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Volume 13;  2012

Database

IntegromeDB: an integrated system and biological search engine
Michael Baitaluk, Sergey Kozhenkov, Yulia Dubinina, Julia Ponomarenko
BMC Genomics. 2012; 13: 35. Published online 2012 January 19. doi: 10.1186/1471-2164-13-35
PMCID:
PMC3293773
Abstract Full Text PDF–811K Supplementary Material
miRdSNP: a database of disease-associated SNPs and microRNA target sites on 3'UTRs of human genes
Andrew E Bruno, Li Li, James L Kalabus, Yuzhuo Pan, Aiming Yu, Zihua Hu
BMC Genomics. 2012; 13: 44. Published online 2012 January 25. doi: 10.1186/1471-2164-13-44
PMCID:
PMC3287127
Abstract Full Text PDF–1.1M
Medicago truncatula transporter database: a comprehensive database resource for M. truncatula transporters
Zhenyan Miao, Daofeng Li, Zhenhai Zhang, Jiangli Dong, Zhen Su, Tao Wang
BMC Genomics. 2012; 13: 60. Published online 2012 February 6. doi: 10.1186/1471-2164-13-60
PMCID:
PMC3298476
Abstract Full Text PDF–1013K Supplementary Material
AtPAN: an integrated system for reconstructing transcriptional regulatory networks in Arabidopsis thaliana
Yi-An Chen, Ying-Chi Wen, Wen-Chi Chang
BMC Genomics. 2012; 13: 85. Published online 2012 March 8. doi: 10.1186/1471-2164-13-85
PMCID:
PMC3314555
Abstract Full Text PDF–3.2M Supplementary Material

Software

GemSIM: general, error-model based simulator of next-generation sequencing data
Kerensa E McElroy, Fabio Luciani, Torsten Thomas
BMC Genomics. 2012; 13: 74. Published online 2012 February 15. doi: 10.1186/1471-2164-13-74
PMCID:
PMC3305602
Abstract Full Text PDF–407K

Research Articles

Yeast-based assay identifies novel Shh/Gli target genes in vertebrate development
Luis A Milla, Claudio R Cortés, Christian Hodar Q, Maritza G Oñate, Veronica Cambiazo, Shawn M Burgess, Verónica Palma
BMC Genomics. 2012; 13: 2. Published online 2012 January 3. doi: 10.1186/1471-2164-13-2
PMCID:
PMC3285088
Abstract Full Text PDF–1.8M Supplementary Material
RAD tag sequencing as a source of SNP markers in Cynara cardunculus L
Davide Scaglione, Alberto Acquadro, Ezio Portis, Matteo Tirone, Steven J Knapp, Sergio Lanteri
BMC Genomics. 2012; 13: 3. Published online 2012 January 3. doi: 10.1186/1471-2164-13-3
PMCID:
PMC3269995
Abstract Full Text PDF–968K Supplementary Material
Diversity in parasitic nematode genomes: the microRNAs of Brugia pahangi and Haemonchus contortus are largely novel
Alan D Winter, William Weir, Martin Hunt, Matthew Berriman, John S Gilleard, Eileen Devaney, Collette Britton
BMC Genomics. 2012; 13: 4. Published online 2012 January 4. doi: 10.1186/1471-2164-13-4
PMCID:
PMC3282659
Abstract Full Text PDF–1.1M Supplementary Material
Controversies in modern evolutionary biology: the imperative for error detection and quality control
Francisco Prosdocimi, Benjamin Linard, Pierre Pontarotti, Olivier Poch, Julie D Thompson
BMC Genomics. 2012; 13: 5. Published online 2012 January 4. doi: 10.1186/1471-2164-13-5
PMCID:
PMC3311146
Abstract Full Text PDF–2.2M Supplementary Material
RNA-Seq and molecular docking reveal multi-level pesticide resistance in the bed bug
Praveen Mamidala, Asela J Wijeratne, Saranga Wijeratne, Karl Kornacker, Babu Sudhamalla, Loren J Rivera-Vega, Andrew Hoelmer, Tea Meulia, Susan C Jones, Omprakash Mittapalli
BMC Genomics. 2012; 13: 6. Published online 2012 January 6. doi: 10.1186/1471-2164-13-6
PMCID:
PMC3273426
Abstract Full Text PDF–5.1M Supplementary Material
Sculpting the maturation, softening and ethylene pathway: The influences of microRNAs on tomato fruits
Jinhua Zuo, Benzhong Zhu, Daqi Fu, Yi Zhu, Yuanzheng Ma, Lihong Chi, Zheng Ju, Yunxiang Wang, Baiqiang Zhai, Yunbo Luo
BMC Genomics. 2012; 13: 7. Published online 2012 January 9. doi: 10.1186/1471-2164-13-7
PMCID:
PMC3266637
Abstract Full Text PDF–546K Supplementary Material
Quantitative Interactor Screening with next-generation Sequencing (QIS-Seq) identifies Arabidopsis thaliana MLO2 as a target of the Pseudomonas syringae type III effector HopZ2
Jennifer D Lewis, Janet Wan, Rachel Ford, Yunchen Gong, Pauline Fung, Hardeep Nahal, Pauline W Wang, Darrell Desveaux, David S Guttman
BMC Genomics. 2012; 13: 8. Published online 2012 January 9. doi: 10.1186/1471-2164-13-8
PMCID:
PMC3320541
Abstract Full Text PDF–2.1M Supplementary Material
Rootstock-regulated gene expression patterns associated with fire blight resistance in apple
Philip J Jensen, Noemi Halbrendt, Gennaro Fazio, Izabela Makalowska, Naomi Altman, Craig Praul, Siela N Maximova, Henry K Ngugi, Robert M Crassweller, James W Travis, Timothy W McNellis
BMC Genomics. 2012; 13: 9. Published online 2012 January 9. doi: 10.1186/1471-2164-13-9
PMCID:
PMC3277459
Abstract Full Text PDF–786K Supplementary Material
Transcriptome changes during fruit development and ripening of sweet orange (Citrus sinensis)
Keqin Yu, Qiang Xu, Xinlei Da, Fei Guo, Yuduan Ding, Xiuxin Deng
BMC Genomics. 2012; 13: 10. Published online 2012 January 10. doi: 10.1186/1471-2164-13-10
PMCID:
PMC3267696
Abstract Full Text PDF–3.0M Supplementary Material
A searchable cross-platform gene expression database reveals connections between drug treatments and disease
Gareth Williams
BMC Genomics. 2012; 13: 12. Published online 2012 January 10. doi: 10.1186/1471-2164-13-12
PMCID:
PMC3305579
Abstract Full Text PDF–1.4M Supplementary Material
SNP mining in C. clementina BAC end sequences; transferability in the Citrus genus (Rutaceae), phylogenetic inferences and perspectives for genetic mapping
Patrick Ollitrault, Javier Terol, Andres Garcia-Lor, Aurélie Bérard, Aurélie Chauveau, Yann Froelicher, Caroline Belzile, Raphaël Morillon, Luis Navarro, Dominique Brunel, Manuel Talon
BMC Genomics. 2012; 13: 13. Published online 2012 January 10. doi: 10.1186/1471-2164-13-13
PMCID:
PMC3320530
Abstract Full Text PDF–1.1M Supplementary Material
Gene fragmentation in bacterial draft genomes: extent, consequences and mitigation
Jonathan L Klassen, Cameron R Currie
BMC Genomics. 2012; 13: 14. Published online 2012 January 10. doi: 10.1186/1471-2164-13-14
PMCID:
PMC3322347
Abstract Full Text PDF–1.4M Supplementary Material
Comprehensive transcriptome analysis reveals novel genes involved in cardiac glycoside biosynthesis and mlncRNAs associated with secondary metabolism and stress response in Digitalis purpurea
Bin Wu, Ying Li, Haixia Yan, Yimian Ma, Hongmei Luo, Lichai Yuan, Shilin Chen, Shanfa Lu
BMC Genomics. 2012; 13: 15. Published online 2012 January 10. doi: 10.1186/1471-2164-13-15
PMCID:
PMC3269984
Abstract Full Text PDF–1.1M Supplementary Material
Polymorphism discovery and allele frequency estimation using high-throughput DNA sequencing of target-enriched pooled DNA samples
Michael P Mullen, Christopher J Creevey, Donagh P Berry, Matt S McCabe, David A Magee, Dawn J Howard, Aideen P Killeen, Stephen D Park, Paul A McGettigan, Matt C Lucy, David E MacHugh, Sinead M Waters
BMC Genomics. 2012; 13: 16. Published online 2012 January 11. doi: 10.1186/1471-2164-13-16
PMCID:
PMC3315736
Abstract Full Text PDF–952K Supplementary Material
Lipopolysaccharide priming enhances expression of effectors of immune defence while decreasing expression of pro-inflammatory cytokines in mammary epithelia cells from cows
Juliane Günther, Wolfram Petzl, Holm Zerbe, Hans-Joachim Schuberth, Dirk Koczan, Leopold Goetze, Hans-Martin Seyfert
BMC Genomics. 2012; 13: 17. Published online 2012 January 12. doi: 10.1186/1471-2164-13-17
PMCID:
PMC3315725
Abstract Full Text PDF–1.4M Supplementary Material
Characterisation of full-length cDNA sequences provides insights into the Eimeria tenellatranscriptome
Nadzirah Amiruddin, Xin-Wei Lee, Damer P Blake, Yutaka Suzuki, Yea-Ling Tay, Lik-Sin Lim, Fiona M Tomley, Junichi Watanabe, Chihiro Sugimoto, Kiew-Lian Wan
BMC Genomics. 2012; 13: 21. Published online 2012 January 13. doi: 10.1186/1471-2164-13-21
PMCID:
PMC3315734
Abstract Full Text PDF–594K Supplementary Material
Genome-wide association scan and phased haplotype construction for quantitative trait loci affecting boar taint in three pig breeds
Vivi R Gregersen, Lene N Conley, Kirsten K Sørensen, Bernt Guldbrandtsen, Ingela H Velander, Christian Bendixen
BMC Genomics. 2012; 13: 22. Published online 2012 January 13. doi: 10.1186/1471-2164-13-22
PMCID:
PMC3315726
Abstract Full Text PDF–281K Supplementary Material
Quantification and accurate normalisation of small RNAs through new custom RT-qPCR arrays demonstrates Salmonella-induced microRNAs in human monocytes
Soroush Sharbati, Jutta Sharbati, Lena Hoeke, Marc Bohmer, Ralf Einspanier
BMC Genomics. 2012; 13: 23. Published online 2012 January 16. doi: 10.1186/1471-2164-13-23
PMCID:
PMC3268085
Abstract Full Text PDF–1.2M Supplementary Material
Estimation of linkage disequilibrium in four US pig breeds
Yvonne M Badke, Ronald O Bates, Catherine W Ernst, Clint Schwab, Juan P Steibel
BMC Genomics. 2012; 13: 24. Published online 2012 January 17. doi: 10.1186/1471-2164-13-24
PMCID:
PMC3269977
Abstract Full Text PDF–304K
The architecture and ppGpp-dependent expression of the primary transcriptome of Salmonella Typhimurium during invasion gene expression
Vinoy K Ramachandran, Neil Shearer, Jobin J Jacob, Cynthia M Sharma, Arthur Thompson
BMC Genomics. 2012; 13: 25. Published online 2012 January 17. doi: 10.1186/1471-2164-13-25
PMCID:
PMC3293720
Abstract Full Text PDF–736K Supplementary Material
Postmortem cardiac tissue maintains gene expression profile even after late harvesting
Simone Gupta, Marc K Halushka, Gina M Hilton, Dan E Arking
BMC Genomics. 2012; 13: 26. Published online 2012 January 17. doi: 10.1186/1471-2164-13-26
PMCID:
PMC3342086
Abstract Full Text PDF–424K Supplementary Material
Dynamic DNA cytosine methylation in the Populus trichocarpa genome: tissue-level variation and relationship to gene expression
Kelly J Vining, Kyle R Pomraning, Larry J Wilhelm, Henry D Priest, Matteo Pellegrini, Todd C Mockler, Michael Freitag, Steven H Strauss
BMC Genomics. 2012; 13: 27. Published online 2012 January 17. doi: 10.1186/1471-2164-13-27
PMCID:
PMC3298464
Abstract Full Text PDF–3.7M Supplementary Material
Increased sensitivity of next generation sequencing-based expression profiling after globin reduction in human blood RNA
Anastasios Mastrokolias, Johan T den Dunnen, GertJan B van Ommen, Peter AC 't Hoen, Willeke MC van Roon-Mom
BMC Genomics. 2012; 13: 28. Published online 2012 January 18. doi: 10.1186/1471-2164-13-28
PMCID:
PMC3275489
Abstract Full Text PDF–2.2M Supplementary Material
Centromere-associated repeat arrays on Trypanosoma brucei chromosomes are much more extensive than predicted
Maria C Echeverry, Christopher Bot, Samson O Obado, Martin C Taylor, John M Kelly
BMC Genomics. 2012; 13: 29. Published online 2012 January 18. doi: 10.1186/1471-2164-13-29
PMCID:
PMC3292466
Abstract Full Text PDF–441K Supplementary Material
Microarray analysis on germfree mice elucidates the primary target of a traditional Japanese medicine juzentaihoto: acceleration of IFN-α response via affecting the ISGF3-IRF7 signaling cascade
Kaori Munakata, Kiyoe Takashima, Mitsue Nishiyama, Naoko Asano, Akihito Mase, Kyoji Hioki, Yasuyuki Ohnishi, Masahiro Yamamoto, Kenji Watanabe
BMC Genomics. 2012; 13: 30. Published online 2012 January 18. doi: 10.1186/1471-2164-13-30
PMCID:
PMC3298487
Abstract Full Text PDF–4.0M Supplementary Material
Sequencing and comparative genomic analysis of 1227 Felis catus cDNA sequences enriched for developmental, clinical and nutritional phenotypes
Kristopher J Irizarry, Sukhaswami B Malladi, Xiangming Gao, Katherine Mitsouras, Lynda Melendez, Patricia A Burris, Jeffrey A Brockman, Samer W Al-Murrani
BMC Genomics. 2012; 13: 31. Published online 2012 January 18. doi: 10.1186/1471-2164-13-31
PMCID:
PMC3278379
Abstract Full Text PDF–781K Supplementary Material
Transcriptional ontogeny of the developing liver
Janice S Lee, William O Ward, Geremy Knapp, Hongzu Ren, Beena Vallanat, Barbara Abbott, Karen Ho, Seth J Karp, J Christopher Corton
BMC Genomics. 2012; 13: 33. Published online 2012 January 19. doi: 10.1186/1471-2164-13-33
PMCID:
PMC3306746
Abstract Full Text PDF–3.9M Supplementary Material
Expression profiling reveals Spot 42 small RNA as a key regulator in the central metabolism of Aliivibrio salmonicida
Geir Å Hansen, Rafi Ahmad, Erik Hjerde, Christopher G Fenton, Nils-Peder Willassen, Peik Haugen
BMC Genomics. 2012; 13: 37. Published online 2012 January 24. doi: 10.1186/1471-2164-13-37
PMCID:
PMC3295665
Abstract Full Text PDF–2.3M Supplementary Material
Comparative genomic analysis of the genus Staphylococcus including Staphylococcus aureus and its newly described sister species Staphylococcus simiae
Haruo Suzuki, Tristan Lefébure, Paulina Pavinski Bitar, Michael J Stanhope
BMC Genomics. 2012; 13: 38. Published online 2012 January 24. doi: 10.1186/1471-2164-13-38
PMCID:
PMC3317825
Abstract Full Text PDF–471K Supplementary Material
The core and unique proteins of haloarchaea
Melinda D Capes, Priya DasSarma, Shiladitya DasSarma
BMC Genomics. 2012; 13: 39. Published online 2012 January 24. doi: 10.1186/1471-2164-13-39
PMCID:
PMC3287961
Abstract Full Text PDF–2.4M Supplementary Material
Genetic diversity of human RNase 8
Calvin C Chan, Jennifer M Moser, Kimberly D Dyer, Caroline M Percopo, Helene F Rosenberg
BMC Genomics. 2012; 13: 40. Published online 2012 January 24. doi: 10.1186/1471-2164-13-40
PMCID:
PMC3295680
Abstract Full Text PDF–1.1M
The miRNAome of globe artichoke: conserved and novel micro RNAs and target analysis
Domenico De Paola, Federica Cattonaro, Domenico Pignone, Gabriella Sonnante
BMC Genomics. 2012; 13: 41. Published online 2012 January 24. doi: 10.1186/1471-2164-13-41
PMCID:
PMC3285030
Abstract Full Text PDF–1.3M Supplementary Material
An evaluation of two-channel ChIP-on-chip and DNA methylation microarray normalization strategies
Michiel E Adriaens, Magali Jaillard, Lars MT Eijssen, Claus-Dieter Mayer, Chris TA Evelo
BMC Genomics. 2012; 13: 42. Published online 2012 January 25. doi: 10.1186/1471-2164-13-42
PMCID:
PMC3293711
Abstract Full Text PDF–2.0M Supplementary Material
Transcriptional profiling of bovine milk using RNA sequencing
Saumya Wickramasinghe, Gonzalo Rincon, Alma Islas-Trejo, Juan F Medrano
BMC Genomics. 2012; 13: 45. Published online 2012 January 25. doi: 10.1186/1471-2164-13-45
PMCID:
PMC3285075
Abstract Full Text PDF–665K Supplementary Material
Identification of differentially expressed genes in SHSY5Y cells exposed to okadaic acid by suppression subtractive hybridization
Vanessa Valdiglesias, Juan Fernández-Tajes, Eduardo Pásaro, Josefina Méndez, Blanca Laffon
BMC Genomics. 2012; 13: 46. Published online 2012 January 27. doi: 10.1186/1471-2164-13-46
PMCID:
PMC3296583
Abstract Full Text PDF–355K Supplementary Material
Xanthomonas oryzae pv oryzae triggers immediate transcriptomic modulations in rice
Rumdeep K Grewal, Sumanti Gupta, Sampa Das
BMC Genomics. 2012; 13: 49. Published online 2012 January 31. doi: 10.1186/1471-2164-13-49
PMCID:
PMC3298507
Abstract Full Text PDF–881K Supplementary Material
Genome-wide landscape of liver X receptor chromatin binding and gene regulation in human macrophages
Petri Pehkonen, Lynn Welter-Stahl, Janine Diwo, Jussi Ryynänen, Anke Wienecke-Baldacchino, Sami Heikkinen, Eckardt Treuter, Knut R Steffensen, Carsten Carlberg
BMC Genomics. 2012; 13: 50. Published online 2012 January 31. doi: 10.1186/1471-2164-13-50
PMCID:
PMC3295715
Abstract Full Text PDF–2.1M Supplementary Material
Genome-wide analysis of hepatic LRH-1 reveals a promoter binding preference and suggests a role in regulating genes of lipid metabolism in concert with FXR
Hansook Kim Chong, Jacob Biesinger, Young-Kyo Seo, Xiaohui Xie, Timothy F Osborne
BMC Genomics. 2012; 13: 51. Published online 2012 February 1. doi: 10.1186/1471-2164-13-51
PMCID:
PMC3295688
Abstract Full Text PDF–1.8M Supplementary Material
Microgravity simulation by diamagnetic levitation: effects of a strong gradient magnetic field on the transcriptional profile of Drosophila melanogaster
Raul Herranz, Oliver J Larkin, Camelia E Dijkstra, Richard JA Hill, Paul Anthony, Michael R Davey, Laurence Eaves, Jack JWA van Loon, F Javier Medina, Roberto Marco
BMC Genomics. 2012; 13: 52. Published online 2012 February 1. doi: 10.1186/1471-2164-13-52
PMCID:
PMC3305489
Abstract Full Text PDF–1.6M Supplementary Material
Gene alterations at Drosophila inversion breakpoints provide prima facie evidence for natural selection as an explanation for rapid chromosomal evolution
Yolanda Guillén, Alfredo Ruiz
BMC Genomics. 2012; 13: 53. Published online 2012 February 1. doi: 10.1186/1471-2164-13-53
PMCID:
PMC3355041
Abstract Full Text PDF–639K Supplementary Material
Zonation related function and ubiquitination regulation in human hepatocellular carcinoma cells in dynamic vs. static culture conditions
Shu Cheng, Jean-Matthieu Prot, Eric Leclerc, Frédéric Y Bois
BMC Genomics. 2012; 13: 54. Published online 2012 February 1. doi: 10.1186/1471-2164-13-54
PMCID:
PMC3295679
Abstract Full Text PDF–672K Supplementary Material
Conservation and divergence of chemical defense system in the tunicate Oikopleura dioica revealed by genome wide response to two xenobiotics
Fekadu Yadetie, Stephen Butcher, Hilde E Førde, Coen Campsteijn, Jean-Marie Bouquet, Odd A Karlsen, France Denoeud, Raghu Metpally, Eric M Thompson, J Robert Manak, Anders Goksøyr, Daniel Chourrout
BMC Genomics. 2012; 13: 55. Published online 2012 February 2. doi: 10.1186/1471-2164-13-55
PMCID:
PMC3292500
Abstract Full Text PDF–932K Supplementary Material
Post-genomic analyses of fungal lignocellulosic biomass degradation reveal the unexpected potential of the plant pathogen Ustilago maydis
Marie Couturier, David Navarro, Caroline Olivé, Didier Chevret, Mireille Haon, Anne Favel, Laurence Lesage-Meessen, Bernard Henrissat, Pedro M Coutinho, Jean-Guy Berrin
BMC Genomics. 2012; 13: 57. Published online 2012 February 2. doi: 10.1186/1471-2164-13-57
PMCID:
PMC3298532
Abstract Full Text PDF–554K Supplementary Material
Analysis of the SOS response of Vibrio and other bacteria with multiple chromosomes
Neus Sanchez-Alberola, Susana Campoy, Jordi Barbé, Ivan Erill
BMC Genomics. 2012; 13: 58. Published online 2012 February 3. doi: 10.1186/1471-2164-13-58
PMCID:
PMC3323433
Abstract Full Text PDF–422K Supplementary Material
Heritable genome-wide variation of gene expression and promoter methylation between wild and domesticated chickens
Daniel Nätt, Carl-Johan Rubin, Dominic Wright, Martin Johnsson, Johan Beltéky, Leif Andersson, Per Jensen
BMC Genomics. 2012; 13: 59. Published online 2012 February 4. doi: 10.1186/1471-2164-13-59
PMCID:
PMC3297523
Abstract Full Text PDF–1.1M Supplementary Material
Ac/Ds-transposon activation tagging in poplar: a powerful tool for gene discovery
Matthias Fladung, Olaf Polak
BMC Genomics. 2012; 13: 61. Published online 2012 February 6. doi: 10.1186/1471-2164-13-61
PMCID:
PMC3295694
Abstract Full Text PDF–1.6M
Transcriptomic and proteomic analyses of the Aspergillus fumigatus hypoxia response using an oxygen-controlled fermenter
Bridget M Barker, Kristin Kroll, Martin Vödisch, Aurélien Mazurie, Olaf Kniemeyer, Robert A Cramer
BMC Genomics. 2012; 13: 62. Published online 2012 February 6. doi: 10.1186/1471-2164-13-62
PMCID:
PMC3293747
Abstract Full Text PDF–3.3M Supplementary Material
Global changes in gene expression by the opportunistic pathogen Burkholderia cenocepacia in response to internalization by murine macrophages
Jennifer S Tolman, Miguel A Valvano
BMC Genomics. 2012; 13: 63. Published online 2012 February 9. doi: 10.1186/1471-2164-13-63
PMCID:
PMC3296584
Abstract Full Text PDF–1.9M Supplementary Material
Transcriptome profiling of low temperature-treated cassava apical shoots showed dynamic responses of tropical plant to cold stress
Dong An, Jun Yang, Peng Zhang
BMC Genomics. 2012; 13: 64. Published online 2012 February 10. doi: 10.1186/1471-2164-13-64
PMCID:
PMC3339519
Abstract Full Text PDF–6.6M Supplementary Material
Relative entropy differences in bacterial chromosomes, plasmids, phages and genomic islands
Jon Bohlin, Mark WJ van Passel, Lars Snipen, Anja B Kristoffersen, David Ussery, Simon P Hardy
BMC Genomics. 2012; 13: 66. Published online 2012 February 10. doi: 10.1186/1471-2164-13-66
PMCID:
PMC3305612
Abstract Full Text PDF–5.5M
Aluminum tolerance association mapping in triticale
Agnieszka Niedziela, Piotr T Bednarek, Henryk Cichy, Grzegorz Budzianowski, Andrzej Kilian, Andrzej Anioł
BMC Genomics. 2012; 13: 67. Published online 2012 February 13. doi: 10.1186/1471-2164-13-67
PMCID:
PMC3313894
Abstract Full Text PDF–341K
Transcription analysis on response of porcine alveolar macrophages to Haemophilus parasuis
Yang Wang, Chong Liu, Ying Fang, Xiaoli Liu, Wentao Li, Shuqing Liu, Yingyu Liu, Yuxi Liu, Catherine Charreyre, Jean-Christophe Audonnet, Pin Chen, Qigai He
BMC Genomics. 2012; 13: 68. Published online 2012 February 13. doi: 10.1186/1471-2164-13-68
PMCID:
PMC3296652
Abstract Full Text PDF–720K Supplementary Material
Orthologous genes identified by transcriptome sequencing in the spider genus Stegodyphus
Tiina M Mattila, Jesper S Bechsgaard, Troels T Hansen, Mikkel H Schierup, Trine Bilde
BMC Genomics. 2012; 13: 70. Published online 2012 February 14. doi: 10.1186/1471-2164-13-70
PMCID:
PMC3350440
Abstract Full Text PDF–568K Supplementary Material
Identification of common genetic modifiers of neurodegenerative diseases from an integrative analysis of diverse genetic screens in model organisms
Xi Chen, Robert D Burgoyne
BMC Genomics. 2012; 13: 71. Published online 2012 February 14. doi: 10.1186/1471-2164-13-71
PMCID:
PMC3292922
Abstract Full Text PDF–701K Supplementary Material
High-throughput proteogenomics of Ruegeria pomeroyi: seeding a better genomic annotation for the whole marine Roseobacter clade
Joseph A Christie-Oleza, Guylaine Miotello, Jean Armengaud
BMC Genomics. 2012; 13: 73. Published online 2012 February 15. doi: 10.1186/1471-2164-13-73
PMCID:
PMC3305630
Abstract Full Text PDF–472K Supplementary Material
Identification and localisation of the NB-LRR gene family within the potato genome
Florian Jupe, Leighton Pritchard, Graham J Etherington, Katrin MacKenzie, Peter JA Cock, Frank Wright, Sanjeev Kumar Sharma, Dan Bolser, Glenn J Bryan, Jonathan DG Jones, Ingo Hein
BMC Genomics. 2012; 13: 75. Published online 2012 February 15. doi: 10.1186/1471-2164-13-75
PMCID:
PMC3297505
Abstract Full Text PDF–1.0M Supplementary Material
Sexual and asexual oogenesis require the expression of unique and shared sets of genes in the insect Acyrthosiphon pisum
Aurore Gallot, Shuji Shigenobu, Tomomi Hashiyama, Stéphanie Jaubert-Possamai, Denis Tagu
BMC Genomics. 2012; 13: 76. Published online 2012 February 15. doi: 10.1186/1471-2164-13-76
PMCID:
PMC3313892
Abstract Full Text PDF–6.6M Supplementary Material
Comprehensive evaluation of SNP identification with the Restriction Enzyme-based Reduced Representation Library (RRL) method
Ye Du, Hui Jiang, Ying Chen, Cong Li, Meiru Zhao, Jinghua Wu, Yong Qiu, Qibin Li, Xiuqing Zhang
BMC Genomics. 2012; 13: 77. Published online 2012 February 16. doi: 10.1186/1471-2164-13-77
PMCID:
PMC3305556
Abstract Full Text PDF–821K Supplementary Material
Whole-Genome sequencing and genetic variant analysis of a quarter Horse mare
Ryan Doan, Noah D Cohen, Jason Sawyer, Noushin Ghaffari, Charlie D Johnson, Scott V Dindot
BMC Genomics. 2012; 13: 78. Published online 2012 February 17. doi: 10.1186/1471-2164-13-78
PMCID:
PMC3309927
Abstract Full Text PDF–5.8M Supplementary Material
A minimal model of peptide binding predicts ensemble properties of serum antibodies
Victor Greiff, Henning Redestig, Juliane Lück, Nicole Bruni, Atijeh Valai, Susanne Hartmann, Sebastian Rausch, Johannes Schuchhardt, Michal Or-Guil
BMC Genomics. 2012; 13: 79. Published online 2012 February 21. doi: 10.1186/1471-2164-13-79
PMCID:
PMC3311590
Abstract Full Text PDF–450K Supplementary Material
High-throughput SNP genotyping in Cucurbita pepo for map construction and quantitative trait loci mapping
Cristina Esteras, Pedro Gómez, Antonio J Monforte, José Blanca, Nelly Vicente-Dólera, Cristina Roig, Fernando Nuez, Belén Picó
BMC Genomics. 2012; 13: 80. Published online 2012 February 22. doi: 10.1186/1471-2164-13-80
PMCID:
PMC3359225
Abstract Full Text PDF–886K Supplementary Material
Altered gene expression profiles in the hippocampus and prefrontal cortex of type 2 diabetic rats
Omar Abdul-Rahman, Maria Sasvari-Szekely, Agota Ver, Klara Rosta, Bernadett K Szasz, Eva Kereszturi, Gergely Keszler
BMC Genomics. 2012; 13: 81. Published online 2012 February 27. doi: 10.1186/1471-2164-13-81
PMCID:
PMC3299604
Abstract Full Text PDF–392K Supplementary Material
RNA-Seq quantification of the human small airway epithelium transcriptome
Neil R Hackett, Marcus W Butler, Renat Shaykhiev, Jacqueline Salit, Larsson Omberg, Juan L Rodriguez-Flores, Jason G Mezey, Yael Strulovici-Barel, Guoqing Wang, Lukas Didon, Ronald G Crystal
BMC Genomics. 2012; 13: 82. Published online 2012 February 29. doi: 10.1186/1471-2164-13-82
PMCID:
PMC3337229
Abstract Full Text PDF–631K Supplementary Material
Identification and characterization of microRNAs in Phaseolus vulgaris by high-throughput sequencing
Pablo Peláez, Minerva S Trejo, Luis P Iñiguez, Georgina Estrada-Navarrete, Alejandra A Covarrubias, José L Reyes, Federico Sanchez
BMC Genomics. 2012; 13: 83. Published online 2012 March 6. doi: 10.1186/1471-2164-13-83
PMCID:
PMC3359237
Abstract Full Text PDF–1.5M Supplementary Material
C57Bl/6 N mice on a western diet display reduced intestinal and hepatic cholesterol levels despite a plasma hypercholesterolemia
Charles Desmarchelier, Christoph Dahlhoff, Sylvia Keller, Manuela Sailer, Gerhard Jahreis, Hannelore Daniel
BMC Genomics. 2012; 13: 84. Published online 2012 March 6. doi: 10.1186/1471-2164-13-84
PMCID:
PMC3319424
Abstract Full Text PDF–721K Supplementary Material
Comparative genomics reveals evidence of marine adaptation in Salinispora species
Kevin Penn, Paul R Jensen
BMC Genomics. 2012; 13: 86. Published online 2012 March 8. doi: 10.1186/1471-2164-13-86
PMCID:
PMC3314556
Abstract Full Text PDF–3.7M Supplementary Material
Genomic variation in Salmonella enterica core genes for epidemiological typing
Pimlapas Leekitcharoenphon, Oksana Lukjancenko, Carsten Friis, Frank M Aarestrup, David W Ussery
BMC Genomics. 2012; 13: 88. Published online 2012 March 12. doi: 10.1186/1471-2164-13-88
PMCID:
PMC3359268
Abstract Full Text PDF–8.1M Supplementary Material
Genome sequencing of ovine isolates of Mycobacterium avium subspecies paratuberculosis offers insights into host association
John P Bannantine, Chia-wei Wu, Chungyi Hsu, Shiguo Zhou, David C Schwartz, Darrell O Bayles, Michael L Paustian, David P Alt, Srinand Sreevatsan, Vivek Kapur, Adel M Talaat
BMC Genomics. 2012; 13: 89. Published online 2012 March 12. doi: 10.1186/1471-2164-13-89
PMCID:
PMC3337245
Abstract Full Text PDF–8.3M Supplementary Material
De novo assembly and Characterisation of the Transcriptome during seed development, and generation of genic-SSR markers in Peanut (Arachis hypogaea L.)
Jianan Zhang, Shan Liang, Jialei Duan, Jin Wang, Silong Chen, Zengshu Cheng, Qiang Zhang, Xuanqiang Liang, Yurong Li
BMC Genomics. 2012; 13: 90. Published online 2012 March 12. doi: 10.1186/1471-2164-13-90
PMCID:
PMC3350410
Abstract Full Text PDF–781K Supplementary Material
Large-scale functional RNAi screen in C. elegans identifies genes that regulate the dysfunction of mutant polyglutamine neurons
François-Xavier Lejeune, Lilia Mesrob, Frédéric Parmentier, Cedric Bicep, Rafael P Vazquez-Manrique, J Alex Parker, Jean-Philippe Vert, Cendrine Tourette, Christian Neri
BMC Genomics. 2012; 13: 91. Published online 2012 March 13. doi: 10.1186/1471-2164-13-91
PMCID:
PMC3331833
Abstract Full Text PDF–1.8M Supplementary Material
A low protein diet during pregnancy provokes a lasting shift of hepatic expression of genes related to cell cycle throughout ontogenesis in a porcine model
Michael Oster, Eduard Murani, Cornelia C Metges, Siriluck Ponsuksili, Klaus Wimmers
BMC Genomics. 2012; 13: 93. Published online 2012 March 16. doi: 10.1186/1471-2164-13-93
PMCID:
PMC3342123
Abstract Full Text PDF–1.1M
Genome wide expression profiling of two accession of G. herbaceum L. in response to drought
Alok Ranjan, Deepti Nigam, Mehar H Asif, Ruchi Singh, Sanjay Ranjan, Shrikant Mantri, Neha Pandey, Ila Trivedi, Krishan Mohan Rai, Satya N Jena, Bhupendra Koul, Rakesh Tuli, Uday V Pathre, Samir V Sawant
BMC Genomics. 2012; 13: 94. Published online 2012 March 16. doi: 10.1186/1471-2164-13-94
PMCID:
PMC3320563
Abstract Full Text PDF–2.7M Supplementary Material
Transcriptome analysis reveals the time of the fourth round of genome duplication in common carp (Cyprinus carpio)
Jin-Tu Wang, Jiong-Tang Li, Xiao-Feng Zhang, Xiao-Wen Sun
BMC Genomics. 2012; 13: 96. Published online 2012 March 19. doi: 10.1186/1471-2164-13-96
PMCID:
PMC3352309
Abstract Full Text PDF–773K Supplementary Material
Sequence signatures involved in targeting the male-specific lethal complex to X-chromosomal genes in Drosophila melanogaster
Philge Philip, Fredrik Pettersson, Per Stenberg
BMC Genomics. 2012; 13: 97. Published online 2012 March 19. doi: 10.1186/1471-2164-13-97
PMCID:
PMC3355045
Abstract Full Text PDF–1.7M Supplementary Material
Quantitative molecular assessment of chimerism across tissues in marmosets and tamarins
Carolyn G Sweeney, Elizabeth Curran, Susan V Westmoreland, Keith G Mansfield, Eric J Vallender
BMC Genomics. 2012; 13: 98. Published online 2012 March 19. doi: 10.1186/1471-2164-13-98
PMCID:
PMC3337283
Abstract Full Text PDF–414K
A new RNASeq-based reference transcriptome for sugar beet and its application in transcriptome-scale analysis of vernalization and gibberellin responses
Effie S Mutasa-Göttgens, Anagha Joshi, Helen F Holmes, Peter Hedden, Berthold Göttgens
BMC Genomics. 2012; 13: 99. Published online 2012 March 19. doi: 10.1186/1471-2164-13-99
PMCID:
PMC3340327
Abstract Full Text PDF–5.2M Supplementary Material
Genomic survey, expression profile and co-expression network analysis of OsWD40 family in rice
Yidan Ouyang, Xiaolong Huang, Zhanhua Lu, Jialing Yao
BMC Genomics. 2012; 13: 100. Published online 2012 March 20. doi: 10.1186/1471-2164-13-100
PMCID:
PMC3329404
Abstract Full Text PDF–6.5M Supplementary Material
Transcriptome sequencing of field pea and faba bean for discovery and validation of SSR genetic markers
Sukhjiwan Kaur, Luke W Pembleton, Noel OI Cogan, Keith W Savin, Tony Leonforte, Jeffrey Paull, Michael Materne, John W Forster
BMC Genomics. 2012; 13: 104. Published online 2012 March 20. doi: 10.1186/1471-2164-13-104
PMCID:
PMC3352077
Abstract Full Text PDF–2.0M Supplementary Material
Evolutionary forces shaping genomic islands of population differentiation in humans
Tamara Hofer, Matthieu Foll, Laurent Excoffier
BMC Genomics. 2012; 13: 107. Published online 2012 March 22. doi: 10.1186/1471-2164-13-107
PMCID:
PMC3317871
Abstract Full Text PDF–933K Supplementary Material
Deciphering neo-sex and B chromosome evolution by the draft genome of Drosophila albomicans
Qi Zhou, Hong-mei Zhu, Quan-fei Huang, Li Zhao, Guo-jie Zhang, Scott W Roy, Beatriz Vicoso, Zhao-lin Xuan, Jue Ruan, Yue Zhang, Ruo-ping Zhao, Chen Ye, Xiu-qing Zhang, Jun Wang, Wen Wang, Doris Bachtrog
BMC Genomics. 2012; 13: 109. Published online 2012 March 22. doi: 10.1186/1471-2164-13-109
PMCID:
PMC3353239
Abstract Full Text PDF–1.7M Supplementary Material
Evolution of the metabolic and regulatory networks associated with oxygen availability in two phytopathogenic enterobacteria
Lavanya Babujee, Jennifer Apodaca, Venkatesh Balakrishnan, Paul Liss, Patricia J Kiley, Amy O Charkowski, Jeremy D Glasner, Nicole T Perna
BMC Genomics. 2012; 13: 110. Published online 2012 March 22. doi: 10.1186/1471-2164-13-110
PMCID:
PMC3349551
Abstract Full Text PDF–979K Supplementary Material
Annotation of primate miRNAs by high throughput sequencing of small RNA libraries
Michael Dannemann, Birgit Nickel, Esther Lizano, Hernán A Burbano, Janet Kelso
BMC Genomics. 2012; 13: 116. Published online 2012 March 27. doi: 10.1186/1471-2164-13-116
PMCID:
PMC3328248
Abstract Full Text PDF–357K
Expression variation in connected recombinant populations of Arabidopsis thaliana highlights distinct transcriptome architectures
Francisco A Cubillos, Jennifer Yansouni, Hamid Khalili, Sandrine Balzergue, Samira Elftieh, Marie-Laure Martin-Magniette, Yann Serrand, Loïc Lepiniec, Sébastien Baud, Bertrand Dubreucq, Jean-Pierre Renou, Christine Camilleri, Olivier Loudet
BMC Genomics. 2012; 13: 117. Published online 2012 March 27. doi: 10.1186/1471-2164-13-117
PMCID:
PMC3359214
Abstract Full Text PDF–1.5M Supplementary Material
Altered expression of testis-specific genes, piRNAs, and transposons in the silkworm ovary masculinized by a W chromosome mutation
Kahori Hara, Tsuguru Fujii, Yutaka Suzuki, Sumio Sugano, Toru Shimada, Susumu Katsuma, Shinpei Kawaoka
BMC Genomics. 2012; 13: 119. Published online 2012 March 28. doi: 10.1186/1471-2164-13-119
PMCID:
PMC3342102
Abstract Full Text PDF–1.3M
Identification of microRNAs from Amur grape (vitis amurensis Rupr.) by deep sequencing and analysis of microRNA variations with bioinformatics
Chen Wang, Jian Han, Chonghuai Liu, Korir Nicholas Kibet, Emrul Kayesh, Lingfei Shangguan, Xiaoying Li, Jinggui Fang
BMC Genomics. 2012; 13: 122. Published online 2012 March 29. doi: 10.1186/1471-2164-13-122
PMCID:
PMC3353164
Abstract Full Text PDF–1.6M Supplementary Material
A genome-wide study of two-component signal transduction systems in eight newly sequenced mutans streptococci strains
Lifu Song, Padhmanand Sudhakar, Wei Wang, Georg Conrads, Anke Brock, Jibin Sun, Irene Wagner-Döbler, An-Ping Zeng
BMC Genomics. 2012; 13: 128. Published online 2012 April 4. doi: 10.1186/1471-2164-13-128
PMCID:
PMC3353171
Abstract Full Text PDF–3.4M Supplementary Material
Gene expression in Atlantic salmon skin in response to infection with the parasitic copepod Lepeophtheirus salmonis, cortisol implant, and their combination
Aleksei Krasnov, Stanko Skugor, Marijana Todorcevic, Kevin A Glover, Frank Nilsen
BMC Genomics. 2012; 13: 130. Published online 2012 April 5. doi: 10.1186/1471-2164-13-130
PMCID:
PMC3338085
Abstract Full Text PDF–445K Supplementary Material
Transcriptome-wide identification and characterization of miRNAs from Pinus densata
Li-Chuan Wan, Haiyan Zhang, Shanfa Lu, Liang Zhang, Zongbo Qiu, Yuanyuan Zhao, Qing-Yin Zeng, Jinxing Lin
BMC Genomics. 2012; 13: 132. Published online 2012 April 6. doi: 10.1186/1471-2164-13-132
PMCID:
PMC3347991
Abstract Full Text PDF–1.0M Supplementary Material
A Gaijin-like miniature inverted repeat transposable element is mobilized in rice during cell differentiation
Hai-Tao Dong, Lu Zhang, Kang-Le Zheng, Hai-Gen Yao, Jack Chen, Feng-Chi Yu, Xiao-Xing Yu, Bi-Zeng Mao, Dong Zhao, Jian Yao, De-Bao Li
BMC Genomics. 2012; 13: 135. Published online 2012 April 13. doi: 10.1186/1471-2164-13-135
PMCID:
PMC3352178
Abstract Full Text PDF–12M Supplementary Material
Analysis of plant LTR-retrotransposons at the fine-scale family level reveals individual molecular patterns
Douglas S Domingues, Guilherme MQ Cruz, Cushla J Metcalfe, Fabio TS Nogueira, Renato Vicentini, Cristiane de S Alves, Marie-Anne Van Sluys
BMC Genomics. 2012; 13: 137. Published online 2012 April 16. doi: 10.1186/1471-2164-13-137
PMCID:
PMC3352295
Abstract Full Text PDF–1.9M Supplementary Material
Complete genome sequence, lifestyle, and multi-drug resistance of the human pathogen Corynebacterium resistens DSM 45100 isolated from blood samples of a leukemia patient
Jasmin Schröder, Irena Maus, Katja Meyer, Stephanie Wördemann, Jochen Blom, Sebastian Jaenicke, Jessica Schneider, Eva Trost, Andreas Tauch
BMC Genomics. 2012; 13: 141. Published online 2012 April 23. doi: 10.1186/1471-2164-13-141
PMCID:
PMC3350403
Abstract Full Text PDF–2.4M Supplementary Material
A framework genetic map for Miscanthus sinensis from RNAseq-based markers shows recent tetraploidy
Kankshita Swaminathan, Won Byoung Chae, Therese Mitros, Kranthi Varala, Liang Xie, Adam Barling, Katarzyna Glowacka, Megan Hall, Stanislaw Jezowski, Ray Ming, Matthew Hudson, John A Juvik, Daniel S Rokhsar, Stephen P Moose
BMC Genomics. 2012; 13: 142. Published online 2012 April 24. doi: 10.1186/1471-2164-13-142
PMCID:
PMC3355032
Abstract Full Text PDF–2.8M Supplementary Material
Genome-wide host responses against infectious laryngotracheitis virus vaccine infection in chicken embryo lung cells
Jeongyoon Lee, Walter G Bottje, Byung-Whi Kong
BMC Genomics. 2012; 13: 143. Published online 2012 April 24. doi: 10.1186/1471-2164-13-143
PMCID:
PMC3353197
Abstract Full Text PDF–548K Supplementary Material
Characterization of the transcriptome profiles related to globin gene switching during in vitro erythroid maturation
Biaoru Li, Lianghao Ding, Wei Li, Michael D Story, Betty S Pace
BMC Genomics. 2012; 13: 153. Published online 2012 April 26. doi: 10.1186/1471-2164-13-153
PMCID:
PMC3353202
Abstract Full Text PDF–1.0M Supplementary Material
Metabolic classification of microbial genomes using functional probes
Chi-Ching Lee, Wei-Cheng Lo, Szu-Ming Lai, Yi-Ping Phoebe Chen, Chuan Yi Tang, Ping-Chiang Lyu
BMC Genomics. 2012; 13: 157. Published online 2012 April 27. doi: 10.1186/1471-2164-13-157
PMCID:
PMC3355368
Abstract Full Text PDF–10M Supplementary Material

Methodology Articles

Optimizing illumina next-generation sequencing library preparation for extremely at-biased genomes
Samuel O Oyola, Thomas D Otto, Yong Gu, Gareth Maslen, Magnus Manske, Susana Campino, Daniel J Turner, Bronwyn MacInnis, Dominic P Kwiatkowski, Harold P Swerdlow, Michael A Quail
BMC Genomics. 2012; 13: 1. Published online 2012 January 3. doi: 10.1186/1471-2164-13-1
PMCID:
PMC3312816
Abstract Full Text PDF–678K Supplementary Material
Rapid gene-based SNP and haplotype marker development in non-model eukaryotes using 3'UTR sequencing
Tyson Koepke, Scott Schaeffer, Vandhana Krishnan, Derick Jiwan, Artemus Harper, Matthew Whiting, Nnadozie Oraguzie, Amit Dhingra
BMC Genomics. 2012; 13: 18. Published online 2012 January 12. doi: 10.1186/1471-2164-13-18
PMCID:
PMC3293726
Abstract Full Text PDF–462K Supplementary Material
Sequence based polymorphic (SBP) marker technology for targeted genomic regions: its application in generating a molecular map of the Arabidopsis thaliana genome
Binod B Sahu, Rishi Sumit, Subodh K Srivastava, Madan K Bhattacharyya
BMC Genomics. 2012; 13: 20. Published online 2012 January 13. doi: 10.1186/1471-2164-13-20
PMCID:
PMC3323429
Abstract Full Text PDF–407K Supplementary Material
Discovery of novel variants in genotyping arrays improves genotype retention and reduces ascertainment bias
John P Didion, Hyuna Yang, Keith Sheppard, Chen-Ping Fu, Leonard McMillan, Fernando Pardo-Manuel de Villena, Gary A Churchill
BMC Genomics. 2012; 13: 34. Published online 2012 January 19. doi: 10.1186/1471-2164-13-34
PMCID:
PMC3305361
Abstract Full Text PDF–2.1M Supplementary Material
Pair-barcode high-throughput sequencing for large-scale multiplexed sample analysis
Jing Tu, Qinyu Ge, Shengqin Wang, Lei Wang, Beili Sun, Qi Yang, Yunfei Bai, Zuhong Lu
BMC Genomics. 2012; 13: 43. Published online 2012 January 25. doi: 10.1186/1471-2164-13-43
PMCID:
PMC3284879
Abstract Full Text PDF–2.4M Supplementary Material
Whole Genome Profiling provides a robust framework for physical mapping and sequencing in the highly complex and repetitive wheat genome
Romain Philippe, Frédéric Choulet, Etienne Paux, Jan van Oeveren, Jifeng Tang, Alexander HJ Wittenberg, Antoine Janssen, Michiel JT van Eijk, Keith Stormo, Adriana Alberti, Patrick Wincker, Eduard Akhunov, Edwin van der Vossen, Catherine Feuillet
BMC Genomics. 2012; 13: 47. Published online 2012 January 30. doi: 10.1186/1471-2164-13-47
PMCID:
PMC3311077
Abstract Full Text PDF–627K Supplementary Material
Combining evidence of selection with association analysis increases power to detect regions influencing complex traits in dairy cattle
Hermann Schwarzenbacher, Marlies Dolezal, Krzysztof Flisikowski, Franz Seefried, Christine Wurmser, Christian Schlötterer, Ruedi Fries
BMC Genomics. 2012; 13: 48. Published online 2012 January 30. doi: 10.1186/1471-2164-13-48
PMCID:
PMC3305582
Abstract Full Text PDF–1.2M Supplementary Material
Peptide markers of aminoacyl tRNA synthetases facilitate taxa counting in metagenomic data
Erez Persi, Uri Weingart, Shiri Freilich, David Horn
BMC Genomics. 2012; 13: 65. Published online 2012 February 10. doi: 10.1186/1471-2164-13-65
PMCID:
PMC3319421
Abstract Full Text PDF–966K Supplementary Material
Reference genome-independent assessment of mutation density using restriction enzyme-phased sequencing
Jennifer Monson-Miller, Diana C Sanchez-Mendez, Joseph Fass, Isabelle M Henry, Thomas H Tai, Luca Comai
BMC Genomics. 2012; 13: 72. Published online 2012 February 14. doi: 10.1186/1471-2164-13-72
PMCID:
PMC3305632
Abstract Full Text PDF–1.2M
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