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Group: ParkinsonLab_at_MaRS - library [204 articles]

Recent papers posted by members of the ParkinsonLab_at_MaRS group
  • Quantification of ortholog losses in insects and vertebrates.
    Genome Biology, Vol. 8 (16 November 2007), R242.
    by Stefan Wyder, Evgenia V Kriventseva, Reinhard Schroder, Tatsuhiko Kadowaki, Evgeny M Zdobnov
    posted to comparative_genomics by grahamc to the group ParkinsonLab_at_MaRS on 2008-03-28 16:52:56 as ** along with 4 people and 1 group cjeans hpaces hlapp svdate Bioinformatics
  • Raising the estimate of functional human sequences.
    Genome Res (9 August 2007)
    by Michael Pheasant, John S S Mattick
    posted to genomics evolution by grahamc to the group ParkinsonLab_at_MaRS on 2007-09-08 03:17:26 as ** along with 9 people and 1 group jyuh jfr andersbj djkt lp2 cabbagezs nklee ljs mimulus_99 microRNA
  • A systems biology approach for pathway level analysis
    Genome Res. (4 September 2007), gr.6202607.
    by Sorin Draghici, Purvesh Khatri, Adi L Tarca, Kashyap Amin, Arina Done, Calin Voichita, Constantin Georgescu, Roberto Romero
    posted to systems_biology pathway_modeling methods by grahamc to the group ParkinsonLab_at_MaRS on 2007-09-08 03:04:47 as ** along with 16 people and 2 groups pengchy tmmurali dragonrez jfr gurkanbebek shigepong zwang cabbagezs cerami xingxu shikin idonaldson Pao-Yang thomaskelder heliopais AlexanderPico Bioinformatics OPIG
  • Is proteomics the new genomics?
    Cell, Vol. 130, No. 3. (10 August 2007), pp. 395-398.
    by J Cox, M Mann
    posted to proteomics mass_spec expression by grahamc to the group ParkinsonLab_at_MaRS on 2007-09-05 03:11:20 as ** along with 4 people fishtank oelemento Pao-Yang anwazo
  • Correlation between structure and temperature in prokaryotic metabolic networks
    BMC Bioinformatics, Vol. 8 (21 August 2007), 303.
    by Kazuhiro Takemoto, Jose C Nacher, Tatsuya Akutsu
    posted to network_topology metabolism by grahamc to the group ParkinsonLab_at_MaRS on 2007-09-05 03:00:31 as **
  • Modular co-evolution of metabolic networks
    BMC Bioinformatics, Vol. 8 (27 August 2007), 311.
    by Jing Zhao, Guo-Hui Ding, Lin Tao, Hong Yu, Zhong-Hao Yu, Jian-Hua Luo, Zhi-Wei Cao, Yi-Xue Li
    posted to network_topology metabolism evolution biological_networks by grahamc to the group ParkinsonLab_at_MaRS on 2007-09-05 02:54:26 as ** along with 1 person Pao-Yang
  • MaxAlign: maximizing usable data in an alignment
    BMC Bioinformatics, Vol. 8 (28 August 2007), 312.
    by Rodrigo Gouveia-Oliveira, Peter W Sackett, Anders G Pedersen
    posted to tools comparative_genomics alignment by grahamc to the group ParkinsonLab_at_MaRS on 2007-09-05 02:50:13 as ** along with 1 person isimpson
  • Tools for Visually Exploring Biological Networks.
    Bioinformatics (25 August 2007)
    by Matthew Suderman, Michael Hallett
    posted to visualization tools protein-protein network_alignment by grahamc to the group ParkinsonLab_at_MaRS on 2007-09-05 02:38:19 as ** along with 12 people and 2 groups jyuh icases dullhunk sebastien_vigneau sgoetz cabbagezs cerami loopback007 Pao-Yang schuylrp AlexanderPico hryk TNT Cancer_Stem_Cells
  • MeTaDoR: A comprehensive resource for membrane targeting domains and their host proteins.
    Bioinformatics (25 August 2007)
    by Nitin Bhardwaj, Robert V V Stahelin, Guijun Zhao, Wonhwa Cho, Hui Lu
    posted to transmembrane_prediction tools methods by grahamc to the group ParkinsonLab_at_MaRS on 2007-09-05 02:36:22 as ** along with 1 person jyuh
  • A review of feature selection techniques in bioinformatics.
    Bioinformatics (24 August 2007)
    by Yvan Saeys, Iñaki Inza, Pedro Larrañaga
    posted to tools review by grahamc to the group ParkinsonLab_at_MaRS on 2007-09-05 02:32:52 as ** along with 13 people and 1 group giovenko jyuh chad_davis aviad_work frohike shigepong lp2 cabbagezs ryanraaum vietanh0 eacosta aaalxy srp33 Bioinformatics
  • TMpro webserver and webservice: Transmembrane helix prediction through amino acid property analysis.
    Bioinformatics (30 August 2007)
    by Madhavi Ganapathiraju, Christopher Jon J Jursa, Hassan A A Karimi, Judith Klein-Seetharaman
    posted to transmembrane_prediction methods algorithm by grahamc to the group ParkinsonLab_at_MaRS on 2007-09-05 02:30:53 as ** along with 1 person cabbagesofdoom
  • Forced unfolding of proteins within cells.
    Science, Vol. 317, No. 5838. (3 August 2007), pp. 663-666.
    by CP Johnson, HY Tang, C Carag, DW Speicher, DE Discher
    posted to proteomics methods cysteine-labeling by grahamc to the group ParkinsonLab_at_MaRS on 2007-08-13 19:45:56 as ** along with 2 people kentsis Jporci
  • The minimum information required for reporting a molecular interaction experiment (MIMIx)
    Nature Biotechnology, Vol. 25, No. 8. (08 August 2007), pp. 894-898.
    by Sandra Orchard, Lukasz Salwinski, Samuel Kerrien, Luisa Montecchi-Palazzi, Matthias Oesterheld, Volker Stümpflen, Arnaud Ceol, Andrew Chatr-Aryamontri, John Armstrong, Peter Woollard, John J Salama, Susan Moore, Jérôme Wojcik, Gary D Bader, Marc Vidal, Michael E Cusick, Mark Gerstein, Anne-Claude Gavin, Giulio Superti-Furga, Jack Greenblatt, Joel Bader, Peter Uetz, Mike Tyers, Pierre Legrain, Stan Fields, Nicola Mulder, Michael Gilson, Michael Niepmann, Lyle Burgoon, Javier, Carlos Prieto, Victoria M Perreau, Chris Hogue, Hans-Werner Mewes, Rolf Apweiler, Ioannis Xenarios, David Eisenberg, Gianni Cesareni, Henning Hermjakob
    posted to standards protein-protein interactions by grahamc to the group ParkinsonLab_at_MaRS on 2007-08-13 19:09:32 as ** along with 6 people jyuh hpiwowar yeastyboy jandot softsimu zwang
  • The protein network of bacterial motility
    Mol Syst Biol, Vol. 3 (31 July 2007)
    by Seesandra V Rajagopala, Bjorn Titz, Johannes Goll, Jodi R Parrish, Katrin Wohlbold, Matthew T Mckevitt, Timothy Palzkill, Hirotada Mori, Russell L Finley, Peter Uetz
    posted to protein-protein interactions by grahamc to the group ParkinsonLab_at_MaRS on 2007-08-13 17:53:19 as ** along with 6 people and 3 groups aswin jmrivort zwang Pao-Yang carlk cerca G-quadruplex Supramolecular OPIG
  • Reconstruction of the vertebrate ancestral genome reveals dynamic genome reorganization in early vertebrates.
    Genome Res (25 July 2007)
    by Yoichiro Nakatani, Hiroyuki Takeda, Yuji Kohara, Shinichi Morishita
    posted to vertebrate_genomics ancestral_genomes by grahamc to the group ParkinsonLab_at_MaRS on 2007-08-13 17:50:49 as ** along with 2 people and 2 groups dchughes maximilianh G4ID Genetics-of-Gambling
  • Accuracy and quality of massively-parallel DNA pyrosequencing
    Genome Biology, Vol. 8 (20 July 2007), R143.
    by Susan M Huse, Julie A Huber, Hilary G Morrison, Mitchell L Sogin, David M Welch
    posted to sequencing methods by grahamc to the group ParkinsonLab_at_MaRS on 2007-08-13 17:27:41 as ** along with 8 people and 2 groups gpappas jmeppley mblwhoi azazello GustavoLacerda blobbybirdman Olaf_Ilzins bozdagd Bioinformatics gatech-compgenomics
  • Microarray-based gene expression profiles in multiple tissues of the domesticated silkworm, Bombyx mori
    Genome Biology, Vol. 8 (04 August 2007), R162.
    by Qingyou Xia, Daojun Cheng, Jun Duan, Genhong Wang, Tingcai Cheng, Xingfu Zha, Chun Liu, Ping Zhao, Fangyin Dai, Ze Zhang, Ningjia He, Liang Zhang, Zhonghuai Xiang
    posted to silkworm genomes by grahamc to the group ParkinsonLab_at_MaRS on 2007-08-13 17:15:22 as **
  • False positive reduction in protein-protein interaction predictions using gene ontology annotations
    BMC Bioinformatics, Vol. 8 (23 July 2007), 262.
    by Mahmoud A Mahdavi, Yen-Han Lin
    posted to protein-protein interactions go_terms by grahamc to the group ParkinsonLab_at_MaRS on 2007-08-13 17:08:46 as ** along with 4 people iris_2001 mingzhi cerca penpen926
  • Semantic integration to identify overlapping functional modules in protein interaction networks
    BMC Bioinformatics, Vol. 8 (24 July 2007), 265.
    by Young-Rae Cho, Woochang Hwang, Murali Ramanathan, Aidong Zhang
    posted to protein-protein interactions go_terms by grahamc to the group ParkinsonLab_at_MaRS on 2007-08-13 17:07:31 as *** along with 4 people and 1 group jyuh tmmurali carlk AbnerCYH csb_journal_club_public
  • Recognizing protein-protein interfaces with empirical potentials and reduced amino acid alphabets
    BMC Bioinformatics, Vol. 8 (27 July 2007), 270.
    by Guillaume Launay, Raul Mendez, Shoshana Wodak, Thomas Simonson
    posted to protein-protein molecular_dynamics interactions by grahamc to the group ParkinsonLab_at_MaRS on 2007-08-13 17:04:55 as * along with 1 person kgutwin
  • An exploration of alternative visualisations of the basic helix-loop-helix protein interaction network
    BMC Bioinformatics, Vol. 8 (06 August 2007), 289.
    by Brian J Holden, John W Pinney, Simon C Lovell, Grigoris D Amoutzias, David L Robertson
    posted to visualization tools protein-protein interactions by grahamc to the group ParkinsonLab_at_MaRS on 2007-08-13 17:00:49 as ** along with 2 people and 1 group zwang Tatelie workshop
  • CLUSS: Clustering of protein sequences based on a new similarity measure
    BMC Bioinformatics, Vol. 8 (04 August 2007), 286.
    by Abdellali Kelil, Shengrui Wang, Ryszard Brzezinski, Alain Fleury
    posted to tools clustering_methods by grahamc to the group ParkinsonLab_at_MaRS on 2007-08-13 16:55:55 as ** along with 3 people nklee ninch bobychan
  • Influence of degree correlations on network structure and stability in protein-protein interaction networks
    BMC Bioinformatics, Vol. 8 (09 August 2007), 297.
    by Caroline C Friedel, Ralf Zimmer
    posted to protein-protein interactions by grahamc to the group ParkinsonLab_at_MaRS on 2007-08-13 16:52:52 as * along with 1 person Pao-Yang
  • BLISS 2.0: a web-based tool for predicting conserved regulatory modules in distantly-related orthologous sequences.
    Bioinformatics (27 July 2007)
    by Hailong Meng, Arunava Banerjee, Lei Zhou
    posted to tools comparative_genomics by grahamc to the group ParkinsonLab_at_MaRS on 2007-08-13 16:47:29 as ** along with 2 people GustavoLacerda maximilianh
  • GENETICS: Evolutionary Insights from Sponges
    Science, Vol. 316, No. 5833. (29 June 2007), pp. 1854-1855.
    by Michael W Taylor, Robert W Thacker, Ute Hentschel
    posted to sponges evolution by grahamc to the group ParkinsonLab_at_MaRS on 2007-08-04 19:48:12 as read along with 1 person ms609
  • Identification of functional modules from conserved ancestral protein protein interactions.
    Bioinformatics, Vol. 23, No. 13. (1 July 2007)
    by J Dutkowski, J Tiuryn
    posted to protein-protein network_alignment interactions by grahamc to the group ParkinsonLab_at_MaRS on 2007-07-26 19:23:54 as ** along with 1 person Pao-Yang
  • A First-Principles Model of Early Evolution: Emergence of Gene Families, Species, and Preferred Protein Folds
    PLoS Computational Biology, Vol. 3, No. 7. (1 July 2007), e139.
    by Konstantin B Zeldovich, Peiqiu Chen, Boris E Shakhnovich, Eugene I Shakhnovich
    posted to protein_evolution modeling by grahamc to the group ParkinsonLab_at_MaRS on 2007-07-25 21:09:57 as ** along with 6 people BioNica cjeans zwang Jporci farhat biinins
  • Protein-Protein Interaction Hotspots Carved into Sequences.
    PLoS Comput Biol, Vol. 3, No. 7. (13 July 2007)
    by Yanay Ofran, Burkhard Rost
    posted to tools protein-protein methods interactions domains by grahamc to the group ParkinsonLab_at_MaRS on 2007-07-25 20:44:10 as ** along with 7 people and 2 groups bicko dchughes cjeans zwang Jporci Pao-Yang higueruelo G4ID Genetics-of-Gambling
  • ENCODE and our very busy genome
    Nature Genetics, Vol. 39, No. 7., pp. 817-818.
    by Steven Henikoff
    posted to genomics by grahamc to the group ParkinsonLab_at_MaRS on 2007-07-25 20:34:25 as ** along with 2 people and 2 groups blobbybirdman yezq Bioinformatics UH - Computational Biology
  • Molecular breeding of polymerases for amplification of ancient DNA.
    Nat Biotechnol (15 July 2007)
    by Marc d'Abbadie, Michael Hofreiter, Alexandra Vaisman, David Loakes, Didier Gasparutto, Jean Cadet, Roger Woodgate, Svante Pääbo, Philipp Holliger
    posted to methods engineered_proteins ancient_dna by grahamc to the group ParkinsonLab_at_MaRS on 2007-07-25 20:29:25 as ** along with 1 person and 2 groups dchughes G4ID Genetics-of-Gambling
  • Nano-enabled synthetic biology
    Mol Syst Biol, Vol. 3 (10 July 2007)
    by Mitchel J Doktycz, Michael L Simpson
    posted to synthetic_biology by grahamc to the group ParkinsonLab_at_MaRS on 2007-07-25 19:43:01 as ** along with 3 people johncumbers Quarem nicholasflann
  • APID2NET: unified interactome graphic analyzer.
    Bioinformatics (21 July 2007)
    by Juan Hernandez H Toro, Carlos Prieto, Javier De Las D Rivas
    posted to tools cytoscape by grahamc to the group ParkinsonLab_at_MaRS on 2007-07-25 18:04:58 as ** along with 1 person jyuh
  • Exploring Biological Network Structure Using Exponential Random Graph Models.
    Bioinformatics (20 July 2007)
    by Zachary M M Saul, Vladimir Filkov
    posted to protein-protein interactions graph_theory by grahamc to the group ParkinsonLab_at_MaRS on 2007-07-25 18:02:38 as ** along with 3 people and 1 group tmmurali iris_2001 Pao-Yang OPIG
  • Automatic extraction of gene ontology annotation and its correlation with clusters in protein networks
    BMC Bioinformatics, Vol. 8 (10 July 2007), 243.
    by Nikolai Daraselia, Anton Yuryev, Sergei Egorov, Ilya Mazo, Iaroslav Ispolatov
    posted to protein-protein interactions graph_theory gene_ontology by grahamc to the group ParkinsonLab_at_MaRS on 2007-07-12 18:39:29 as **** along with 4 people jyuh sgoetz carlk yas
  • Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization.
    Science, Vol. 317, No. 5834. (6 July 2007), pp. 86-94.
    by NH Putnam, M Srivastava, U Hellsten, B Dirks, J Chapman, A Salamov, A Terry, H Shapiro, E Lindquist, VV Kapitonov, J Jurka, G Genikhovich, IV Grigoriev, SM Lucas, RE Steele, JR Finnerty, U Technau, MQ Martindale, DS Rokhsar
    posted to sequenced_organisms genomics evolution cnidaria by grahamc to the group ParkinsonLab_at_MaRS on 2007-07-11 21:30:20 as ** along with 3 people madhadron xxxxxxxxxxx nhp
  • Genetic Properties Influencing the Evolvability of Gene Expression.
    Science (24 May 2007)
    by Christian R R Landry, Bernardo Lemos, Scott A A Rifkin, W J J Dickinson, Daniel L L Hartl
    posted to gene_expression evolution by grahamc to the group ParkinsonLab_at_MaRS on 2007-07-11 21:21:51 as ** along with 10 people and 2 groups jjray brant balicea sebastien_vigneau emarker heliopais cisevol caseybrown emptyhb klo EisenLab cis-regulatory-evolution
  • Not All Scale-Free Networks Are Born Equal: The Role of the Seed Graph in PPI Network Evolution.
    PLoS Comput Biol, Vol. 3, No. 7. (6 July 2007)
    by Fereydoun Hormozdiari, Petra Berenbrink, Nataša Pr Ulj, S Cenk C Sahinalp
    posted to protein-protein interactions by grahamc to the group ParkinsonLab_at_MaRS on 2007-07-11 21:17:45 as *
  • Sexually antagonistic genetic variation for fitness in red deer
    Nature, Vol. 447, No. 7148., pp. 1107-1110.
    by Katharina Foerster, Tim Coulson, Ben C Sheldon, Josephine M Pemberton, Tim H Clutton-Brock, Loeske EB Kruuk
    posted to selection evolution by grahamc to the group ParkinsonLab_at_MaRS on 2007-07-11 21:14:17 as **
  • Expandable DNA repeats and human disease
    Nature, Vol. 447, No. 7147. (21 June 2007), pp. 932-940.
    by Sergei M Mirkin
    posted to evolution biology by grahamc to the group ParkinsonLab_at_MaRS on 2007-07-11 21:09:19 as ** along with 1 person and 2 groups dchughes G4ID Genetics-of-Gambling
  • Replication and protection of telomeres
    Nature, Vol. 447, No. 7147. (21 June 2007), pp. 924-931.
    by Ramiro E Verdun, Jan Karlseder
    posted to evolution biology by grahamc to the group ParkinsonLab_at_MaRS on 2007-07-11 21:08:02 as ** along with 1 person and 2 groups dchughes G4ID Genetics-of-Gambling
  • The immortal strand hypothesis: segregation and reconstruction.
    Cell, Vol. 129, No. 7. (29 June 2007), pp. 1239-1243.
    by TA Rando
    posted to evolution by grahamc to the group ParkinsonLab_at_MaRS on 2007-07-10 03:50:58 as **
  • High-throughput identification of Interacting Protein-Protein Binding Sites
    BMC Bioinformatics, Vol. 8 (27 June 2007), 223.
    by Jo-Lan Chung, Wei Wang, Philip E Bourne
    posted to tools protein-protein methods interactions domains by grahamc to the group ParkinsonLab_at_MaRS on 2007-07-09 23:18:48 as ** along with 3 people bicko zwang Evangelia
  • Relationship between insertion/deletion (indel) frequency of proteins and essentiality
    BMC Bioinformatics, Vol. 8 (28 June 2007), 227.
    by Simon K Chan, Michael Hsing, Fereydoun Hormozdiari, Artem Cherkasov
    posted to protein-protein interactions by grahamc to the group ParkinsonLab_at_MaRS on 2007-07-09 23:11:51 as **
  • Probabilistic prediction and ranking of human protein-protein interactions
    BMC Bioinformatics, Vol. 8 (05 July 2007), 239.
    by Michelle S Scott, Geoffrey J Barton
    posted to protein-protein methods interactions by grahamc to the group ParkinsonLab_at_MaRS on 2007-07-09 23:08:06 as ** along with 3 people wnpx zwang mingzhi
  • Interaction-Site Prediction for Protein Complexes: a Critical Assessment.
    Bioinformatics (22 June 2007)
    by Huan-Xiang X Zhou, Sanbo Qin
    posted to review protein-protein interactions domains by grahamc to the group ParkinsonLab_at_MaRS on 2007-07-09 23:02:40 as ***
  • A statistical approach using network structure in the prediction of protein characteristics
    Bioinformatics (28 June 2007), btm342.
    by Pao-Yang Chen, Charlotte M Deane, Gesine Reinert
    posted to tools protein-protein interactions by grahamc to the group ParkinsonLab_at_MaRS on 2007-07-09 22:57:16 as *** along with 5 people iris_2001 zwang cabbagezs cdeane Pao-Yang
  • QPRIMER: A Quick Web-based Application for Designing Conserved PCR Primers from Multigenome Alignments.
    Bioinformatics (28 June 2007)
    by Namshin Kim, Christopher Lee
    posted to tools methods by grahamc to the group ParkinsonLab_at_MaRS on 2007-07-09 22:54:00 as ** along with 4 people jyuh sebastien_vigneau ryanraaum asddd
  • A procedure for assessing GO annotation consistency.
    Bioinformatics, Vol. 21 Suppl 1 (June 2005)
    by ME Dolan, L Ni, E Camon, JA Blake
    posted to gene_ontology by grahamc to the group ParkinsonLab_at_MaRS on 2007-06-18 18:24:06 as ****
  • Co-evolutionary Analysis of Domains in Interacting Proteins Reveals Insights into Domain-Domain Interactions Mediating Protein-Protein Interactions
    Journal of Molecular Biology, Vol. 362, No. 4. (29 September 2006), pp. 861-875.
    by Raja Jothi, Praveen F Cherukuri, Asba Tasneem, Teresa M Przytycka
    posted to protein-protein interactions domains by grahamc to the group ParkinsonLab_at_MaRS on 2007-06-18 18:22:15 as ** along with 3 people marti choonpeng iris_2001
  • Improving the success rate of proteome analysis by modeling protein-abundance distributions and experimental designs
    Nature Biotechnology, Vol. 25, No. 6., pp. 651-655.
    by Jan Eriksson, David Fenyö
    posted to proteomics methods by grahamc to the group ParkinsonLab_at_MaRS on 2007-06-18 18:07:26 as ** along with 3 people jyuh nedwards brianb
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