Building Block and Building Rule: Dual Descriptor Method for Biological Sequence Analysis [PDF]
, 2008 The emergence of “Systems Biology” in recent years highlights the systematic viewpoint of bio-system modeling. Building on such a background, Dual Descriptor Method, a generic methodology for biological sequence analysis is proposed. From a
Bin-Guang Ma
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Dynamics of Unperturbed and Noisy Generalized Boolean Networks
, 2009 For years, we have been building models of gene regulatory networks, where recent advances in molecular biology shed some light on new structural and dynamical properties of such highly complex systems.
Darabos, Christian +2 more
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Sequence modeling and design from molecular to genome scale with Evo
bioRxivThe genome is a sequence that completely encodes the DNA, RNA, and proteins that orchestrate the function of a whole organism. Advances in machine learning combined with massive datasets of whole genomes could enable a biological foundation model that ...
Eric Nguyen +15 more
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Journal of Molecular Biology, 1999 An improved dynamic programming algorithm is reported for RNA secondary structure prediction by free energy minimization. Thermodynamic parameters for the stabilities of secondary structure motifs are revised to include expanded sequence dependence as ...
D. Mathews +3 more
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Mapping the evolution of mitochondrial complex I through structural variation
FEBS Letters, EarlyView.Respiratory complex I (CI) is crucial for bioenergetic metabolism in many prokaryotes and eukaryotes. It is composed of a conserved set of core subunits and additional accessory subunits that vary depending on the organism. Here, we categorize CI subunits from available structures to map the evolution of CI across eukaryotes. Respiratory complex I (CI)
Dong‐Woo Shin +2 more
wiley +1 more source
Profile Context-Sensitive HMMs for Probabilistic Modeling of Sequences With Complex Correlations [PDF]
, 2006 The profile hidden Markov model is a specific type of HMM that is well suited for describing the common features of a set of related sequences. It has been extensively used in computational biology, where it is still one of the most popular tools.
Vaidyanathan, P. P., Yoon, Byung-Jun
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SIG-DB: leveraging homomorphic encryption to Securely Interrogate privately held Genomic DataBases
, 2018 Genomic data are becoming increasingly valuable as we develop methods to utilize the information at scale and gain a greater understanding of how genetic information relates to biological function.
Flower, Audrey +8 more
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Simple sequence repeats in zebra finch (Taeniopygia guttata) expressed sequence tags: a new resource for evolutionary genetic studies of passerines [PDF]
, 2007 Background Passerines (perching birds) are widely studied across many biological disciplines including ecology, population biology, neurobiology, behavioural ecology and evolutionary biology.
Birkhead, T.R., Hale, M.C., Slate, J.
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Synthetic biology open language (SBOL) version 3.0.0
Journal of Integrative Bioinformatics, 2020 Synthetic biology builds upon genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems.
Baig Hasan +14 more
doaj +1 more source
Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk
Nature Genetics, 2018 Key challenges for human genetics, precision medicine and evolutionary biology include deciphering the regulatory code of gene expression and understanding the transcriptional effects of genome variation.
Jian Zhou +5 more
semanticscholar +1 more source