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From origins to open questions – Ten years of BMC Biology

Collection published: 15 April 2013

Last updated: 2 September 2013

BMC Biology was launched as the flagship journal of BioMed Central in 2003, and we cannot leave a ten-year anniversary unmarked. But suspecting a reluctance to dwell on history, in this age when it is enough trouble to keep up with the breakneck present, we have in this collection of anniversary articles looked resolutely forward, and invited the authors of some of our most highly cited articles to produce updates on progress since they were published, and our Editorial Board members to contribute the open questions they would like to see answered in their fields.

Even Patrick Brown, who spoke to us about the origins of open access, had his eyes so firmly fixed on the far horizon ten years ago that his vision remains in the future; and Peter Walter, with whom we did indulge in a little history in his interview on the origins of re-review opt-out, addresses an issue that remains perennial.

		Comment Open questions: Zombie projects, translational research, and the real secret of the inside of the cell Gregory A Petsko BMC Biology 2013, 11:97 (2 September 2013) Abstract \| Full text \| PDF \| 1 comment \| Editor’s summary Gregory Petsko, writing for the BMC Biology tenth birthday Open questions series, argues, with his usual forthrightness, that we need to pay more attention to where the balance of ‘big’ and ‘little’ science is going, and remember how little we know about the interior of the cell.
		Comment Open questions: two challenges in chemical biology - chemical engineering and the science of diet Philip A Cole BMC Biology 2013, 11:87 (30 July 2013) Full text \| PDF \| PubMed \| Editor’s summary In his contribution to the 10th anniversary Open questions series in BMC Biology, Philip Cole proposes synthetic biology for probing the mysteries of protein modifications and dynamics, and chemoprevention through diet for improving public health.
		Comment Open questions: A logic (or lack thereof) of genome organization Laurence D Hurst BMC Biology 2013, 11:58 (28 May 2013) Full text \| PDF \| PubMed \| Editor’s summary Laurence Hurst reflects on the range of genome biological factors determining whether mutations have a selective effect, and how knowing more might help us to predict which will cause disease.
		Anniversary Update Tropical rain forest evolution: palms as a model group Thomas LP Couvreur, William J Baker BMC Biology 2013, 11:48 (15 April 2013) Full text \| PDF \| PubMed \| Cited on BioMed Central
		Anniversary Update White-nose syndrome in bats: illuminating the darkness Paul M Cryan, Carol Meteyer, Justin G Boyles, David S Blehert BMC Biology 2013, 11:47 (15 April 2013) Full text \| PDF \| PubMed \| Cited on BioMed Central
		Anniversary Update Seeing the Tree of Life behind the phylogenetic forest Pere Puigbò, Yuri I Wolf, Eugene V Koonin BMC Biology 2013, 11:46 (15 April 2013) Full text \| PDF \| PubMed \| Cited on BioMed Central
		Anniversary Update Arthropods and inherited bacteria: from counting the symbionts to understanding how symbionts count Olivier Duron, Gregory DD Hurst BMC Biology 2013, 11:45 (15 April 2013) Full text \| PDF \| PubMed \| Cited on BioMed Central
		Anniversary Update Segment assembly, structure alignment and iterative simulation in protein structure prediction Yang Zhang, Jeffrey Skolnick BMC Biology 2013, 11:44 (15 April 2013) Full text \| PDF \| PubMed \| Cited on BioMed Central
		Anniversary Update Systematic curation of protein and genetic interaction data for computable biology Kara Dolinski, Andrew Chatr-aryamontri, Mike Tyers BMC Biology 2013, 11:43 (15 April 2013) Full text \| PDF \| PubMed \| Cited on BioMed Central
		Anniversary Update Neurosensory transmission without a synapse: new perspectives on taste signaling Sue C Kinnamon BMC Biology 2013, 11:42 (15 April 2013) Full text \| PDF \| PubMed \| Cited on BioMed Central
		Anniversary Update Fuzzy species revisited William P Hanage BMC Biology 2013, 11:41 (15 April 2013) Full text \| PDF \| PubMed \| Cited on BioMed Central
		Anniversary Update The new micro-kingdoms of eukaryotes Jan Pawlowski BMC Biology 2013, 11:40 (15 April 2013) Full text \| PDF \| PubMed \| Cited on BioMed Central
		Editorial Tenth anniversary updates from our authors Penelope Austin, Kester Jarvis BMC Biology 2013, 11:39 (15 April 2013) Full text \| PDF \| PubMed \| Cited on BioMed Central
		Opinion Of flies and men: insights on organismal metabolism from fruit flies Akhila Rajan, Norbert Perrimon BMC Biology 2013, 11:38 (15 April 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary For many reasons metabolism is now a high-profile topic, and in an update to mark the tenth anniversary of BMC Biology, Norbert Perrimon and Akhila Rajan review the remarkable similarities that make Drosophila a model for mammalian metabolism, and some recent advances made possible by the advantages of this model organism.
		Review Drugging Hedgehog: signaling the pathway to translation Tom J Carney, Philip W Ingham BMC Biology 2013, 11:37 (15 April 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Ten years ago Jeff Porter and colleagues published a screen for small-molecule modulators of the Hedgehog signaling pathway in the Journal of Biology. For BMC Biology’s 10^th anniversary, Tom Carney and Philip Ingham discuss the far-reaching clinical impact of some of the agonists and antagonists they discovered.
		Review LKB1 and AMPK and the cancer-metabolism link - ten years after D Hardie, Dario R Alessi BMC Biology 2013, 11:36 (15 April 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Ten years ago Grahame Hardie published in Journal of Biology (now BMC Biology) the discovery that the upstream activating kinase he was seeking for the multifarious energy sensor AMPK was the tumor suppressor, LKB1, that Dario Alessi was working on in a neighboring lab. For BMC Biology’s tenth anniversary they review some of what they have discovered since.
		Comment Domesticating the beast Virginia Walbot BMC Biology 2013, 11:35 (15 April 2013) Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary In 2009, Virginia Walbot commented ‘Are we training pit bulls to review our manuscripts?’ Revisiting the topic, she asks if we can tame our pit bull reviewers by involving students more in peer review and teaching them to see things from an authors’ perspective and the perspective of the journal that is responsible for making a decision on publication.
		Interview Two structure papers, a call from Frankfurt airport, and how to escape from reviewer delays: An interview with Peter Walter Peter Walter, Miranda Robertson BMC Biology 2013, 11:34 (15 April 2013) Full text \| PDF \| PubMed \| Cited on BioMed Central
		Interview An interview with Patrick O Brown on the origins and future of open access Patrick O Brown BMC Biology 2013, 11:33 (15 April 2013) Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary In an interview for the BMC Biology tenth anniversary collection, Patrick O Brown excavates his memory for the origins of open access publishing, and finds a vision of the future still to be fulfilled.
		Editorial A view forward from ten years of BMC Biology Miranda Robertson BMC Biology 2013, 11:32 (15 April 2013) Full text \| PDF
		Comment Open questions: Reflections on plant development and genetics Virginia Walbot BMC Biology 2013, 11:25 (28 March 2013) Full text \| PDF \| PubMed \| Editor’s summary For the BMC Biology 10^th anniversary series of open questions, Virginia Walbot reflects on how genomics has contributed to our understanding of plants over the last ten years, and the challenge of understanding how the flexible phenotypes of plants may adapt to environmental effects in future.
		Comment Open questions: Epigenetics and the role of heterochromatin in development Susan M Gasser BMC Biology 2013, 11:21 (4 March 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary As part of BMC Biology’s 10^th anniversary collection, Susan Gasser’s open questions link heterochromatin-mediated silencing, nuclear localisation and the true nature of epigenetic control.
		Editorial Q&A: Re-review opt-out and painless publishing Miranda Robertson BMC Biology 2013, 11:18 (28 February 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary BMC Biology operates on the principle that the function of a journal is to facilitate publication of sound research results. Miranda Robertson reviews in Q&A format the journal’s re-review opt-out policy and how it has worked over the four years of its operation.
		Comment Open questions: What is there left for cell biologists to do? Sean Munro BMC Biology 2013, 11:16 (27 February 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary In a contribution to the 10^th anniversary series on open questions in biology, Sean Munro asks provocatively what there is left for cell biologists to do, and with great elan and a touch of waspish humor produces five unanswered questions on issues from the special properties of non-dividing cells to the architecture of the brain.
		Comment Open questions: Chromosome condensation - Why does a chromosome look like a chromosome? Frank Uhlmann BMC Biology 2013, 11:9 (31 January 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary In his contribution to the ‘Open questions’ anniversary collection for BMC Biology, Frank Uhlmann poses the unsolved problem of chromosome packaging
		Comment Open questions - in brief: Beyond -omics, missing motor proteins, and getting from molecules to organisms Stephen J Benkovic, Julie Theriot, Dagmar Ringe BMC Biology 2013, 11:8 (31 January 2013) Abstract \| Full text \| PDF \| PubMed
		Comment Open questions: missing pieces from the immunological jigsaw puzzle Gillian M Griffiths BMC Biology 2013, 11:10 (31 January 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Gillian Griffiths, in her ‘Open questions’ contribution for BMC Biology, pinpoints some critical missing links in the cell-biological specializations of immune cells
		Comment Are we training pit bulls to review our manuscripts? Virginia Walbot Journal of Biology 2009, 8:24 (9 March 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 4 comments \| Editor’s summary Virginia Walbot accepts some of the blame for remorselessly negative reviewers, and suggests a training program for graduate students and post docs that will deliver a fairer assessment of manuscripts.

		Comment Open questions: Zombie projects, translational research, and the real secret of the inside of the cell Gregory A Petsko BMC Biology 2013, 11:97 (2 September 2013) Abstract \| Full text \| PDF \| 1 comment \| Editor’s summary Gregory Petsko, writing for the BMC Biology tenth birthday Open questions series, argues, with his usual forthrightness, that we need to pay more attention to where the balance of ‘big’ and ‘little’ science is going, and remember how little we know about the interior of the cell.
		Comment Open questions: two challenges in chemical biology - chemical engineering and the science of diet Philip A Cole BMC Biology 2013, 11:87 (30 July 2013) Full text \| PDF \| PubMed \| Editor’s summary In his contribution to the 10th anniversary Open questions series in BMC Biology, Philip Cole proposes synthetic biology for probing the mysteries of protein modifications and dynamics, and chemoprevention through diet for improving public health.
		Comment Open questions: A logic (or lack thereof) of genome organization Laurence D Hurst BMC Biology 2013, 11:58 (28 May 2013) Full text \| PDF \| PubMed \| Editor’s summary Laurence Hurst reflects on the range of genome biological factors determining whether mutations have a selective effect, and how knowing more might help us to predict which will cause disease.
		Anniversary Update Tropical rain forest evolution: palms as a model group Thomas LP Couvreur, William J Baker BMC Biology 2013, 11:48 (15 April 2013) Full text \| PDF \| PubMed \| Cited on BioMed Central
		Anniversary Update White-nose syndrome in bats: illuminating the darkness Paul M Cryan, Carol Meteyer, Justin G Boyles, David S Blehert BMC Biology 2013, 11:47 (15 April 2013) Full text \| PDF \| PubMed \| Cited on BioMed Central
		Anniversary Update Seeing the Tree of Life behind the phylogenetic forest Pere Puigbò, Yuri I Wolf, Eugene V Koonin BMC Biology 2013, 11:46 (15 April 2013) Full text \| PDF \| PubMed \| Cited on BioMed Central
		Anniversary Update Arthropods and inherited bacteria: from counting the symbionts to understanding how symbionts count Olivier Duron, Gregory DD Hurst BMC Biology 2013, 11:45 (15 April 2013) Full text \| PDF \| PubMed \| Cited on BioMed Central
		Anniversary Update Segment assembly, structure alignment and iterative simulation in protein structure prediction Yang Zhang, Jeffrey Skolnick BMC Biology 2013, 11:44 (15 April 2013) Full text \| PDF \| PubMed \| Cited on BioMed Central
		Anniversary Update Systematic curation of protein and genetic interaction data for computable biology Kara Dolinski, Andrew Chatr-aryamontri, Mike Tyers BMC Biology 2013, 11:43 (15 April 2013) Full text \| PDF \| PubMed \| Cited on BioMed Central
		Anniversary Update Neurosensory transmission without a synapse: new perspectives on taste signaling Sue C Kinnamon BMC Biology 2013, 11:42 (15 April 2013) Full text \| PDF \| PubMed \| Cited on BioMed Central
		Anniversary Update Fuzzy species revisited William P Hanage BMC Biology 2013, 11:41 (15 April 2013) Full text \| PDF \| PubMed \| Cited on BioMed Central
		Anniversary Update The new micro-kingdoms of eukaryotes Jan Pawlowski BMC Biology 2013, 11:40 (15 April 2013) Full text \| PDF \| PubMed \| Cited on BioMed Central
		Editorial Tenth anniversary updates from our authors Penelope Austin, Kester Jarvis BMC Biology 2013, 11:39 (15 April 2013) Full text \| PDF \| PubMed \| Cited on BioMed Central
		Opinion Of flies and men: insights on organismal metabolism from fruit flies Akhila Rajan, Norbert Perrimon BMC Biology 2013, 11:38 (15 April 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary For many reasons metabolism is now a high-profile topic, and in an update to mark the tenth anniversary of BMC Biology, Norbert Perrimon and Akhila Rajan review the remarkable similarities that make Drosophila a model for mammalian metabolism, and some recent advances made possible by the advantages of this model organism.
		Review Drugging Hedgehog: signaling the pathway to translation Tom J Carney, Philip W Ingham BMC Biology 2013, 11:37 (15 April 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Ten years ago Jeff Porter and colleagues published a screen for small-molecule modulators of the Hedgehog signaling pathway in the Journal of Biology. For BMC Biology’s 10^th anniversary, Tom Carney and Philip Ingham discuss the far-reaching clinical impact of some of the agonists and antagonists they discovered.
		Review LKB1 and AMPK and the cancer-metabolism link - ten years after D Hardie, Dario R Alessi BMC Biology 2013, 11:36 (15 April 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Ten years ago Grahame Hardie published in Journal of Biology (now BMC Biology) the discovery that the upstream activating kinase he was seeking for the multifarious energy sensor AMPK was the tumor suppressor, LKB1, that Dario Alessi was working on in a neighboring lab. For BMC Biology’s tenth anniversary they review some of what they have discovered since.
		Comment Domesticating the beast Virginia Walbot BMC Biology 2013, 11:35 (15 April 2013) Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary In 2009, Virginia Walbot commented ‘Are we training pit bulls to review our manuscripts?’ Revisiting the topic, she asks if we can tame our pit bull reviewers by involving students more in peer review and teaching them to see things from an authors’ perspective and the perspective of the journal that is responsible for making a decision on publication.
		Interview Two structure papers, a call from Frankfurt airport, and how to escape from reviewer delays: An interview with Peter Walter Peter Walter, Miranda Robertson BMC Biology 2013, 11:34 (15 April 2013) Full text \| PDF \| PubMed \| Cited on BioMed Central
		Interview An interview with Patrick O Brown on the origins and future of open access Patrick O Brown BMC Biology 2013, 11:33 (15 April 2013) Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary In an interview for the BMC Biology tenth anniversary collection, Patrick O Brown excavates his memory for the origins of open access publishing, and finds a vision of the future still to be fulfilled.
		Editorial A view forward from ten years of BMC Biology Miranda Robertson BMC Biology 2013, 11:32 (15 April 2013) Full text \| PDF
		Comment Open questions: Reflections on plant development and genetics Virginia Walbot BMC Biology 2013, 11:25 (28 March 2013) Full text \| PDF \| PubMed \| Editor’s summary For the BMC Biology 10^th anniversary series of open questions, Virginia Walbot reflects on how genomics has contributed to our understanding of plants over the last ten years, and the challenge of understanding how the flexible phenotypes of plants may adapt to environmental effects in future.
		Comment Open questions: Epigenetics and the role of heterochromatin in development Susan M Gasser BMC Biology 2013, 11:21 (4 March 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary As part of BMC Biology’s 10^th anniversary collection, Susan Gasser’s open questions link heterochromatin-mediated silencing, nuclear localisation and the true nature of epigenetic control.
		Editorial Q&A: Re-review opt-out and painless publishing Miranda Robertson BMC Biology 2013, 11:18 (28 February 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary BMC Biology operates on the principle that the function of a journal is to facilitate publication of sound research results. Miranda Robertson reviews in Q&A format the journal’s re-review opt-out policy and how it has worked over the four years of its operation.
		Comment Open questions: What is there left for cell biologists to do? Sean Munro BMC Biology 2013, 11:16 (27 February 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary In a contribution to the 10^th anniversary series on open questions in biology, Sean Munro asks provocatively what there is left for cell biologists to do, and with great elan and a touch of waspish humor produces five unanswered questions on issues from the special properties of non-dividing cells to the architecture of the brain.
		Comment Open questions: Chromosome condensation - Why does a chromosome look like a chromosome? Frank Uhlmann BMC Biology 2013, 11:9 (31 January 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary In his contribution to the ‘Open questions’ anniversary collection for BMC Biology, Frank Uhlmann poses the unsolved problem of chromosome packaging
		Comment Open questions - in brief: Beyond -omics, missing motor proteins, and getting from molecules to organisms Stephen J Benkovic, Julie Theriot, Dagmar Ringe BMC Biology 2013, 11:8 (31 January 2013) Abstract \| Full text \| PDF \| PubMed
		Comment Open questions: missing pieces from the immunological jigsaw puzzle Gillian M Griffiths BMC Biology 2013, 11:10 (31 January 2013) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Gillian Griffiths, in her ‘Open questions’ contribution for BMC Biology, pinpoints some critical missing links in the cell-biological specializations of immune cells
		Comment Are we training pit bulls to review our manuscripts? Virginia Walbot Journal of Biology 2009, 8:24 (9 March 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| 4 comments \| Editor’s summary Virginia Walbot accepts some of the blame for remorselessly negative reviewers, and suggests a training program for graduate students and post docs that will deliver a fairer assessment of manuscripts.