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		Question and Answer Q&A: What is regeneration, and why look to planarians for answers? Alejandro Sánchez Alvarado BMC Biology 2012, 10:88 (8 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary What controls regeneration? Alejandro Sanchez Alvarado explores this old question in biology in a Q&A explaining what we understand from planarians - non-parasitic flatworms all of whose tissues can regenerate.
		Commentary In search of noise-induced bimodality Kyung Kim, Herbert M Sauro BMC Biology 2012, 10:89 (7 November 2012) Abstract \| Full text \| PDF \| PubMed
		Comment From taxonomic literature to cybertaxonomic content Jeremy Miller, Torsten Dikow, Donat Agosti, Guido Sautter, Terry Catapano, Lyubomir Penev, ZhiQiang Zhang, Dean Pentcheff, Richard Pyle, Stan Blum, Cynthia Parr, Chris Freeland, Tom Garnett, Linda S Ford, Burgert Muller, Leo Smith, Ginger Strader, Teodor Georgiev, Laurence Bénichou BMC Biology 2012, 10:87 (31 October 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Hot on the heels of the ICZN's decision to allow species descriptions to be filed electronically, Miller and colleagues argue for a concerted effort towards integrating existing taxonomic content by journals' semantic tagging of legacy and contemporary literature.
		Research article Multiparameter behavioral profiling reveals distinct thermal response regimes in Caenorhabditis elegans Rajarshi Ghosh, Aylia Mohammadi, Leonid Kruglyak, William S Ryu BMC Biology 2012, 10:85 (31 October 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary By developing a novel assay to quantitate C elegans thermal avoidance behavior, William Ryu and colleagues discovered that different genes are utilized to provide the same phenotypic response, depending on the severity of the applied stimulus.
		Commentary Chromatin roadblocks to reprogramming 50 years on Peter J Skene, Steven Henikoff BMC Biology 2012, 10:83 (29 October 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary This year, John Gurdon, with Shinya Yamanaka, won the Nobel Prize in Physiology or Medicine for the discovery that nuclei from adult cells can be reprogrammed to an undifferentiated state. In a commentary on a paper in Epigenetics & Chromatin from John Gurdon and colleagues, Skene and Henikoff explain how the variant histone H3.3 links the findings of the two prizewinners.
		Research article A spruce gene map infers ancient plant genome reshuffling and subsequent slow evolution in the gymnosperm lineage leading to extant conifers Nathalie Pavy, Betty Pelgas, Jérôme Laroche, Philippe Rigault, Nathalie Isabel, Jean Bousquet BMC Biology 2012, 10:84 (26 October 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Software MESSA: MEta-Server for protein Sequence Analysis Qian Cong, Nick V Grishin BMC Biology 2012, 10:82 (2 October 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Using amalgamated sequence alignments to generate information about local sequence properties, 3D structure and protein function, the new meta-server MESSA provides an integrated, holistic view of proteins via a user-friendly interface.
		Research article Evidence for gill slits and a pharynx in Cambrian vetulicolians: implications for the early evolution of deuterostomes Qiang Ou, Simon Morris, Jian Han, Zhifei Zhang, Jianni Liu, Ailin Chen, Xingliang Zhang, Degan Shu BMC Biology 2012, 10:81 (2 October 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The correct phylogenetic position of vetulicolians is a longstanding paleontological controversy. Here, Degan Shu and colleagues present new fossil findings supporting the placement of this enigmatic Cambrian taxon within the deuterostomes.
		Commentary Cambrian problematica and the diversification of deuterostomes Andrew B Smith BMC Biology 2012, 10:79 (2 October 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Commenting on new fossil findings from the ancient vetulicolian clade, Andrew Smith discusses how far we can - or sometimes can't - make generalizations from fossil taxa to the ancestors of existing species.
		Methodology article Rapid production of antigen-specific monoclonal antibodies from a variety of animals Nobuyuki Kurosawa, Megumi Yoshioka, Rika Fujimoto, Fuminori Yamagishi, Masaharu Isobe BMC Biology 2012, 10:80 (28 September 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Using a fluorescent dye to label the greatly expanded endoplasmic reticulum characteristic of antibody-secreting cells, Kurosawa and colleagues demonstrate how monoclonal antibodies can be produced from a variety of immunized animals in just one week.
		Commentary Autophagy impairment: a crossroad between neurodegeneration and tauopathies Melissa Nassif, Claudio Hetz BMC Biology 2012, 10:78 (21 September 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A connection between autophagy impairment and Tau pathology of the kind seen in Alzheimer's is suggested by research published in Molecular Neurodegeneration. Nassif and Hetz discuss how this adds to emerging evidence for defective autophagy contributing to neurodegenerative disease.
		Methodology article Conditional gene expression systems in the transgenic rat brain Kai Schönig, Tillmann Weber, Ariana Frömmig, Lena Wendler, Brigitte Pesold, Dominik Djandji, Hermann Bujard, Dusan Bartsch BMC Biology 2012, 10:77 (3 September 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The advantages of rats over mice for biomedical research have to date been offset by a dearth of proven methods for their genetic manipulation. Addressing this deficit, Bartsch and coauthors develop transgenic rats with inducible reporter gene expression in forebrain neurons.
		Editorial What is wrong with this picture? Miranda Robertson BMC Biology 2012, 10:76 (3 September 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary BMC Biology has always acknowledged that the phylogeny encompassed in its iconic microcell is an artistic distortion of the reality, but had not realized it is actually wrong. Miranda Robertson explains in a short editorial, and invites further corrections.
		Commentary Different noses for different mice and men Andreas Keller BMC Biology 2012, 10:75 (21 August 2012) Abstract \| Full text \| PDF \| PubMed \| 1 comment \| Editor’s summary The astounding genetic diversity underlying chemoreception in both mice and men is explored in two articles in BMC Genomics. Andreas Keller discusses how this diversity evolved, and the consequences of each nose being different.
		Correction A novel deconvolution method for modeling UDP-N-acetyl-D-glucosamine biosynthetic pathways based on ¹³C mass isotopologue profiles under non-steady-state conditions Hunter NB Moseley, Andrew N Lane, Alex C Belshoff, Richard M Higashi, Teresa WM Fan BMC Biology 2012, 10:74 (17 August 2012) Abstract \| Full text \| PDF \| PubMed
		Commentary Movement adds bite to the evolutionary morphology of mammalian teeth P David Polly BMC Biology 2012, 10:69 (16 August 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The need for teeth to function effectively imposes constraints upon their morphological evolution. David Polly discusses research in BMC Evolutionary Biology that emphasizes mandibular movement as a key quantitative feature influencing the evolution of tooth shape.
		Research article TWIST1 associates with NF-κB subunit RELA via carboxyl-terminal WR domain to promote cell autonomous invasion through IL8 production Shan Li, Stephen E Kendall, Raquel Raices, James Finlay, Maricela Covarrubias, Zheng Liu, Gina Lowe, Yu-Huey Lin, Yuan Teh, Victoria Leigh, Simi Dhillon, Steven Flanagan, Karen S Aboody, Carlotta A Glackin BMC Biology 2012, 10:73 (14 August 2012) Abstract \| Full text \| PDF \| PubMed
		Research article A novel Rho-dependent pathway that drives interaction of fascin-1 with p-Lin-11/Isl-1/Mec-3 kinase (LIMK) 1/2 to promote fascin-1/actin binding and filopodia stability Asier Jayo, Maddy Parsons, Josephine C Adams BMC Biology 2012, 10:72 (10 August 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The actin-binding protein fascin is important for cell migration and its up-regulation is implicated in metastasis in several human carcinomas. Adams and colleagues visualize a direct interaction between fascin and LIM kinase 1/2, Rho-activated kinases, which regulate the stability of filopodia.
		Research article Untangling the evolution of Rab G proteins: implications of a comprehensive genomic analysis Tobias H Klöpper, Nickias Kienle, Dirk Fasshauer, Sean Munro BMC Biology 2012, 10:71 (8 August 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The functional complexity made possible by the proteins that direct traffic between the internal membranes of eukaryotic cells lies at the heart of metazoan evolution. Sean Munro and colleagues trace the Rab family of membrane traffic proteins to its evolutionary roots.
		Commentary The Rabs: A family at the root of metazoan evolution Harald Stenmark BMC Biology 2012, 10:68 (8 August 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Harald Stenmark explains the interest in the phylogenetic analysis of Rab GTPases reported in a paper in BMC Biology, and sketches (literally) the diversity of membrane transport functions that correspond to the six functional groups proposed.
		Correction Rapid sympatric ecological differentiation of crater lake cichlid fishes within historic times Kathryn R Elmer, Topi K Lehtonen, Andreas F Kautt, Chris Harrod, Axel Meyer BMC Biology 2012, 10:70 (7 August 2012) Abstract \| Full text \| PDF \| PubMed
		Research article Excessive folate synthesis limits lifespan in the C. elegans: E. coli aging model Bhupinder Virk, Gonçalo Correia, David P Dixon, Inna Feyst, Jie Jia, Nikolin Oberleitner, Zoe Briggs, Emily Hodge, Robert Edwards, John Ward, David Gems, David Weinkove BMC Biology 2012, 10:67 (31 July 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary David Weinkove and colleagues report an accidental discovery in C. elegans that has led them to a series of studies implicating folate in excess of needs in limiting lifespan, with interesting hints from the effects of sulfonamide drugs that the same may apply to mammals.
		Commentary Folate status of gut microbiome affects Caenorhabditis elegans lifespan Theresa PT Nguyen, Catherine F Clarke BMC Biology 2012, 10:66 (31 July 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Commenting on a recent report in BMC Biology on an adventitious discovery in nematode worms, Theresa Nguyen and Catherine Clarke speculate on the implications for human lifespan of folate supplementation and the effects of sulfonamide drugs on the microbiome.
		Research article Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria) Ylenia Chiari, Vincent Cahais, Nicolas Galtier, Frédéric Delsuc BMC Biology 2012, 10:65 (27 July 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Turtles have traditionally been hard to place taxonomically because of their unique morphology, and recent research based on microRNA has stirred the pot once again. Contrary to that work, phylogenomic analysis of a large new sequence data set adds strong support to the previous conclusion that turtles' closest evolutionary relatives are birds and crocodiles.
		Commentary Amniote phylogeny and the position of turtles S Blair Hedges BMC Biology 2012, 10:64 (27 July 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Commenting on research on the disputed evolutionary placement of turtles, Blair Hedges discusses how integration of data from different sources – DNA, morphology, and biogeography – can help to resolve evolutionary disputes.

	All
		Question and Answer Q&A: What is regeneration, and why look to planarians for answers? Alejandro Sánchez Alvarado BMC Biology 2012, 10:88 (8 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary What controls regeneration? Alejandro Sanchez Alvarado explores this old question in biology in a Q&A explaining what we understand from planarians - non-parasitic flatworms all of whose tissues can regenerate.
		Commentary In search of noise-induced bimodality Kyung Kim, Herbert M Sauro BMC Biology 2012, 10:89 (7 November 2012) Abstract \| Full text \| PDF \| PubMed
		Comment From taxonomic literature to cybertaxonomic content Jeremy Miller, Torsten Dikow, Donat Agosti, Guido Sautter, Terry Catapano, Lyubomir Penev, ZhiQiang Zhang, Dean Pentcheff, Richard Pyle, Stan Blum, Cynthia Parr, Chris Freeland, Tom Garnett, Linda S Ford, Burgert Muller, Leo Smith, Ginger Strader, Teodor Georgiev, Laurence Bénichou BMC Biology 2012, 10:87 (31 October 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Hot on the heels of the ICZN's decision to allow species descriptions to be filed electronically, Miller and colleagues argue for a concerted effort towards integrating existing taxonomic content by journals' semantic tagging of legacy and contemporary literature.
		Research article Multiparameter behavioral profiling reveals distinct thermal response regimes in Caenorhabditis elegans Rajarshi Ghosh, Aylia Mohammadi, Leonid Kruglyak, William S Ryu BMC Biology 2012, 10:85 (31 October 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary By developing a novel assay to quantitate C elegans thermal avoidance behavior, William Ryu and colleagues discovered that different genes are utilized to provide the same phenotypic response, depending on the severity of the applied stimulus.
		Commentary Chromatin roadblocks to reprogramming 50 years on Peter J Skene, Steven Henikoff BMC Biology 2012, 10:83 (29 October 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary This year, John Gurdon, with Shinya Yamanaka, won the Nobel Prize in Physiology or Medicine for the discovery that nuclei from adult cells can be reprogrammed to an undifferentiated state. In a commentary on a paper in Epigenetics & Chromatin from John Gurdon and colleagues, Skene and Henikoff explain how the variant histone H3.3 links the findings of the two prizewinners.
		Research article A spruce gene map infers ancient plant genome reshuffling and subsequent slow evolution in the gymnosperm lineage leading to extant conifers Nathalie Pavy, Betty Pelgas, Jérôme Laroche, Philippe Rigault, Nathalie Isabel, Jean Bousquet BMC Biology 2012, 10:84 (26 October 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Software MESSA: MEta-Server for protein Sequence Analysis Qian Cong, Nick V Grishin BMC Biology 2012, 10:82 (2 October 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Using amalgamated sequence alignments to generate information about local sequence properties, 3D structure and protein function, the new meta-server MESSA provides an integrated, holistic view of proteins via a user-friendly interface.
		Research article Evidence for gill slits and a pharynx in Cambrian vetulicolians: implications for the early evolution of deuterostomes Qiang Ou, Simon Morris, Jian Han, Zhifei Zhang, Jianni Liu, Ailin Chen, Xingliang Zhang, Degan Shu BMC Biology 2012, 10:81 (2 October 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The correct phylogenetic position of vetulicolians is a longstanding paleontological controversy. Here, Degan Shu and colleagues present new fossil findings supporting the placement of this enigmatic Cambrian taxon within the deuterostomes.
		Commentary Cambrian problematica and the diversification of deuterostomes Andrew B Smith BMC Biology 2012, 10:79 (2 October 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Commenting on new fossil findings from the ancient vetulicolian clade, Andrew Smith discusses how far we can - or sometimes can't - make generalizations from fossil taxa to the ancestors of existing species.
		Methodology article Rapid production of antigen-specific monoclonal antibodies from a variety of animals Nobuyuki Kurosawa, Megumi Yoshioka, Rika Fujimoto, Fuminori Yamagishi, Masaharu Isobe BMC Biology 2012, 10:80 (28 September 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Using a fluorescent dye to label the greatly expanded endoplasmic reticulum characteristic of antibody-secreting cells, Kurosawa and colleagues demonstrate how monoclonal antibodies can be produced from a variety of immunized animals in just one week.
		Commentary Autophagy impairment: a crossroad between neurodegeneration and tauopathies Melissa Nassif, Claudio Hetz BMC Biology 2012, 10:78 (21 September 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A connection between autophagy impairment and Tau pathology of the kind seen in Alzheimer's is suggested by research published in Molecular Neurodegeneration. Nassif and Hetz discuss how this adds to emerging evidence for defective autophagy contributing to neurodegenerative disease.
		Methodology article Conditional gene expression systems in the transgenic rat brain Kai Schönig, Tillmann Weber, Ariana Frömmig, Lena Wendler, Brigitte Pesold, Dominik Djandji, Hermann Bujard, Dusan Bartsch BMC Biology 2012, 10:77 (3 September 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The advantages of rats over mice for biomedical research have to date been offset by a dearth of proven methods for their genetic manipulation. Addressing this deficit, Bartsch and coauthors develop transgenic rats with inducible reporter gene expression in forebrain neurons.
		Editorial What is wrong with this picture? Miranda Robertson BMC Biology 2012, 10:76 (3 September 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary BMC Biology has always acknowledged that the phylogeny encompassed in its iconic microcell is an artistic distortion of the reality, but had not realized it is actually wrong. Miranda Robertson explains in a short editorial, and invites further corrections.
		Commentary Different noses for different mice and men Andreas Keller BMC Biology 2012, 10:75 (21 August 2012) Abstract \| Full text \| PDF \| PubMed \| 1 comment \| Editor’s summary The astounding genetic diversity underlying chemoreception in both mice and men is explored in two articles in BMC Genomics. Andreas Keller discusses how this diversity evolved, and the consequences of each nose being different.
		Correction A novel deconvolution method for modeling UDP-N-acetyl-D-glucosamine biosynthetic pathways based on ¹³C mass isotopologue profiles under non-steady-state conditions Hunter NB Moseley, Andrew N Lane, Alex C Belshoff, Richard M Higashi, Teresa WM Fan BMC Biology 2012, 10:74 (17 August 2012) Abstract \| Full text \| PDF \| PubMed
		Commentary Movement adds bite to the evolutionary morphology of mammalian teeth P David Polly BMC Biology 2012, 10:69 (16 August 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The need for teeth to function effectively imposes constraints upon their morphological evolution. David Polly discusses research in BMC Evolutionary Biology that emphasizes mandibular movement as a key quantitative feature influencing the evolution of tooth shape.
		Research article TWIST1 associates with NF-κB subunit RELA via carboxyl-terminal WR domain to promote cell autonomous invasion through IL8 production Shan Li, Stephen E Kendall, Raquel Raices, James Finlay, Maricela Covarrubias, Zheng Liu, Gina Lowe, Yu-Huey Lin, Yuan Teh, Victoria Leigh, Simi Dhillon, Steven Flanagan, Karen S Aboody, Carlotta A Glackin BMC Biology 2012, 10:73 (14 August 2012) Abstract \| Full text \| PDF \| PubMed
		Research article A novel Rho-dependent pathway that drives interaction of fascin-1 with p-Lin-11/Isl-1/Mec-3 kinase (LIMK) 1/2 to promote fascin-1/actin binding and filopodia stability Asier Jayo, Maddy Parsons, Josephine C Adams BMC Biology 2012, 10:72 (10 August 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The actin-binding protein fascin is important for cell migration and its up-regulation is implicated in metastasis in several human carcinomas. Adams and colleagues visualize a direct interaction between fascin and LIM kinase 1/2, Rho-activated kinases, which regulate the stability of filopodia.
		Research article Untangling the evolution of Rab G proteins: implications of a comprehensive genomic analysis Tobias H Klöpper, Nickias Kienle, Dirk Fasshauer, Sean Munro BMC Biology 2012, 10:71 (8 August 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The functional complexity made possible by the proteins that direct traffic between the internal membranes of eukaryotic cells lies at the heart of metazoan evolution. Sean Munro and colleagues trace the Rab family of membrane traffic proteins to its evolutionary roots.
		Commentary The Rabs: A family at the root of metazoan evolution Harald Stenmark BMC Biology 2012, 10:68 (8 August 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Harald Stenmark explains the interest in the phylogenetic analysis of Rab GTPases reported in a paper in BMC Biology, and sketches (literally) the diversity of membrane transport functions that correspond to the six functional groups proposed.
		Correction Rapid sympatric ecological differentiation of crater lake cichlid fishes within historic times Kathryn R Elmer, Topi K Lehtonen, Andreas F Kautt, Chris Harrod, Axel Meyer BMC Biology 2012, 10:70 (7 August 2012) Abstract \| Full text \| PDF \| PubMed
		Research article Excessive folate synthesis limits lifespan in the C. elegans: E. coli aging model Bhupinder Virk, Gonçalo Correia, David P Dixon, Inna Feyst, Jie Jia, Nikolin Oberleitner, Zoe Briggs, Emily Hodge, Robert Edwards, John Ward, David Gems, David Weinkove BMC Biology 2012, 10:67 (31 July 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary David Weinkove and colleagues report an accidental discovery in C. elegans that has led them to a series of studies implicating folate in excess of needs in limiting lifespan, with interesting hints from the effects of sulfonamide drugs that the same may apply to mammals.
		Commentary Folate status of gut microbiome affects Caenorhabditis elegans lifespan Theresa PT Nguyen, Catherine F Clarke BMC Biology 2012, 10:66 (31 July 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Commenting on a recent report in BMC Biology on an adventitious discovery in nematode worms, Theresa Nguyen and Catherine Clarke speculate on the implications for human lifespan of folate supplementation and the effects of sulfonamide drugs on the microbiome.
		Research article Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria) Ylenia Chiari, Vincent Cahais, Nicolas Galtier, Frédéric Delsuc BMC Biology 2012, 10:65 (27 July 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Turtles have traditionally been hard to place taxonomically because of their unique morphology, and recent research based on microRNA has stirred the pot once again. Contrary to that work, phylogenomic analysis of a large new sequence data set adds strong support to the previous conclusion that turtles' closest evolutionary relatives are birds and crocodiles.
		Commentary Amniote phylogeny and the position of turtles S Blair Hedges BMC Biology 2012, 10:64 (27 July 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Commenting on research on the disputed evolutionary placement of turtles, Blair Hedges discusses how integration of data from different sources – DNA, morphology, and biogeography – can help to resolve evolutionary disputes.