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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

  •     Annotation Transfer Between Genomes: Protein?Protein Interologs and Protein?DNA Regulogs

•             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