Study designs

Good experiments start with good planning. The analysis of genetic and molecular information involves increasingly sophisticated tools and methodologies, many of which are advancing at a fast pace. The articles in this series provide detailed advice on the most appropriate and up-to-date means for designing experiments, with the aim of helping researchers to maximise the value of their data.


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2017

May 2017 Volume 18 No 5

Detecting RNA modifications in the epitranscriptome: predict and validate

Mark Helm & Yuri Motorin

doi:10.1038/nrg.2016.169

April 2017 Volume 18 No 4

The evolution of tumour phylogenetics: principles and practice

Russell Schwartz & Alejandro A. Schäffer

doi:10.1038/nrg.2016.170

February 2017 Volume 18 No 2

Making sense of genomic islands of differentiation in light of speciation

Jochen B. W. Wolf & Hans Ellegren

doi:10.1038/nrg.2016.133

January 2017 Volume 18 No 1

Loss-of-function genetic tools for animal models: cross-species and cross-platform differences

Benjamin E. Housden, Matthias Muhar, Matthew Gemberling, Charles A. Gersbach, Didier Y. R. Stainier, Geraldine Seydoux, Stephanie E. Mohr, Johannes Zuber & Norbert Perrimon

doi:10.1038/nrg.2016.118

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2016

December 2016 Volume 17 No 12

The state of play in higher eukaryote gene annotation

Jonathan M. Mudge & Jennifer Harrow

doi:10.1038/nrg.2016.119

August 2016 Volume 17 No 8

Crowdsourcing biomedical research: leveraging communities as innovation engines

Julio Saez-Rodriguez, James C. Costello, Stephen H. Friend, Michael R. Kellen, Lara Mangravite, Pablo Meyer, Thea Norman & Gustavo Stolovitzky

doi:10.1038/nrg.2016.69

March 2016 Volume 17 No 3

Unravelling the human genome–phenome relationship using phenome-wide association studies

William S. Bush, Matthew T. Oetjens & Dana C. Crawford

doi:10.1038/nrg.2015.36

February 2016 Volume 17 No 2

Harnessing the power of RADseq for ecological and evolutionary genomics

Kimberly R. Andrews, Jeffrey M. Good, Michael R. Miller, Gordon Luikart & Paul A. Hohenlohe

doi:10.1038/nrg.2015.28

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2015

July 2015 Volume 16 No 7

Methods for the directed evolution of proteins

Michael S. Packer & David R. Liu

doi:10.1038/nrg3927

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2015

May 2015 Volume 16 No 5

Genetic linkage analysis in the age of whole-genome sequencing

Jurg Ott, Jing Wang & Suzanne M. Leal

doi:10.1038/nrg3908

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2014

November 2014 Volume 15 No 11

Identifying and mitigating bias in next-generation sequencing methods for chromatin biology

Clifford A. Meyer & X. Shirley Liu

doi:10.1038/nrg3788

May 2014 Volume 15 No 5

Statistical power and significance testing in large-scale genetic studies

Pak C. Sham & Shaun M. Purcell

doi:10.1038/nrg3706

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2013

February 2013 Volume 14 No 2

The heritability of human disease: estimation, uses and abuses

Albert Tenesa & Chris S. Haley

doi:10.1038/nrg3377

January 2013 Volume 14 No 1

Cancer pharmacogenomics: strategies and challenges

Heather E. Wheeler, Michael L. Maitland, M. Eileen Dolan, Nancy J. Cox & Mark J. Ratain

doi:10.1038/nrg3352

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2012

December 2012 Volume 13 No 12

ChIP–seq and beyond: new and improved methodologies to detect and characterize protein–DNA interactions

Terrence S. Furey

doi:10.1038/nrg3306

November 2012 Volume 13 No 11

Genetic variation in metabolic phenotypes: study designs and applications

Karsten Suhre & Christian Gieger

doi:10.1038/nrg3314

September 2012 Volume 13 No 9

The continuing value of twin studies in the omics era

Jenny van Dongen, P. Eline Slagboom, Harmen H. M. Draisma, Nicholas G. Martin & Dorret I. Boomsma

doi:10.1038/nrg3243

August 2012 Volume 13 No 8

Studying and modelling dynamic biological processes using time-series gene expression data

Ziv Bar-Joseph, Anthony Gitter & Itamar Simon

doi:10.1038/nrg3244

May 2012 Volume 13 No 5

Molecular phylogenetics: principles and practice

Ziheng Yang & Bruce Rannala

doi:10.1038/nrg3186

May 2012 Volume 13 No 5

Harnessing genomics and genome biology to understand malaria biology

Sarah K. Volkman, Daniel E. Neafsey, Stephen F. Schaffner, Daniel J. Park & Dyann F. Wirth

doi:10.1038/nrg3187

May 2012 Volume 13 No 5

A beginner's guide to eukaryotic genome annotation

Mark Yandell and Daniel Ence

doi:10.1038/nrg3186

February 2012 Volume 13 No 2

Computer simulations: tools for population and evolutionary genetics

Sean Hoban, Giorgio Bertorelle & Oscar E. Gaggiotti

doi:10.1038/nrg3130

January 2012 Volume 13 No 1

Experimental and analytical tools for studying the human microbiome

Justin Kuczynski, Christian L. Lauber, William A. Walters, Laura Wegener Parfrey, José C. Clemente, Dirk Gevers & Rob Knight

doi:10.1038/nrg3129

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2011

December 2011 Volume 12 No 12

Software for systems biology: from tools to integrated platforms

Samik Ghosh, Yukiko Matsuoka, Yoshiyuki Asai, Kun-Yi Hsin & Hiroaki Kitano

doi:10.1038/nrg3096

November 2011 Volume 12 No 11

Molecular spandrels: tests of adaptation at the genetic level

Rowan D. H. Barrett & Hopi E. Hoekstra

doi:10.1038/nrg3015

November 2011 Volume 12 No 11

Exome sequencing as a tool for Mendelian disease gene discovery

Michael J. Bamshad, Sarah B. Ng, Abigail W. Bigham, Holly K. Tabor, Mary J. Emond, Deborah A. Nickerson & Jay Shendure

doi:10.1038/nrg3031

October 2011 Volume 12 No 10

Next-generation transcriptome assembly

Jeffrey A. Martin & Zhong Wang

doi:10.1038/nrg3068

October 2011 Volume 12 No 10

Haplotype phasing: existing methods and new developments

Sharon R. Browning & Brian L. Browning

doi:10.1038/nrg3054

August 2011 Volume 12 No 8

New approaches to disease mapping in admixed populations

Michael F. Seldin, Bogdan Pasaniuc & Alkes L. Price

doi:10.1038/nrg3002

August 2011 Volume 12 No 8

Epigenome-wide association studies for common human diseases

Vardhman K. Rakyan, Thomas A. Down, David J. Balding & Stephan Beck

doi:10.1038/nrg3000

July 2011 Volume 12 No 7

Genome-wide genetic marker discovery and genotyping using next-generation sequencing

John W. Davey, Paul A. Hohenlohe, Paul D. Etter, Jason Q. Boone, Julian M. Catchen & Mark L. Blaxter

doi:10.1038/nrg3012

June 2011 Volume 12 No 6

Genotype and SNP calling from next-generation sequencing data

Rasmus Nielsen, Joshua S. Paul, Anders Albrechtsen & Yun S. Song

doi:10.1038/nrg2986

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2010

December 2010 Volume 11 No 12

Predicting genetic predisposition in humans: the promise of whole-genome markers

Gustavo de los Campos, Daniel Gianola & David B. Allison

doi:10.1038/nrg2898

November 2010 Volume 11 No 11

Statistical analysis strategies for association studies involving rare variants

Vikas Bansal, Ondrej Libiger, Ali Torkamani & Nicholas J. Schork

doi:10.1038/nrg2867

Reconciling the analysis of IBD and IBS in complex trait studies

Joseph E. Powell, Peter M. Visscher & Michael E. Goddard

doi:10.1038/nrg2865

October 2010 Volume 11 No 10

Evaluating genome-scale approaches to eukaryotic DNA replication

David M. Gilbert

doi:10.1038/nrg2830

Advances in understanding cancer genomes through second-generation sequencing

Matthew Meyerson, Stacey Gabriel and Gad Getz

doi:10.1038/nrg2841

April 2010 Volume 11 No 4

Gene–environment-wide association studies: emerging approaches

Duncan Thomas

doi:10.1038/nrg2764

March 2010 Volume 11 No 3

Principles and challenges of genome-wide DNA methylation analysis

Peter W. Laird

doi:10.1038/nrg2732

February 2010 Volume 11 No 2

Methodological challenges of genome-wide association analysis in Africa

Yik-Ying Teo, Kerrin S. Small & Dominic P. Kwiatkowski

doi:10.1038/nrg2731

January 2010 Volume 11 No 1

Sequencing technologies — the next generation

Michael L. Metzker

doi:10.1038/nrg2626

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2009

October 2009 Volume 10 No 10

Bayesian statistical methods for genetic association studies

Matthew Stephens & David J. Balding

doi:10.1038/nrg2615

ChIP–seq: advantages and challenges of a maturing technology

Peter J. Park

doi:10.1038/nrg2641

September 2009 Volume 10 No 9

Genetics of human gene expression: mapping DNA variants that influence gene expression

Vivian G. Cheung & Richard S. Spielman

doi:10.1038/nrg2630

Applying mass spectrometry-based proteomics to genetics, genomics and network biology

Matthias Gstaiger & Ruedi Aebersold

doi:10.1038/nrg2633

Microfluidic devices for measuring gene network dynamics in single cells

Matthew R. Bennett & Jeff Hasty

doi:10.1038/nrg2625

Genetics in geographically structured populations: defining, estimating and interpreting FST

Kent E. Holsinger & Bruce S. Weir

doi:10.1038/nrg2611

June 2009 Volume 10 No 6

Detecting gene–gene interactions that underlie human diseases

Heather J Cordell

doi:10.1038/nrg2579

May 2009 Volume 10 No 5

Validating, augmenting and refining genome-wide association signals

John P. A. Ioannidis, Gilles Thomas & Mark J. Daly

doi:10.1038/nrg2544

March 2009 Volume 10 No 3

Mapping complex disease traits with global gene expression

William Cookson, Liming Liang, Gonçalo Abecasis, Miriam Moffatt & Mark Lathrop

doi:10.1038/nrg2537

February 2009 Volume 10 No 2

Stochastic modelling for quantitative description of heterogeneous biological systems

Darren J. Wilkinson

doi:10.1038/nrg2509

January 2009 Volume 10 No 1

RNA-Seq: a revolutionary tool for transcriptomics

Zhong Wang, Mark Gerstein & Michael Snyder

doi:10.1038/nrg2484

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2008

July 2008 Volume 9 No 7

The art and design of genetic screens: RNA interference

Michael Boutros & Julie Ahringer

doi:10.1038/nrg2364

May 2008 Volume 9 No 5

Genome-wide association studies for complex traits: consensus, uncertainty and challenges

Mark I. McCarthy, Gonçalo R. Abecasis, Lon R. Cardon, David B. Goldstein, Julian Little, John P. A. Ioannidis & Joel N. Hirschhorn

doi:10.1038/nrg2344