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1
Tackling the widespread and critical impact of batch effects in high-throughput data
Tackling the widespread and critical impact of batch effects in high-throughput data
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Tackling the widespread and critical impact of batch effects in high-throughput data

Nature reviews. Genetics, 2010-10, Vol.11 (10), p.733-739 [Peer Reviewed Journal]

2015 INIST-CNRS ;COPYRIGHT 2010 Nature Publishing Group ;COPYRIGHT 2010 Nature Publishing Group ;Copyright Nature Publishing Group Oct 2010 ;2010 Macmillan Publishers Limited. All rights reserved 2010 ;ISSN: 1471-0056 ;EISSN: 1471-0064 ;DOI: 10.1038/nrg2825 ;PMID: 20838408

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2
BioSeq-Analysis: a platform for DNA, RNA and protein sequence analysis based on machine learning approaches
BioSeq-Analysis: a platform for DNA, RNA and protein sequence analysis based on machine learning approaches
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BioSeq-Analysis: a platform for DNA, RNA and protein sequence analysis based on machine learning approaches

Briefings in bioinformatics, 2019-07, Vol.20 (4), p.1280-1294 [Peer Reviewed Journal]

The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com 2017 ;The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com. ;The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com ;ISSN: 1467-5463 ;EISSN: 1477-4054 ;DOI: 10.1093/bib/bbx165 ;PMID: 29272359

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3
Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing
Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing
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Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing

BMC genomics, 2011-05, Vol.12 (1), p.245-245, Article 245 [Peer Reviewed Journal]

COPYRIGHT 2011 BioMed Central Ltd. ;COPYRIGHT 2011 BioMed Central Ltd. ;Attribution ;Copyright ©2011 Gilles et al; licensee BioMed Central Ltd. 2011 Gilles et al; licensee BioMed Central Ltd. ;ISSN: 1471-2164 ;EISSN: 1471-2164 ;DOI: 10.1186/1471-2164-12-245 ;PMID: 21592414

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4
NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy
NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy
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NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

Nucleic acids research, 2012-01, Vol.40 (D1), p.D130-D135 [Peer Reviewed Journal]

Published by Oxford University Press, 2011. 2011 ;ISSN: 0305-1048 ;EISSN: 1362-4962 ;DOI: 10.1093/nar/gkr1079 ;PMID: 22121212

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5
Microbial resolution of whole genome shotgun and 16S amplicon metagenomic sequencing using publicly available NEON data
Microbial resolution of whole genome shotgun and 16S amplicon metagenomic sequencing using publicly available NEON data
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Microbial resolution of whole genome shotgun and 16S amplicon metagenomic sequencing using publicly available NEON data

PloS one, 2020-02, Vol.15 (2), p.e0228899 [Peer Reviewed Journal]

2020 Brumfield et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. ;2020 Brumfield et al 2020 Brumfield et al ;ISSN: 1932-6203 ;EISSN: 1932-6203 ;DOI: 10.1371/journal.pone.0228899 ;PMID: 32053657

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6
Repetitive DNA and next-generation sequencing: computational challenges and solutions
Repetitive DNA and next-generation sequencing: computational challenges and solutions
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Repetitive DNA and next-generation sequencing: computational challenges and solutions

Nature reviews. Genetics, 2012-01, Vol.13 (1), p.36-46 [Peer Reviewed Journal]

COPYRIGHT 2012 Nature Publishing Group ;COPYRIGHT 2012 Nature Publishing Group ;Copyright Nature Publishing Group Jan 2012 ;2012 Macmillan Publishers Limited. All rights reserved 2012 ;ISSN: 1471-0056 ;EISSN: 1471-0064 ;DOI: 10.1038/nrg3117 ;PMID: 22124482

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7
Sequencing technologies - the next generation
Sequencing technologies - the next generation
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Sequencing technologies - the next generation

Nature reviews. Genetics, 2010-01, Vol.11 (1), p.31-46 [Peer Reviewed Journal]

2015 INIST-CNRS ;COPYRIGHT 2010 Nature Publishing Group ;COPYRIGHT 2010 Nature Publishing Group ;Copyright Nature Publishing Group Jan 2010 ;ISSN: 1471-0056 ;EISSN: 1471-0064 ;DOI: 10.1038/nrg2626 ;PMID: 19997069

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8
BioSeq-Analysis2.0: an updated platform for analyzing DNA, RNA and protein sequences at sequence level and residue level based on machine learning approaches
BioSeq-Analysis2.0: an updated platform for analyzing DNA, RNA and protein sequences at sequence level and residue level based on machine learning approaches
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BioSeq-Analysis2.0: an updated platform for analyzing DNA, RNA and protein sequences at sequence level and residue level based on machine learning approaches

Nucleic acids research, 2019-11, Vol.47 (20), p.e127-e127 [Peer Reviewed Journal]

The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. 2019 ;The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. ;ISSN: 0305-1048 ;EISSN: 1362-4962 ;DOI: 10.1093/nar/gkz740 ;PMID: 31504851

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9
Genome structural variation discovery and genotyping
Genome structural variation discovery and genotyping
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Genome structural variation discovery and genotyping

Nature reviews. Genetics, 2011-05, Vol.12 (5), p.363-376 [Peer Reviewed Journal]

2015 INIST-CNRS ;COPYRIGHT 2011 Nature Publishing Group ;COPYRIGHT 2011 Nature Publishing Group ;Copyright Nature Publishing Group May 2011 ;2011 Macmillan Publishers Limited. All rights reserved 2011 ;ISSN: 1471-0056 ;EISSN: 1471-0064 ;DOI: 10.1038/nrg2958 ;PMID: 21358748

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10
The beginning of the end for microarrays?
The beginning of the end for microarrays?
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The beginning of the end for microarrays?

Nature methods, 2008-07, Vol.5 (7), p.585-587 [Peer Reviewed Journal]

COPYRIGHT 2008 Nature Publishing Group ;Copyright Nature Publishing Group Jul 2008 ;ISSN: 1548-7091 ;EISSN: 1548-7105 ;DOI: 10.1038/nmeth0708-585 ;PMID: 18587314

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11
De novo assembly of human genomes with massively parallel short read sequencing
De novo assembly of human genomes with massively parallel short read sequencing
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De novo assembly of human genomes with massively parallel short read sequencing

Genome research, 2010-02, Vol.20 (2), p.265-272 [Peer Reviewed Journal]

Copyright © 2010 by Cold Spring Harbor Laboratory Press ;ISSN: 1088-9051 ;EISSN: 1549-5469 ;DOI: 10.1101/gr.097261.109 ;PMID: 20019144

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12
Pse-in-One: a web server for generating various modes of pseudo components of DNA, RNA, and protein sequences
Pse-in-One: a web server for generating various modes of pseudo components of DNA, RNA, and protein sequences
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Pse-in-One: a web server for generating various modes of pseudo components of DNA, RNA, and protein sequences

Nucleic acids research, 2015-07, Vol.43 (W1), p.W65-W71 [Peer Reviewed Journal]

The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. ;The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. 2015 ;ISSN: 0305-1048 ;EISSN: 1362-4962 ;DOI: 10.1093/nar/gkv458 ;PMID: 25958395

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13
Next-generation transcriptome assembly
Next-generation transcriptome assembly
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Next-generation transcriptome assembly

Nature reviews. Genetics, 2011-10, Vol.12 (10), p.671-682 [Peer Reviewed Journal]

2015 INIST-CNRS ;COPYRIGHT 2011 Nature Publishing Group ;COPYRIGHT 2011 Nature Publishing Group ;Copyright Nature Publishing Group Oct 2011 ;ISSN: 1471-0056 ;EISSN: 1471-0064 ;DOI: 10.1038/nrg3068 ;PMID: 21897427

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14
DNA sequencing at 40: past, present and future
DNA sequencing at 40: past, present and future
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DNA sequencing at 40: past, present and future

Nature (London), 2017-10, Vol.550 (7676), p.345-353 [Peer Reviewed Journal]

COPYRIGHT 2017 Nature Publishing Group ;COPYRIGHT 2017 Nature Publishing Group ;Copyright Nature Publishing Group Oct 19, 2017 ;ISSN: 0028-0836 ;EISSN: 1476-4687 ;DOI: 10.1038/nature24286 ;PMID: 29019985

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15
Limitations of next-generation genome sequence assembly
Limitations of next-generation genome sequence assembly
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Limitations of next-generation genome sequence assembly

Nature methods, 2011-01, Vol.8 (1), p.61-65 [Peer Reviewed Journal]

COPYRIGHT 2011 Nature Publishing Group ;Copyright Nature Publishing Group Jan 2011 ;2011 Nature America, Inc. All rights reserved. 2011 ;ISSN: 1548-7091 ;EISSN: 1548-7105 ;DOI: 10.1038/nmeth.1527 ;PMID: 21102452

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16
The MEME Suite
The MEME Suite
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The MEME Suite

Nucleic acids research, 2015-07, Vol.43 (W1), p.W39-W49 [Peer Reviewed Journal]

The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. ;The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. 2015 ;ISSN: 0305-1048 ;EISSN: 1362-4962 ;DOI: 10.1093/nar/gkv416 ;PMID: 25953851

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17
ggseqlogo: a versatile R package for drawing sequence logos
ggseqlogo: a versatile R package for drawing sequence logos
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ggseqlogo: a versatile R package for drawing sequence logos

Bioinformatics (Oxford, England), 2017-11, Vol.33 (22), p.3645-3647 [Peer Reviewed Journal]

The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com ;ISSN: 1367-4803 ;EISSN: 1367-4811 ;DOI: 10.1093/bioinformatics/btx469 ;PMID: 29036507

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18
limma powers differential expression analyses for RNA-sequencing and microarray studies
limma powers differential expression analyses for RNA-sequencing and microarray studies
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limma powers differential expression analyses for RNA-sequencing and microarray studies

Nucleic acids research, 2015-04, Vol.43 (7), p.e47-e47 [Peer Reviewed Journal]

The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. ;The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. 2015 ;ISSN: 0305-1048 ;EISSN: 1362-4962 ;DOI: 10.1093/nar/gkv007 ;PMID: 25605792

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19
Hybrid selection of discrete genomic intervals on custom-designed microarrays for massively parallel sequencing
Hybrid selection of discrete genomic intervals on custom-designed microarrays for massively parallel sequencing
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Hybrid selection of discrete genomic intervals on custom-designed microarrays for massively parallel sequencing

Nature protocols, 2009-06, Vol.4 (6), p.960-974 [Peer Reviewed Journal]

COPYRIGHT 2009 Nature Publishing Group ;Copyright Nature Publishing Group Jun 2009 ;2009 Nature Publishing Group 2009 ;ISSN: 1754-2189 ;EISSN: 1750-2799 ;DOI: 10.1038/nprot.2009.68 ;PMID: 19478811

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20
Power analysis of single-cell RNA-sequencing experiments
Power analysis of single-cell RNA-sequencing experiments
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Power analysis of single-cell RNA-sequencing experiments

Nature methods, 2017-04, Vol.14 (4), p.381-387 [Peer Reviewed Journal]

Copyright Nature Publishing Group Apr 2017 ;ISSN: 1548-7091 ;EISSN: 1548-7105 ;DOI: 10.1038/nmeth.4220 ;PMID: 28263961

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