Educational papers from Nature Biotechnology and PLoS Computational Biology.

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Nature Biotechnology

Computational Biology Primers

This is a list of explanatory papers that have appeared as primer in the Computational Biology section of the journal Nature Biotechnology, in reverse chronological order. (Last addition November 2013 / checked July 2017).

So you want to be a computational biologist? ("Commentary")
(Nick Loman & Mick Watson)
November 2013, Vol 31, No 11; pp 996 - 998
doi: 10.1038/nbt.2740 (?)

The anatomy of successful computational biology software ("Feature")
(Stephen Altschul, Barry Demchak, Richard Durbin, Robert Gentleman, Martin Krzywinski, Heng Li, Anton Nekrutenko, James Robinson, Wayne Rasband, James Taylor & Cole Trapnell)
October 2013, Vol 31, No 10; pp 894 - 897
doi: 10.1038/nbt.2721 (?)

How to apply de Bruijn graphs to genome assembly
(Phillip E C Compeau, Pavel A Pevzner & Glenn Tesler)
November 2011, Vol 29, No 11; pp 987 - 991
doi: 10.1038/nbt.2023 (?)

Analyzing 'omics data using hierarchical models
(Hongkai Ji & X Shirley Liu)
April 2010, Vol 28, No 4; pp 337 - 340
doi: 10.1038/nbt.1619 (?)

What is flux balance analysis?
(Jeffrey D Orth, Ines Thiele & Bernhard Ø Palsson)
March 2010, Vol 28, No 3; pp 245 - 248
doi: 10.1038/nbt.1614 (?)

How does multiple testing correction work?
(William S Noble)
December 2009, Vol 27, No 12 ; pp 1135 - 1137
doi: 10.1038/nbt1209-1135 (?)

How to visually interpret biological data using networks
(Daniele Merico, David Gfeller & Gary D Bader)
October 2009, Vol 27 No 10 ; pp 921 - 924
doi: 10.1038/nbt.1567 (?)

How to map billions of short reads onto genomes
(Cole Trapnell & Steven L Salzberg)
May 2009, Vol 27, No 5; pp 455 - 457
doi: 10.1038/nbt0509-455 (?)

SNP imputation in association studies
(Eran Halperin & Dietrich A Stephan)
April 2009, Vol 27, No 4; pp 349 - 351
doi: 10.1038/nbt0409-349 (?)

Maximizing power in association studies
(Eran Halperin & Dietrich A Stephan)
March 2009, Vol 27, No 3; pp 255 - 256
doi: 10.1038/nbt0309-255 (?)

Understanding genome browsing
(Melissa S Cline & W James Kent)
February 2009, Vol 27, No 2; pp 153 - 155
doi: 10.1038/nbt0209-153 (?)

What are decision trees?
(Carl Kingsford & Steven L Salzberg)
September 2008, Volume 26, No 9; pp 1011 - 1013
doi: 10.1038/nbt0908-1011 (?)

What is the expectation maximization algorithm?
(Chuong B Do & Serafim Batzoglou)
August 2008, Volume 26 No 8; pp 897 - 899
doi: 10.1038/nbt1406 (?)

What is principal component analysis?
(Markus Ringnér)
March 2008, Volume 26, No 3; pp 303 - 304
doi: 10.1038/nbt0308-303 (?)

What are artificial neural networks?
(Anders Krogh)
February 2008, Volume 26, No 2; pp 195 - 197
doi: 10.1038/nbt1386 (?)

How does eukaryotic gene prediction work?
(Michael R Brent)
August 2007, Volume 25, No 8; pp 883 - 885
doi: 10.1038/nbt0807-883 (?)

How do shotgun proteomics algorithms identify proteins?
(Edward M Marcotte)
July 2007, Volume 25, No 7; pp 755 - 757
doi: 10.1038/nbt0707-755 (?)

What is a support vector machine?
(William S Noble)
December 2006, Volume 24, No 12; pp 1565 - 1567
doi: 10.1038/nbt1206-1565 (?)

How does DNA sequence motif discovery work?
(Patrik D'haeseleer)
August 2006, Volume 24, No 8; pp 959 - 961
doi: 10.1038/nbt0806-959 (?)

What are DNA sequence motifs?
(Patrik D'haeseleer)
April 2006, Volume 24, No 4; pp 423 - 425
doi: 10.1038/nbt0406-423 (?)

Inference in Bayesian networks
(Chris J Needham, James R Bradford, Andrew J Bulpitt & David R Westhead)
January 2006, Volume 24, No 1; pp 51 - 53
doi: 10.1038/nbt0106-51 (?)

How does gene expression clustering work?
(Patrik D'haeseleer)
December 2005, Volume 23, No 12; pp 1499 - 1501
doi: 10.1038/nbt1205-1499 (?)

How do RNA folding algorithms work?
(Sean R Eddy)
November 2004, Volume 22, No 11; pp 1457 - 1458
doi: 10.1038/nbt1104-1457 (?)

What is a hidden Markov model?
(Sean R Eddy)
October 2004, Volume 22, No 10; pp 1315 - 1316
doi: 10.1038/nbt1004-1315 (?)

What is Bayesian statistics?
(Sean R Eddy)
September 2004, Volume 22, No 9; pp 1177 - 1178
doi: 10.1038/nbt0904-1177 (?)

Where did the BLOSUM62 alignment score matrix come from?
(Sean R Eddy)
August 2004, Volume 22, No 8; pp 1035 - 1036
doi: 10.1038/nbt0804-1035 (?)

What is dynamic programming?
(Sean R Eddy)
July 2004, Volume 22, No 7; pp 909 - 910
doi: 10.1038/nbt0704-909 (?)

Journal home

PloS Computational Biology

Several Captions have been used to indicate educationally relevant papers in Plos CompBio. Here we have collected some other papers.

Getting Started in ...

Getting Started in Gene Orthology and Functional Analysis
(Fang G, Bhardwaj N, Robilotto R, Gerstein MB)
PLoS Comput Biol (2010) 6(3): e1000703;
doi: 10.1371/journal.pcbi.1000703 (?)

Getting Started in Structural Phylogenomics
(Sjölander K )
PLoS Comput Biol (2010) 6(1): e1000621 ;
doi: 10.1371/journal.pcbi.1000621 (?)

Getting Started in Gene Expression Microarray Analysis
(Slonim DK, Yanai I)
PLoS Comput Biol (2009) 5(10): e1000543;
doi: 10.1371/journal.pcbi.1000543 (?)

Getting Started in Text Mining: Part Two.
(Rzhetsky A, Seringhaus M, Gerstein MB)
PLoS Comput Biol (2009) 5(7): e1000411. ;
doi: 10.1371/journal.pcbi.1000411 (?)

Getting Started in Computational Mass Spectrometry-Based Proteomics.
(Vitek O)
PLoS Comput Biol (2009) 5(5): e1000366. ;
doi: 10.1371/journal.pcbi.1000366 (?)

Getting Started in Computational Immunology.
(Kleinstein SH )
PLoS Comput Biol (2008) 4(8): e1000128;
doi: 10.1371/journal.pcbi.1000128 (?)

Getting Started in Biological Pathway Construction and Analysis.
(Viswanathan GA, Seto J, Patil S, Nudelman G, Sealfon SC )
PLoS Comput Biol (2008) 4(2): e16;
doi: 10.1371/journal.pcbi.0040016 (?)

Getting Started in Text Mining
(Cohen KB, Hunter L)
PLoS Comput Biol (2008) 4(1): e20;
doi: 10.1371/journal.pcbi.0040020 (?)

Getting Started in Probabilistic Graphical Models.
(Airoldi EM )
PLoS Comput Biol (2007) 3(12): e252. ;
doi: 10.1371/journal.pcbi.0030252 (?)

Getting Started in Tiling Microarray Analysis
(Liu XS)
PLoS Comput Biol (2007) 3(10): e183;
doi: 10.1371/journal.pcbi.0030183 (?)

Ten Simple Rules

PLOS CB publishes a series "Ten Simple Rules" with titles like 'Ten Simple Rules for Getting Published' or '...for a Good Poster Presentation', etc. We could no longer find an overview. Try to find them using the search page.

On the Process of Becoming a Great Scientist
(Giddings MC)
PLoS Comput Biol (2008) 4(2): e33;
doi: 10.1371/journal.pcbi.0040033 (?)