1.1 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 1.2 +++ b/grant.bib Mon Apr 20 17:19:47 2009 -0700 1.3 @@ -0,0 +1,364 @@ 1.4 + 1.5 +@misc{_zotero_????, 1.6 + title = {Zotero - Quick Start Guide}, 1.7 + url = {http://www.zotero.org/documentation/quick_start_guide} 1.8 +}, 1.9 + 1.10 +@article{chin_genome-scale_2007, 1.11 + title = {A genome-scale map of expression for a mouse brain section obtained using voxelation}, 1.12 + volume = {30}, 1.13 + url = {http://physiolgenomics.physiology.org/cgi/content/abstract/30/3/313}, 1.14 + doi = {10.1152/physiolgenomics.00287.2006}, 1.15 + abstract = {Gene expression signatures in the mammalian brain hold the key to understanding neural development and neurological diseases. We have reconstructed two-dimensional images of gene expression for 20,000 genes in a coronal slice of the mouse brain at the level of the striatum by using microarrays in combination with voxelation at a resolution of 1 mm3. Good reliability of the microarray results were confirmed using multiple replicates, subsequent quantitative {RT-PCR} voxelation, mass spectrometry voxelation, and publicly available in situ hybridization data. Known and novel genes were identified with expression patterns localized to defined substructures within the brain. In addition, genes with unexpected patterns were identified, and cluster analysis identified a set of genes with a gradient of dorsal/ventral expression not restricted to known anatomical boundaries. The genome-scale maps of gene expression obtained using voxelation will be a valuable tool for the neuroscience community.}, 1.16 + number = {3}, 1.17 + journal = {Physiol. Genomics}, 1.18 + author = {Mark H. Chin and Alex B. Geng and Arshad H. Khan and {Wei-Jun} Qian and Vladislav A. Petyuk and Jyl Boline and Shawn Levy and Arthur W. Toga and Richard D. Smith and Richard M. Leahy and Desmond J. Smith}, 1.19 + month = aug, 1.20 + year = {2007}, 1.21 + pages = {313--321} 1.22 +}, 1.23 + 1.24 +@article{lein_genome-wide_2007, 1.25 + title = {Genome-wide atlas of gene expression in the adult mouse brain}, 1.26 + volume = {445}, 1.27 + issn = {0028-0836}, 1.28 + url = {http://dx.doi.org/10.1038/nature05453}, 1.29 + doi = {10.1038/nature05453}, 1.30 + number = {7124}, 1.31 + journal = {Nature}, 1.32 + author = {Ed S. Lein and Michael J. Hawrylycz and Nancy Ao and Mikael Ayres and Amy Bensinger and Amy Bernard and Andrew F. Boe and Mark S. Boguski and Kevin S. Brockway and Emi J. Byrnes and Lin Chen and Li Chen and {Tsuey-Ming} Chen and Mei Chi Chin and Jimmy Chong and Brian E. Crook and Aneta Czaplinska and Chinh N. Dang and Suvro Datta and Nick R. Dee and Aimee L. Desaki and Tsega Desta and Ellen Diep and Tim A. Dolbeare and Matthew J. Donelan and {Hong-Wei} Dong and Jennifer G. Dougherty and Ben J. Duncan and Amanda J. Ebbert and Gregor Eichele and Lili K. Estin and Casey Faber and Benjamin A. Facer and Rick Fields and Shanna R. Fischer and Tim P. Fliss and Cliff Frensley and Sabrina N. Gates and Katie J. Glattfelder and Kevin R. Halverson and Matthew R. Hart and John G. Hohmann and Maureen P. Howell and Darren P. Jeung and Rebecca A. Johnson and Patrick T. Karr and Reena Kawal and Jolene M. Kidney and Rachel H. Knapik and Chihchau L. Kuan and James H. Lake and Annabel R. Laramee and Kirk D. Larsen and Christopher Lau and Tracy A. Lemon and Agnes J. Liang and Ying Liu and Lon T. Luong and Jesse Michaels and Judith J. Morgan and Rebecca J. Morgan and Marty T. Mortrud and Nerick F. Mosqueda and Lydia L. Ng and Randy Ng and Geralyn J. Orta and Caroline C. Overly and Tu H. Pak and Sheana E. Parry and Sayan D. Pathak and Owen C. Pearson and Ralph B. Puchalski and Zackery L. Riley and Hannah R. Rockett and Stephen A. Rowland and Joshua J. Royall and Marcos J. Ruiz and Nadia R. Sarno and Katherine Schaffnit and Nadiya V. Shapovalova and Taz Sivisay and Clifford R. Slaughterbeck and Simon C. Smith and Kimberly A. Smith and Bryan I. Smith and Andy J. Sodt and Nick N. Stewart and {Kenda-Ruth} Stumpf and Susan M. Sunkin and Madhavi Sutram and Angelene Tam and Carey D. Teemer and Christina Thaller and Carol L. Thompson and Lee R. Varnam and Axel Visel and Ray M. Whitlock and Paul E. Wohnoutka and Crissa K. Wolkey and Victoria Y. Wong and Matthew Wood and Murat B. Yaylaoglu and Rob C. Young and Brian L. Youngstrom and Xu Feng Yuan and Bin Zhang and Theresa A. Zwingman and Allan R. Jones}, 1.33 + year = {2007}, 1.34 + pages = {168--176} 1.35 +}, 1.36 + 1.37 +@article{ng_anatomic_2009, 1.38 + title = {An anatomic gene expression atlas of the adult mouse brain}, 1.39 + volume = {12}, 1.40 + issn = {1097-6256}, 1.41 + url = {http://dx.doi.org/10.1038/nn.2281}, 1.42 + doi = {10.1038/nn.2281}, 1.43 + number = {3}, 1.44 + journal = {Nat Neurosci}, 1.45 + author = {Lydia Ng and Amy Bernard and Chris Lau and Caroline C Overly and {Hong-Wei} Dong and Chihchau Kuan and Sayan Pathak and Susan M Sunkin and Chinh Dang and Jason W Bohland and Hemant Bokil and Partha P Mitra and Luis Puelles and John Hohmann and David J Anderson and Ed S Lein and Allan R Jones and Michael Hawrylycz}, 1.46 + month = mar, 1.47 + year = {2009}, 1.48 + pages = {356--362} 1.49 +}, 1.50 + 1.51 +@article{thompson_genomic_2008, 1.52 + title = {Genomic Anatomy of the Hippocampus}, 1.53 + volume = {60}, 1.54 + issn = {0896-6273}, 1.55 + url = {http://www.sciencedirect.com/science/article/B6WSS-4V70FHY-9/2/a4de532b1bf60f0d033eacad345b935e}, 1.56 + doi = {10.1016/j.neuron.2008.12.008}, 1.57 + abstract = {Summary 1.58 +Availability of genome-scale in situ hybridization data allows systematic analysis of genetic neuroanatomical architecture. Within the hippocampus, electrophysiology and lesion and imaging studies demonstrate functional heterogeneity along the septotemporal axis, although precise underlying circuitry and molecular substrates remain uncharacterized. Application of unbiased statistical component analyses to genome-scale hippocampal gene expression data revealed robust septotemporal molecular heterogeneity, leading to the identification of a large cohort of genes with robust regionalized hippocampal expression. Manual mapping of heterogeneous {CA3} pyramidal neuron expression patterns demonstrates an unexpectedly complex molecular parcellation into a relatively coherent set of nine expression domains in the septal/temporal and proximal/distal axes with reciprocal, nonoverlapping boundaries. Unique combinatorial profiles of adhesion molecules within these domains suggest corresponding differential connectivity, which is demonstrated for {CA3} projections to the lateral septum using retrograde labeling. This complex, discrete molecular architecture provides a novel paradigm for predicting functional differentiation across the full septotemporal extent of the hippocampus.}, 1.59 + number = {6}, 1.60 + journal = {Neuron}, 1.61 + author = {Carol L. Thompson and Sayan D. Pathak and Andreas Jeromin and Lydia L. Ng and Cameron R. {MacPherson} and Marty T. Mortrud and Allison Cusick and Zackery L. Riley and Susan M. Sunkin and Amy Bernard and Ralph B. Puchalski and Fred H. Gage and Allan R. Jones and Vladimir B. Bajic and Michael J. Hawrylycz and Ed S. Lein}, 1.62 + month = dec, 1.63 + year = {2008}, 1.64 + keywords = {{MOLNEURO,SYSBIO,SYSNEURO}}, 1.65 + pages = {1010--1021} 1.66 +}, 1.67 + 1.68 +@inproceedings{shanks_wikigateway:library_2005, 1.69 + address = {San Diego, California}, 1.70 + title = {{WikiGateway:} a library for interoperability and accelerated wiki development}, 1.71 + isbn = {1-59593-111-2}, 1.72 + url = {http://portal.acm.org/citation.cfm?id=1104973.1104979}, 1.73 + doi = {10.1145/1104973.1104979}, 1.74 + abstract = {{WikiGateway} is an open-source suite of tools for automated interaction with wikis:• Python and Perl modules with functions like {getPage,} {putPage,} {getRecentChanges,} and more.• A mechanism to add {DAV,} Atom, or {XMLRPC} capabilities to any supported wiki server.• A command-line tool with functionality similar to the Perl and Python modules.• Demo applications built on top of these tools include a wiki copy command, a spam-cleaning bot, and a tool to recursively upload text files inside a directory structure as wiki {pages.All} {WikiGateway} tools are compatible with a number of different wiki engines. Developers can use {WikiGateway} to hide the differences between wiki engines and build applications which interoperate with many different wiki engines.}, 1.75 + booktitle = {Proceedings of the 2005 international symposium on Wikis}, 1.76 + publisher = {{ACM}}, 1.77 + author = {Bayle Shanks}, 1.78 + year = {2005}, 1.79 + keywords = {atom,client-side wiki,interoperability,interwiki,middleware,webdav,wiki,wikiclient,wikigateway,wikirpcinterface,wiki xmlrpc}, 1.80 + pages = {53--66} 1.81 +}, 1.82 + 1.83 +@article{zhang_v3_2008, 1.84 + title = {V3 Spinal Neurons Establish a Robust and Balanced Locomotor Rhythm during Walking}, 1.85 + volume = {60}, 1.86 + issn = {0896-6273}, 1.87 + url = {http://www.sciencedirect.com/science/article/B6WSS-4TMK33J-C/2/9281fbcc359d1ad037a368824abbd871}, 1.88 + doi = {10.1016/j.neuron.2008.09.027}, 1.89 + abstract = {Summary 1.90 +A robust and well-organized rhythm is a key feature of many neuronal networks, including those that regulate essential behaviors such as circadian rhythmogenesis, breathing, and locomotion. Here we show that excitatory V3-derived neurons are necessary for a robust and organized locomotor rhythm during walking. When V3-mediated neurotransmission is selectively blocked by the expression of the tetanus toxin light chain subunit {(TeNT),} the regularity and robustness of the locomotor rhythm is severely perturbed. A similar degeneration in the locomotor rhythm occurs when the excitability of V3-derived neurons is reduced acutely by ligand-induced activation of the allatostatin receptor. The V3-derived neurons additionally function to balance the locomotor output between both halves of the spinal cord, thereby ensuring a symmetrical pattern of locomotor activity during walking. We propose that the V3 neurons establish a regular and balanced motor rhythm by distributing excitatory drive between both halves of the spinal cord.}, 1.91 + number = {1}, 1.92 + journal = {Neuron}, 1.93 + author = {Ying Zhang and Sujatha Narayan and Eric Geiman and Guillermo M. Lanuza and Tomoko Velasquez and Bayle Shanks and Turgay Akay and Jason Dyck and Keir Pearson and Simon Gosgnach and {Chen-Ming} Fan and Martyn Goulding}, 1.94 + month = oct, 1.95 + year = {2008}, 1.96 + keywords = {{MOLNEURO}}, 1.97 + pages = {84--96} 1.98 +}, 1.99 + 1.100 +@article{van_essen_integrated_2001, 1.101 + title = {An integrated software suite for surface-based analyses of cerebral cortex}, 1.102 + volume = {8}, 1.103 + issn = {1067-5027}, 1.104 + url = {http://www.ncbi.nlm.nih.gov/pubmed/11522765}, 1.105 + abstract = {The authors describe and illustrate an integrated trio of software programs for carrying out surface-based analyses of cerebral cortex. The first component of this trio, {SureFit} {(Surface} Reconstruction by Filtering and Intensity Transformations), is used primarily for cortical segmentation, volume visualization, surface generation, and the mapping of functional neuroimaging data onto surfaces. The second component, Caret {(Computerized} Anatomical Reconstruction and Editing Tool Kit), provides a wide range of surface visualization and analysis options as well as capabilities for surface flattening, surface-based deformation, and other surface manipulations. The third component, {SuMS} {(Surface} Management System), is a database and associated user interface for surface-related data. It provides for efficient insertion, searching, and extraction of surface and volume data from the database.}, 1.106 + number = {5}, 1.107 + journal = {Journal of the American Medical Informatics Association: {JAMIA}}, 1.108 + author = {D C Van Essen and H A Drury and J Dickson and J Harwell and D Hanlon and C H Anderson}, 1.109 + year = {2001}, 1.110 + note = {{PMID:} 11522765}, 1.111 + keywords = {Anatomy, {Artistic,Anatomy,} {Cross-Sectional,Brain,Cerebral} {Cortex,Databases,} {Factual,Humans,Image} Processing, {Computer-Assisted,Magnetic} Resonance {Imaging,Medical} {Illustration,Neuroanatomy,Software,Systems} Integration}, 1.112 + pages = {443--59} 1.113 +}, 1.114 + 1.115 +@misc{sonnenburg_large_2006, 1.116 + type = {Article}, 1.117 + title = {Large scale multiple kernel learning}, 1.118 + url = {http://eprints.pascal-network.org/archive/00003035/}, 1.119 + author = {Sören Sonnenburg and Gunnar Raetsch and Christin Schaefer and Bernhard Schölkopf}, 1.120 + year = {2006}, 1.121 + note = {While classical kernel-based learning algorithms are based on a single kernel, in practice it is often desirable to use multiple kernels. Lanckriet et al. (2004) considered conic combinations of kernel matrices for classification, leading to a convex quadratically constrained quadratic program. We show that it can be rewritten as a semi-infinite linear program that can be efficiently solved by recycling the standard {SVM} implementations. Moreover, we generalize the formulation and our method to a larger class of problems, including regression and one-class classification. Experimental results show that the proposed algorithm works for hundred thousands of examples or hundreds of kernels to be combined, and helps for automatic model selection, improving the interpretability of the learning result. In a second part we discuss general speed up mechanism for {SVMs,} especially when used with sparse feature maps as appear for string kernels, allowing us to train a string kernel {SVM} on a 10 million real-world splice data set from computational biology. We integrated multiple kernel learning in our machine learning toolbox {SHOGUN} for which the source code is publicly available at http://www.fml.tuebingen.mpg.de/raetsch/projects/shogun.}, 1.122 + keywords = {{Learning/Statistics} \& {Optimisation,Multimodal} {Integration,Theory} \& Algorithms}, 1.123 + howpublished = {http://eprints.pascal-network.org/archive/00003035/} 1.124 +}, 1.125 + 1.126 +@book{swanson_brain_2003, 1.127 + edition = {3}, 1.128 + title = {Brain Maps: Structure of the Rat Brain}, 1.129 + isbn = {0126105820}, 1.130 + publisher = {Academic Press}, 1.131 + author = {Larry Swanson}, 1.132 + month = nov, 1.133 + year = {2003} 1.134 +}, 1.135 + 1.136 +@book{paxinos_mouse_2001, 1.137 + edition = {2}, 1.138 + title = {The Mouse Brain in Stereotaxic Coordinates}, 1.139 + isbn = {{012547637X}}, 1.140 + publisher = {Academic Press}, 1.141 + author = {George Paxinos and Keith {B.J.} Franklin}, 1.142 + month = jul, 1.143 + year = {2001} 1.144 +}, 1.145 + 1.146 +@article{waterston_initial_2002, 1.147 + title = {Initial sequencing and comparative analysis of the mouse genome}, 1.148 + volume = {420}, 1.149 + issn = {0028-0836}, 1.150 + url = {http://www.ncbi.nlm.nih.gov/pubmed/12466850}, 1.151 + doi = {10.1038/nature01262}, 1.152 + abstract = {The sequence of the mouse genome is a key informational tool for understanding the contents of the human genome and a key experimental tool for biomedical research. Here, we report the results of an international collaboration to produce a high-quality draft sequence of the mouse genome. We also present an initial comparative analysis of the mouse and human genomes, describing some of the insights that can be gleaned from the two sequences. We discuss topics including the analysis of the evolutionary forces shaping the size, structure and sequence of the genomes; the conservation of large-scale synteny across most of the genomes; the much lower extent of sequence orthology covering less than half of the genomes; the proportions of the genomes under selection; the number of protein-coding genes; the expansion of gene families related to reproduction and immunity; the evolution of proteins; and the identification of intraspecies polymorphism.}, 1.153 + number = {6915}, 1.154 + journal = {Nature}, 1.155 + author = {Robert H Waterston and Kerstin {Lindblad-Toh} and Ewan Birney and Jane Rogers and Josep F Abril and Pankaj Agarwal and Richa Agarwala and Rachel Ainscough and Marina Alexandersson and Peter An and Stylianos E Antonarakis and John Attwood and Robert Baertsch and Jonathon Bailey and Karen Barlow and Stephan Beck and Eric Berry and Bruce Birren and Toby Bloom and Peer Bork and Marc Botcherby and Nicolas Bray and Michael R Brent and Daniel G Brown and Stephen D Brown and Carol Bult and John Burton and Jonathan Butler and Robert D Campbell and Piero Carninci and Simon Cawley and Francesca Chiaromonte and Asif T Chinwalla and Deanna M Church and Michele Clamp and Christopher Clee and Francis S Collins and Lisa L Cook and Richard R Copley and Alan Coulson and Olivier Couronne and James Cuff and Val Curwen and Tim Cutts and Mark Daly and Robert David and Joy Davies and Kimberly D Delehaunty and Justin Deri and Emmanouil T Dermitzakis and Colin Dewey and Nicholas J Dickens and Mark Diekhans and Sheila Dodge and Inna Dubchak and Diane M Dunn and Sean R Eddy and Laura Elnitski and Richard D Emes and Pallavi Eswara and Eduardo Eyras and Adam Felsenfeld and Ginger A Fewell and Paul Flicek and Karen Foley and Wayne N Frankel and Lucinda A Fulton and Robert S Fulton and Terrence S Furey and Diane Gage and Richard A Gibbs and Gustavo Glusman and Sante Gnerre and Nick Goldman and Leo Goodstadt and Darren Grafham and Tina A Graves and Eric D Green and Simon Gregory and Roderic Guigó and Mark Guyer and Ross C Hardison and David Haussler and Yoshihide Hayashizaki and {LaDeana} W Hillier and Angela Hinrichs and Wratko Hlavina and Timothy Holzer and Fan Hsu and Axin Hua and Tim Hubbard and Adrienne Hunt and Ian Jackson and David B Jaffe and L Steven Johnson and Matthew Jones and Thomas A Jones and Ann Joy and Michael Kamal and Elinor K Karlsson and Donna Karolchik and Arkadiusz Kasprzyk and Jun Kawai and Evan Keibler and Cristyn Kells and W James Kent and Andrew Kirby and Diana L Kolbe and Ian Korf and Raju S Kucherlapati and Edward J Kulbokas and David Kulp and Tom Landers and J P Leger and Steven Leonard and Ivica Letunic and Rosie Levine and Jia Li and Ming Li and Christine Lloyd and Susan Lucas and Bin Ma and Donna R Maglott and Elaine R Mardis and Lucy Matthews and Evan Mauceli and John H Mayer and Megan {McCarthy} and W Richard {McCombie} and Stuart {McLaren} and Kirsten {McLay} and John D {McPherson} and Jim Meldrim and Beverley Meredith and Jill P Mesirov and Webb Miller and Tracie L Miner and Emmanuel Mongin and Kate T Montgomery and Michael Morgan and Richard Mott and James C Mullikin and Donna M Muzny and William E Nash and Joanne O Nelson and Michael N Nhan and Robert Nicol and Zemin Ning and Chad Nusbaum and Michael J {O'Connor} and Yasushi Okazaki and Karen Oliver and Emma {Overton-Larty} and Lior Pachter and Genís Parra and Kymberlie H Pepin and Jane Peterson and Pavel Pevzner and Robert Plumb and Craig S Pohl and Alex Poliakov and Tracy C Ponce and Chris P Ponting and Simon Potter and Michael Quail and Alexandre Reymond and Bruce A Roe and Krishna M Roskin and Edward M Rubin and Alistair G Rust and Ralph Santos and Victor Sapojnikov and Brian Schultz and Jörg Schultz and Matthias S Schwartz and Scott Schwartz and Carol Scott and Steven Seaman and Steve Searle and Ted Sharpe and Andrew Sheridan and Ratna Shownkeen and Sarah Sims and Jonathan B Singer and Guy Slater and Arian Smit and Douglas R Smith and Brian Spencer and Arne Stabenau and Nicole {Stange-Thomann} and Charles Sugnet and Mikita Suyama and Glenn Tesler and Johanna Thompson and David Torrents and Evanne Trevaskis and John Tromp and Catherine Ucla and Abel {Ureta-Vidal} and Jade P Vinson and Andrew C Von Niederhausern and Claire M Wade and Melanie Wall and Ryan J Weber and Robert B Weiss and Michael C Wendl and Anthony P West and Kris Wetterstrand and Raymond Wheeler and Simon Whelan and Jamey Wierzbowski and David Willey and Sophie Williams and Richard K Wilson and Eitan Winter and Kim C Worley and Dudley Wyman and Shan Yang and {Shiaw-Pyng} Yang and Evgeny M Zdobnov and Michael C Zody and Eric S Lander}, 1.156 + month = dec, 1.157 + year = {2002}, 1.158 + note = {{PMID:} 12466850}, 1.159 + keywords = {{Animals,Base} {Composition,Chromosomes,} {Mammalian,Conserved} {Sequence,CpG} {Islands,Evolution,} {Molecular,Gene} Expression {Regulation,Genes,Genetic} {Variation,Genome,Genome,} {Human,Genomics,Humans,Mice,Mice,} {Knockout,Mice,} {Transgenic,Models,} {Animal,Multigene} {Family,Mutagenesis,Neoplasms,Physical} Chromosome {Mapping,Proteome,Pseudogenes,Quantitative} Trait {Loci,Repetitive} Sequences, Nucleic {Acid,RNA,} {Untranslated,Selection} {(Genetics),Sequence} Analysis, {DNA,Sex} {Chromosomes,Species} {Specificity,Synteny}}, 1.160 + pages = {520--62} 1.161 +}, 1.162 + 1.163 +@article{curwen_ensembl_2004, 1.164 + title = {The Ensembl Automatic Gene Annotation System}, 1.165 + volume = {14}, 1.166 + url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=479124}, 1.167 + doi = {10.1101/gr.1858004}, 1.168 + number = {5}, 1.169 + journal = {Genome Research}, 1.170 + author = {Val Curwen and Eduardo Eyras and T. Daniel Andrews and Laura Clarke and Emmanuel Mongin and Steven {M.J.} Searle and Michele Clamp}, 1.171 + month = may, 1.172 + year = {2004}, 1.173 + note = {{PMC479124}}, 1.174 + pages = {942–950} 1.175 +}, 1.176 + 1.177 +@article{gong_gene_2003, 1.178 + title = {A gene expression atlas of the central nervous system based on bacterial artificial chromosomes}, 1.179 + volume = {425}, 1.180 + issn = {0028-0836}, 1.181 + url = {http://dx.doi.org/10.1038/nature02033}, 1.182 + doi = {10.1038/nature02033}, 1.183 + number = {6961}, 1.184 + journal = {Nature}, 1.185 + author = {Shiaoching Gong and Chen Zheng and Martin L. Doughty and Kasia Losos and Nicholas Didkovsky and Uta B. Schambra and Norma J. Nowak and Alexandra Joyner and Gabrielle Leblanc and Mary E. Hatten and Nathaniel Heintz}, 1.186 + month = oct, 1.187 + year = {2003}, 1.188 + pages = {917--925} 1.189 +}, 1.190 + 1.191 +@article{visel_genepaint.org:atlas_2004, 1.192 + title = {{GenePaint.org:} an atlas of gene expression patterns in the mouse embryo}, 1.193 + volume = {32}, 1.194 + url = {http://nar.oxfordjournals.org/cgi/content/abstract/32/suppl_1/D552}, 1.195 + doi = {10.1093/nar/gkh029}, 1.196 + abstract = {High-throughput instruments were recently developed to determine gene expression patterns on tissue sections by {RNA} in situ hybridization. The resulting images of gene expression patterns, chiefly of E14.5 mouse embryos, are accessible to the public at http://www.genepaint.org. This relational database is searchable for gene identifiers and {RNA} probe sequences. Moreover, patterns and intensity of expression in [{\textasciitilde}]100 different embryonic tissues are annotated and can be searched using a standardized catalog of anatomical structures. A virtual microscope tool, the Zoom Image Server, was implemented in {GenePaint.org} and permits interactive zooming and panning across [{\textasciitilde}]15 000 high-resolution images.}, 1.197 + number = {suppl\_1}, 1.198 + journal = {Nucl. Acids Res.}, 1.199 + author = {Axel Visel and Christina Thaller and Gregor Eichele}, 1.200 + year = {2004}, 1.201 + pages = {D552--556} 1.202 +}, 1.203 + 1.204 +@article{magdaleno_bgem:in_2006, 1.205 + title = {{BGEM:} An In Situ Hybridization Database of Gene Expression in the Embryonic and Adult Mouse Nervous System}, 1.206 + volume = {4}, 1.207 + url = {http://dx.doi.org/10.1371%2Fjournal.pbio.0040086}, 1.208 + doi = {10.1371/journal.pbio.0040086}, 1.209 + number = {4}, 1.210 + journal = {{PLoS} Biology}, 1.211 + author = {Susan Magdaleno and Patricia Jensen and Craig L. Brumwell and Anna Seal and Karen Lehman and Andrew Asbury and Tony Cheung and Tommie Cornelius and Diana M. Batten and Christopher Eden and Shannon M. Norland and Dennis S. Rice and Nilesh Dosooye and Sundeep Shakya and Perdeep Mehta and Tom Curran}, 1.212 + month = apr, 1.213 + year = {2006}, 1.214 + pages = {e86 {EP} --} 1.215 +}, 1.216 + 1.217 +@inproceedings{carson_data_2005, 1.218 + title = {Data Mining in situ gene expression patterns at cellular resolution}, 1.219 + doi = {{10.1109/CSBW.2005.49}}, 1.220 + abstract = {Non-radioactive in situ hybridization {(ISH)} is a powerful technique for revealing gene expression in individual cells, the level of detail necessary for investigating how genes control cell type identity, cell differentiation, and cell-cell signaling. Although the availability of robotic {ISH} enables the expeditious determination of expression patterns for thousands of genes in serially sectioned tissues, a large collection of {ISH} images is, per se, of limited benefit. However, via accurate detection of expression strength and spatial normalization of expression location across different specimens, {ISH} images become a minable resource of annotated gene expression capable of advancing functional genomics in a mode similar to {DNA} sequence databases. We have developed computational methods to automate robotic {ISH} image annotation and applied these to over 200 genes throughout the postnatal mouse brain. Gene expression strengths were quantified for each cell tissue section images, and these images were subjected to atlas-based segmentation using a series of subdivision mesh maps that comprise our atlas of the postnatal mouse brain. With this common geometric representation of gene expression, patterns are automatically annotated and spatial searches success fully find the genes expressed in a similar fashion to custom query patterns. Cluster analysis of spatially normalized expression patterns identifies potential relationships in gene networks. Annotated gene expression patterns and query interfaces are publicly accessible at wv/w. geneattas. org.}, 1.221 + booktitle = {Computational Systems Bioinformatics Conference, 2005. Workshops and Poster Abstracts. {IEEE}}, 1.222 + author = {J. Carson and T. Ju and C. Thaller and M. Bello and I. Kakadiaris and J. Warren and G. Eichele and W. Chiu}, 1.223 + year = {2005}, 1.224 + keywords = {atlas-based segmentation,automate robotic in situ hybridization image annotation,biological techniques,biological tissues,biology {computing,Brain,cell-cell} signaling,cell differentiation,cellular biophysics,cellular resolution,cluster analysis,data {mining,DNA} sequence database,functional genomics,gene expression pattern,genetics,image classification,image segmentation,mesh maps,pattern clustering,postnatal mouse brain,query interface,statistical analysis,tissue}, 1.225 + pages = {358} 1.226 +}, 1.227 + 1.228 +@article{venkataraman_emage_2008, 1.229 + title = {{EMAGE} Edinburgh Mouse Atlas of Gene Expression: 2008 update}, 1.230 + volume = {36}, 1.231 + url = {http://nar.oxfordjournals.org/cgi/content/abstract/36/suppl_1/D860}, 1.232 + doi = {10.1093/nar/gkm938}, 1.233 + abstract = {{EMAGE} {(http://genex.hgu.mrc.ac.uk/Emage/database)} is a database of in situ gene expression patterns in the developing mouse embryo. Domains of expression from raw data images are spatially integrated into a set of standard {3D} virtual mouse embryos at different stages of development, allowing data interrogation by spatial methods. Sites of expression are also described using an anatomy ontology and data can be queried using text-based methods. Here we describe recent enhancements to {EMAGE} which include advances in spatial search methods including: a refined local spatial similarity search algorithm, a method to allow global spatial comparison of patterns in {EMAGE} and subsequent hierarchical-clustering, and spatial searches across multiple stages of development. In addition, we have extended data access by the introduction of web services and new {HTML-based} search interfaces, which allow access to data that has not yet been spatially annotated. We have also started incorporating full {3D} images of gene expression that have been generated using optical projection tomography {(OPT).}}, 1.234 + number = {suppl\_1}, 1.235 + journal = {Nucl. Acids Res.}, 1.236 + author = {Shanmugasundaram Venkataraman and Peter Stevenson and Yiya Yang and Lorna Richardson and Nicholas Burton and Thomas P. Perry and Paul Smith and Richard A. Baldock and Duncan R. Davidson and Jeffrey H. Christiansen}, 1.237 + year = {2008}, 1.238 + pages = {D860--865} 1.239 +}, 1.240 + 1.241 +@inbook{hemert_matching_2008, 1.242 + series = {Communications in Computer and Information Science}, 1.243 + title = {Matching Spatial Regions with Combinations of Interacting Gene Expression Patterns}, 1.244 + volume = {13}, 1.245 + url = {http://dx.doi.org/10.1007/978-3-540-70600-7_26}, 1.246 + abstract = {The Edinburgh Mouse Atlas aims to capture in-situ gene expression patterns in a common spatial framework. In this study, we construct a grammar to define spatial regions by 1.247 +combinations of these patterns. Combinations are formed by applying operators to curated gene expression patterns from the 1.248 +atlas, thereby resembling gene interactions in a spatial context. The space of combinations is searched using an evolutionary 1.249 +algorithm with the objective of finding the best match to a given target pattern. We evaluate the method by testing its robustness 1.250 +and the statistical significance of the results it finds.}, 1.251 + booktitle = {Bioinformatics Research and Development}, 1.252 + publisher = {Springer Berlin Heidelberg}, 1.253 + author = {Jano Hemert and Richard Baldock}, 1.254 + year = {2008}, 1.255 + pages = {347--361} 1.256 +}, 1.257 + 1.258 +@inbook{van_hemert_mining_2007, 1.259 + series = {Lecture Notes in Computer Science}, 1.260 + title = {Mining Spatial Gene Expression Data for Association Rules}, 1.261 + volume = {4414/2007}, 1.262 + isbn = {978-3-540-71232-9}, 1.263 + url = {http://dx.doi.org/10.1007/978-3-540-71233-6_6}, 1.264 + abstract = {We analyse data from the Edinburgh Mouse Atlas {Gene-Expression} Database {(EMAGE)} which is a high quality data source for spatio-temporal 1.265 +gene expression patterns. Using a novel process whereby generated patterns are used to probe spatially-mapped gene expression 1.266 +domains, we are able to get unbiased results as opposed to using annotations based predefined anatomy regions. We describe 1.267 +two processes to form association rules based on spatial configurations, one that associates spatial regions, the other associates 1.268 +genes.}, 1.269 + booktitle = {Bioinformatics Research and Development}, 1.270 + publisher = {Springer Berlin / Heidelberg}, 1.271 + author = {Jano van Hemert and Richard Baldock}, 1.272 + year = {2007}, 1.273 + pages = {66--76} 1.274 +}, 1.275 + 1.276 +@article{sprague_zebrafish_2006, 1.277 + title = {The Zebrafish Information Network: the zebrafish model organism database}, 1.278 + volume = {34}, 1.279 + issn = {1362-4962}, 1.280 + url = {http://www.ncbi.nlm.nih.gov/pubmed/16381936}, 1.281 + doi = {10.1093/nar/gkj086}, 1.282 + abstract = {The Zebrafish Information Network {(ZFIN;} http://zfin.org) is a web based community resource that implements the curation of zebrafish genetic, genomic and developmental data. {ZFIN} provides an integrated representation of mutants, genes, genetic markers, mapping panels, publications and community resources such as meeting announcements and contact information. Recent enhancements to {ZFIN} include (i) comprehensive curation of gene expression data from the literature and from directly submitted data, (ii) increased support and annotation of the genome sequence, (iii) expanded use of ontologies to support curation and query forms, (iv) curation of morpholino data from the literature, and (v) increased versatility of gene pages, with new data types, links and analysis tools.}, 1.283 + number = {Database issue}, 1.284 + journal = {Nucleic Acids Research}, 1.285 + author = {Judy Sprague and Leyla Bayraktaroglu and Dave Clements and Tom Conlin and David Fashena and Ken Frazer and Melissa Haendel and Douglas G Howe and Prita Mani and Sridhar Ramachandran and Kevin Schaper and Erik Segerdell and Peiran Song and Brock Sprunger and Sierra Taylor and Ceri E Van Slyke and Monte Westerfield}, 1.286 + year = {2006}, 1.287 + note = {{PMID:} 16381936}, 1.288 + keywords = {{Animals,Databases,} {Genetic,Gene} {Expression,Genomics,Internet,Models,} {Animal,Oligonucleotides,} {Antisense,Systems} {Integration,User-Computer} {Interface,Vocabulary,} {Controlled,Zebrafish,Zebrafish} Proteins}, 1.289 + pages = {D581--5} 1.290 +}, 1.291 + 1.292 +@article{bell_geishawhole-mount_2004, 1.293 + title = {{GEISHA,} a whole-mount in situ hybridization gene expression screen in chicken embryos}, 1.294 + volume = {229}, 1.295 + url = {http://dx.doi.org/10.1002/dvdy.10503}, 1.296 + doi = {10.1002/dvdy.10503}, 1.297 + abstract = {Despite the increasing quality and quantity of genomic sequence that is available to researchers, predicting gene function from sequence information remains a challenge. One method for obtaining rapid insight into potential functional roles of novel genes is through gene expression mapping. We have performed a high throughput whole-mount in situ hybridization {(ISH)} screen with chick embryos to identify novel, differentially expressed genes. Approximately 1,200 5prime expressed sequence tags {(ESTs)} were generated from {cDNA} clones of a Hamburger and Hamilton {(HH)} stage 4-7 (late gastrula) chick embryo endoderm-mesoderm library. After screening to remove ubiquitously expressed {cDNAs} and internal clustering and after comparison to {GenBank} sequences, remaining {cDNAs} (representing both characterized and uncharacterized genes) were screened for expression in {HH} stage 3-14 embryos by automated high throughput {ISH.} Of 786 {cDNAs} for which {ISH} was successfully performed, approximately 30\% showed ubiquitous expression, 40\% were negative, and approximately 30\% showed a restricted expression pattern. {cDNAs} were identified that showed restricted expression in every embryonic region, including the primitive streak, somites, developing cardiovascular system and neural tube/neural crest. A relational database was developed to hold all {EST} sequences, {ISH} images, and corresponding {BLAST} report information, and to enable browsing and querying of data. A user interface is freely accessible at . Results show that high throughput whole-mount {ISH} provides an effective approach for identifying novel genes that are differentially expressed in the developing chicken embryo. Developmental Dynamics 229:677-687, 2004. � 2004 {Wiley-Liss,} Inc.}, 1.298 + number = {3}, 1.299 + journal = {Developmental Dynamics}, 1.300 + author = {George W. Bell and Tatiana A. Yatskievych and Parker B. Antin}, 1.301 + year = {2004}, 1.302 + pages = {677--687} 1.303 +}, 1.304 + 1.305 +@article{tomancak_systematic_2002, 1.306 + title = {Systematic determination of patterns of gene expression during Drosophila embryogenesis}, 1.307 + volume = {3}, 1.308 + url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=151190}, 1.309 + doi = {10.1186/gb-2002-3-12-research0088}, 1.310 + number = {12}, 1.311 + journal = {Genome Biology}, 1.312 + author = {Pavel Tomancak and Amy Beaton and Richard Weiszmann and Elaine Kwan and {ShengQiang} Shu and Suzanna E Lewis and Stephen Richards and Michael Ashburner and Volker Hartenstein and Susan E Celniker and Gerald M Rubin}, 1.313 + year = {2002}, 1.314 + note = {{PMC151190}}, 1.315 + pages = {research00881–8814} 1.316 +}, 1.317 + 1.318 +@article{carson_digital_2005, 1.319 + title = {A Digital Atlas to Characterize the Mouse Brain Transcriptome}, 1.320 + volume = {1}, 1.321 + url = {http://dx.plos.org/10.1371%2Fjournal.pcbi.0010041}, 1.322 + doi = {10.1371/journal.pcbi.0010041}, 1.323 + abstract = {Massive amounts of data are being generated in an effort to represent for the brain the expression of all genes at cellular resolution. Critical to exploiting this effort is the ability to place these data into a common frame of reference. Here we have developed a computational method for annotating gene expression patterns in the context of a digital atlas to facilitate custom user queries and comparisons of this type of data. This procedure has been applied to 200 genes in the postnatal mouse brain. As an illustration of utility, we identify candidate genes that may be related to Parkinson disease by using the expression of a dopamine transporter in the substantia nigra as a search query pattern. In addition, we discover that transcription factor Rorb is down-regulated in the barrelless mutant relative to control mice by quantitative comparison of expression patterns in layer {IV} somatosensory cortex. The semi-automated annotation method developed here is applicable to a broad spectrum of complex tissues and data modalities.}, 1.324 + number = {4}, 1.325 + journal = {{PLoS} Comput Biol}, 1.326 + author = {James P Carson and Tao Ju and {Hui-Chen} Lu and Christina Thaller and Mei Xu and Sarah L Pallas and Michael C Crair and Joe Warren and Wah Chiu and Gregor Eichele}, 1.327 + year = {2005}, 1.328 + pages = {e41} 1.329 +}, 1.330 + 1.331 +@article{lee_high-resolution_2007, 1.332 + title = {A {High-Resolution} Anatomical Framework of the Neonatal Mouse Brain for Managing Gene Expression Data}, 1.333 + volume = {1}, 1.334 + url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2525996}, 1.335 + doi = {10.3389/neuro.11.006.2007}, 1.336 + journal = {Frontiers in Neuroinformatics}, 1.337 + author = {{Erh-Fang} Lee and Jyl Boline and Arthur W. Toga}, 1.338 + year = {2007}, 1.339 + note = {{PMC2525996}}, 1.340 + pages = {6} 1.341 +}, 1.342 + 1.343 +@article{barrett_ncbi_2007, 1.344 + title = {{NCBI} {GEO:} mining tens of millions of expression profiles--database and tools update}, 1.345 + volume = {35}, 1.346 + url = {http://nar.oxfordjournals.org/cgi/content/abstract/35/suppl_1/D760}, 1.347 + doi = {10.1093/nar/gkl887}, 1.348 + abstract = {The Gene Expression Omnibus {(GEO)} repository at the National Center for Biotechnology Information {(NCBI)} archives and freely disseminates microarray and other forms of high-throughput data generated by the scientific community. The database has a minimum information about a microarray experiment {(MIAME)-compliant} infrastructure that captures fully annotated raw and processed data. Several data deposit options and formats are supported, including web forms, spreadsheets, {XML} and Simple Omnibus Format in Text {(SOFT).} In addition to data storage, a collection of user-friendly web-based interfaces and applications are available to help users effectively explore, visualize and download the thousands of experiments and tens of millions of gene expression patterns stored in {GEO.} This paper provides a summary of the {GEO} database structure and user facilities, and describes recent enhancements to database design, performance, submission format options, data query and retrieval utilities. {GEO} is accessible at http://www.ncbi.nlm.nih.gov/geo/}, 1.349 + number = {suppl\_1}, 1.350 + journal = {Nucl. Acids Res.}, 1.351 + author = {Tanya Barrett and Dennis B. Troup and Stephen E. Wilhite and Pierre Ledoux and Dmitry Rudnev and Carlos Evangelista and Irene F. Kim and Alexandra Soboleva and Maxim Tomashevsky and Ron Edgar}, 1.352 + year = {2007}, 1.353 + pages = {D760--765} 1.354 +}, 1.355 + 1.356 +@article{smith_mouse_2007, 1.357 + title = {The mouse Gene Expression Database {(GXD):} 2007 update}, 1.358 + volume = {35}, 1.359 + url = {http://nar.oxfordjournals.org/cgi/content/abstract/35/suppl_1/D618}, 1.360 + doi = {10.1093/nar/gkl1003}, 1.361 + abstract = {The Gene Expression Database {(GXD)} provides the scientific community with an extensive and easily searchable database of gene expression information about the mouse. Its primary emphasis is on developmental studies. By integrating different types of expression data, {GXD} aims to provide comprehensive information about expression patterns of transcripts and proteins in wild-type and mutant mice. Integration with the other Mouse Genome Informatics {(MGI)} databases places the gene expression information in the context of genetic, sequence, functional and phenotypic information, enabling valuable insights into the molecular biology that underlies developmental and disease processes. In recent years the utility of {GXD} has been greatly enhanced by a large increase in data content, obtained from the literature and provided by researchers doing large-scale in situ and {cDNA} screens. In addition, we have continued to refine our query and display features to make it easier for users to interrogate the data. {GXD} is available through the {MGI} web site at http://www.informatics.jax.org/ or directly at http://www.informatics.jax.org/menus/expression\_menu.shtml.}, 1.362 + number = {suppl\_1}, 1.363 + journal = {Nucl. Acids Res.}, 1.364 + author = {Constance M. Smith and Jacqueline H. Finger and Terry F. Hayamizu and Ingeborg J. {McCright} and Janan T. Eppig and James A. Kadin and Joel E. Richardson and Martin Ringwald}, 1.365 + year = {2007}, 1.366 + pages = {D618--623} 1.367 +} 1.368 \ No newline at end of file