Abstract：
:Regardless of how creative, innovative, and elegant our computational methods, the ultimate proof of an algorithm's worth is the experimentally validated quality of its predictions. Unfortunately, this truism is hard to reduce to practice. Usually, modelers produce hundreds to hundreds of thousands of predictions, most (if not all) of which go untested. In a best-case scenario, a small subsample of predictions (three to ten usually) is experimentally validated, as a quality control step to attest to the global soundness of the full set of predictions. However, whether this small set is even representative of the global algorithm's performance is a question usually left unaddressed. Thus, a clear understanding of the strengths and weaknesses of an algorithm most often remains elusive, especially to the experimental biologists who must decide which tool to use to address a specific problem. In this chapter, we describe the first systematic set of challenges posed to the systems biology community in the framework of the DREAM (Dialogue for Reverse Engineering Assessments and Methods) project. These tests, which came to be known as the DREAM2 challenges, consist of data generously donated by participants to the DREAM project and curated in such a way as to become problems of network reconstruction and whose solutions, the actual networks behind the data, were withheld from the participants. The explanation of the resulting five challenges, a global comparison of the submissions, and a discussion of the best performing strategies are the main topics discussed.
journal_name
Ann N Y Acad Scijournal_title
Annals of the New York Academy of Sciencesauthors
Stolovitzky G,Prill RJ,Califano Adoi
10.1111/j.1749-6632.2009.04497.xsubject
Has Abstractpub_date
2009-03-01 00:00:00pages
159-95eissn
0077-8923issn
1749-6632pii
NYAS04497journal_volume
1158pub_type
杂志文章abstract：:The current trend in antipoverty policy emphasizes mandated empowerment: the poor are being handed the responsibility for making things better for themselves, largely without being asked whether this is what they want. Beneficiary control is now being built into public service delivery, while microcredit and small bus...
journal_title：Annals of the New York Academy of Sciences
pub_type： 杂志文章
doi：10.1196/annals.1425.019
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journal_title：Annals of the New York Academy of Sciences
pub_type： 杂志文章,评审
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abstract：:In a retrospective studies of spontaneous abortion, bias can arise if the investigator restricts attention to the outcome of the most recent pregnancy. Bias happens because couples tend to replace spontaneous abortions with other pregnancies until they achieve a live birth, after which they may avoid conception for a ...
journal_title：Annals of the New York Academy of Sciences
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doi：10.1111/j.1749-6632.1994.tb30416.x
更新日期：1994-02-18 00:00:00
abstract：:This paper describes the flight experiment, supporting ground science, and the design rationale for a project on spaceflight holography investigation in a virtual apparatus (SHIVA). SHIVA is a fundamental study of particle dynamics in fluids in microgravity. Gravitation effects and steady Stokes drag often dominate th...
journal_title：Annals of the New York Academy of Sciences
pub_type： 杂志文章
doi：10.1196/annals.1324.042
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journal_title：Annals of the New York Academy of Sciences
pub_type： 杂志文章
doi：10.1111/j.1749-6632.2002.tb02097.x
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journal_title：Annals of the New York Academy of Sciences
pub_type： 杂志文章,评审
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journal_title：Annals of the New York Academy of Sciences
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doi：
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journal_title：Annals of the New York Academy of Sciences
pub_type： 杂志文章,评审
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更新日期：2003-09-01 00:00:00
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journal_title：Annals of the New York Academy of Sciences
pub_type： 杂志文章
doi：10.1111/j.1749-6632.1986.tb20954.x
更新日期：1986-01-01 00:00:00
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journal_title：Annals of the New York Academy of Sciences
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更新日期：2009-04-01 00:00:00
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journal_title：Annals of the New York Academy of Sciences
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更新日期：2017-02-01 00:00:00
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journal_title：Annals of the New York Academy of Sciences
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journal_title：Annals of the New York Academy of Sciences
pub_type： 杂志文章
doi：10.1111/j.1749-6632.1982.tb43423.x
更新日期：1982-12-10 00:00:00
abstract：:Learning theory proposes that drug seeking is a synthesis of multiple controllers. Whereas goal-directed drug seeking is determined by the anticipated incentive value of the drug, habitual drug seeking is elicited by stimuli that have formed a direct association with the response. Moreover, drug-paired stimuli can tra...
journal_title：Annals of the New York Academy of Sciences
pub_type： 杂志文章,评审
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更新日期：2013-04-01 00:00:00
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journal_title：Annals of the New York Academy of Sciences
pub_type： 杂志文章,评审
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更新日期：2006-08-01 00:00:00
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journal_title：Annals of the New York Academy of Sciences
pub_type： 杂志文章
doi：10.1196/annals.1423.047
更新日期：2007-09-01 00:00:00
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journal_title：Annals of the New York Academy of Sciences
pub_type： 杂志文章,评审
doi：10.1111/j.1749-6632.2008.03988.x
更新日期：2009-01-01 00:00:00
abstract：:The aim of this prospective study was to assess the prevalence of antiphospholipid antibodies (aPL) in women who had undergone in vitro fertilization (IVF) and the relationship between aPL and IVF outcome. A total of 101 infertile women with at least three unsuccessful IVF attempts were consecutively included in this ...
journal_title：Annals of the New York Academy of Sciences
pub_type： 杂志文章
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更新日期：2007-06-01 00:00:00
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journal_title：Annals of the New York Academy of Sciences
pub_type： 杂志文章,评审
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更新日期：2004-12-01 00:00:00
abstract：:Curcumin (diferuloylmethane) is a nontoxic dietary pigment in tumeric and curry and a potent inhibitor of the common transcription factor Nuclear Factor kappaB (NF-kappaB) in several cell types. It is well established that some of the catabolic effects of the proinflammatory cytokines interleukin-1beta (IL-1beta) and ...
journal_title：Annals of the New York Academy of Sciences
pub_type： 杂志文章
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更新日期：2004-12-01 00:00:00
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journal_title：Annals of the New York Academy of Sciences
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更新日期：2003-12-01 00:00:00
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journal_title：Annals of the New York Academy of Sciences
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更新日期：1990-01-01 00:00:00
abstract：:How can people adaptively analyze and "work through" negative feelings without ruminating? This paper will briefly review findings from an integrative program of research, which suggests that a critical factor determining whether people's attempts to adaptively reason about negative experiences succeed or fail is the ...
journal_title：Annals of the New York Academy of Sciences
pub_type： 杂志文章,评审
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更新日期：2009-06-01 00:00:00
abstract：:The objectives of ExoMars are to inject an orbiter around Mars and to land a rover on the surface to look for possible traces of life. During the first stages of the feasibility analysis, the mass margin of the orbiter was very small for a direct transfer in the Soyuz/Fregat scenario. An analysis of the combined use o...
journal_title：Annals of the New York Academy of Sciences
pub_type： 杂志文章
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更新日期：2005-12-01 00:00:00
abstract：:Various mechanisms have been identified by which hormones and neurotransmitters, interacting with heptahelical receptors, modulate the intracellular Ca2+ concentration in neuronal, endocrine, and neuroendocrine cells. All of them involve heterotrimeric G proteins. Best documented are hormonal stimulations and inhibiti...
journal_title：Annals of the New York Academy of Sciences
pub_type： 杂志文章,评审
doi：10.1111/j.1749-6632.1994.tb17280.x
更新日期：1994-09-15 00:00:00
abstract：:The effect of combined treatment with ribavirin and tiazofurin on the development of experimental autoimmune encephalomyelitis, the best characterized animal model for human autoimmune disease multiple sclerosis, was investigated. The disease was induced in highly susceptible Dark Agouti rats with spinal cord homogena...
journal_title：Annals of the New York Academy of Sciences
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abstract：UNLABELLED:Hepatocarcinogenesis is a multistep process characterized by hepatocyte inflammation, regeneration, and proliferation. These changes are believed to depend on the aberrant expression of various tumor suppressor genes, oncogenes and growth factors. Several studies have shown the involvement of cyclooxygenase-...
journal_title：Annals of the New York Academy of Sciences
pub_type： 杂志文章
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更新日期：2009-02-01 00:00:00
abstract：:Mammalian spermatogenesis is a complex developmental process. Spermatozoa, like ova, are uniquely capable of supporting embryonic development. Our approach to understanding this process is to identify genes whose developmental pattern of expression suggests that they may play a role in spermatogenesis. Experiments on ...
journal_title：Annals of the New York Academy of Sciences
pub_type： 杂志文章
doi：10.1111/j.1749-6632.1987.tb25002.x
更新日期：1987-01-01 00:00:00
abstract：:Cancer remains one of the leading causes of death worldwide. Thus, to identify any useful biomarkers is still a need. We performed "cancer immunomics" to identify autoantibody signatures produced in response to the presence of either breast or colorectal cancer. SERological proteome analysis (SERPA) was performed by t...
journal_title：Annals of the New York Academy of Sciences
pub_type： 杂志文章
doi：10.1196/annals.1381.024
更新日期：2007-06-01 00:00:00
abstract：:Bone marrow transplantation (BMT) is currently a procedure that is associated with high morbidity and mortality. Thus, the clinical application of this technique is limited to the treatment of life-threatening hematopoietic malignancies. The morbidity and mortality of BMT is mainly related to graft-versus-host disease...
journal_title：Annals of the New York Academy of Sciences
pub_type： 杂志文章,评审
doi：10.1111/j.1749-6632.1999.tb08482.x
更新日期：1999-04-30 00:00:00
