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	1. 16448 Accesses	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.
	2. 14262 Accesses	Research article The first metazoa living in permanently anoxic conditions Roberto Danovaro, Antonio Dell'Anno, Antonio Pusceddu, Cristina Gambi, Iben Heiner, Reinhardt Møbjerg Kristensen BMC Biology 2010, 8:30 (6 April 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 2 comments \| F1000 Biology \| Editor’s summary An expedition to a deep sea hypersaline anoxic basin in the Mediterranean has discovered the first multicellular animals that live and reproduce in the absence of oxygen.
	3. 10864 Accesses	Question and Answer Q&A: What is the Golgi apparatus, and why are we asking? Sean Munro BMC Biology 2011, 9:63 (30 September 2011) Full text \| PDF \| PubMed \| 2 comments \| Editor’s summary Sean Munro explains in Q&A format why the Golgi apparatus remains a gently seething cauldron of controversy more than 120 years after its discovery.
	4. 10589 Accesses	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.
	5. 10106 Accesses	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.
	6. 9798 Accesses	Forum What does the concept of the stem cell niche really mean today? Arthur D Lander, Judith Kimble, Hans Clevers, Elaine Fuchs, Didier Montarras, Margaret Buckingham, Anne L Calof, Andreas Trumpp, Thordur Oskarsson BMC Biology 2012, 10:19 (9 March 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary How do current researchers view the stem cell niche? Eight experts from different fields provide their perspective, and ask how stem cells evolve in such an environment, launching a new Forum article type within the cross-journal collection on stem cells.
	7. 9787 Accesses	Commentary Sex, sex chromosomes and gene expression Xuemei Lu, Chung-I Wu BMC Biology 2011, 9:30 (4 May 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Commenting on a paper in BMC Biology challenging current beliefs on the evolution of X inactivation and the distribution of genes on sex chromosomes, Lu and Wu weigh alternative theories, including sexual antagonism and tissue-specific expression.
	8. 9152 Accesses	Editorial Pit-bull reviewing, the pursuit of perfection and the victims of success Miranda Robertson BMC Biology 2011, 9:84 (1 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The festering discontent with reviewing and editorial practices in the high-profile biology journals has erupted into a new high-quality open access journal to be launched in 2012. Miranda Robertson explores the problem and the solutions offered, and revisits the re-review opt-out policy operated by BMC Biology.
	9. 8838 Accesses	Review Molecular dynamics simulations and drug discovery Jacob D Durrant, J Andrew McCammon BMC Biology 2011, 9:71 (28 October 2011) Abstract \| Full text \| PDF \| PubMed \| F1000 Biology \| Editor’s summary Modeling the movements of atoms within macromolecules can predict their conformational flexibility to inform drug discovery. Jacob Durrant and Andrew McCammon explain how this is done in molecular dynamics simulations, reviewing both the successes and current limitations of the approach.
	10. 8700 Accesses	Question and Answer Q&A: What is a pathogen? A question that begs the point Liise-anne Pirofski, Arturo Casadevall BMC Biology 2012, 10:6 (31 January 2012) Abstract \| Full text \| PDF \| PubMed \| 1 comment \| Editor’s summary Arturo Casadevall and Liise-anne Pirofski explain in Q&A format the emergent properties of microbial pathogenesis that make the question impossible to answer, and the emergence of new pathogens almost impossible to predict.
	11. 7421 Accesses	Opinion Origins of cellular geometry Wallace F Marshall BMC Biology 2011, 9:57 (31 August 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Many cells, both protozoan and metazoan, have extremely elaborate architectures, and most have organelles that obey scaling laws. Wallace Marshall discusses what is known of these remarkably ill understood properties.
	12. 7061 Accesses	Question and Answer Q&A: ChIP-seq technologies and the study of gene regulation Edison T Liu, Sebastian Pott, Mikael Huss BMC Biology 2010, 8:56 (14 May 2010) Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Edison Liu and colleagues explain in Q&A format how ChIP-seq technology allows investigation of transcriptional regulation on a genomic scale, and what is next.
	13. 7008 Accesses	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.
	14. 6974 Accesses	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.
	15. 6860 Accesses	Comment Dangerous for ferrets: lethal for humans? Peter C Doherty, Paul G Thomas BMC Biology 2012, 10:10 (20 February 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Research on how highly pathogenic H5N1 viruses might become transmissible between humans has ignited heated debate on the balance of risks and benefits of such experiments. Peter Doherty and Paul Thomas give their view.
	16. 6835 Accesses	Research article Evidence that a West-East admixed population lived in the Tarim Basin as early as the early Bronze Age Chunxiang Li, Hongjie Li, Yinqiu Cui, Chengzhi Xie, Dawei Cai, Wenying Li, Victor H Mair, Zhi Xu, Quanchao Zhang, Idelisi Abuduresule, Li Jin, Hong Zhu, Hui Zhou BMC Biology 2010, 8:15 (17 February 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Genetic analysis of human remains from the Tarim Basin in China reveals that the Xiaohe people comprised an admixture of populations originating from both the East and the West dating from the early Bronze Age.
	17. 6823 Accesses	Question and Answer Q&A: Who is H. sapiens really, and how do we know? Mason Liang, Rasmus Nielsen BMC Biology 2011, 9:20 (31 March 2011) Full text \| PDF \| PubMed \| 1 comment \| Editor’s summary Modern sequencing technology has made it possible to scavenge the DNA of extinct hominin ancestors for evidence of interbreeding with Homo sapiens. Liang and Nielsen examine the evidence, what it tells us and how sure we can be
	18. 6358 Accesses	Commentary Toward a comprehensive language for biological systems James R Faeder BMC Biology 2011, 9:68 (17 October 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Biology is complex, and biologists are (mostly) resistant to modeling. James Faeder, lucidly challenging this resistance, welcomes a new rule-based software package reported in a recent paper in BMC Systems Biology that begins to confront the complexity.
	19. 6314 Accesses	Methodology article Use of the viral 2A peptide for bicistronic expression in transgenic mice Georgios Trichas, Jo Begbie, Shankar Srinivas BMC Biology 2008, 6:40 (15 September 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Germline transmission of a bicistronic vector using the 2A peptide to allow co-translational cleavage is stable in mice and shows no developmental side-effects, giving a superior alternative to the internal ribosomal entry site for expressing multiple transgenes.
	20. 6256 Accesses	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 \| 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.
	21. 6250 Accesses	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.
	22. 6086 Accesses	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.
	23. 5789 Accesses	Commentary Difficult phylogenetic questions: more data, maybe; better methods, certainly Hervé Philippe, Béatrice Roure BMC Biology 2011, 9:91 (29 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Niels Bohr said that 'Prediction is very difficult, especially about the future,' but phylogeneticists would just be happy with the past. Philippe and Roure discuss some methods for dealing with particularly difficult evolutionary problems, and how corroboration is the key to success.
	24. 5761 Accesses	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 \| 1 comment \| 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.
	25. 5714 Accesses	Commentary Inferring the Tree of Life: chopping a phylogenomic problem down to size? Olaf RP Bininda-Emonds BMC Biology 2011, 9:59 (20 September 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The recent rapid increase in molecular sequence data has been a boon for phylogeneticists, but brings with it a greater need to separate bad data from good. Bininda-Emonds explains how this is being done, and discusses some of the problems that remain to be solved before we might reconstruct the entire tree of life.