Journal of Molecular Biology

1959

Citations in the corpus

• Algebraic Statistics for Computational Biology: Preface (2005, methodology): “First, we give a self-contained explanation of the Needleman–Wunsch algorithm [Needleman and Wunsch, 1970] for aligning biological sequences.”
• Inverse statistical physics of protein sequences: a key issues review (2017, methodology): “After having adressed inverse models in statistical physics from the methodological point of view, we will give a few exemplary results from using these methodologies with real protein sequence data.”
• Hoeffding Races: Accelerating Model Selection Search for Classification and Function Approximation (1993, methodology): “This is the famous protein secondary structure database, with some preprocessing [Zhang et al., 1992].”
• Protein Secondary Structure Prediction Using Cascaded Convolutional and Recurrent Neural Networks (2016, methodology): “In the 1990s, significant improvements were achieved by exploiting the evolutionary information of proteins from the same structural family [Rost and Sander, 1993] and position-specific scoring matrices [Jones, 1999].”
• Power-Law Distributions in Empirical Data (2007, background): “In some cases it is known that the sampling procedure used can be biased, e.g., for the protein interactions (Sprinzak et al., 2003), citations and authorships (Bhattacharya and Getoor, 2007), and the Internet (Achlioptas et al., 2005; Dimitropoulos et al., 2007).”
• Integrated protein function prediction by mining function associations, sequences, and protein–protein and gene–gene interaction networks (2015, unknown): “protein function at the whole molecular level [17, 18], some methods predict protein function based on amino acid sequences [19, 20] .”
• The physics of epigenetics (2015, background): “It is therefore relevant to include the three-dimensional structure in the theoretical modeling of the spreading of epigenetic marks.”
• Robustness, evolvability, and neutrality (2005, unknown): “Keywords: Molecular evolution; Evolutionary novelty; Innovation”
• The transmission sense of information (2008, background): “coli (Bennetzen and Hall, 1982; Ikemura, 1981; Sharp and Li). While the underlying mechanisms for the correlations are not fully understood, simple models of mutation and selection can explain much of the observed variance (Bulmer, 1987; Knight et al., 2001). As another intriguing example, Mitarai e”