Genome Biology | Volume 10 Issue 11

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	Volume 10 Issue 11
	Comment
	Comment Advice and dissent Gregory A Petsko Genome Biology 2009, 10:113 (24 November 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Greg Petsko reflects on what can happen when governments and their scientific advisors disagree.
	Review
	Minireview Ubiquitous RNA-dependent RNA polymerase and gene silencing James A Birchler Genome Biology 2009, 10:243 (26 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The discovery of a ubiquitous RNA-dependent RNA polymerase raises new questions about small RNA silencing mechanisms.
	Minireview Panmixia postponed: ancestry-related assortative mating in contemporary human populations Andrew S Burrell, Todd R Disotell Genome Biology 2009, 10:245 (27 November 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A population study using human ancestry-informative markers reveals that the choice of a mate tends to be non-random in regard to specific ancestries within the group.
	Minireview Transcriptional regulation of metastatic [Id]entity by KLF17 Marcin P Iwanicki, Joan S Brugge Genome Biology 2009, 10:244 (30 November 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new player identified in the regulation of epithelial-to-mesenchyme transition, cell invasiveness and metastasis.
	Opinion Evolution, ecology and the engineered organism: lessons for synthetic biology Jeffrey M Skerker, Julius B Lucks, Adam P Arkin Genome Biology 2009, 10:114 (30 November 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An understanding of evolution and ecology will be critical to the success of synthetic biology.
	Report
	Meeting report Biology inspires engineering Reine Byun, Attila Becskei Genome Biology 2009, 10:317 (19 November 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the Cold Spring Harbor Laboratory/Wellcome Trust Meeting on Engineering Principles in Biology, Cambridge, UK, 14-16 October 2009.
	Research
	Research Divergence of exonic splicing elements after gene duplication and the impact on gene structures Zhenguo Zhang, Li Zhou, Ping Wang, Yang Liu, Xianfeng Chen, Landian Hu, Xiangyin Kong Genome Biology 2009, 10:R120 (2 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of human exonic splicing elements in duplicated genes reveals their important role in the generation of new gene structures.
	Research Regulatory interdependence of myeloid transcription factors revealed by Matrix RNAi analysis Yasuhiro Tomaru, Christophe Simon, Alistair RR Forrest, Hisashi Miura, Atsutaka Kubosaki, Yoshihide Hayashizaki, Masanori Suzuki Genome Biology 2009, 10:R121 (2 November 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The knockdown of 78 transcription factors in differentiating human THP-1 cells using matrix RNAi reveals their interdependence
	Research Genome-wide analysis reveals rapid and dynamic changes in miRNA and siRNA sequence and expression during ovule and fiber development in allotetraploid cotton (Gossypium hirsutum L.) Mingxiong Pang, Andrew W Woodward, Vikram Agarwal, Xueying Guan, Misook Ha, Vanitharani Ramachandran, Xuemei Chen, Barbara A Triplett, David M Stelly, Z Jeffrey Chen Genome Biology 2009, 10:R122 (4 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Rapid and dynamic changes in the expression of small RNAs are seen during ovule and fiber development in allotetraploid cotton.
	Research Serum-dependent transcriptional networks identify distinct functional roles for H-Ras and N-Ras during initial stages of the cell cycle Esther Castellano, Carmen Guerrero, Alejandro Núñez, Javier De Las Rivas, Eugenio Santos Genome Biology 2009, 10:R123 (6 November 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Transcriptional and functional analysis reveals that the H-Ras and N-Ras isoforms have different roles in the initial phases of the mouse cell cycle
	Research Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness Ana C Marques, Chris P Ponting Genome Biology 2009, 10:R124 (6 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comparative evolutionary analysis of two mouse long noncoding RNA libraries reveals a much larger pool of noncoding RNAs remains yet to be discovered.
	Research High resolution discovery and confirmation of copy number variants in 90 Yoruba Nigerians Hajime Matsuzaki, Pei-Hua Wang, Jing Hu, Rich Rava, Glenn K Fu Genome Biology 2009, 10:R125 (9 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Most microRNAs have a stronger inhibitory effect in estrogen receptor-negative than in estrogen receptor-positive breast cancers.
	Research Construction of a high-resolution genetic linkage map and comparative genome analysis for the reef-building coral Acropora millepora Shi Wang, Lingling Zhang, Eli Meyer, Mikhail V Matz Genome Biology 2009, 10:R126 (10 November 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A high-resolution genetic linkage map for the coral Acropora millepora is constructed and compared with other metazoan genomes, revealing syntenic blocks.
	Research Genomic transcriptional profiling identifies a candidate blood biomarker signature for the diagnosis of septicemic melioidosis Rungnapa Pankla, Surachat Buddhisa, Matthew Berry, Derek M Blankenship, Gregory J Bancroft, Jacques Banchereau, Ganjana Lertmemongkolchai, Damien Chaussabel Genome Biology 2009, 10:R127 (10 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A diagnostic signature for sepsis caused by Burkholderia pseudomallei infection was identified from transcriptional profiling of the blood of septicemia patients.
	Research Differential binding and co-binding pattern of FOXA1 and FOXA3 and their relation to H3K4me3 in HepG2 cells revealed by ChIP-seq Mehdi Motallebipour, Adam Ameur, Madhu Sudhan Reddy Bysani, Kalicharan Patra, Ola Wallerman, Jonathan Mangion, Melissa A Barker, Kevin J McKernan, Jan Komorowski, Claes Wadelius Genome Biology 2009, 10:R129 (17 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary FOXA1 and FOXA3 binding patterns in HepG2 cells, together with their possible molecular interactions with FOXA2 and each other, are revealed by ChIP-seq.
	Research CTCF binding site classes exhibit distinct evolutionary, genomic, epigenomic and transcriptomic features Kobby Essien, Sebastien Vigneau, Sofia Apreleva, Larry N Singh, Marisa S Bartolomei, Sridhar Hannenhalli Genome Biology 2009, 10:R131 (18 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary CTCF DNA binding sites are classified into distinct functional classes, with distinct biological properties, shedding light on the differing functional roles of CTCF binding.
	Research Ancestry-related assortative mating in Latino populations Neil Risch, Shweta Choudhry, Marc Via, Analabha Basu, Ronnie Sebro, Celeste Eng, Kenneth Beckman, Shannon Thyne, Rocio Chapela, Jose R Rodriguez-Santana, William Rodriguez-Cintron, Pedro C Avila, Elad Ziv, Esteban Gonzalez Burchard Genome Biology 2009, 10:R132 (20 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Examination of ancestry-informative genetic markers shows that Puerto Rican and Mexican populations have shown strong assortative mating that continues to this day.
	Research Expansion of the human mitochondrial proteome by intra- and inter-compartmental protein duplication Radek Szklarczyk, Martijn A Huynen Genome Biology 2009, 10:R135 (24 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The human mitochondrial proteome is shown to have expanded due to duplication of protein encoding genes and re-localization of these duplicated proteins.
	Method Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays Tatiana Popova, Elodie Manié, Dominique Stoppa-Lyonnet, Guillem Rigaill, Emmanuel Barillot, Marc Stern Genome Biology 2009, 10:R128 (11 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary GAP, a method for analyzing complex cancer genome profiles from SNP arrays, performs well even with poor quality data and rearranged genomes
	Method COMIT: identification of noncoding motifs under selection in coding sequences Deniz Kural, Yang Ding, Jiantao Wu, Alicia M Korpi, Jeffrey H Chuang Genome Biology 2009, 10:R133 (20 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary COMIT is presented; an algorithm for detecting functional non-coding motifs in coding regions, separating nucleotide and amino acid effects.
	Software BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources Chunlei Wu, Camilo Orozco, Jason Boyer, Marc Leglise, James Goodale, Serge Batalov, Christopher L Hodge, James Haase, Jeff Janes, Jon W Huss, Andrew I Su Genome Biology 2009, 10:R130 (17 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary BioGPS is a community based customisable gene annotation portal bringing together gene annotation resources on to a single platform.
	Software Searching for SNPs with cloud computing Ben Langmead, Michael C Schatz, Jimmy Lin, Mihai Pop, Steven L Salzberg Genome Biology 2009, 10:R134 (20 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Novel software utilizing cloud computing technology to cost-effectively align and map SNPs from a human genome in three.

	Volume 10 Issue 11
	Comment
	Comment Advice and dissent Gregory A Petsko Genome Biology 2009, 10:113 (24 November 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Greg Petsko reflects on what can happen when governments and their scientific advisors disagree.
	Review
	Minireview Ubiquitous RNA-dependent RNA polymerase and gene silencing James A Birchler Genome Biology 2009, 10:243 (26 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The discovery of a ubiquitous RNA-dependent RNA polymerase raises new questions about small RNA silencing mechanisms.
	Minireview Panmixia postponed: ancestry-related assortative mating in contemporary human populations Andrew S Burrell, Todd R Disotell Genome Biology 2009, 10:245 (27 November 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A population study using human ancestry-informative markers reveals that the choice of a mate tends to be non-random in regard to specific ancestries within the group.
	Minireview Transcriptional regulation of metastatic [Id]entity by KLF17 Marcin P Iwanicki, Joan S Brugge Genome Biology 2009, 10:244 (30 November 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new player identified in the regulation of epithelial-to-mesenchyme transition, cell invasiveness and metastasis.
	Opinion Evolution, ecology and the engineered organism: lessons for synthetic biology Jeffrey M Skerker, Julius B Lucks, Adam P Arkin Genome Biology 2009, 10:114 (30 November 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary An understanding of evolution and ecology will be critical to the success of synthetic biology.
	Report
	Meeting report Biology inspires engineering Reine Byun, Attila Becskei Genome Biology 2009, 10:317 (19 November 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A report of the Cold Spring Harbor Laboratory/Wellcome Trust Meeting on Engineering Principles in Biology, Cambridge, UK, 14-16 October 2009.
	Research
	Research Divergence of exonic splicing elements after gene duplication and the impact on gene structures Zhenguo Zhang, Li Zhou, Ping Wang, Yang Liu, Xianfeng Chen, Landian Hu, Xiangyin Kong Genome Biology 2009, 10:R120 (2 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary An analysis of human exonic splicing elements in duplicated genes reveals their important role in the generation of new gene structures.
	Research Regulatory interdependence of myeloid transcription factors revealed by Matrix RNAi analysis Yasuhiro Tomaru, Christophe Simon, Alistair RR Forrest, Hisashi Miura, Atsutaka Kubosaki, Yoshihide Hayashizaki, Masanori Suzuki Genome Biology 2009, 10:R121 (2 November 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The knockdown of 78 transcription factors in differentiating human THP-1 cells using matrix RNAi reveals their interdependence
	Research Genome-wide analysis reveals rapid and dynamic changes in miRNA and siRNA sequence and expression during ovule and fiber development in allotetraploid cotton (Gossypium hirsutum L.) Mingxiong Pang, Andrew W Woodward, Vikram Agarwal, Xueying Guan, Misook Ha, Vanitharani Ramachandran, Xuemei Chen, Barbara A Triplett, David M Stelly, Z Jeffrey Chen Genome Biology 2009, 10:R122 (4 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Rapid and dynamic changes in the expression of small RNAs are seen during ovule and fiber development in allotetraploid cotton.
	Research Serum-dependent transcriptional networks identify distinct functional roles for H-Ras and N-Ras during initial stages of the cell cycle Esther Castellano, Carmen Guerrero, Alejandro Núñez, Javier De Las Rivas, Eugenio Santos Genome Biology 2009, 10:R123 (6 November 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Transcriptional and functional analysis reveals that the H-Ras and N-Ras isoforms have different roles in the initial phases of the mouse cell cycle
	Research Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness Ana C Marques, Chris P Ponting Genome Biology 2009, 10:R124 (6 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A comparative evolutionary analysis of two mouse long noncoding RNA libraries reveals a much larger pool of noncoding RNAs remains yet to be discovered.
	Research High resolution discovery and confirmation of copy number variants in 90 Yoruba Nigerians Hajime Matsuzaki, Pei-Hua Wang, Jing Hu, Rich Rava, Glenn K Fu Genome Biology 2009, 10:R125 (9 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Most microRNAs have a stronger inhibitory effect in estrogen receptor-negative than in estrogen receptor-positive breast cancers.
	Research Construction of a high-resolution genetic linkage map and comparative genome analysis for the reef-building coral Acropora millepora Shi Wang, Lingling Zhang, Eli Meyer, Mikhail V Matz Genome Biology 2009, 10:R126 (10 November 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A high-resolution genetic linkage map for the coral Acropora millepora is constructed and compared with other metazoan genomes, revealing syntenic blocks.
	Research Genomic transcriptional profiling identifies a candidate blood biomarker signature for the diagnosis of septicemic melioidosis Rungnapa Pankla, Surachat Buddhisa, Matthew Berry, Derek M Blankenship, Gregory J Bancroft, Jacques Banchereau, Ganjana Lertmemongkolchai, Damien Chaussabel Genome Biology 2009, 10:R127 (10 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary A diagnostic signature for sepsis caused by Burkholderia pseudomallei infection was identified from transcriptional profiling of the blood of septicemia patients.
	Research Differential binding and co-binding pattern of FOXA1 and FOXA3 and their relation to H3K4me3 in HepG2 cells revealed by ChIP-seq Mehdi Motallebipour, Adam Ameur, Madhu Sudhan Reddy Bysani, Kalicharan Patra, Ola Wallerman, Jonathan Mangion, Melissa A Barker, Kevin J McKernan, Jan Komorowski, Claes Wadelius Genome Biology 2009, 10:R129 (17 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary FOXA1 and FOXA3 binding patterns in HepG2 cells, together with their possible molecular interactions with FOXA2 and each other, are revealed by ChIP-seq.
	Research CTCF binding site classes exhibit distinct evolutionary, genomic, epigenomic and transcriptomic features Kobby Essien, Sebastien Vigneau, Sofia Apreleva, Larry N Singh, Marisa S Bartolomei, Sridhar Hannenhalli Genome Biology 2009, 10:R131 (18 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary CTCF DNA binding sites are classified into distinct functional classes, with distinct biological properties, shedding light on the differing functional roles of CTCF binding.
	Research Ancestry-related assortative mating in Latino populations Neil Risch, Shweta Choudhry, Marc Via, Analabha Basu, Ronnie Sebro, Celeste Eng, Kenneth Beckman, Shannon Thyne, Rocio Chapela, Jose R Rodriguez-Santana, William Rodriguez-Cintron, Pedro C Avila, Elad Ziv, Esteban Gonzalez Burchard Genome Biology 2009, 10:R132 (20 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Examination of ancestry-informative genetic markers shows that Puerto Rican and Mexican populations have shown strong assortative mating that continues to this day.
	Research Expansion of the human mitochondrial proteome by intra- and inter-compartmental protein duplication Radek Szklarczyk, Martijn A Huynen Genome Biology 2009, 10:R135 (24 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The human mitochondrial proteome is shown to have expanded due to duplication of protein encoding genes and re-localization of these duplicated proteins.
	Method Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays Tatiana Popova, Elodie Manié, Dominique Stoppa-Lyonnet, Guillem Rigaill, Emmanuel Barillot, Marc Stern Genome Biology 2009, 10:R128 (11 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary GAP, a method for analyzing complex cancer genome profiles from SNP arrays, performs well even with poor quality data and rearranged genomes
	Method COMIT: identification of noncoding motifs under selection in coding sequences Deniz Kural, Yang Ding, Jiantao Wu, Alicia M Korpi, Jeffrey H Chuang Genome Biology 2009, 10:R133 (20 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary COMIT is presented; an algorithm for detecting functional non-coding motifs in coding regions, separating nucleotide and amino acid effects.
	Software BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources Chunlei Wu, Camilo Orozco, Jason Boyer, Marc Leglise, James Goodale, Serge Batalov, Christopher L Hodge, James Haase, Jeff Janes, Jon W Huss, Andrew I Su Genome Biology 2009, 10:R130 (17 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary BioGPS is a community based customisable gene annotation portal bringing together gene annotation resources on to a single platform.
	Software Searching for SNPs with cloud computing Ben Langmead, Michael C Schatz, Jimmy Lin, Mihai Pop, Steven L Salzberg Genome Biology 2009, 10:R134 (20 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Novel software utilizing cloud computing technology to cost-effectively align and map SNPs from a human genome in three.

Explore Genome Biology

Articles

Volume 10 Issue 11

Comment

Review

Report

Research