF Lareau, D Lazarevic, L Lipovich, J Liu, S Liuni, S McWilliam, M Madan 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, KC Pang, WJ Pavan, G Pavesi, G Pesole, N Petrovsky, S Piazza, J Reed, JF Reid, BZ Ring, M Ringwald, B Rost, Y Ruan, SL Salzberg, A Sandelin, C Schneider, C Schönbach, K Sekiguchi, CA 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, SL Tan, S Tang, MS Taylor, J Tegner, SA Teichmann, HR Ueda, E van Nimwegen, R Verardo, CL Wei, K Yagi, H Yamanishi, E Zabarovsky, S Zhu, A Zimmer, W Hide, C Bult, SM Grimmond, RD Teasdale, ET Liu, V Brusic, J Quackenbush, C Wahlestedt, JS Mattick, DA Hume, 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, ,
  • Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs.
    Nature, Vol. 420, No. 6915. (5 December 2002), pp. 563-573.
  • Topology of three-way junctions in folded RNAs.
    RNA, Vol. 12, No. 1. (January 2006), pp. 83-93.
    posted to junction rna by eckart_bindewald on 2006-12-04 13:30:12 as ***** along with 1 person jarasch
  • RNA structural motifs: building blocks of a modular biomolecule.
    Q Rev Biophys, Vol. 38, No. 3. (August 2005), pp. 221-243.
    by DK Hendrix, SE Brenner, SR Holbrook
  • RNA structure: the long and the short of it.
    Curr Opin Struct Biol, Vol. 15, No. 3. (June 2005), pp. 302-308.
    by SR Holbrook
  • Rethinking some mechanisms invoked to explain translational regulation in eukaryotes
    Gene, Vol. In Press, Corrected Proof
    by Marilyn Kozak
  • Regulation of matrix metalloproteinase-9 (MMP-9) by translational efficiency in murine prostate carcinoma cells.
    Cancer Res, Vol. 62, No. 6. (15 March 2002), pp. 1910-1914.
    by Y Jiang, RJ Muschel
    posted to cancer efficiency translation_initiation by eckart_bindewald on 2006-09-18 17:17:01 as *****
  • Comparative analysis of orthologous eukaryotic mRNAs: potential hidden functional signals.
    Nucleic Acids Res, Vol. 32, No. 5. (2004), pp. 1774-1782.
    by SA Shabalina, AY Ogurtsov, IB Rogozin, EV Koonin, DJ Lipman
    posted to initiation translation utr by eckart_bindewald on 2006-07-17 12:02:57 as *****
  • The mammalian transcriptome and the function of non-coding DNA sequences.
    Genome Biol, Vol. 5, No. 4. (2004)
    posted to noncoding transcription translation utr by eckart_bindewald on 2006-07-17 12:01:19 as *****
  • Prediction of Genomic Functional Elements.
    Annu Rev Genomics Hum Genet (9 August 2005)
    by Steven J M J Jones
    posted to genome noncoding prediction by eckart_bindewald on 2006-07-11 16:45:29 as *****
  • Prediction of eukaryotic mRNA translational properties.
    Bioinformatics, Vol. 15, No. 7-8. (g 1999), pp. 704-712.
    posted to prediction translation by eckart_bindewald on 2006-06-06 15:18:45 as *****
  • Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change.
    BMC Bioinformatics, Vol. 7, No. 1. (27 March 2006)
    by Andrew V Uzilov, Joshua M Keegan, David H Mathews
  • Oncomirs — microRNAs with a role in cancer
    Nature Reviews Cancer, Vol. 6, No. 4., pp. 259-269.
    by Aurora Esquela-Kerscher, Frank J Slack
  • Identification and Classification of Conserved RNA Secondary Structures in the Human Genome.
    PLoS Comput Biol, Vol. 2, No. 4. (21 April 2006)
    by Jakob Skou S Pedersen, Gill Bejerano, Adam Siepel, Kate Rosenbloom, Kerstin Lindblad-Toh, Eric S S Lander, Jim Kent, Webb Miller, David Haussler
  • Computational identification of noncoding RNAs in E. coli by comparative genomics.
    Curr Biol, Vol. 11, No. 17. (4 September 2001), pp. 1369-1373.
    by E Rivas, RJ Klein, TA Jones, SR Eddy
  • De novo design of sequences for nucleic acid structural engineering.
    J Biomol Struct Dyn, Vol. 8, No. 3. (December 1990), pp. 573-581.
    by NC Seeman
    posted to design dna nanotechnology sequence by eckart_bindewald on 2006-02-07 16:24:20 as ***** along with 1 person dna
  • Genomics of microRNA.
    Trends Genet (27 January 2006)
    by V Narry N Kim, Jin-Wu W Nam
  • The Widespread Impact of Mammalian MicroRNAs on mRNA Repression and Evolution.
    Science (24 November 2005)
    by Kyle Kai-How K Farh, Andrew Grimson, Calvin Jan, Benjamin P P Lewis, Wendy K K Johnston, Lee P P Lim, Christopher B B Burge, David P P Bartel
  • Profile-based detection of microRNA precursors in animal genomes
    Bioinformatics, Vol. 21, No. 7. (01 April 2005), pp. 841-845.
    by Legendre Matthieu, Lambert Andre, Gautheret Daniel
    posted to microrna prediction by eckart_bindewald on 2006-01-16 12:39:50 as *****
  • Camels and zebrafish, viruses and cancer: a microRNA update.
    Hum Mol Genet, Vol. 14 Spec No. 2 (15 October 2005)
    posted to cancer microrna by eckart_bindewald on 2006-01-04 15:50:43 as ***** along with 1 person ajeffs
  • MicroRNA functions in animal development and human disease.
    Development, Vol. 132, No. 21. (November 2005), pp. 4653-4662.
    posted to cancer microrna by eckart_bindewald on 2006-01-04 15:50:03 as ***** along with 1 person maralena
  • MicroRNA-21 is an antiapoptotic factor in human glioblastoma cells.
    Cancer Res, Vol. 65, No. 14. (15 July 2005), pp. 6029-6033.
    by JA Chan, AM Krichevsky, KS Kosik
    posted to cancer microrna by eckart_bindewald on 2006-01-04 15:43:10 as ***** along with 2 people maralena mtagaya
  • Combinatorial microRNA target predictions
    Nature Genetics, Vol. 37, No. 5. (03 April 2005), pp. 495-500.
    by Azra Krek, Dominic Grün, Matthew N Poy, Rachel Wolf, Lauren Rosenberg, Eric J Epstein, Philip Macmenamin, Isabelle d da Piedade, Kristin C Gunsalus, Markus Stoffel, Nikolaus Rajewsky
  • Systematic discovery of regulatory motifs in human promoters and 3[prime] UTRs by comparison of several mammals
    Nature, Vol. aop, No. current. (27 February 2005)
    by Xiaohui Xie, Jun Lu, EJ Kulbokas, Todd R Golub, Vamsi Mootha, Kerstin Lindblad-Toh, Eric S Lander, Manolis Kellis
  • Human MicroRNA targets.
    PLoS Biol, Vol. 2, No. 11. (November 2004)
    by B John, AJ Enright, A Aravin, T Tuschl, C Sander, DS Marks
  • A combined computational-experimental approach predicts human microRNA targets.
    Genes Dev, Vol. 18, No. 10. (15 May 2004), pp. 1165-1178.
  • Thermodynamics of three-way multibranch loops in RNA.
    Biochemistry, Vol. 40, No. 23. (12 June 2001), pp. 6971-6981.
    by JM Diamond, DH Turner, DH Mathews
    posted to loop multibranch rna secondary structure thermodynamics by eckart_bindewald on 2005-12-14 14:44:45 as *****
  • GORouter: an RDF model for providing semantic query and inference services for Gene Ontology and its associations
    BMC Bioinformatics, Vol. 9, No. Suppl 1. (2008)
    by Qingwei Xu, Yixiang Shi, Qiang Lu, Guoqing Zhang, Qingming Luo, Yixue Li
  • Combining Statistical Alignment and Phylogenetic Footprinting to Detect Regulatory Elements.
    Bioinformatics (18 March 2008)
    by R Satija, L Pachter, J Hein
  • GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes.
    BMC Bioinformatics, Vol. 5 (18 November 2004)
    by DM Martin, M Berriman, GJ Barton
  • Global self-organization of all known protein sequences reveals inherent biological signatures
    Journal of Molecular Biology, Vol. 268, No. 2. (2 May 1997), pp. 539-556.
    by Michal Linial, Nathan Linial, Naftali Tishby, Golan Yona
    posted to fingerprint function gene prediction protein signature by eckart_bindewald on 2008-03-14 16:41:33 as ****
  • Detection of a MicroRNA Signal in an In Vivo Expression Set of mRNAs.
    PLoS ONE, Vol. 2, No. 8. (2007)
    by T Liu, T Papagiannakopoulos, K Puskar, S Qi, F Santiago, W Clay, K Lao, Y Lee, SF Nelson, HI Kornblum, F Doyle, L Petzold, B Shraiman, KS Kosik
  • Members of the miRNA-200 family regulate olfactory neurogenesis.
    Neuron, Vol. 57, No. 1. (10 January 2008), pp. 41-55.
    by PS Choi, L Zakhary, WY Choi, S Caron, E Alvarez-Saavedra, EA Miska, M McManus, B Harfe, AJ Giraldez, RH Horvitz, AF Schier, C Dulac
  • Term-tissue specific models for prediction of gene ontology biological processes using transcriptional profiles of aging in drosophila melanogaster
    BMC Bioinformatics, Vol. 9 (28 February 2008), 129.
    by Wensheng Zhang, Sige Zou, Jiuzhou Song
    posted to function microarray prediction protein by eckart_bindewald on 2008-03-03 15:19:20 as ****
  • Detecting genetic variation in microarray expression data
    Genome Res. (3 July 2007), gr.6307307.
    by Jennifer A Greenhall, Matthew A Zapala, Mario Caceres, Ondrej Libiger, Carrolee Barlow, Nicholas J Schork, David J Lockhart
  • A Glycine-Dependent Riboswitch That Uses Cooperative Binding to Control Gene Expression
    Science, Vol. 306, No. 5694. (8 October 2004), pp. 275-279.
    by Maumita Mandal, Mark Lee, Jeffrey E Barrick, Zasha Weinberg, Gail M Emilsson, Walter L Ruzzo, Ronald R Breaker
  • Cooperative binding of effectors by an allosteric ribozyme
    Nucl. Acids Res., Vol. 29, No. 7. (1 April 2001), pp. 1631-1637.
    by Antony M Jose, Garrett A Soukup, Ronald R Breaker
    posted to aptamer cooperative design effector ribozyme rna by eckart_bindewald on 2007-11-06 15:51:26 as ****
  • Inter- and intra-combinatorial regulation by transcription factors and microRNAs
    BMC Genomics, Vol. 8 (30 October 2007), 396.
    by Yiming Zhou, John Ferguson, Joseph T Chang, Yuval Kluger