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Journal Articles
- 2023
[j22]Joeri van Strien
, Felix Evers, Madhurya Lutikurti, Stijn L. Berendsen, Alejandro Garanto, Geert-Jan van Gemert, Alfredo Cabrera-Orefice, Richard J. Rodenburg, Ulrich Brandt, Taco W. A. Kooij, Martijn A. Huynen:
Comparative Clustering (CompaCt) of eukaryote complexomes identifies novel interactions and sheds light on protein complex evolution. PLoS Comput. Biol. 19(8) (2023)- 2021
- [j21]Lisette Meerstein-Kessel, Jeron Venhuizen, Daniel Garza, Nicolas Pröllochs, Emma J. Vos, Joshua M. Obiero, Philip L. Felgner, Robert W. Sauerwein, Marynthe Peters, Annie S. P. Yang, Martijn A. Huynen:
Novel insights from the Plasmodium falciparum sporozoite-specific proteome by probabilistic integration of 26 studies. PLoS Comput. Biol. 17(4) (2021) - 2019
- [j20]Joeri van Strien, Sergio Guerrero-Castillo, Iliana A Chatzispyrou, Riekelt H. Houtkooper, Ulrich Brandt, Martijn A. Huynen:
COmplexome Profiling ALignment (COPAL) reveals remodeling of mitochondrial protein complexes in Barth syndrome. Bioinform. 35(17): 3083-3091 (2019) - 2016
- [j19]Radek Szklarczyk, Wout Megchelenbrink, Pavel Cizek, Marie Ledent, Gonny Velemans, Damian Szklarczyk, Martijn A. Huynen:
WeGET: predicting new genes for molecular systems by weighted co-expression. Nucleic Acids Res. 44(Database-Issue): 567-573 (2016) - 2015
- [j18]Qingzhen Hou, Bas E. Dutilh, Martijn A. Huynen, Jaap Heringa, K. Anton Feenstra:
Sequence specificity between interacting and non-interacting homologs identifies interface residues - a homodimer and monomer use case. BMC Bioinform. 16: 325:1-325:12 (2015) - [j17]Robin van der Lee, Qian Feng, Martijn A. Langereis, Rob ter Horst, Radek Szklarczyk, Mihai G. Netea, Arno C. Andeweg, Frank J. M. van Kuppeveld, Martijn A. Huynen:
Integrative Genomics-Based Discovery of Novel Regulators of the Innate Antiviral Response. PLoS Comput. Biol. 11(10) (2015) - 2013
- [j16]Sergio Rossell, Martijn A. Huynen, Richard A. Notebaart:
Inferring Metabolic States in Uncharacterized Environments Using Gene-Expression Measurements. PLoS Comput. Biol. 9(3) (2013) - 2011
- [j15]Jaime Huerta-Cepas, Joaquín Dopazo, Martijn A. Huynen, Toni Gabaldón:
Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication. Briefings Bioinform. 12(5): 442-448 (2011) - [j14]Bas E. Dutilh, Rasa Jurgelenaite, Radek Szklarczyk, Sacha A. F. T. van Hijum, Harry R. Harhangi, Markus Schmid, Bart de Wild, Kees-Jan Françoijs, Henk Stunnenberg, Marc Strous, Mike S. M. Jetten, Huub J. M. Op den Camp, Martijn A. Huynen:
FACIL: Fast and Accurate Genetic Code Inference and Logo. Bioinform. 27(14): 1929-1933 (2011) - 2010
- [j13]Iziah Edwin Sama, Martijn A. Huynen:
Measuring the physical cohesiveness of proteins using physical interaction enrichment. Bioinform. 26(21): 2737-2743 (2010) - 2009
- [j12]Bas E. Dutilh, Martijn A. Huynen, Marc Strous:
Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly. Bioinform. 25(21): 2878-2881 (2009) - 2008
- [j11]Martin Oti, Jeroen van Reeuwijk, Martijn A. Huynen, Han G. Brunner:
Conserved co-expression for candidate disease gene prioritization. BMC Bioinform. 9 (2008) - [j10]Bas E. Dutilh, Ying He, Maarten L. Hekkelman, Martijn A. Huynen:
Signature, a web server for taxonomic characterization of sequence samples using signature genes. Nucleic Acids Res. 36(Web-Server-Issue): 470-474 (2008) - 2007
- [j9]Bas E. Dutilh, Vera van Noort, René T. J. M. van der Heijden, T. Boekhout, Berend Snel, Martijn A. Huynen:
Assessment of phylogenomic and orthology approaches for phylogenetic inference. Bioinform. 23(7): 815-824 (2007) - [j8]René T. J. M. van der Heijden, Berend Snel, Vera van Noort, Martijn A. Huynen:
Orthology prediction at scalable resolution by phylogenetic tree analysis. BMC Bioinform. 8 (2007) - [j7]Fiona G. G. Nielsen, Stefan Gräf, Xinmin Zhang, Stefan Kurtz, Sergei Denissov, Roland Green, Ewan Birney, Paul Flicek, Martijn A. Huynen, Henk Stunnenberg:
Optimising oligonucleotide array design for ChIP-on-chip. BMC Bioinform. 8(S-8) (2007) - [j6]Toni Gabaldón, Martijn A. Huynen:
From Endosymbiont to Host-Controlled Organelle: The Hijacking of Mitochondrial Protein Synthesis and Metabolism. PLoS Comput. Biol. 3(11) (2007) - 2005
- [j5]Victor Kunin, Sarah A. Teichmann, Martijn A. Huynen, Christos A. Ouzounis:
The properties of protein family space depend on experimental design. Bioinform. 21(11): 2618-2622 (2005) - [j4]Christian von Mering, Lars Juhl Jensen, Berend Snel, Sean D. Hooper, Markus Krupp, Mathilde Foglierini, Nelly Jouffre, Martijn A. Huynen, Peer Bork:
STRING: known and predicted protein-protein associations, integrated and transferred across organisms. Nucleic Acids Res. 33(Database-Issue): 433-437 (2005) - 2004
- [j3]Harm van Bakel, Martijn A. Huynen, Cisca Wijmenga:
Prokaryotic diversity of the Saccharomyces cerevisiae Atx1p-mediated copper pathway. Bioinform. 20(16): 2644-2655 (2004) - 2003
- [j2]Christian von Mering, Martijn A. Huynen, Daniel Jaeggi, Steffen Schmidt, Peer Bork, Berend Snel:
STRING: a database of predicted functional associations between proteins. Nucleic Acids Res. 31(1): 258-261 (2003) - 1996
- [j1]Martijn A. Huynen, Alan S. Perelson, W. A. Vieira, Peter F. Stadler:
Base Pairing Probabilities in a Complete HIV-1 RNA. J. Comput. Biol. 3(2): 253-274 (1996)
Conference and Workshop Papers
- 2011
- [c6]Wout Megchelenbrink, Martijn A. Huynen, Elena Marchiori:
Flux Measurement Selection in Metabolic Networks. PRIB 2011: 214-224 - 2007
- [c5]Stefan Gräf, Fiona G. G. Nielsen, Stefan Kurtz, Martijn A. Huynen, Ewan Birney, Henk Stunnenberg, Paul Flicek:
Optimized design and assessment of whole genome tiling arrays. ISMB/ECCB (Supplement of Bioinformatics) 2007: 195-204 - 2005
- [c4]Toni Gabaldón, Martijn A. Huynen:
Lineage-specific gene loss following mitochondrial endosymbiosis and its potential for function prediction in eukaryotes. ECCB/JBI 2005: 150 - 1998
- [c3]Thomas Dandekar, Stefan Schuster, Martijn A. Huynen, Peer Bork:
Pathway alignment: Application in the comparative analysis of glycolysis. German Conference on Bioinformatics 1998 - 1996
- [c2]Ivo L. Hofacker, Martijn A. Huynen, Peter F. Stadler, Paul E. Stolorz:
Knowledge Discovery in RNA Sequence Families of HIV Using Scalable Computers. KDD 1996: 20-25 - 1989
- [c1]Martijn A. Huynen, Paulien Hogeweg:
Genetic Algorithms and Information Accumulation during the Evolution of Gene Regulation. ICGA 1989: 225-230
Coauthor Index
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