2011
Fíla J, Honys D (2011): Enrichment techniques employed in phosphoproteomics. Amino Acids, on-line first, doi: 10.1007/s00726-011-1111-z.
Szabová J,Růžička P, Verner Z, Hampl V, Lukeš J: Experimental Examination of EFL and MATX Eukaryotic Horizontal Gene Transfers: Coexistence of Mutually Exclusive Transcripts Predates Functional Rescue. Mol. Biol. Evol., 28(8): 2371–2378, 2011.
Hafidh S, Čapková V, Honys D: mRNP Complexes Tweaking after Transcription. In Lesley J. Collins (ed.) RNA infrastructure and networks, Landes Bioscience and Springer Science+Business Media, 2010.
Fíla J, Čapková V, Feciková J, Honys D: Impact of homogenization and protein extraction conditions on the obtained tobacco pollen proteomic patterns. Biologia Plantarum 55 (3): 499-506, 2011.
2009
Honys D, Reňák D, Feciková J, Jedelský PL, Nebesářová J, Dobrev P, Čapková V: Cytoskeleton-associated large RNP complexes in tobacco male gametopyte (EPPs) are associated with ribosomes and are involved in protein synthesis, processing and localisation. Journal of Proteome Research, 8(4): 2015-2031, 2009.
Gibalová A, Reňák D, Matczuk K, Dupľáková N, Cháb D, Twell D, Honys D: AtbZIP34 is required for Arabidopsis pollen wall patterning and the control of several metabolic pathways in developing pollen. Plant Molecular Biology, 70(5): 581-601, 2009.
2008
Honys, D., Dupľáková, N., Reňák, D. (2008) On Line Tools for Presentation and Analysis of Plant Microarray Data. In Martina K. Moretti and Lorenzo J. Rizzo (eds.) Oligonucleotide Array Sequence Analysis, Nova Publishers, ISBN 978-1-60456-542-3, pp 265-295.
Kosová K, Holková L, Prášil IT, Prášilová P, Bradáčova M, Vitámvás P, Čapková V: Expression of dehydrin 5 during the development of frost tolerance in barley (Hordeum vulgare). Journal of Plant Physiology 165 (11): 1142-1151, 2008
2007
Dupľáková N, Reňák D, Hovanec P, Honysová B, Twell D, Honys D: Arabidopsis Gene Family Profiler (aGFP) - user-oriented transcriptomic database with easy-to-use graphic interface. BMC Plant Biology, 7:39, 2007.
Vitámvás P, Saalbach G, Prášil IT, Čapková V, Opatrná J, Ahmed J: WCS120 protein family and proteins soluble upon boiling in cold-acclimated winter wheat. Journal of Plant Physiology 164(9): 1197-1207, 2007.
2006
Honys D, Reňák D, Twell D: Male gametophyte development and function. In: Jaime Teixeira da Silva (ed.) Floriculture, Ornamental and Plant Biotechnology: advances and topical issues (1st Edition), Global Science Books, London, 76-87, 2006.
Twell D, Oh S-A, Honys D: Pollen development, a genetic and transcriptomic view. In: Rui Malhó (ed.) Plant Cell Monographs vol. 3, The Pollen Tube. Springer-Verlag Berlin, Heidelberg, ISBN 3540311211, pp 15-45, 2006.
Novak JP. Kim S-Y, Xu J, Modlich O, Volsky DJ, Honys D, Slonczewski JL, Bell DA, Blattner FR, Blumwald E, Boerma M, BonDurant SS, Cosio M, Gatalica Z, Hajduch M, Hidalgo J, McInnes RR, Miller MC, Nambara E, Rolph M, Sottosanto J, St-Arnaud R, Szego MJ, Tatematsu K, Wang C: Generalization of DNA microarray dispersion properties: microarray equivalent of t-distribution. Biology Direct, 1:27, 2006.
Honys D, Oh S-A, Reňák D, Johnson A, Šolcová B, Boudová R, Twell D: Identification of microspore-active promoters that allow targeted manipulation of gene expression at early stages of microgametogenesis in Arabidopsis. BMC Plant Biology 6(1):31, 2006.
Bock KW, Honys D, Ward JM, Padmanaban S, Nawrocki EP, Hirschi KD, Twell D, Sze H: Integrating membrane transport with male gametophyte development and function through transcriptomics. Plant Physiol. 140: 1151-1168, 2006.
Lapčík O, Honys D, Koblovská R, Macková Z, Vítková M, Klejdus B: Isoflavonoids are present in Arabidopsis thaliana despite the absence of any homologue to known isoflavonoid synthases. Plant Physiol. Biochem. 44: 106-114, 2006.
2005
Hájek T, Honys D, Witters E, Čapková V: Identification of stress-induced mitochondrial proteins in cultured tobacco cells. Physiol. Plant. 124: 12-24, 2005.
Hrubá P, Honys D, Twell D, Čapková V, Tupý J: Expression of beta-galactosidase and beta-xylosidase during microspore and pollen development. Planta 220: 931-940, 2005.
Hrubá P, Honys D, Tupý J: Expression and thermotolerance of calreticulin during pollen development in tobacco. Sex. Plant Reprod. 18: 143-148, 2005.
2004
Honys D, Twell D: Transcriptome analysis of developing haploid male gametophytes in Arabidopsis thaliana. Genome Biology 5: R85, 2004.
Honys D, Twell D: Male gametogenesis In: R.M. Goodman (ed.) Encyclopedia of Plant & Crop Science, Marcel Dekker Inc., New York, ISBN 0824709446, 2004.
 
Sze H, Padmanaban S, Cellier F, Honys D, Cheng N, Bock KW, Conéjéro G, Li X, Twell D, Ward JM, Hirschi KD: Expression Patterns of a Novel AtCHX Gene Family Highlight Potential Roles in Osmotic Adjustment and K1 Homeostasis in Pollen Development. Plant Physiol. 136: 2532-2547, 2004.
Hájek T, Honys D, Čapková V: New method of plant mitochondria isolation and sub-fractionation for proteomic analyses. Plant Science 167: 389-395, 2004.
Pokorná J, Schwarzerová K, Zelenková S, Petrášek J, Janotová I, Čapková V, Opatrný Z: Sites of actin filament initiation and reorganization in cold-treated tobacco cells. Plant, Cell and Environment 27: 641-653, 2004.
Lalanne E, Honys D, Johnson A, Borner G, Lilley K, Dupree P, Grossniklaus U, Twell D: SETH1 and SETH2, two components of the glycosylphosphatidylinositol anchor biosynthetic pathway, are required for pollen germination and tube growth in Arabidopsis. Plant Cell 16: 229-240, 2004.
2003
Honys D, Twell D: Comparative analysis of Arabidopsis pollen transcriptome. Plant Physiol. 132: 640-652, 2003.
Motyka V, Vaňková R, Čapková V, Petrášek J, Kamínek M, Schmülling T: Citokinin-induced upregulation of cytokinin oxidase activity in tobacco includes changes in enzyme glycosylation and secretion. Physiol. Plant. 1117: 11-21, 2003.
Schwarzerová K, Pokorná J, Petrášek J, Zelenková S, Čapková V, Janotová I, Opatrný Z: The structure of cortical cytoplasm in cold-treated tobacco cells. The role of the cytoskeleton and the endomembrane system. Cell Biol. International 27:263-265, 2003.
2001
Honys D: Isolation of proteins comprising native gene-specific messenger ribonucleoprotein particles using paramagnetic beads. Plant Sci. 161: 605-611, 2001 Biol. Plant. 44: 321-324, 2001
Haisel D, Hofman P, Vágner M, Lipavská H, Tichá I, Schäfer C, Čapková V: Ex vitro phenotype stability is affected by in vitro cultivation. Biol. Plant. 44: 321-324, 2001
Kadleček P, Tichá I, Haisel D, Čapková V, Schäfer Ch: Importance of in vitro pretreatment for ex vitro acclimation and growth. Plant. Sci. 161: 695-701, 2001
Fidlerová A, Smýkal P, Tupý J, Čapková V: Glycoproteins 66 and 69 kDa of pollen tube wall: properties and distribution in Angiosperms. J. Plant Physiol. 158: 1367-1374, 2001
2000
Honys D, Čapková V: Temporal changes in the RNA distribution between polysomes and postpolysomal ribonucleoprotein particles in tobacco male gametophyte. Biol. Plant. 43: 517-522, 2000.
Wittink FRA, Knuiman B, Derksen J, Čapková V, Twell D, Schrauwen JAM, Wullems GJ: The pollen-specific gene ntp303 encodes a 69-kDa glycoprotein associated with the vegetative membrane and the cell wall. Sex. Plant Reprod. 12: 276-284, 2000.
Honys D, Combe JP, Twell D, Čapková V: The translationally repressed pollen-specific ntp303 mRNA is stored in non-polysomal mRNPs during pollen maturation. Sex. Plant Reprod. 13: 135-144, 2000.
Mašek T, Smýkal P, Janotová I, Honys D, Čapková V, Pechan P: Isolation of the Brassica napus L. cDNA encoding a putative high-mobility-group HMG I/Y protein. Plant Science 159: 197-204, 2000.
1998
Tichá I, Čáp F, Pacovská D, Haisel D, Čapková V, Schäffer C: Photosynthesis and photoinhibition in tobacco plantlets grown in vitro: an ontogenetic approach. In: Garab, G. (ed.): Photosynthesis: Mechanisms and Effects. Pp. 2233-2236. Kluwer Academic Publishers, Dorrecht 1998
Tichá I, Čáp F, Pacovská D, Hofman P, Haisel D, Čapková V, Schäffer C.: Culture on sugar medium enhances photosynthetic capacity and high light resistance of plantlets grown in vitro. Physiol. Plant. 102: 155-162, 1998
1997
Čapková V, Fidlerová A, Amstel van AS, Croes FA, Mata C, Schrauwen JAM, Wullems GJ, Tupý J: Role of N-glycosylation of 66 and 69 kDa gyĺycoproteins in wall formation during pollen tube growth in vitro. European J. Cell Biol. 72: 282-285, 1997.
1996
Říhová L, Čapková V, Tupý J: Changes in glycoprotein patterns associated with male gametophyte development and with induction of pollen embryogenesis in Nicotiana tabacum L. J. Plant Physiol. 147: 573-582, 1996.
1994
Čapková V, Zbrožek J, Tupý J: Protein synthesis in tobacco pollen tubes: preferential synthesis of cell wall 69 kDa and 66 kDa glycoproteins. Sex. Plant Reprod. 7: 57-66, 1994.
Štorchová H, Čapková V, Tupý J: A Nicotiana tabacum mRNA encoding a 69 kDa glycoprotein occuring abundantly in pollen tubes is transcribed but not translated during pollen development in the anthers. Planta 192: 441-445, 1994.
Čapková V, Zbrožek J, Tupý J: Protein synthesis in tobacco pollen tubes: preferential synthesis of cell wall 69 kDa and 66 kDa glycoproteins. Sex. Plant Reprod. 7: 57-66, 1994.
Štorchová H, Čapková V, Tupý J: A Nicotiana tabacum mRNA encoding a 69 kDa glycoprotein occuring abundantly in pollen tubes is transcribed but not translated during pollen development in the anthers. Planta 192: 441-445, 1994.
1988
Čapková V, Hrabětová E, Tupý J: Protein synthesis in pollen tubes: preferential formation of new species independent of transcription. Sex. Plant reprod. 1: 150-155, 1988.