QuanTest2: benchmarking multiple sequence alignments using secondary structure prediction.

Desmond G. Higgins https://scholar.google.com/citations?user=Ap0K7rUAAAAJ https://en.wikipedia.org/wiki/Desmond_G._Higgins https://orcid.org/0000-0002-3952-3285 https://www.wikidata.org/entity/Q20058405 https://www.researcherid.com/rid/J-6314-2012 http://isni.org/isni/000000004617439X https://viaf.org/viaf/32217080 https://id.loc.gov/authorities/names/no2001006610

Fabian Sievers Desmond G. Higgins QuanTest2: benchmarking multiple sequence alignments using secondary structure prediction. 90-95 2020 36 Bioinform. 1 https://doi.org/10.1093/bioinformatics/btz552 https://www.wikidata.org/entity/Q91777104 db/journals/bioinformatics/bioinformatics36.html#SieversH20

Quan Le Fabian Sievers Desmond G. Higgins Protein multiple sequence alignment benchmarking through secondary structure prediction. 1331-1337 2017 33 Bioinform. 9 https://doi.org/10.1093/bioinformatics/btw840 https://www.wikidata.org/entity/Q39017728 db/journals/bioinformatics/bioinformatics33.html#LeSH17

Gearoid Fox Fabian Sievers Desmond G. Higgins Using <i>de novo</i> protein structure predictions to measure the quality of very large multiple sequence alignments. 814-820 2016 32 Bioinform. 6 https://doi.org/10.1093/bioinformatics/btv592 https://www.wikidata.org/entity/Q30381372 db/journals/bioinformatics/bioinformatics32.html#FoxSH16

Peter Jehl Jean Manguy Denis C. Shields Desmond G. Higgins Norman E. Davey ProViz - a web-based visualization tool to investigate the functional and evolutionary features of protein sequences. W11-W15 2016 44 Nucleic Acids Res. Webserver-Issue https://doi.org/10.1093/nar/gkw265 https://www.wikidata.org/entity/Q39845548 db/journals/nar/nar44.html#JehlMSHD16

Kieran Boyce Fabian Sievers Desmond G. Higgins Instability in progressive multiple sequence alignment algorithms. 26 2015 10 Algorithms Mol. Biol. https://doi.org/10.1186/s13015-015-0057-1 https://www.wikidata.org/entity/Q40442593 db/journals/almob/almob10.html#BoyceSH15

Peter Jehl Fabian Sievers Desmond G. Higgins OD-seq: outlier detection in multiple sequence alignments. 269:1-269:11 2015 16 BMC Bioinform. https://doi.org/10.1186/s12859-015-0702-1 https://www.wikidata.org/entity/Q35754160 db/journals/bmcbi/bmcbi16.html#JehlSH15

Fabian Sievers Graham M. Hughes Desmond G. Higgins Systematic exploration of guide-tree topology effects for small protein alignments. 338 2014 15 BMC Bioinform. https://doi.org/10.1186/1471-2105-15-338 https://www.wikidata.org/entity/Q35302259 db/journals/bmcbi/bmcbi15.html#SieversHH14

Audrey M. Michel Gearoid Fox Anmol M. Kiran Christof De Bo Patrick B. F. O'Connor Stephen M. Heaphy James P. A. Mullan Claire A. Donohue Desmond G. Higgins Pavel V. Baranov GWIPS-viz: development of a ribo-seq genome browser. 859-864 2014 42 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkt1035 https://www.wikidata.org/entity/Q37661931 db/journals/nar/nar42.html#MichelFKBOHMDHB14

Fabian Sievers David Dineen Andreas Wilm Desmond G. Higgins Making automated multiple alignments of very large numbers of protein sequences. 989-995 2013 29 Bioinform. 8 https://doi.org/10.1093/bioinformatics/btt093 https://www.wikidata.org/entity/Q47913155 db/journals/bioinformatics/bioinformatics29.html#SieversDWH13

Gordon Blackshields Fabian Sievers Weifeng Shi Andreas Wilm Desmond G. Higgins Sequence embedding for fast construction of guide trees for multiple sequence alignment. 21 2010 5 Algorithms Mol. Biol. https://doi.org/10.1186/1748-7188-5-21 https://www.wikidata.org/entity/Q41504368 db/journals/almob/almob5.html#BlackshieldsSSWH10

Stephen F. Madden Susan B. Carpenter Ian B. Jeffery Harry Björkbacka Katherine A. Fitzgerald Luke A. O'Neill Desmond G. Higgins Detecting microRNA activity from gene expression data. 257 2010 11 BMC Bioinform. https://doi.org/10.1186/1471-2105-11-257 https://www.wikidata.org/entity/Q33581163 db/journals/bmcbi/bmcbi11.html#MaddenCJBFOH10

Gordon Blackshields Mark A. Larkin Iain M. Wallace Andreas Wilm Desmond G. Higgins Fast embedding methods for clustering tens of thousands of sequences. 282-286 2008 32 Comput. Biol. Chem. 4 https://doi.org/10.1016/j.compbiolchem.2008.03.005 https://www.wikidata.org/entity/Q43473840 db/journals/candc/candc32.html#BlackshieldsLWWH08

Simon J. Furney Stephen F. Madden Tomasz A. Kisiel Desmond G. Higgins Núria López-Bigas Distinct Patterns in the Regulation and Evolution of Human Cancer Genes. 33-46 2008 8 Silico Biol. 1 http://content.iospress.com/articles/in-silico-biology/isb00341 db/journals/isb/isb8.html#FurneyMKHL08

Sébastien Moretti Andreas Wilm Desmond G. Higgins Ioannis Xenarios Cédric Notredame R-Coffee: a web server for accurately aligning noncoding RNA sequences. 10-13 2008 36 Nucleic Acids Res. Web-Server-Issue https://doi.org/10.1093/nar/gkn278 https://www.wikidata.org/entity/Q24646160 db/journals/nar/nar36.html#MorettiWHXN08

Ian B. Jeffery Stephen F. Madden Paul A. McGettigan Guy Perrière Aedín C. Culhane Desmond G. Higgins Integrating transcription factor binding site information with gene expression datasets. 298-305 2007 23 Bioinform. 3 https://doi.org/10.1093/bioinformatics/btl597 https://www.wikidata.org/entity/Q48422980 db/journals/bioinformatics/bioinformatics23.html#JefferyMMPCH07

Mark A. Larkin Gordon Blackshields Nigel P. Brown R. Chenna Paul A. McGettigan Hamish McWilliam Franck Valentin Iain M. Wallace Andreas Wilm Rodrigo Lopez Julie Dawn Thompson Toby J. Gibson Desmond G. Higgins Clustal W and Clustal X version 2.0. 2947-2948 2007 23 Bioinform. 21 https://doi.org/10.1093/bioinformatics/btm404 https://www.wikidata.org/entity/Q27860517 db/journals/bioinformatics/bioinformatics23.html#LarkinBBCMMVWWLTGH07

Iain M. Wallace Desmond G. Higgins Supervised multivariate analysis of sequence groups to identify specificity determining residues. 2007 8 BMC Bioinform. https://doi.org/10.1186/1471-2105-8-135 https://www.wikidata.org/entity/Q33282473 db/journals/bmcbi/bmcbi8.html#WallaceH07

Sébastien Moretti Fabrice Armougom Iain M. Wallace Desmond G. Higgins C. Victor Jongeneel Cédric Notredame The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods. 645-648 2007 35 Nucleic Acids Res. Web-Server-Issue https://doi.org/10.1093/nar/gkm333 https://www.wikidata.org/entity/Q35914038 db/journals/nar/nar35.html#MorettiAWHJN07

Fabrice Armougom Olivier Poirot Sébastien Moretti Desmond G. Higgins Phillip Bucher Vladimir Keduas Cédric Notredame APDB: a web server to evaluate the accuracy of sequence alignments using structural information. 2439-2440 2006 22 Bioinform. 19 https://doi.org/10.1093/bioinformatics/btl404 https://www.wikidata.org/entity/Q42600333 db/journals/bioinformatics/bioinformatics22.html#ArmougomPMHBKN06

Ian B. Jeffery Desmond G. Higgins Aedín C. Culhane Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data. 359 2006 7 BMC Bioinform. https://doi.org/10.1186/1471-2105-7-359 https://www.wikidata.org/entity/Q31050008 db/journals/bmcbi/bmcbi7.html#JefferyHC06

Gordon Blackshields Iain M. Wallace Mark A. Larkin Desmond G. Higgins Analysis and Comparison of Benchmarks for Multiple Sequence Alignment. 321-339 2006 6 Silico Biol. 4 http://content.iospress.com/articles/in-silico-biology/isb00245 db/journals/isb/isb6.html#BlackshieldsWLH06

Iain M. Wallace Orla O'Sullivan Desmond G. Higgins Evaluation of iterative alignment algorithms for multiple alignment. 1408-1414 2005 21 Bioinform. 8 https://doi.org/10.1093/bioinformatics/bti159 https://www.wikidata.org/entity/Q50762597 db/journals/bioinformatics/bioinformatics21.html#WallaceOH05

Aedín C. Culhane Jean Thioulouse Guy Perrière Desmond G. Higgins MADE4: an R package for multivariate analysis of gene expression data. 2789-2790 2005 21 Bioinform. 11 https://doi.org/10.1093/bioinformatics/bti394 https://www.wikidata.org/entity/Q30986013 db/journals/bioinformatics/bioinformatics21.html#CulhaneTPH05

Aedín C. Culhane Guy Perrière Desmond G. Higgins Cross-platform comparison and visualisation of gene expression data using co-inertia analysis. 59 2003 4 BMC Bioinform. https://doi.org/10.1186/1471-2105-4-59 https://www.wikidata.org/entity/Q24804635 db/journals/bmcbi/bmcbi4.html#CulhanePH03

Chenna Ramu Hideaki Sugawara Tadashi Koike Rodrigo Lopez Toby J. Gibson Desmond G. Higgins Julie Dawn Thompson Multiple sequence alignment with the Clustal series of programs. 3497-3500 2003 31 Nucleic Acids Res. 13 db/journals/nar/nar31.html#ChennaSKLGHT03 https://doi.org/10.1093/nar/gkg500 https://www.wikidata.org/entity/Q24672842

Steven D. Prestwich Desmond G. Higgins Orla O'Sullivan A SAT-Based Approach to Multiple Sequence Alignment. 940-944 https://doi.org/10.1007/978-3-540-45193-8_83 2003 conf/cp/2003 CP db/conf/cp/cp2003.html#PrestwichHO03 Orla O'Sullivan Mark Zehnder Desmond G. Higgins Philipp Bucher Aurélien Grosdidier Cédric Notredame APDB: a novel measure for benchmarking sequence alignment methods without reference alignments. 215-221 2003 conf/ismb/2003 ISMB (Supplement of Bioinformatics) https://doi.org/10.1093/bioinformatics/btg1029 db/conf/ismb/ismb2003.html#OSullivanZHBGN03

Aedín C. Culhane Guy Perrière Elizabeth C. Considine Thomas G. Cotter Desmond G. Higgins Between-group analysis of microarray data. 1600-1608 2002 18 Bioinform. 12 db/journals/bioinformatics/bioinformatics18.html#CulhanePCCH02 https://doi.org/10.1093/bioinformatics/18.12.1600 https://www.wikidata.org/entity/Q30756692

Patricia Thébault Pierre Monestie Annette McGrath Desmond G. Higgins MIAH: automatic alignment of eukaryotic SSU rRNAs. 341-342 1999 15 Bioinform. 4 db/journals/bioinformatics/bioinformatics15.html#ThebaultMMH99 https://doi.org/10.1093/bioinformatics/15.4.341 https://www.wikidata.org/entity/Q57252773

Emmet A. O'Brien Cédric Notredame Desmond G. Higgins Optimization of ribosomal RNA profile alignments. 332-341 1998 14 Bioinform. 4 db/journals/bioinformatics/bioinformatics14.html#OBrienNH98 https://doi.org/10.1093/bioinformatics/14.4.332 https://www.wikidata.org/entity/Q47953417

Cédric Notredame Liisa Holm Desmond G. Higgins COFFEE: an objective function for multiple sequence alignments. 407-422 1998 14 Bioinform. 5 db/journals/bioinformatics/bioinformatics14.html#NotredameHH98 https://doi.org/10.1093/bioinformatics/14.5.407 https://www.wikidata.org/entity/Q32049136

Emmet A. O'Brien Desmond G. Higgins Empirical estimation of the reliability of ribosomal RNA alignments. 830-838 1998 14 Bioinform. 10 db/journals/bioinformatics/bioinformatics14.html#OBrienH98 https://doi.org/10.1093/bioinformatics/14.10.830 https://www.wikidata.org/entity/Q48705624

Julie Dawn Thompson Desmond G. Higgins Toby J. Gibson Improved sensitivity of profile searches through the use of sequence weights and gap excision. 19-29 1994 10 Comput. Appl. Biosci. 1 db/journals/bioinformatics/bioinformatics10.html#ThompsonHG94 https://doi.org/10.1093/bioinformatics/10.1.19 https://www.wikidata.org/entity/Q52381755

Catherine M. Rice Rainer Fuchs Desmond G. Higgins Peter Stoehr Graham Cameron The EMBL data library. 2967-2971 1993 21 Nucleic Acids Res. 13 db/journals/nar/nar21.html#RiceFHSC93 https://doi.org/10.1093/nar/21.13.2967 https://www.wikidata.org/entity/Q57252775

Desmond G. Higgins Sequence ordinations: a multivariate analysis approach to analysing large sequence data sets. 15-22 1992 8 Comput. Appl. Biosci. 1 db/journals/bioinformatics/bioinformatics8.html#Higgins92 https://doi.org/10.1093/bioinformatics/8.1.15 https://www.wikidata.org/entity/Q30981731

Desmond G. Higgins Peter Stoehr EMBLSCAN: fast approximate DNA database searches on compact disc. 137-139 1992 8 Comput. Appl. Biosci. 2 db/journals/bioinformatics/bioinformatics8.html#HigginsS92 https://doi.org/10.1093/bioinformatics/8.2.137

Desmond G. Higgins Alan J. Bleasby Rainer Fuchs CLUSTAL V: improved software for multiple sequence alignment. 189-191 1992 8 Comput. Appl. Biosci. 2 db/journals/bioinformatics/bioinformatics8.html#HigginsBF92 https://doi.org/10.1093/bioinformatics/8.2.189 https://www.wikidata.org/entity/Q55880085

Denis C. Shields Desmond G. Higgins P. M. Sharp GCWIND: a microcomputer program for identifying open reading frames according to codon positional G+C content. 521-523 1992 8 Comput. Appl. Biosci. 5 db/journals/bioinformatics/bioinformatics8.html#ShieldsHS92 https://doi.org/10.1093/bioinformatics/8.5.521

Jaap Heringa Hubert Sommerfeldt Desmond G. Higgins Patrick Argos OBSTRUCT: a program to obtain largest cliques from a protein sequence set according to structural resolution and sequence similarity. 599-600 1992 8 Comput. Appl. Biosci. 6 db/journals/bioinformatics/bioinformatics8.html#HeringaSHA92 https://doi.org/10.1093/bioinformatics/8.6.599 https://www.wikidata.org/entity/Q67969041

Desmond G. Higgins P. M. Sharp Fast and sensitive multiple sequence alignments on a microcomputer. 151-153 1989 5 Comput. Appl. Biosci. 2 db/journals/bioinformatics/bioinformatics5.html#HigginsS89 https://doi.org/10.1093/bioinformatics/5.2.151 https://www.wikidata.org/entity/Q29618252

Desmond G. Higgins Manolo Gouy Interfacing similarity search software with the sequence retrieval system ACNUC. 239-241 1987 3 Comput. Appl. Biosci. 3 db/journals/bioinformatics/bioinformatics3.html#HigginsG87 https://doi.org/10.1093/bioinformatics/3.3.239 https://www.wikidata.org/entity/Q57252778

Patrick Argos Fabrice Armougom Pavel V. Baranov Harry Björkbacka Gordon Blackshields Alan J. Bleasby Christof De Bo Kieran Boyce Nigel P. Brown Philipp Bucher Phillip Bucher Graham Cameron Susan B. Carpenter R. Chenna Elizabeth C. Considine Thomas G. Cotter Aedín C. Culhane Norman E. Davey David Dineen Claire A. Donohue Katherine A. Fitzgerald Gearoid Fox Rainer Fuchs Simon J. Furney Toby J. Gibson Manolo Gouy Aurélien Grosdidier Stephen M. Heaphy Jaap Heringa Liisa Holm Graham M. Hughes Ian B. Jeffery Peter Jehl C. Victor Jongeneel Vladimir Keduas Anmol M. Kiran Tomasz A. Kisiel Tadashi Koike Mark A. Larkin Quan Le Rodrigo Lopez Núria López-Bigas Stephen F. Madden Jean Manguy Paul A. McGettigan Annette McGrath Hamish McWilliam Audrey M. Michel Pierre Monestie Sébastien Moretti James P. A. Mullan Cédric Notredame Emmet A. O'Brien Patrick B. F. O'Connor Luke A. O'Neill Orla O'Sullivan Guy Perrière Olivier Poirot Steven D. Prestwich Chenna Ramu Catherine M. Rice P. M. Sharp Weifeng Shi Denis C. Shields Fabian Sievers Hubert Sommerfeldt Peter Stoehr Hideaki Sugawara Patricia Thébault Jean Thioulouse Julie Dawn Thompson Franck Valentin Iain M. Wallace Andreas Wilm Ioannis Xenarios Mark Zehnder