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  • Algorithms in Biology

    The exhaustive list of topics in Algorithms in Biology in which we provide Help with Homework Assignment and Help with Project is as follows:

    Genomic Rearrangements

    •  Genome Rearrangements in Mammalian Evolution

    •  Reconstructing contiguous regions of an ancestral genome

    Repetitive DNA Detection and Classification

    •  Piler: identification and classification of genomic repeats

    •  De novo identification of repeat families in large genomes

    Index-based search of single sequences

    •  BLAT -- The BLAST-like alignment tool

    •  Designing seeds for similarity search

    Multiple indexes and multiple alignments

    •  Designing Multiple Simultaneous Seeds for DNA Similarity Search

    •  Using multiple alignments to improve seeded local alignment algorithms

    Multiple Sequence Alignment

    •   An algorithm for progressive multiple alignment of sequences with insertions

    •   Probabilistic consistency-based multiple sequence alignment

    Inverse Alignment

    •   Simple and fast inverse alignment

    •  CONTRAlign: discriminative training for protein sequence alignment

    Ab initio motif finding

    •  Ab initio prediction of transcription factor targets using structural knowledge

    •  MotifCut: regulatory motif finding with maximum density subgraphs

    Comparative motif finding

    •  Discovery of regulatory elements by a computational method for phylogenetic footprinting

    •  Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals

    RNA Secondary Structure Prediction

    •  A study of accessible motifs and RNA folding complexity

    •  CONTRAfold: RNA secondary structure prediction without physics-based models

    RNA regulation

    •  Identification of hundreds of conserved and nonconserved human microRNAs

    •  RNA regulation: a new genetics?

    •  Challenging the dogma: the hidden layer of non-protein-coding RNAs in complex organisms

    RNA finding

    •  Searching genomes for noncoding RNA using FastR

    •   A sequence-based filtering method for ncRNA identification and its application to searching for riboswitch elements

    Evolution of Multidomain Proteins

    •  Graph theoretical insights into evolution of multidomain proteins

    •  Evolution of the protein repertoire

    Stochastic roadmap simulations of protein kinetics

    •  Stochastic roadmap simulation: an efficient representation and algorithm for analyzing molecular motion

    •  Predicting experimental quantities in protein folding kinetics using stochastic roadmap simulation

    Protein Folding Dynamics

    •   Simulating protein motions with rigidity analysis

    •   Markov methods for hierarchical coarse-graining of large protein dynamics

    Inference of phylogenetic trees

    •  A structural EM algorithm for phylogenetic inference

    •  Disc-covering, a fast converging method for phylogenetic tree reconstruction

    Gene trees

    •  Orthology, paralogy, and proposed classification for paralog subtypes

    •   A hybrid micro-macro evolutionary approach to gene tree reconstruction

    Comparison of Networks Across Species

    •  Conserved patterns of protein interaction in multiple species

    •  Graemlin: General and robust alignment of multiple large interaction networks

    Human-Chimp Speciation

    •   Inferring the Mode of Speciation From Genomic Data: A Study of the Great Apes

    •   Genetic evidence for complex speciation of humans and chimpanzees

    Protein Structure Alignment

    •   Approximate protein structure alignment in polynomial time

    •   A parameterized algorithm for protein structure alignment

    Machine Learning for Protein Classification

    •  Mismatch string kernels for discriminative protein classification

    •  Semi-supervised protein classification using cluster kernels

    Construction of Networks from Diverse Data Sources

    •  A probabilistic functional network of yeast genes

    •   Integrated Protein Interaction Networks for 11 Microbes

    Robust Self-Assembly of DNA

    •  Error free self-assembly using error prone tilesProperties of Interaction Networks

    •  Self-healing tile sets

    •  Complexity of self-assembled shapes

    •  Evidence for dynamically organized modularity in the yeast protein-protein interaction network

    •  Subnets of scale-free networks are not scale free: sampling properties of networks

    Human Migrations

    •  The application of molecular approaches to the study of human evolution

    •  Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa

    •   Recovering the geographic origin of early modern humans by realistic and spatially explicit simulations

    Human Evolution

    •   Positive natural selection in the human lineage

    •   Global landscape of recent inferred Darwinian selection for Homo sapiens

    •   A map of recent positive selection in the Human genome

    Transforming Cells into Automata

    •  Predicting post-synaptic activity in proteins with data mining

    •  Filtering erroneous protein annotation

    •   Engineering Life: building a FAB for Biology

    •   Genetic Circuit Building Blocks for Cellular Computation, Communications, and Signal Processing