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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