Advances in technology across all areas of science have ushered in an era of big data, providing researchers with unprecedented opportunities to understand how biological systems function and interact. Scientists are now faced with the challenge of developing sophisticated computational tools capable of unravelling these data and uncovering important biological signals. Computational biology will continue to play a key role in facilitating multi-disciplinary collaborations, encouraging data sharing and establishing experimental and analytical standards in the life sciences.

Produced with support from IBM Research and IBM Watson Health.






Nature Biotechnology Primers

What is flux balance analysis?

Jeffrey D Orth, Ines Thiele and Bernhard θ Palsson

doi:10.1038/nbt.1614

Nature Biotechnology 28, 245-248 (2010)

What is a support vector machine?

William S Noble

doi:10.1038/nbt1206-1565

Nature Biotechnology 24, 1565-1567 (2006)

What is principal component analysis?

Markus Ringnér

doi:10.1038/nbt0308-303

Nature Biotechnology 26, 303-304 (2008)

How does gene expression clustering work?

Patrik D'haeseleer

doi:10.1038/nbt1205-1499

Nature Biotechnology 23, 1499-1501 (2005)

How to map billions of short reads onto genomes

Cole Trapnell and Steven L Salzberg

doi:10.1038/nbt0509-455

Nature Biotechnology 27, 455-457 (2009)

What is a hidden Markov model?

Sean R Eddy

doi:10.1038/nbt1004-1315

Nature Biotechnology 22, 1315-1316 (2004)

How does multiple testing correction work?

William S Noble

doi:10.1038/nbt1209-1135

Nature Biotechnology 27, 1135-1137 (2009)

Where did the BLOSUM62 alignment score matrix come from?

Sean R Eddy

doi:10.1038/nbt0804-1035

Nature Biotechnology 22, 1035-1036 (2004)

What are DNA sequence motifs?

Patrik D'haeseleer

doi:10.1038/nbt0406-423

Nature Biotechnology 24, 423-425 (2006)

How to apply de Bruijn graphs to genome assembly

Phillip E C Compeau, Pavel A Pevzner and Glenn Tesler

doi:10.1038/nbt.2023

Nature Biotechnology 29, 987-991 (2011)

What is the expectation maximization algorithm?

Chuong B Do and Serafim Batzoglou

doi:10.1038/nbt1406

Nature Biotechnology 26, 897-899 (2008)

What are artificial neural networks?

Anders Krogh

doi:10.1038/nbt1386

Nature Biotechnology 26, 195-197 (2008)

How do RNA folding algorithms work?

Sean R Eddy

doi:10.1038/nbt1104-1457

Nature Biotechnology 22, 1457-1458 (2004)

How do shotgun proteomics algorithms identify proteins?

Edward M Marcotte

doi:10.1038/nbt0707-755

Nature Biotechnology 25, 755-757 (2007)

Inference in Bayesian networks

Chris J Needham, James R Bradford, Andrew J Bulpitt and David R Westhead

doi:10.1038/nbt0106-51

Nature Biotechnology 24, 51-53 (2006)

What are decision trees?

Carl Kingsford and Steven L Salzberg

doi:10.1038/nbt0908-1011

Nature Biotechnology 26, 1011-1013 (2008)

How does DNA sequence motif discovery work?

Patrik D'haeseleer

doi:10.1038/nbt0806-959

Nature Biotechnology 24, 959-961 (2006)

What is dynamic programming?

Sean R Eddy

doi:10.1038/nbt0704-909

Nature Biotechnology 22, 909-910 (2004)

What is Bayesian statistics?

Sean R Eddy

doi:10.1038/nbt0904-1177

Nature Biotechnology 22, 1177-1178 (2004)

How to visually interpret biological data using networks

Daniele Merico, David Gfeller and Gary D Bader

doi:10.1038/nbt.1567

Nature Biotechnology 27, 921-924 (2009)

SNP imputation in association studies

Eran Halperin and Dietrich A Stephan

doi:10.1038/nbt0409-349

Nature Biotechnology 27, 349-351 (2009)

Analyzing 'omics data using hierarchical models

Hongkai Ji and X Shirley Liu

doi:10.1038/nbt.1619

Nature Biotechnology 28, 337-340 (2010)

How does eukaryotic gene prediction work?

Michael R Brent

doi:10.1038/nbt0807-883

Nature Biotechnology 25, 883-885 (2007)

Understanding genome browsing

Melissa S Cline and W James Kent

doi:10.1038/nbt0209-153

Nature Biotechnology 27, 153-155 (2009)

Maximizing power in association studies

Eran Halperin and Dietrich A Stephan

doi:10.1038/nbt0309-255

Nature Biotechnology 27, 255-256 (2009)

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Nature Biotechnology Research Articles


Discovering microRNAs from deep sequencing data using miRDeep

Marc R Friedländer, Wei Chen, Catherine Adamidi, Jonas Maaskola, Ralf Einspanier, Signe Knespel and Nikolaus Rajewsky

doi:10.1038/nbt1394

Nature Biotechnology 26, 407-415 (2008)

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

Morgan G I Langille, Jesse Zaneveld, J Gregory Caporaso, Daniel McDonald, Dan Knights, Joshua A Reyes, Jose C Clemente, Deron E Burkepile, Rebecca L Vega Thurber, Rob Knight, Robert G Beiko and Curtis Huttenhower

doi:10.1038/nbt.2676

Nature Biotechnology 31, 814-821 (2013)

Extracting a cellular hierarchy from high-dimensional cytometry data with SPADE

Peng Qiu, Erin F Simonds, Sean C Bendall, Kenneth D Gibbs, Robert V Bruggner, Michael D Linderman, Karen Sachs, Garry P Nolan and Sylvia K Plevritis

doi:10.1038/nbt.1991

Nature Biotechnology 29, 886-891 (2011)

viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia

El-ad David Amir, Kara L Davis, Michelle D Tadmor, Erin F Simonds, Jacob H Levine, Sean C Bendall, Daniel K Shenfeld, Smita Krishnaswamy, Garry P Nolan and Dana Pe'er

doi:10.1038/nbt.2594

Nature Biotechnology 31, 545-552 (2013)

Systematic comparison of phenome-wide association study of electronic medical record data and genome-wide association study data

Joshua C Denny, Lisa Bastarache, Marylyn D Ritchie, Robert J Carroll, Raquel Zink, Jonathan D Mosley, Julie R Field, Jill M Pulley, Andrea H Ramirez, Erica Bowton, Melissa A Basford, David S Carrell, Peggy L Peissig, Abel N Kho, Jennifer A Pacheco, Luke V Rasmussen, David R Crosslin, Paul K Crane, Jyotishman Pathak, Suzette J Bielinski, Sarah A Pendergrass, Hua Xu, Lucia A Hindorff, Rongling Li, Teri A Manolio, Christopher G Chute, Rex L Chisholm, Eric B Larson, Gail P Jarvik, Murray H Brilliant, Catherine A McCarty, Iftikhar J Kullo, Jonathan L Haines, Dana C Crawford, Daniel R Masys and Dan M Roden

doi:10.1038/nbt.27494

Nature Biotechnology 31, 1102-1111 (2013)

Crowdsourced analysis of clinical trial data to predict amyotrophic lateral sclerosis progression

Robert Küffner, Neta Zach, Raquel Norel, Johann Hawe, David Schoenfeld, Liuxia Wang, Guang Li, Lilly Fang, Lester Mackey, Orla Hardiman, Merit Cudkowicz, Alexander Sherman, Gokhan Ertaylan, Moritz Grosse-Wentrup, Torsten Hothorn, Jules van Ligtenberg, Jakob H Macke, Timm Meyer, Bernhard Schölkopf, Linh Tran, Rubio Vaughan, Gustavo Stolovitzky and Melanie L Leitner

doi:10.1038/nbt.3051

Nature Biotechnology 33, 51-57 (2014)

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

Babak Alipanahi, Andrew Delong, Matthew T Weirauch and Brendan J Frey

doi:10.1038/nbt.3300

Nature Biotechnology 33, 831-838 (2015)

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

Jürgen Cox and Matthias Mann

doi:10.1038/nbt.1511

Nature Biotechnology 26, 1367-1372 (2008)

Full-length transcriptome assembly from RNA-Seq data without a reference genome

Manfred G Grabherr, Brian J Haas, Moran Yassour, Joshua Z Levin, Dawn A Thompson, Ido Amit, Xian Adiconis, Lin Fan, Raktima Raychowdhury, Qiandong Zeng, Zehua Chen, Evan Mauceli, Nir Hacohen, Andreas Gnirke, Nicholas Rhind, Federica di Palma, Bruce W Birren, Chad Nusbaum, Kerstin Lindblad-Toh, Nir Friedman and Aviv Regev

doi:10.1038/nbt.1883

Nature Biotechnology 29, 644-652 (2011)

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

Cole Trapnell, Brian A Williams, Geo Pertea, Ali Mortazavi, Gordon Kwan, Marijke J van Baren, Steven L Salzberg, Barbara J Wold and Lior Pachter

doi:10.1038/nbt.1621

Nature Biotechnology 28, 511-515 (2010)

Network-based prediction of human tissue-specific metabolism

Tomer Shlomi, Moran N Cabili, Markus J Herrgârd, Bernhard θ Palsson and Eytan Ruppin

doi:10.1038/nbt.1487

Nature Biotechnology 26, 1003-1010 (2008)

Hybrid error correction and de novo assembly of single-molecule sequencing reads

Sergey Koren, Michael C Schatz, Brian P Walenz, Jeffrey Martin, Jason T Howard, Ganeshkumar Ganapathy, Zhong Wang, David A Rasko, W Richard McCombie, Erich D Jarvis and Adam M Phillippy

doi:10.1038/nbt.2280

Nature Biotechnology 30, 693-700 (2012)


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