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		Commentary Is sex necessary? Sheng Sun, Joseph Heitman BMC Biology 2011, 9:56 (31 August 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Sexuality is the reproductive mode of choice for eukaryotes, but fungal species often evolve apparent asexuality. Sun and Heitman explain why this might happen, but add a word of caution about the experimental difficulty of definitively identifying a fungus as asexual.
		Research article The taming of an impossible child: a standardized all-in approach to the phylogeny of Hymenoptera using public database sequences Ralph S Peters, Benjamin Meyer, Lars Krogmann, Janus Borner, Karen Meusemann, Kai Schütte, Oliver Niehuis, Bernhard Misof BMC Biology 2011, 9:55 (18 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 2 comments \| Editor’s summary Ralph Peters and colleagues feed the available data on the super-diverse insect order of wasps, bees, sawflies and ants into an improved bioinformatic pipeline designed to generate phylogenetic trees from rapidly accumulating sequence data, and demonstrate its usefulness, and the need for more data to resolve outstanding phylogenetic issues.
		Research article Identification and characterization of a set of conserved and new regulators of cytoskeletal organization, cell morphology and migration Siau Bai, Maria Herrera-Abreu, Jennifer L Rohn, Victor Racine, Virginia Tajadura, Narendra Suryavanshi, Stephanie Bechtel, Stefan Wiemann, Buzz Baum, Anne J Ridley BMC Biology 2011, 9:54 (11 August 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Anne Ridley and colleagues identify novel regulators of cytoskeletal organization and cell migration in human cells through a genome-wide RNAi screen in Drosophila cells.
		Research article Identification of specificity determining residues in peptide recognition domains using an information theoretic approach applied to large-scale binding maps Kevin Y Yip, Lukas Utz, Simon Sitwell, Xihao Hu, Sachdev S Sidhu, Benjamin E Turk, Mark Gerstein, Philip M Kim BMC Biology 2011, 9:53 (11 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Editorial The noncoding universe Kester Jarvis, Miranda Robertson BMC Biology 2011, 9:52 (28 July 2011) Abstract \| Full text \| PDF \| PubMed \| 1 comment \| Editor’s summary In an editorial revisiting the controversy on the extent of the noncoding transcriptome, BMC Biology concludes that the bioinformatic facts are becoming clearer but their biological meaning remains obscure.
		Commentary Tracing lineages to uncover neuronal identity Lia Panman, Thomas Perlmann BMC Biology 2011, 9:51 (19 July 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Understanding the development of the diverse dopamine-secreting neurons that populate the ventral midbrain may help in the treatment of disorders such as Parkinson's disease and schizophrenia. Lia Panman and Thomas Perlmann comment on a paper in Neural Development which elucidates the early life history of these cells.
		Commentary Noncoding RNA, antigenic variation, and the virulence genes of Plasmodium falciparum A Taylor Bright, Elizabeth A Winzeler BMC Biology 2011, 9:50 (19 July 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The malaria parasite P. falciparum has 60 variants of the gene encoding the major virulence factor PfEMP, variably expressed on the red blood cell surface so that it evades immune detection. Taylor Bright and Elizabeth Winzeler discuss a recent report in Genome Biology on a new family of long noncoding RNAs that may explain the selective suppression of these genes.
		Research article Mouse maternal systemic inflammation at the zygote stage causes blunted cytokine responsiveness in lipopolysaccharide-challenged adult offspring Charlotte L Williams, Jessica L Teeling, V Hugh Perry, Tom P Fleming BMC Biology 2011, 9:49 (19 July 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Systemic inflammation induced in female mice at the time of conception has consequences for the behavior, adiposity and innate immune responses of their adult offspring.
		Research article Cofactor-mediated conformational control in the bifunctional kinase/RNase Ire1 Alexei V Korennykh, Pascal F Egea, Andrei A Korostelev, Janet Finer-Moore, Robert M Stroud, Chao Zhang, Kevan M Shokat, Peter Walter BMC Biology 2011, 9:48 (6 July 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Korennykh and colleagues show how ADP binding can tune the kinase in the activation of the bifunctional kinase-RNase that invokes the transcriptional rescue program in response to the toxic accumulation of unfolded proteins in the ER.
		Research article Structural and functional basis for RNA cleavage by Ire1 Alexei V Korennykh, Andrei A Korostelev, Pascal F Egea, Janet Finer-Moore, Robert M Stroud, Chao Zhang, Kevan M Shokat, Peter Walter BMC Biology 2011, 9:47 (6 July 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The unfolded protein response to ER stress is activated by nonconventional splicing of the mRNAs encoding proteins that relieve the stress by the bifunctional kinase-RNase Ire1. Korennykh and colleagues propose a mechanism for the RNase that contradicts the current view.
		Commentary Robustness and fault tolerance make brains harder to study Shyam Srinivasan, Charles F Stevens BMC Biology 2011, 9:46 (29 June 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method commonly used to infer functional connectivity in neural circuits, Granger causality, has been put to the test on the well-defined crab pyloric network by Eve Marder and colleagues in a paper in Neural Systems and Circuits. Commenting in BMC Biology, Charles Stevens and Shyam Srinivasan posit that the need for nervous systems to be robust and fault tolerant makes it inevitable that inferential techniques of this kind will be error-prone.
		Research article Centriole polarisation to the immunological synapse directs secretion from cytolytic cells of both the innate and adaptive immune systems Jane C Stinchcombe, Mariolina Salio, Vincenzo Cerundolo, Daniela Pende, Maurizo Arico, Gillian M Griffiths BMC Biology 2011, 9:45 (28 June 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Centrosome repositioning occurs in cytolytic cells of the innate immune system, just as it does in those of the adaptive system, focusing the release of cytotoxic granules at the site of contact with the target cell.
		Research article Origin and global diversification patterns of tropical rain forests: inferences from a complete genus-level phylogeny of palms Thomas LP Couvreur, Félix Forest, William J Baker BMC Biology 2011, 9:44 (16 June 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 2 comments \| Editor’s summary Knowing how rainforest biodiversity arose will be useful in predicting reactions to its loss. A synthesis of molecular and fossil data on palms suggests diversity has slowly accumulated over the past 100 million years, rather than being the product of a rapid diversification.
		Commentary Selecting synaptic partners: GRASPing the role of UNC-6/netrin QueeLim Ch'ng BMC Biology 2011, 9:43 (10 June 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The UNC-6/netrin molecule, known to be important for guiding axons as they develop, is now found to play a key role in selecting the synaptic connections they make. QueeLim Ch'ng comments on the significance of these findings, published today in Neural Development.
		Review Stem cell biology and drug discovery Lee L Rubin, Kelly M Haston BMC Biology 2011, 9:42 (7 June 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Lee Rubin and Kelly Haston survey recent research on the contribution of pluripotent cells to modeling disease with the aim of improving the efficiency of drug discovery and prediction of unexpected drug toxicities.
		Opinion Stochastic dynamics and the evolution of mutations in stem cells David Dingli, Jorge M Pacheco BMC Biology 2011, 9:41 (7 June 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Stem cell populations are small and therefore clonal expansion of mutant cells is susceptible to stochastic effects. Dingli and Pacheco propose that such effects may result in the unfavorable acquisition of mutations causing potentially lethal disease and occasionally, stochastic extinction could explain the disappearance of mutant clones.
		Comment The individuality of stem cells Arthur D Lander BMC Biology 2011, 9:40 (7 June 2011) Full text \| PDF \| PubMed \| Editor’s summary Arthur Lander reflects on how current assumptions that stem cells divide asymmetrically and are programmed to produce the right differentiated cell types at the right times may fail to acknowledge a fundamental contribution of stem cell individuality.
		Commentary Following autophagy step by step Tom Hansen, Terje Johansen BMC Biology 2011, 9:39 (2 June 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Autophagy, whereby cells digest their own contents and can remove damaging aggregates and pathogens, is a current focus of interest for therapeutic intervention. Hansen and Johansen explain in a Commentary on a paper from Brady and colleagues a new advance in screening for modulators that allows resolution of distinct steps in the pathway.
		Methodology article Concurrent detection of autolysosome formation and lysosomal degradation by flow cytometry in a high-content screen for inducers of autophagy Phillip Hundeshagen, Anne Hamacher-Brady, Roland Eils, Nathan R Brady BMC Biology 2011, 9:38 (2 June 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary There is much interest in activating autophagy, by which cells deliver their own contents to the lysosomal system, in cancer therapy. Nathan Brady and colleagues report a flow cytometric method whereby drug candidates may be screened for effects on separate steps in the process.
		Methodology article 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 2011, 9:37 (31 May 2011) Abstract \| Full text \| PDF \| PubMed
		Commentary DNA replication: archaeal oriGINS Stephen D Bell BMC Biology 2011, 9:36 (31 May 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary With the structure for an important archaeal DNA replication factor recently published in BMC Biology, Stephen Bell discusses its similarities to and differences from the same human tetramer, and lays out a model for its role in the replication machinery.
		Commentary No small feat: microRNA responses during vocal communication in songbirds Claudio V Mello, Peter V Lovell BMC Biology 2011, 9:35 (31 May 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The male zebrafinch is one of few animals other than humans that communicates through complex vocal signals. Claudio Mello and Peter Lovell comment on genomic approaches to unravelling the neural basis of song-learning, including a paper in BMC Genomics that profiles the microRNA response to conspecific birdsong
		Review Microarrays, deep sequencing and the true measure of the transcriptome John H Malone, Brian Oliver BMC Biology 2011, 9:34 (31 May 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Global measures of gene expression can now be extracted either from microarrays or from RNA-seq, which do not always seem to give the same answer. Malone and Oliver review the advantages and limitations of each and conclude that, with some important exceptions, they tell the same story.
		Research article Identification of a functional docking site in the Rpn1 LRR domain for the UBA-UBL domain protein Ddi1 Tara A Gomez, Natalie Kolawa, Marvin Gee, Michael J Sweredoski, Raymond J Deshaies BMC Biology 2011, 9:33 (31 May 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Proteasomal degradation of proteins is an important regulatory mechanism for many cellular processes including the cell cycle. Raymond Deshaies and colleagues identify crucial interactions between the proteasome and one of the shuttle proteins that delivers ubiquitinated proteins for destruction.
		Research article PKC isoforms interact with and phosphorylate DNMT1 Geneviève Lavoie, Pierre-Olivier Estève, Nathalie Laulan, Sriharsa Pradhan, Yves St-Pierre BMC Biology 2011, 9:31 (27 May 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central

	All
		Commentary Is sex necessary? Sheng Sun, Joseph Heitman BMC Biology 2011, 9:56 (31 August 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Sexuality is the reproductive mode of choice for eukaryotes, but fungal species often evolve apparent asexuality. Sun and Heitman explain why this might happen, but add a word of caution about the experimental difficulty of definitively identifying a fungus as asexual.
		Research article The taming of an impossible child: a standardized all-in approach to the phylogeny of Hymenoptera using public database sequences Ralph S Peters, Benjamin Meyer, Lars Krogmann, Janus Borner, Karen Meusemann, Kai Schütte, Oliver Niehuis, Bernhard Misof BMC Biology 2011, 9:55 (18 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 2 comments \| Editor’s summary Ralph Peters and colleagues feed the available data on the super-diverse insect order of wasps, bees, sawflies and ants into an improved bioinformatic pipeline designed to generate phylogenetic trees from rapidly accumulating sequence data, and demonstrate its usefulness, and the need for more data to resolve outstanding phylogenetic issues.
		Research article Identification and characterization of a set of conserved and new regulators of cytoskeletal organization, cell morphology and migration Siau Bai, Maria Herrera-Abreu, Jennifer L Rohn, Victor Racine, Virginia Tajadura, Narendra Suryavanshi, Stephanie Bechtel, Stefan Wiemann, Buzz Baum, Anne J Ridley BMC Biology 2011, 9:54 (11 August 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Anne Ridley and colleagues identify novel regulators of cytoskeletal organization and cell migration in human cells through a genome-wide RNAi screen in Drosophila cells.
		Research article Identification of specificity determining residues in peptide recognition domains using an information theoretic approach applied to large-scale binding maps Kevin Y Yip, Lukas Utz, Simon Sitwell, Xihao Hu, Sachdev S Sidhu, Benjamin E Turk, Mark Gerstein, Philip M Kim BMC Biology 2011, 9:53 (11 August 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Editorial The noncoding universe Kester Jarvis, Miranda Robertson BMC Biology 2011, 9:52 (28 July 2011) Abstract \| Full text \| PDF \| PubMed \| 1 comment \| Editor’s summary In an editorial revisiting the controversy on the extent of the noncoding transcriptome, BMC Biology concludes that the bioinformatic facts are becoming clearer but their biological meaning remains obscure.
		Commentary Tracing lineages to uncover neuronal identity Lia Panman, Thomas Perlmann BMC Biology 2011, 9:51 (19 July 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Understanding the development of the diverse dopamine-secreting neurons that populate the ventral midbrain may help in the treatment of disorders such as Parkinson's disease and schizophrenia. Lia Panman and Thomas Perlmann comment on a paper in Neural Development which elucidates the early life history of these cells.
		Commentary Noncoding RNA, antigenic variation, and the virulence genes of Plasmodium falciparum A Taylor Bright, Elizabeth A Winzeler BMC Biology 2011, 9:50 (19 July 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The malaria parasite P. falciparum has 60 variants of the gene encoding the major virulence factor PfEMP, variably expressed on the red blood cell surface so that it evades immune detection. Taylor Bright and Elizabeth Winzeler discuss a recent report in Genome Biology on a new family of long noncoding RNAs that may explain the selective suppression of these genes.
		Research article Mouse maternal systemic inflammation at the zygote stage causes blunted cytokine responsiveness in lipopolysaccharide-challenged adult offspring Charlotte L Williams, Jessica L Teeling, V Hugh Perry, Tom P Fleming BMC Biology 2011, 9:49 (19 July 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Systemic inflammation induced in female mice at the time of conception has consequences for the behavior, adiposity and innate immune responses of their adult offspring.
		Research article Cofactor-mediated conformational control in the bifunctional kinase/RNase Ire1 Alexei V Korennykh, Pascal F Egea, Andrei A Korostelev, Janet Finer-Moore, Robert M Stroud, Chao Zhang, Kevan M Shokat, Peter Walter BMC Biology 2011, 9:48 (6 July 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Korennykh and colleagues show how ADP binding can tune the kinase in the activation of the bifunctional kinase-RNase that invokes the transcriptional rescue program in response to the toxic accumulation of unfolded proteins in the ER.
		Research article Structural and functional basis for RNA cleavage by Ire1 Alexei V Korennykh, Andrei A Korostelev, Pascal F Egea, Janet Finer-Moore, Robert M Stroud, Chao Zhang, Kevan M Shokat, Peter Walter BMC Biology 2011, 9:47 (6 July 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The unfolded protein response to ER stress is activated by nonconventional splicing of the mRNAs encoding proteins that relieve the stress by the bifunctional kinase-RNase Ire1. Korennykh and colleagues propose a mechanism for the RNase that contradicts the current view.
		Commentary Robustness and fault tolerance make brains harder to study Shyam Srinivasan, Charles F Stevens BMC Biology 2011, 9:46 (29 June 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method commonly used to infer functional connectivity in neural circuits, Granger causality, has been put to the test on the well-defined crab pyloric network by Eve Marder and colleagues in a paper in Neural Systems and Circuits. Commenting in BMC Biology, Charles Stevens and Shyam Srinivasan posit that the need for nervous systems to be robust and fault tolerant makes it inevitable that inferential techniques of this kind will be error-prone.
		Research article Centriole polarisation to the immunological synapse directs secretion from cytolytic cells of both the innate and adaptive immune systems Jane C Stinchcombe, Mariolina Salio, Vincenzo Cerundolo, Daniela Pende, Maurizo Arico, Gillian M Griffiths BMC Biology 2011, 9:45 (28 June 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Centrosome repositioning occurs in cytolytic cells of the innate immune system, just as it does in those of the adaptive system, focusing the release of cytotoxic granules at the site of contact with the target cell.
		Research article Origin and global diversification patterns of tropical rain forests: inferences from a complete genus-level phylogeny of palms Thomas LP Couvreur, Félix Forest, William J Baker BMC Biology 2011, 9:44 (16 June 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 2 comments \| Editor’s summary Knowing how rainforest biodiversity arose will be useful in predicting reactions to its loss. A synthesis of molecular and fossil data on palms suggests diversity has slowly accumulated over the past 100 million years, rather than being the product of a rapid diversification.
		Commentary Selecting synaptic partners: GRASPing the role of UNC-6/netrin QueeLim Ch'ng BMC Biology 2011, 9:43 (10 June 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The UNC-6/netrin molecule, known to be important for guiding axons as they develop, is now found to play a key role in selecting the synaptic connections they make. QueeLim Ch'ng comments on the significance of these findings, published today in Neural Development.
		Review Stem cell biology and drug discovery Lee L Rubin, Kelly M Haston BMC Biology 2011, 9:42 (7 June 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Lee Rubin and Kelly Haston survey recent research on the contribution of pluripotent cells to modeling disease with the aim of improving the efficiency of drug discovery and prediction of unexpected drug toxicities.
		Opinion Stochastic dynamics and the evolution of mutations in stem cells David Dingli, Jorge M Pacheco BMC Biology 2011, 9:41 (7 June 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Stem cell populations are small and therefore clonal expansion of mutant cells is susceptible to stochastic effects. Dingli and Pacheco propose that such effects may result in the unfavorable acquisition of mutations causing potentially lethal disease and occasionally, stochastic extinction could explain the disappearance of mutant clones.
		Comment The individuality of stem cells Arthur D Lander BMC Biology 2011, 9:40 (7 June 2011) Full text \| PDF \| PubMed \| Editor’s summary Arthur Lander reflects on how current assumptions that stem cells divide asymmetrically and are programmed to produce the right differentiated cell types at the right times may fail to acknowledge a fundamental contribution of stem cell individuality.
		Commentary Following autophagy step by step Tom Hansen, Terje Johansen BMC Biology 2011, 9:39 (2 June 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Autophagy, whereby cells digest their own contents and can remove damaging aggregates and pathogens, is a current focus of interest for therapeutic intervention. Hansen and Johansen explain in a Commentary on a paper from Brady and colleagues a new advance in screening for modulators that allows resolution of distinct steps in the pathway.
		Methodology article Concurrent detection of autolysosome formation and lysosomal degradation by flow cytometry in a high-content screen for inducers of autophagy Phillip Hundeshagen, Anne Hamacher-Brady, Roland Eils, Nathan R Brady BMC Biology 2011, 9:38 (2 June 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary There is much interest in activating autophagy, by which cells deliver their own contents to the lysosomal system, in cancer therapy. Nathan Brady and colleagues report a flow cytometric method whereby drug candidates may be screened for effects on separate steps in the process.
		Methodology article 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 2011, 9:37 (31 May 2011) Abstract \| Full text \| PDF \| PubMed
		Commentary DNA replication: archaeal oriGINS Stephen D Bell BMC Biology 2011, 9:36 (31 May 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary With the structure for an important archaeal DNA replication factor recently published in BMC Biology, Stephen Bell discusses its similarities to and differences from the same human tetramer, and lays out a model for its role in the replication machinery.
		Commentary No small feat: microRNA responses during vocal communication in songbirds Claudio V Mello, Peter V Lovell BMC Biology 2011, 9:35 (31 May 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The male zebrafinch is one of few animals other than humans that communicates through complex vocal signals. Claudio Mello and Peter Lovell comment on genomic approaches to unravelling the neural basis of song-learning, including a paper in BMC Genomics that profiles the microRNA response to conspecific birdsong
		Review Microarrays, deep sequencing and the true measure of the transcriptome John H Malone, Brian Oliver BMC Biology 2011, 9:34 (31 May 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Global measures of gene expression can now be extracted either from microarrays or from RNA-seq, which do not always seem to give the same answer. Malone and Oliver review the advantages and limitations of each and conclude that, with some important exceptions, they tell the same story.
		Research article Identification of a functional docking site in the Rpn1 LRR domain for the UBA-UBL domain protein Ddi1 Tara A Gomez, Natalie Kolawa, Marvin Gee, Michael J Sweredoski, Raymond J Deshaies BMC Biology 2011, 9:33 (31 May 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Proteasomal degradation of proteins is an important regulatory mechanism for many cellular processes including the cell cycle. Raymond Deshaies and colleagues identify crucial interactions between the proteasome and one of the shuttle proteins that delivers ubiquitinated proteins for destruction.
		Research article PKC isoforms interact with and phosphorylate DNMT1 Geneviève Lavoie, Pierre-Olivier Estève, Nathalie Laulan, Sriharsa Pradhan, Yves St-Pierre BMC Biology 2011, 9:31 (27 May 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central