Arthur Ram
Professor Fungal genetics and Biotechnology
- Name
- Prof.dr. A.F.J. Ram
- Telephone
- +31 71 527 4914
- a.f.j.ram@biology.leidenuniv.nl
- ORCID iD
- 0000-0002-2487-8016
I am associate professor Molecular Microbiology and Biotechnology at the Institute of Biology (IBL). I am interested in the several aspects related to the growth and development of the filamentous fungi. These include elucidation of molecular mechanisms related to the transcriptional regulation of enzymes involved in plant polysaccharide degradation, polarized secretion and cell growth, and mechanisms related to fungal cell wall biosynthesis and remodeling.
More information about Arthur Ram
PhD Candidates
News
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How fungi are helping us be more sustainable -
BRAIN appoints University of Leiden as partner for BEC-Enabled production strain development
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Arthur Ram receives NWO grant to improve enzyme factory -
Parade of creative science communication products -
European collaboration shines a light on enzyme discovery for industry -
Amy Montanje receives the 'Kees Bakker Award' -
Martienke Baaij receives the “Kees Bakker Award” -
Pam Engelberts receives the “Kees Bakker Award” -
New Directors of Education IBL
Courses
Former PhD candidates
Brief Biography
I obtained my PhD in 1996 at the University of Amsterdam with molecular genetic study on Isolation and characterization of cell wall mutants in Saccharomyces cerevisiae. The biosynthesis and remodeling of the fungal cell wall is still in important part of my research area, focusing on signal transduction pathway responsible for cell wall remodeling and identification of enzymes important for biosynthesis and crosslinking of cell wall polymers such as alpha glucan, chitin and galactomannan. In 1999 moved to Leiden after a two-years post doc at TNO Nutrition in Zeist, to start, together with Prof Kees van den Hondel and developed two other research lines in relation to transcriptional regulation of plant polysaccharides degrading enzyme networks and in relation to polarized growth and protein secretion in the filamentous fungus Aspergillus niger.
At Leiden University I’m currently head of the departments Molecular Microbiology and Biotechnology.
Research
My research is focused at the understanding of the molecular mechanisms that underlay cellular processes which are specific for filamentous fungi. Aspergillus niger is chosen as our main model system due its fascinating biology in terms of growth and development and its many applications in biotechnology related to protein and metabolite production. The cellular processes that are studied include processes related to enzyme production, polarized growth, cell wall biosynthesis, and carbon utilization. In the last years we have also included as a model species Aspergillus fumigatus as this fungus is the most commonly found fungus in human patients and therir medically relevant. We are also studying Trichoderma reesei as another important industrial fungus.
To study these fundamental processes, we have developed many important molecular and cell-biological tools including i) state of the art molecular tools to analyze gene function (creating knockout strain, tools for targeting integration, controlled expression and fluorescent protein labeling, CRISPR/CAS technology), ii) use of available microscope infrastructure within the IBL to perform protein localization studies in time and space, iii) develop classical genetic tools such as bulk segregant analysis, to perform mutant identification via whole genome sequencing approaches, iv) we have build-up and financed a state-of-the art bioreactor cultivation platform for filamentous fungi, Such a platform is an absolute requirement for microbiological research in the field of filamentous fungi as such as system is the only way by which the growth of the fungus can be adequately controlled.
Research Interests
1. Transcription regulation of carbohydrate modifying enzymes
Filamentous fungi, including Aspergillus niger are well known for its ability to secrete a wide variety of plant-polysaccharide modifying enzymes. The secreted enzymes are able to degrade the plant cell wall polysaccharides pectin, hemicellulose and cellulose, as well as plant storage polysaccharides like starch and inulin. We are interested in the mechanism(s) by which the fungus can sense and transport the presence of different (often complex) carbon sources in its vicinity and how the presence of a certain carbohydrate activates the expression of a network of genes encoding enzymes to degrade the carbon source. Special focus is on the identification of so-called inducer molecules and transcription factors that are required for expression of enzyme networks involved in the breakdown and uptake of starch, inulin and pectin. In 2016, we identified a novel transcription factor and repressor module that controls the expression of pectin degrading enzymes in A. niger.
Related projects:
- New regulators involved in plant cell wall degradation (Jing Niu, PhD, Ebru Alazi, PhD)
- Responses to carbon starvation (Annemarie Burggraaf, PhD)
- Improving the filamentous fungus Aspergillus niger as cell factory for starch degrading jean paul enzymes (Mark Arentshorst)
2. Morphology and enzyme production
Cell morphology and secretion capacity are two important parameters in relation to optimizing enzyme production in filamentous fungi . Fundamental research on fungal morphology and secretion in the industrial host Aspergillus niger is aimed at a much deeper understanding of the mechanisms that temporally and spatially regulate different steps of the hyphal morphogenesis and secretion. Knowledge of the complex networks and molecular interactions will generate new possibilities to control and manipulate the morphology of A. niger for industrial applications. The cell wall of filamentous fungi is an essential part of the cell protecting its integrity, forming a barrier with the surrounding environment and permitting interactions with possible substrates and hosts to be infected. Recent research in the group has revealed that galactofuranose is essential for the integrity of the cell wall and is required for proper morphology. In its absence the mycelium grows much slower and forms abnormal hyphae with increased branching.
Related projects:
- Cell architecture and pathways for parallel secretion in the filamentous fungus Aspergillus niger (Min Jin Kwon PhD, Vera Meyer)
- Galactofuranose biosynthesis in the filamentous fungus Aspergillus niger (Joohae Park PhD)
- Cell Wall Dynamics in Aspergillus niger (Benjamin Nitsche PhD)
- Efficient targeting of the Trichoderma genome for industrial protein engineering (Jean Paul Ouedraogo, post-doc)
3 Robustness of the Fungal Cell Factory
The cell wall of yeasts and fungi is of vital importance to the cell. It is required to resist the turgor pressure of the protoplasts to prevent cell lysis. It further protects against potentially damaging enzymes from the environment and acts as a scaffold for exposing cell wall proteins that play a role during cell-cell interactions. The cell wall strength and permeability is mainly accomplished by crosslinking of individual cell wall components to each other. We are interested in the crosslinking of these components with the aim to improve enzyme production and increase extractability of cell wall components such as chitin. The cell wall of spores of A. niger is much more resistant to environmental stress (heat stress and oxidative stress) compared to vegetative cells. We are interested in the cell wall related adaptation that create the stress tolerance of spores as well as understanding mechanisms that are important to create the heterogeneity of stress resistance among fungal spores.
Related projects:
- Cell wall strength in Aspergillus niger (Tim van Leeuwe, PhD)
- Heterogeneity of resistance in spores of food spoilage fungi (Sjoerd Seekles, PhD)
Professor Fungal genetics and Biotechnology
- Science
- Instituut Biologie Leiden
- IBL Microbial Sciences
- Richter A., Blei F., Hu G., Schwitalla J.W., Lozano-Andrade C.N., Xie J., Jarmusch S.A., Wibowo M., Kjeldgaard B., Surabhi S., Xu X., Jautzus T., Phippen C.B.W., Tyc O., Arentshorst M., Wang Y., Garbeva P., Larsen T.O., Ram A.F.J., Hondel C.A.M. van den, Maróti G. & Kovács Á.T. (2024), Enhanced surface colonisation and competition during bacterial adaptation to a fungus, Nature Communications 15: 4486.
- Verschoor J., Croese M.R.J., Lakemeier S.E., Mugge A., Burgers C.M.C., Innocenti P., Willemse J.J., Crooijmans M.E., Wezel G.P. van, Ram A.F.J. & Winde J.H. de (2024), Polyester degradation by soil bacteria: identification of conserved BHETase enzymes in Streptomyces, Communications Biology 7: 725.
- Forrer S.N., Arentshorst M., Kooloth Valappil P., Visser J. & Ram A.F.J. (2024), Competition between homologous chromosomal DNA and exogenous donor DNA to repair CRISPR/Cas9-induced double-strand breaks in Aspergillus niger, Fungal Biology and Biotechnology 11(1): 15.
- Sidar A., Volshol G.P., Arentshorst M., Ram A.F.J., Vijgenboom E. & Punt P.J. (2024), Deciphering domain structures of Aspergillus and Streptomyces GH3-β-Glucosidases: a screening system for enzyme engineering and biotechnological applications, BMC Research Notes 17(1): 257.
- Pre S. du, Konings M., Schoorl D.J.A., Fahal A.H., Arentshorst M., Ram A.F.J. & Sande W.W.J. van de (2024), Protoplast-mediated transformation of Madurella mycetomatis using hygromycin resistance as a selection marker, PLoS Neglected Tropical Diseases 18(4): e0012092.
- Seekles S.J., Brule T. van den, Punt M., Dijksterhuis J., Arentshorst M., Ljadpanahsaravj M., Roseboom W., Meuken G., Ongenae V.M.A., Zwerus J., Ohm R.A., Kramer G.J., Wösten H.A.B., Winde J.H. de & Ram A.F.J. (2023), Compatible solutes determine the heat resistance of conidia, Fungal Biology and Biotechnology 10: 21.
- Arentshorst M., Kooloth Valappil P., Mózsik L., Regensburg-Tuïnk A.J.G., Seekles S.J., Tjallings G., Fraaije M.W., Visser J. & Ram A.F.J. (2023), A CRISPR/Cas9‐based multicopy integration system for protein production in Aspergillus niger, FEBS Journal 290(21): 5127-5140.
- Tjallinks G., Boverio A., Maric I., Rozeboom H., Arentshorst M., Visser J., Ram A.F.J., Mattevi A. & Fraaije M.W. (2023), Structure elucidation and characterization of patulin synthase, insights into the formation of a fungal mycotoxin, FEBS Journal 290(21): 5114-5126.
- Forn Cuni G., Welvaarts L., Stel F.M., Hondel C.A.M.J.J. van den, Arentshorst M., Ram A.F.J. & Meijer A.H. (2023), Stimulating the autophagic-lysosomal axis enhances host defense against fungal infection in a zebrafish model of invasive Aspergillosis, Autophagy 1986(1): 324-337.
- Verschoor J.A., Kusumawardhani H., Ram A.F.J. & Winde J.H. de (2022), Toward microbial recycling and upcycling of plastics: prospects and challenges, Frontiers in Microbiology 13: 821629.
- Seekles S.J., Dam J. van, Arentshorst M. & Ram A.F.J. (2022), Natural variation and the role of Zn2Cys6 transcription factors SdrA, WarA and WarB in sorbic acid resistance of aspergillus niger, Microorganisms 10(2): 221.
- Brule T. van den, Punt M., Seekles S.J., Segers F.J.J., Houbraken J., Hazeleger W.C., Ram A.F.J., Wösten H.A.B., Zwietering M.H., Dijksterhuis J. & Besten H.M.W. den (2022), Intraspecific variability in heat resistance of fungal conidia, Food Research International 156: 111302.
- Punt M., Seekles S.J., Dam J.L. van, Adelhart Toorop C. de, Martina R.R., Houbraken J., Ram A.F.J., Wösten H.A.B. & Ohm R.A. (2022), High sorbic acid resistance of Penicillium roqueforti is mediated by the SORBUS gene cluster, PLoS Genetics 18(6): e1010086.
- Seekles S.J., Punt M., Savelkoel N., Houbraken J., Wösten H.A.B., Ohm R.A. & Ram A.F.J (2022), Genome sequences of 24 Aspergillus niger sensu stricto strains to study strain diversity, heterokaryon compatibility, and sexual reproduction, G3: Genes | Genomes | Genetics 12(7): jkac124.
- Escobar N., Keizer E.M., Neer J.F. van, Arentshorst M., Strijp J.A.G. van, Haas P.J.A., Ram A.F.J., Punt P.J., Wösten H.A.B. & Cock H. de (2022), LaeA-dependent production of small molecules of Aspergillus niger that compete with specific antibodies that bind to human immune receptors. bioRxiv. [working paper].
- Seekles S.J., Teunisse P. P. P., Punt M., Brule T. van den, Dijksterhuis J., Houbraken J., Wösten H.A.B. & Ram A.F.J. (2021), Preservation stress resistance of melanin deficient conidia from Paecilomyces variotii and Penicillium roqueforti mutants generated via CRISPR/Cas9 genome editing, Fungal Biology and Biotechnology 8: 4.
- Ellena V., Seekles S.J., Vignolle G.A., Ram A.F.J. & Steiger M.G. (2021), Genome sequencing of the neotype strain CBS 554.65 reveals the MAT1–2 locus of Aspergillus niger, BMC Genomics 22: 679.
- Boer C. de, McGregor N.G.S., Peterse E., Schröder S.P., Florea B.I., Jiang J., Reijngoud J., Ram A.F.J., Wezel G.P. van, Marel G.A. van der, Codee J.D.C., Overkleeft H.S. & Davies G.J. (2021), Glycosylated cyclophellitol-derived activity-based probes and inhibitors for cellulases, RSC Chemical Biology 2(6): 1701.
- Arentshorst M., Di Falco M., Moisan M.C., Reid I.D., Spaapen T.O.M., Dam J. van, Demirci E., Powlowski J., Punt P.J., Tsang A. & Ram A.F.J. (2021), Identification of a conserved transcriptional activator-repressor module controlling the expression of genes involved in tannic acid degradation and gallic acid utilization in aspergillus niger, Fungal Biology 2: 681631.
- Demirci E., Arentshorst M., Yilmaz B., Swinkels A., Reid I.D., Visser J., Tsang A. & Ram A.F.J. (2021), Genetic characterization of mutations related to conidiophore stalk length development in aspergillus niger laboratory strain N402, Frontiers in Genetics 12: 666684.
- Reijngoud J., Arentshorst M., Ruijmbeek C., Reid I., Alazi E., Punt P.J., Tsang A. & Ram A.F.J. (2021), Loss of function of the carbon catabolite repressor CreA leads to low but inducer-independent expression from the feruloyl esterase B promoter in Aspergillus niger, Biotechnology Letters 43(7): 1323-1336.
- McGregor N.G.S., Artola M., Nin-Hill A., Linzel D., Haon M., Reijngoud J., Ram A., Rosso M.N., Marel G.A. van der, Codée J.D.C., Wezel G.P. van, Berrin J.G., Rovira C., Overkleeft H.S. & Davies G.J. (2020), Rational Design of Mechanism-Based Inhibitors and Activity-Based Probes for the Identification of Retaining α-l-Arabinofuranosidases, Journal of the American Chemical Society 142(10): 4648-4662.
- Boer C. de, McGregor N.G.S., Peterse E., Schröder S.P., Florea B.I., Jiang J., Reijngoud J., Ram A.F.J., Wezel G.P. van, Marel G.A. van der, Codée J.D.C., Overkleeft H.S. & Davies G.J. (2020), Glycosylated cyclophellitol-derived activity-based probes and inhibitors for cellulases, RSC Chemical Biology 1(3): 148-155.
- Leeuwe T.M. van, Arentshorst M., Forn-Cuní G., Geoffrion N., Tsang A., Delvigne F., Meijer A.H., Ram A.F.J. & Punt P.J. (2020), Deletion of the Aspergillus niger pro-protein processing protease gene kexB results in a pH-dependent morphological transition during submerged cultivations and increases cell wall chitin content , Microorganisms 8(12): 1918.
- Leeuwe T.M. van, Wattjes J., Niehues A., Forn-Cuní G., Geoffrion N., Mélida H., Arentshorst M., Molina A.,Tsang A., Meijer A.H., Moerschbacher B.M., Punt P.J. & Ram A.F.J. (2020), A seven-membered cell wall related transglycosylase gene family in Aspergillus niger is relevant for cell wall integrity in cell wall mutants with reduced α-glucan or galactomannan, Cell Surface 6: 100039.
- Miyauchi S., Hage H., Drula E., Lesage-Meessen L., Berrin J., Navarro D., Favel A., Chaduli D., Grisel S., Haon M., Piumi F., Levasseur A., Lomascolo A., Ahrendt S., Barry K., LaButti K.M., Chevret D., Daum C., Mariette J., Klopp C., Cullen D., Vries R.P. de, Gathman A.C., Hainaut M., Henrissat B., Hildén K.S., Kües U., Lilly W., Lipzen A., Mäkelä M.R., Martinez A.T., Morel-Rouhier M., Morin E., Pangilinan J., Ram A.F.J., Wösten H.A.B., Ruiz-Dueñas F.J., Riley R., Record E., Grigoriev I.V. & Rosso M. (2020), Conserved white-rot enzymatic mechanism for wood decay in the Basidiomycota genus pycnoporus , DNA Research 27(2): dsaa011.
- Sidar A., Albuquerque E.D., Voshol G.P., Ram A.F.J., Vijgenboom E. & Punt P.J. (2020), Carbohydrate binding modules: diversity of domain architecture in amylases and cellulases from filamentous microorganisms , Frontiers in Bioengineering and Biotechnology 8: 871.
- Meyer V., Basenko E.Y., Benz J.P., Braus G.H., Caddick M.X., Csukai M., Vries R.P. de, Endy D., Frisvad J.C., Gunde-Cimerman N., Haarmann T., Hadar Y., Hansen K., Johnson R.I., Keller N.P., Kraševec N., Mortensen U.H., Perez R., Ram A.F.J., Record E., Ross P., Shapaval V., Steiniger C., Brink H. van den, Munster J. van, Yarden O. & Wösten H.A.B. (2020), Growing a circular economy with fungal biotechnology: a white paper, Fungal Biology and Biotechnology 7: 5.
- Jørgensen T.R., Burggraaf A.M., Arentshorst M., Schutze T., Lamers G.E.M., Niu J., Kwon M.J., Park J., Frisvad J.C., Nielsen K.F., Meyer V., Hondel C.A.M.J.J. van den, Dyer P.S. & Ram A.F.J. (2020), Identification of SclB, a Zn(II)2Cys6 transcription factor involved in sclerotium formation in Aspergillus niger, Fungal Genetics and Biology 139: 103377.
- Leeuwe T.M. van , Arentshorst M., Punt P.J. & Ram A.F.J. (2020), Interrogation of the cell wall integrity pathway in Aspergillus niger identifies a putative negative regulator of transcription involved in chitin deposition, Gene: X 5: 100028.
- Tegelaar M., Bleichrodt R-J., Nitsche B., Ram A.F.J. & Wösten H.A.B. (2020), Subpopulations of hyphae secrete proteins or resist heat stress in Aspergillus oryzae colonies, Environmental Microbiology 22(1): 447-455.
- Leeuwe T.M. van, Gerritsen A., Arentshorst M., Punt P.J. & Ram A.F.J. (2020), Rab GDP-dissociation inhibitor gdiA is an essential gene required for cell wall chitin deposition in Aspergillus niger, Fungal Genetics and Biology 136: 103319.
- Koch B.E.V., Hajdamowicz N.H., Lagendijk E., Ram A.F.J. & Meijer A.H. (2019), Aspergillus fumigatus establishes infection in zebrafish by germination of phagocytized conidia, while Aspergillus niger relies on extracellular germination, Scientific Reports 9: 12791.
- Reijngoud J., Deseke M., Halbesma E.T.M., Alazi E., Arentshorst M., Punt P.J. & Ram A.F.J. (2019), Correction to: Mutations in AraR leading to constitutive of arabinolytic genes in Aspergillus niger under derepressing conditions, Applied Microbiology and Biotechnology 103(12): 5063-5063.
- Arentshorst M., Lange D. de, Park J., Lagendijk E.L., Alazi E., Hondel C.A.M.J.J. van den & Ram A.F.J. (2019), Functional analysis of three putative galactofuranosyltransferases with redundant functions in galactofuranosylation in Aspergillus niger, Archives of Microbiology 202(1): 197-203.
- Leeuwe T.M. van, Arentshorst M., Ernst T., Alazi E., Punt P.J. & Ram A.F.J. (2019), Efficient marker free CRISPR/Cas9 genome editing for functional analysis of gene families in filamentous fungi, Fungal Biology and Biotechnology 6: 13.
- Tegelaar M., Bleichrodt R.J., Nitsche B.M., Ram A.F.J. & Wösten H.A.B. (2019), Subpopulations of hyphae secrete proteins or resist heat stress in Aspergillus oryzae colonies, Environmental Microbiology 22(1): 447-455.
- Niu J., Ram A.F.J. & Punt P.J. (2019), Meeting a challenge: a view on studying transcriptional control of genes involved in plant biomass degradation in aspergillus niger. In: Nevalainen H. (Ed.), Grand Challenges in Fungal Biotechnology. Grand Challenges in Biology and Bioechnology. Cham: Springer. 211-235.
- Reijngoud J., Deseke M., Halbesma E.T.M., Alazi E., Arentshorst M., Punt P.J. & Ram A.F.R. (2019), Mutations in AraR leading to constitutive of arabinolytic genes in Aspergillus niger under depressing conditions, Applied Microbiology and Biotechnology 103(10): 4125-4136.
- Leeuwe T.M. van, Gerritsen A., Arentshorst M., Punt P.J. & Ram A.F.J. (2019), Rab GDP-dissociation inhibitor gdiA is an essential gene required for cell wall chitin deposition in aspergillus niger, Fungal Genetics and Biology 136: 103319.
- Aerts D., Bergh S.G. van den, Post H., Altelaar M.A.F., Arentshorst M., Ram A.F.J., Ohm R.A. & Wösten H.A.B. (2019), FlbA-regulated gene rpnR is involved in stress resistance and impacts protein secretion when Aspergillus niger is grown on xylose, Applied and Environmental Microbiology 85(2): e02282-18.
- Aerts D., Hauer E.E., Ohm R.A., Arentshorst M., Teertstra W.R., Phippen C., Ram A.F.J., Frisvad J.C. & Wösten H.A.B. (2018), The FlbA-regulated predicted transcription factor Fum21 of Aspergillus niger is involved in fumonisin production, Antonie van Leeuwenhoek 111(3): 311-322.
- Alazi E. & Ram A.F.J. (2018), Modulating Transcriptional Regulation of Plant Biomass Degrading Enzyme Networks for Rational Design of Industrial Fungal Strains, Frontiers in Bioengineering and Biotechnology 6: 113.
- Alazi E., Niu J., Otto S.B., Arentshorst M., Pham T.T.M., Tsang A. & Ram A.F.J. (2018), W361R mutation in GaaR, the regulator of D-galacturonic acid-responsive genes, leads to constitutive production of pectinases in Aspergillus niger, MicrobiologyOpen 8(5): e00732.
- Brandl J., Aguilar-Pontes M.V., Schäpe P., Noerregaard A., Arvas M., Ram A.F.J., Meyer V., Tsang A., Vries R.P. de & Andersen M.R. (2018), A community-driven reconstruction of the Aspergillus niger metabolic network, Fungal Biology and Biotechnology 5: 16.
- Thieme K.G., Gerke J., Sasse C., Valerius O., Thieme S., Karimi R., Heinrich A.K., Finkernagel F., Smith K., Bode H.B., Freitag M., Ram A.F.J. & Braus G.H. (2018), Velvet domain protein VosA represses the zinc cluster transcription factor SclB regulatory network for Aspergillus nidulans asexual development, oxidative stress response and secondary metabolism, PLoS Genetics 14(7): e1007511.
- Arentshorst M. & Ram A.F.J. (2018), Parasexual crossings for bulk segregant analysis in aspergillus niger to facilitate mutant identification via whole genome sequencing. In: Vries R. de, Tsang A. & Grigoriev I. (Eds.), Fungal Genomics. Methods in Molecular Biology no. MMB 1775. New York, NY, U.S.A.: Humana Press. 277-287.
- Alazi E., Knetsch T.G.J., Di Falco M., Reid I.D., Arentshorst M., Visser J., Tsang A. & Ram A.F.J. (2018), Inducer-independent production of pectinases in Aspergillus niger by overexpression of the D-galacturonic acid-responsive transcription factor gaaR, Applied Microbiology and Biotechnology 102(6): 2723–2736.
- Alazi E., Khosravi C., Homan T.G., Pré S. du, Arentshorst M., Falco M. di, Pham Thi T.M., Peng M., Aguilar-Pontes M.V., Visser J., Tsang A., Vries R.P. de & Ram A.F.J. (2017), The pathway intermediate 2-keto-3-deoxy-L-galactonate mediates the induction of genes involved in D-galacturonic acid utilization in Aspergillus niger, FEBS Letters 591(10): 1408-1418.
- Vries R.P. de, Riley R., Wiebenga A., Aguilar-Osorio G., Amillis S., Uchima C.A., Anderluh G., Asadollahi M., Askin M., Barry K., Battaglia E., Bayram Ö., Benocci T., Braus-Stromeyer S.A., Caldana C., Cánovas D., Cerqueira G.C., Chen F., Chen W., Choi C., Clum A., Dos Santos R.A., Damásio A.R., Diallinas G., Emri T., Fekete E., Flipphi M., Freyberg S., Gallo A., Gournas C., Habgood R., Hainaut M., Harispe M.L., Henrissat B., Hildén K.S., Hope R., Hossain A., Karabika E., Karaffa L., Karányi Z., Kraševec N., Kuo A., Kusch H., LaButti K., Lagendijk E.L., Lapidus A., Levasseur A., Lindquist E., Lipzen A., Logrieco A.F., MacCabe A., Mäkelä M.R., Malavazi I., Melin P., Meyer V., Mielnichuk N., Miskei M., Molnár Á.P., Mulé G., Ngan C.Y., Orejas M., Orosz E., Ouedraogo J.P., Overkamp M., Park H.S., Perrone G., Piumi F., Punt P.J., Ram A.F.J., Ramón A., Rauscher S., Record E., Riaño-Pachón D.M., Robert V., Röhrig J., Ruller R., Salamov A., Salih N.S., Samson R.A., Sándor E., Sanguinetti M., Schütze T., Sepčić K., Shelest E., Sherlock G., Sophianopoulou V., Squina F.M., Sun H., Susca A., Todd R.B., Tsang A., Unkles S.E., Wiele N. van de, Rossen-Uffink D. van, Oliveira J.V., Vesth T.C., Visser J., Yu J.H., Zhou M., Andersen M.R., Archer D.B., Baker S.E., Benoit I., Brakhage A.A., Braus G.H., Fischer R., Frisvad J.C., Goldman G.H., Houbraken J., Oakley B., Pócsi I., Scazzocchio C., Seiboth B., vanKuyk P.A., Wortman J., Dyer P.S. & Grigoriev I.V. (2017), Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus, Genome Biology 18: 28.
- Niu J., Alazi E., Reid I.D., Arentshorst M., Punt P.J., Visser J., Tsang A. & Ram A.F.J. (2017), An Evolutionarily Conserved Transcriptional Activator-Repressor Module Controls Expression of Genes for D-Galacturonic Acid Utilization in Aspergillus niger, Genetics 205(1): 169-183.
- Niu J., Arentshorst M., Nair P.D., Dai Z., Baker S., Frisvad J.C., Nielsen K.F., Punt P.J. & Ram A.F.J. (2016), Identification of a classical mutant in the industrial host Aspergillus niger by systems genetics: LaeA Is required for citric acid production and regulates the formation of some secondary metabolites.G3 (Bethesda), G3: Genes | Genomes | Genetics 6(1): 193-204.
- Niu J., Arentshorst M., Seelinger F., Ram A.F.J. & Ouedraogo J.P. (2016), A set of isogenic auxotrophic strains for constructing multiple gene deletion mutants and parasexual crossings in Aspergillus niger, Archives of Microbiology 198(9): 861-868.
- Park J., Hulsman M., Arentshorst M., Breeman M., Alazi E., Lagendijk E.L., Rocha M.C., Malavazi I., Nitsche B.M., Hondel C.A.M.J.J. van den, Meyer V. & Ram A.F.J. (2016), Transcriptomic and molecular genetic analysis of the cell wall salvage response of Aspergillus niger to the absence of galactofuranose synthesis, Cellular Microbiology 18(9): 1268-1284.
- Burggraaf A.M., Punt P.J., Ram A.F. & Poeggeler S. (2016), The unconventional secretion of PepN is independent of a functional autophagy machinery in the filamentous fungus Aspergillus niger, FEMS Microbiology Letters 363(15): 152.
- Alazi E., Niu J., Kowalczyk J.E., Peng M., Pontes M.V.A., Kan J.A.L. van, Visser J., Vries R.P. de & Ram A.F.J. (2016), The transcriptional activator GaaR of Aspergillus niger is required for release and utilization of D-galacturonic acid from pectin, FEBS Letters 590(12): 1804-1815.
- Ouedraogo J., Arentshorst M., Nikolaev I., Barends S. & Ram A.F.J. (2016), I-Scel enzyme mediated integration (SEMI) for fast and efficient gene targeting in Trichoderma reesei, Journal of Biotechnology 222: 25-28.
- Wanka F., Arentshorst M., Cairns T.C., Jorgensen T., Ram A.F.J. & Meyer V. (2016), Highly active promoters and native secretion signals for protein production during extremely low growth rates in Aspergillus niger, Microbial Cell Factories 15: 145.
- Patyshakuliyeva A., Arentshorst M., Allijn I.E., Ram A.F.J., Vries R.P. de & Gelber I.B. (2016), Improving cellulase production by Aspergillus niger using adaptive evolution, Biotechnology Letters 38(6): 969-974.
- Burggraaf A.M. & Ram A.F.J. (2016), Autophagy is dispensable to overcome ER stress in the filamentous fungus Aspergillus niger, MicrobiologyOpen 5(4): 647-658.
- Steiger M.G., Punt P.J., Ram A.F.J., Mattanovich D. & Sauer M. (2016), Characterizing MttA as a mitochondrial cis-aconitic acid transporter by metabolic engineering, Metabolic Engineering 35: 95-104.
- Paege N., Jung S., Schape P., Muller-Hagen D., Ouedraogo J.P., Heiderich C., Jedamzick J., Nitsche B.M., Hondel C.A.M.J.J. van den, Ram A.F.J. & Meyer V. (2016), A Transcriptome Meta-Analysis Proposes Novel Biological Roles for the Antifungal Protein AnAFP in Aspergillus niger, PLoS ONE 11(11): 0165755.
- Rocha M.C., Tadini M.F.J.H., Godoy K.F. de, Castro P.A. de, Hori J.I., Cunha A.F. da, Arentshorst M., Ram A.F.J., Hondel C.A.M.J.J. van den, Goldman G.H. & Malavazi I. (2016), Aspergillus fumigatus MADS-Box Transcription Factor rlmA Is Required for Regulation of the Cell Wall Integrity and Virulence, G3: Genes | Genomes | Genetics 6(9): 2983-3002.
- Paun L., Nitsche B., Homan T.G., Ram A.F.J. & Kempken F. (2016), An inducible tool for random mutagenesis in Aspergillus niger based on the transposon Vader, Applied Microbiology and Biotechnology 100(14): 6309-6317.
- Ouedraogo J.P., Arentshorst M., Nikolaev I., Barends S. & Ram A.F.J. (2015), I-SceI-mediated double-strand DNA breaks stimulate efficient gene targeting in the industrial fungus Trichoderma reesei, Applied Microbiology and Biotechnology 99(23): 10083-10095.
- Arentshorst M., Lagendijk E.L. & Ram A.F.J. (2015), A new vector for efficient gene targeting to the pyrG locus in Aspergillus niger, Fungal Biology and Biotechnology 2: 2.
- Munster J.M. van, Nitsche B.M., Akeroyd M., Dijkhuizen L., Maarel M.J.E.C. van der & Ram A.F.J. (2015), Systems Approaches to Predict the Functions of Glycoside Hydrolases during the Life Cycle of Aspergillus niger Using Developmental Mutants Delta brlA and Delta flbA, PLoS ONE 10(1): e0116269.
- Arenthorst M., Jing N. & Ram A.F.J. (2015), Efficient generation of Aspergillus niger knock out strains by combining NHEJ mutants and a split Marker Approach. In: Berg M.A. van den & Maruthachalam K. (Eds.), Genetic Transformation Systems in Fungi. Fungal Biology no. 1. Cham: Springer. 263-272.
- Wu C., Zacchetti B., Ram A.F.J., Wezel G.P. van, Claessen D. & Choi Y.H. (2015), Expanding the chemical space for natural products by Aspergillus-Streptomyces co-cultivation and biotransformation, Scientific Reports 2015(5): 10868.
- Park J.H., Tefsen B., Heemskerk M.J., Lagendijk E.L., Hondel C.A.M.J.J. van den, Die I. van & Ram A.F.J. (2015), Identification and functional analysis of two Golgi-localized UDP-galactofuranose transporters with overlapping functions in Aspergillus niger, BMC Microbiology 15: 253.
- Ercan O., Bisschops M.M.M., Overkamp W., Jorgensen T.R., Ram A.F.J., Smid E.J., Pronk J.T., Kuipers O.P., Daran-Lapujade P. & Kleerebezem M. (2015), Physiological and Transcriptional Responses of Different Industrial Microbes at Near-Zero Specific Growth Rates, Applied and Environmental Microbiology 81(17): 5662-5670.
- Niu J., Homan T.G., Arentshorst M., Vries R.P. de, Visser J. & Ram A.F.J. (2015), The interaction of induction and repression mechanisms in the regulation of galacturonic acid-induced genes in Aspergillus niger, Fungal Genetics and Biology 82: 32-42.
- Park J.P., Tefsen B., Arentshorst M., Lagendijk E., Hondel C.A.M.J.J. van den, Die I. van & Ram A.F.J. (2014), Identification of the UDP-glucose-4-epimerase required for galactofuranose biosynthesis and galactose metabolism in A. niger, Fungal Biology and Biotechnology 1: 6.
- Levasseur A., Lomascolo A., Chabrol O., Ruiz-Dueñas F.J., Boukhris-Uzan E., Piumi F., Kues U., Ram A.F.J., Murat C., Haon M., Benoit I., Arfi Y., Chevret D., Drula E., Kwon M.J., Gouret P., Lesage-Meessen L., Lombard V., Mariette J., Noirot C., Park J.H., Patyshakuliyeva A., Sigoillot J.C., Wieneger R.A., Wösten H.A.B., Martin F., Coutinho P.M., Vries R.P. de, Martinez A.T., Klopp C., Pontarotti P., Henrissat B. & Record E. (2014), The genome of the white-rot fungus Pycnoporus cinnabarinus : a basidiomycete model with a versatile arsenal for lignocellulosic biomass breakdown, BMC Genomics 15: 486.
- Franken A.C.W., Lechner B.E., Werner E.R., Haas H., Lokman B.C., Ram A.F.J., Hondel C.A.M.J.J. van den, Weert S. de & Punt P.J. (2014), Genome mining and functional genomics for siderophore production in Aspergillus niger, Briefings in Functional Genomics 13(6): 482-492.
- Kwon M.J., Arentshorst M., Fiedler M., Groen F.L. de, Punt P.J., Meyer V. & Ram A.F.J. (2014), Molecular genetic analysis of vesicular transport in Aspergillus niger reveals partial conservation of the molecular mechanism of exocytosis in fungi, Microbiology 160(14-01): 316-329.
- Arentshorst M., Jing N. & Ram A.F.J. (2014), Efficient Generation of Aspergillus niger Knock Out Strains by Combining NHEJ Mutants and a Split Marker Approach. Genetic Transformation Systems in Fungi. In: , Genetic Transformation Systems in Fungi I.
- Fiedler M.R.M., Lorenz A., Nitsche B.M., Hondel C.A.M.J.J. van den, Ram A.F.J. & Meyer V. (2014), The capacity of Aspergillus niger to sense and respond to cell wall stress requires at least three transcription factors: RlmA, MsnA and CrzA, Fungal Biology and Biotechnology 1: 5.
- Chiodo F, Marradi M, Park J, Ram A.F., Penadés S, Van Die I & Tefsen B. (2014), Galactofuranose-coated gold nanoparticles elicit a pro-inflammatory response in human monocyte-derived dendritic cells and are recognized by DC-SIGN, ACS Chemical Biology : .
- Schachtschabel D., Arentshorst M., Nitsche B.M., Morris S., Nielsen K.F., Hondel C.A. van den, Klis F.M. & Ram A.F.J. (2013), The transcriptional repressor TupA in Aspergillus niger is involved in controlling gene expression related to cell wall biosynthesis, development, and nitrogen source availability, PLoS ONE 8(10): e78102.
- Ouedraogo J.P., Lagendijk E.L., Van den Hondel C.A., Ram A.F.J., Meyer & V. (2013), Screening for compounds with antifungal activities, Fungal Biology (Springer) : 225-230.
- Kwon M.J., Arentshorst M., Fiedler M., De Groen F.L., Punt P.J., Meyer V. & Ram A.F. (2013), Molecular genetic analysis of vesicular transport in Aspergillus niger reveals partial conservation of the molecular mechanism of exocytosis in fungi, Microbiology : .
- Krijgsheld P., Nitsche B.M., Post H., Levin A.M., Müller W.H., Heck A.J., Ram A.F.J., Altelaar A.F. & Wösten H.A. (2013), Deletion of flbA Results in Increased Secretome Complexity and Reduced Secretion Heterogeneity in Colonies of Aspergillus niger, Journal of Proteome Research : .
- Kwon M.J., Nitsche B.M., Arentshorst M., Jørgensen T.R., Ram A.F.J. & Meyer V. (2013), The transcriptomic signature of RacA activation and inactivation provides new insights into the morphogenetic network of Aspergillus niger, PLoS ONE 8(7): e68946.
- Franken A.C., Werner E.R., Haas H., Lokman B.C., Van den Hondel C.A., Ram A.F., De Weert S. & Punt P.J. (2013), The role of coproporphyrinogen III oxidase and ferrochelatase genes in heme biosynthesis and regulation in Aspergillus niger, Applied Microbiology and Biotechnology 97(22):9773-85: .
- Van Munster J.M., Nitsche B.M., Krijgsheld P., Van Wijk A., Dijkhuizen L., Wösten H.A., Ram A.F. & Van der Maarel M.J. (2013), Chitinases CtcB and CfcI modify the cell wall in sporulating aerial mycelium of Aspergillus niger, Microbiology 159(Pt 9):1853-67: .
- Ram A.F.J. (2013), Modern Technologies Boost Classical Genetics: Whole Genome Sequencing Revives Forward Genetic Mutant Screens in Filamentous Fungi, Fungal Genomics & Biology 2: e105: .
- Esbelin J., Mallea S.J., Ram A.F.J. & Carlin F. (2013), Role of Pigmentation in Protecting Aspergillus niger Conidiospores Against Pulsed Light Radiation, Photochemical & Photobiological Sciences 89(3):758-61: .
- Nitsche B.M., Burggraaf-van Welzen A.M., Lamers G., Meyer V. & Ram A.F. (2013), Autophagy promotes survival in aging submerged cultures of the filamentous fungus Aspergillus niger, Applied Microbiology and Biotechnology 97(18): 8205-8218.
- Van Veluw G.J., Teertstra W.R., De Bekker C., Vinck A., Van Beek N., Muller W.H., Arentshorst M., Van der Mei H.C., Ram A.F., Dijksterhuis J. & Wösten H.A. (2013), Heterogeneity in liquid shaken cultures of Aspergillus niger inoculated with melanised conidia or conidia of pigmentation mutants, Studies in Mycology 74(1): 47-57.
- Nitsche B.M., Jørgensen T.R., Akeroyd M., Meyer V. & Ram A.F.J. (2012), The carbon starvation response of Aspergillus niger during submerged cultivation: Insights from the transcriptome and secretome, BMC Genomics 13: 380.
- Arentshorst M., Ram A.F.J. & Meyer V. (2012), Using non-homologous end-joining-deficient strains for functional gene analyses in filamentous fungi, Methods in Molecular Biology 835: 133-150.
- Carvalho N.D.S.P., Jørgensen T.R., Arentshorst M., Nitsche B.M., Hondel C.A.M.J.J. van den, Archer D.B. & Ram A.F.J. (2012), Genome-wide expression analysis upon constitutive activation of the HacA bZIP transcription factor in Aspergillus niger reveals a coordinated cellular response to counteract ER stress, BMC Genomics 13: 350.
- Kwon M.J., Jørgensen T.R., Nitsche B.M., Arentshorst M., Park J., Ram A.F.J. & Meyer V. (2012), The transcriptomic fingerprint of glucoamylase over-expression in Aspergillus niger, BMC Genomics 13: 701.
- Ouedraogo J.P., Lagendijk E.L., Hondel C.A.M.J.J. van den, Ram A.F.J. & Meyer V. (2012), Screening for compounds exerting antifungal activities. In: Kumar Gupta V., Tuohy M.G., Ayyachamy M., O'Donovan A. & Turner K.M. (Eds.), Laboratory Protocols in Fungal Biology. New York: Humana Press/Springer. 225-230.
- Nitsche B.M., Ram A.F.J. & Meyer V. (2012), The use of open source bioinformatics tools to dissect transcriptomic data, Methods in Molecular Biology 835: 311-331.
- Tefsen B., Ram A.F.J., Die I. van & Routier F.H. (2012), Galactofuranose in eukaryotes: aspects of biosynthesis and functional impact, Glycobiology 22(4): 456-469.
- Franken A.C., Lokman B.C., Ram A.F.J., Hondel C.A.M.J.J. van den, Weert S. de & Punt P.J. (2012), Analysis of the role of the Aspergillus niger aminolevulinic acid synthase (hemA) gene illustrates the difference between regulation of yeast and fungal hem - and sirohaem-dependent pathways, FEMS Microbiology Letters 335(2): 104-112.
- Tefsen B., Lagendijk E.L., Park J., Akeroyd M., Schachtschabel D., Winkler R., Die I. van & Ram A.F.J. (2012), Fungal α-arabinofuranosidases of glycosyl hydrolase families 51 and 54 show a dual arabinofuranosyl- and galactofuranosyl-hydrolyzing activity, Biological Chemistry 393(8): 767-775.
- Schachtschabel D., Arentshorst M., Lagendijk E.L. & Ram A.F.J. (2012), Vacuolar H(+)-ATPase plays a key role in cell wall biosynthesis of Aspergillus niger, Fungal Genetics and Biology 49(4): 284-293.
- Meyer V., Wu B. & Ram A.F.J. (2011), Aspergillus as a multi-purpose cell factory: Current status and perspectives, Biotechnology Letters 33: 469-476.
- Carvalho N.D.S.P., Arentshorst M., Kooistra R., Stam H., Sagt C.M., Hondel C.A.M.J.J. van den & Ram A.F.J. (2011), Effects of a defective ERAD pathway on growth and heterologous protein production in Aspergillus niger, Applied Microbiology and Biotechnology 89: 357-373.
- Franken A.C., Lokman B.C., Ram A.F.J., Punt P.J., Hondel C.A.M.J.J. van den & Weert S. de (2011), Heme biosynthesis and its regulation: towards understanding and improvement of heme biosynthesis in filamentous fungi, Applied Microbiology and Biotechnology 91: 447-460.
- Tefsen B., Ram A.F.J., Die I. van & Routier F.H. (2011), Galactofuranose in eukaryotes: aspects of biosynthesis and functionl impact, Glycobiology : .
- Arentshorst M., Ram A.F.J. & Meyer V. (2011), Using NHEJ-deficient strains for functional gene analyses in filamentous fungi. In: , Methods in Molecular Biology.
- Nitsche B.M., Ram A.F.J. & Meyer V. (2011), The use of open source bioinformatics tools to dissect fungal transcriptomic data. In: , Methods in Molecular Biology.
- Kwon M.J., Arentshorst M., Roos E.D., Hondel C.A.M.J.J. van den, Meyer V. & Ram A.F.J. (2011), Functional characterization of Rho GTPases in Aspergillus niger uncovers conserved and diverged roles of Rho proteins within filamentous fungi, Molecular Microbiology 79(5): 1151-1167.
- Meyer V., Wanka F., Gent J. van, Arentshorst M., Hondel C.A.M.J.J. van den & Ram A.F.J. (2011), Fungal gene expression on demand: an inducible, tunable and metabolism independent expression system for Aspergillus niger, Applied and Environmental Microbiology 77(9): 2975-2983.
- Carvalho N.D.S.P., Arentshorst M., Weenink X., Punt P.J., Hondel C.A.M.J.J. van den & Ram A.F.J. (2011), Functional YFP-tagging of the essential GDP-mannose transporter reveals an important role for the secretion related small GTPase SrgC protein in maintenance of Golgi bodies in Aspergillus niger, Fungal Biology 115(3): 253-264.
- Jørgensen T.R., Nielsen K.F., Arentshorst M., Park J., Hondel C.A.M.J.J. van den, Frisvad J.C. & Ram A.F.J. (2011), Submerged conidiation and product formation by Aspergillus niger at low specific growth rates are affected in aerial developmental mutants, Applied and Environmental Microbiology 77(15): 5270-5277.
- Nitsche B.M., Crabtree J., Cerqueira G.C., Meyer V., Ram A.F.J. & Wortman J.R. (2011), New resources for functional analysis of omics data for the genus Aspergillus, BMC Genomics 12: 486.
- Jørgensen T.R., Park J.-H., Arentshorst M., Welzen A.M. van, Lamers G., VanKuyk P.A., Damveld R.A., Hondel C.A.M.J.J. van den, Nielsen K.F., Frisvad J.C. & Ram A.F.J. (2011), The molecular and genetic basis of conidial pigmentation in Aspergillus niger, Fungal Genetics and Biology 48(5): 544-553.
- Guillemette T., Ram A.F.J., Carvalho N.D.S.P., Joubert A., Simoneau P. & Archer D.B. (2011), Methods for investigating the UPR in filamentous fungi, Methods in Enzymology 490: 1-29.
- Carvalho N.D.S.P., Arentshorst M., Kwon M.J., Meyer V. & Ram A.F.J. (2011), Expanding the ku70 toolbox analyses, Applied Microbiology and Biotechnology 87: 1463-1473.
- Jørgensen T.R., Nitsche B.M., Lamers G.E.M., Arentshorst M., Hondel C.A.M.J.J. van den & Ram A.F.J. (2010), Transcriptomic insights into the physiology of Aspergillus niger approaching a specific growth rate of zero, Applied and Environmental Microbiology 76(16): 5344-5355.
- Meyer V., Ram A.F.J. & Punt P.J. (2010), Genetics, Genetic Manipulation, and Approaches to Strain Improvement of Filamentous Fungi. In: Manual of Industrial Microbiology and Biotechnology. Washington DC: ASM Press.
- Kaaij R.M. van der, Ram A.F.J., Schaap P. & Punt P.J. (2010), Genomic approaches for identification of the biopolymer degrading enzyme network of Aspergillus niger. The Mycota. Berlin Heidelberg: Springer-Verlag Berlin Heidelberg.
- Meyer V., Minkwitz S., Schütze T., Hondel C.A.M.J.J. van den & Ram A.F.J. (2010), The Aspergillus niger RmsA protein: a node in a genetic network?, Communicative and Integrative Biology 3(2): 195-197.
- Jacobs D.I., Olsthoorn M.M., Maillet I., Akeroyd M., Breestraat S., Donkers S., Hoeven R.A.M. van der, Hondel C.A.M.J.J. van den, Kooistra R.A., Lapointe T., Menke H., Meulenberg R., Misset M., Muller W.H., Peij N.N. van, Ram A.F.J., Rodriguez S., Roelofs M.S., Roubos J.A., Tilborg M.W. van, Verkleij A.J., Pel H.J., Stam H. & Sagt C.M. (2009), Effective lead selection for improved protein production in Aspergillus niger based on integrated genomics, Fungal Genetics and Biology 46(1 Supplement): S141-S152.
- Groot P.W.J. de, Brandt B.W., Horiuchi H., Ram A.F.J., Koster C.G. de & Klis F.M. (2009), Comprehensive genomic analysis of cell wall genes in Aspergillus nidulans, Fung. Genet. Biol. 46(Suppl. 1): S72-81.
- Jørgensen T.R., Goosen T., Hondel C.A.M.J.J. van den, Ram A.F.J. & Iversen J.J. (2009), Transcriptomic comparison of Aspergillus niger growing on two different sugars reveals coordinated regulation of the secretory pathway, BMC Genomics 10: 44.
- Wortman J.R., Gilsenan J.M., Joardar V., Deegan J., Clutterbuck J., Andersen M.R., Archer D., Bencina M., Braus G., Coutinho P., Doehren H. von der, Doonan J., Driessen A., Durek P., Espeso E., Fekete E., Flipphi M., Garcia Estrada C., Geysens S., Goldman G., Groot P. de, Hansen K., Harris S.D., Heinekamp T., Helmstaedt K., Henrissat B., Hofmann G., Homan T., Horio T., Horiuchi H., James S., Jones M., Karányi Z., Kato M., Keller N., Kelly D.E., Kiel J.A.K.W., Kim J-M., Klei IJ. van der, Klis F., Kovalchuk A., Kraševec N., Kubicek C.P., Levente K., Liu B., MacCabe A., Meyer V., Mirabito P., Miskei M., Mos M. de, Mullins J., Nelson D.R., Nielsen J., Oakley B.R., Osmani S.A., Pakula T., Paszewski A., Paulsen I., Pilsyk S., Pócsi I., Punt P.J., Ram A.F.J., Ren Q., Robson G., Seiboth B., Solingen P. van, Specht T., Sun J., Taheri-Talesh N., Takeshita N., Ussery D., VanKuyk P.A., Visser H., Vondervoort P. & Vries R.P. de (2009), The 2008 update of the Aspergillus nidulans genome annotation: a community effort, Fung. Genet. Biol. 46(Supp 1): S2-13.
- Meyer V., Arentshorst M., Flitter S.J., Nitsche B.M., Kwon M.J., Reynaga-Pena C.G., Bartnicki-Garcia S., Hondel C.A.M.J.J. van den & Ram A.F.J. (2009), Reconstruction of signalling networks regulating fungal morphogenesis by transcriptomics, Eukaryotic Cell 8(11): 1677-1691.
- Kaaij R.M. van der, Ram A.F.J., Schaap P. & Punt P.J. (2009), Genomic approaches for identification of the biopolymer degrading enzyme network of Aspergillus niger, The Mycota : .
- Yuan X., Roubos J.A., Hondel C.A.M.J.J. van den & Ram A.F.J. (2008), Identification of InuR, a new Zn(II)2Cys6 transcriptional activator involved in the regulation of inulinolytic genes in Aspergillus niger, Molecular Genetics and Genomics 279: 11-26.
- Rodriguez E., Ruiz-Duenas F.J., Kooistra R.A., Ram A.F.J., Martinez A.T. & Martinez M.J. (2008), Isolation of two laccase genes from the white-rot fungus Pleurotus eryngii and heterologous expression of the pel3 encoded protein, Journal of Biotechnology 134: 9-19.
- Damveld R.A., Franken A., Arentshorst M., Punt P.J., Klis F.M., Hondel C.A.M.J.J. van den & Ram A.F.J. (2008), A novel screening method for cell wall mutants in Aspergillus niger identifies UDP-galactopyranose mutase as an important protein in fungal cell wall biosynthesis, Genetics 178(2): 873-881.
- Yuan X., Kaaij R.M. van der, Hondel C.A.M.J.J. van den, Punt P.J., Maarel M.J., Dijkhuizen L. & Ram A.F.J. (2008), Aspergillus niger genome-wide analysis reveals a large number of novel alpha-glucan acting enzymes with unexpected expression profiles, Molecular Genetics and Genomics 279: 545-561.
- Deng S., Gerrits A.H.G., Ende A. van der, Ram A.F.J., Arentshorst M., Gräser Y., Hu H. & Hoog G.S. de (2008), Evolution of CDC42, a putative virulence factor triggering meristematic growth in black yeasts, Studies in Mycology 61: 121-129.
- Groot P.W.J. de, Brandt B.W., Horiuchi H., Ram A.F.J., Koster C.G. de & Klis F.M. (2008), Comprehensive Genomic Analysis of Cell Wall Genes in Aspergillus nidulans, Fungal Genetics and Biology : .
- Homan T.G., Ram A.F.J. & Hondel C.A.M.J.J. van den (2008), The 2008 update of the Aspergillus nidulans genome annotation: a community effort, Fungal Genetics and Biology 46(1): S2-S13.
- Michielse C.B., Hooykaas P.J.J., Hondel C.A.M.J.J. van den & Ram A.F.J. (2008), Agrobacterium-mediated transformation of the filamentous fungus Aspergillus awamori, Nature Physics 3: 1671-1678.
- Meyer V., Arentshorst M., Hondel C.A.M.J.J. van den & Ram A.F.J. (2008), The polarisome component SpaA localises to hyphal tips of Aspergillus niger and is important for polar growth, Fungal Genetics and Biology 45(2): 152-164.
- Hagen S., Marx F., Ram A.F.J. & Meyer V. (2007), The antifungal protein AFP from Aspergillus giganteus inhibits chitin synthesis in sensitive fungi, Applied and Environmental Microbiology 73(7): 2128-2134.
- Meyer V., Arentshorst M., El-Ghezal A., Drews A.C., Kooistra R.A., Hondel C.A.M.J.J. van den & Ram A.F.J. (2007), Highly efficient gene targeting in the Aspergillus niger kusA mutant, Journal of Biotechnology 128(4): 770-775.
- Goosen C., Yuan X., Munster J.M. van, Ram A.F.J., Maarel M.J. & Dijkhuizen L. (2007), Molecular and biochemical characterization of a novel intracellular invertase from Aspergillus niger with transfructosylating activity, Eukaryotic Cell 6: 674-681.
- Vondervoort P.J.I. van de, Langeveld S.M.J., Visser J., Peij N.N. van, Pel H.J., Hondel C.A.M.J.J. van den & Ram A.F.J. (2007), Identification of a mitotic recombination hotspot on chromosome III of the asexual fungus Aspergillus niger and its possible correlation with [corrected] elevated basal transcription, Current Genetics 52: 107-114.
- Kaaij R.M. van der, Yuan X., Franken A., Ram A.F.J., Punt P.J., Maarel M.J. & Dijkhuizen L. (2007), Two novel, putatively cell wall-associated and glycosylphosphatidylinositol-anchored alpha-glucanotransferase enzymes of Aspergillus niger, Eukaryotic Cell 6: 1178-1188.
- Pel H.J., Winde J.H. de, Ram A.F.J., Hondel C.A.M.J.J. van den, Vondervoort P.J.I. van de & et al. (2007), Genome sequencing and analysis of the versatile cell factory Aspergillus niger CBS 513.88, Nature Biotechnology 25(2): 221-231.
- Sumthong P., Damveld R.A., Choi Y.H., Arentshorst M., Ram A.F.J., Hondel C.A.M.J.J. van den & Verpoorte R. (2006), Activity of quinones from teak (Tectona grandis) on fungal cell wall stress, Planta Medica 72(10): 943-944.
- Weenink X.O., Punt P.J., Hondel C.A.M.J.J. van den & Ram A.F.J. (2006), A new method for screening and isolation of hypersecretion mutants in Aspergillus niger, Applied Microbiology and Biotechnology 69: 711-717.
- Ram A.F.J. & Klis F.M. (2006), Identification of fungal cell wall mutants using susceptibility assays based on Calcofluor White and Congo Red, Nature Physics 1: 2253-2256.
- Yuan X.L., Goosen C., Kools H., Maarel M.J., Hondel C.A.M.J.J. van den, Dijkhuizen L. & Ram A.F.J. (2006), Database mining and transcriptional analysis of genes encoding inulin-modifying enzymes of Aspergillus niger, Microbiology 152(10): 3061-3073.
- Vinck A., Terlou M., Pestman W.R., Martens E.P., Ram A.F.J., Hondel C.A.M.J.J. van den & Worsten H.A. (2005), Hyphal differentiation in the exploring mycelium of Aspergillus niger, Molecular Microbiology 58(3): 693-699.
- Damveld R.A., Kuyk P.A. van, Arentshorst M., Klis F.M., Hondel C.A.M.J.J. van den & Ram A.F.J. (2005), Expression of agsA, one of five 1,3-α-d-glucan synthase-encoding genes in Aspergillus niger, is induced in response to cell wall stress, Fungal Genetics and Biology 42(5): 165-177.
- Michielse C.B., Arentshorst M., Ram A.F.J. & Hondel C.A.M.J.J. van den (2005), Agrobacterium-mediated transformation leads to improved gene replacement efficiency in Aspergillus awamori, Fungal Genetics and Biology 42(1): 9-19.
- Groot P.W. de, Ram A.F.J. & Klis F.M. (2005), Features and functions of covalently linked proteins in fungal cell walls, Fungal Genetics and Biology 42(8): 657-675.
- Michielse C.B., Hooykaas P.J.J., Hondel C.A.M.J.J. van den & Ram A.F.J. (2005), Agrobacterium-mediated transformation as a tool for functional genomics in fungi, Current Genetics 48(1): 1-17.
- Damveld R.A., Arentshorst M., VanKuyk P.A., Klis F.M., Hondel C.A.M.J.J. van den & Ram A.F.J. (2005), The Aspergillus niger MADS-box transcription factor RlmA is required for cell wall reinforcement in response to cell wall stress, Molecular Microbiology 58(1): 305-319.
- Damveld R.A., Arentshorst M., Kuyk P.A. van, Klis F.M., Hondel C.A.M.J.J. van den & Ram A.F.J. (2005), Characterisation of CwpA, a putative glycosylphosphatidylinositol-anchored cell wall mannoprotein in the filamentous fungus Aspergillus niger, Fungal Genetics and Biology 42(10): 873-885.
- Michielse C.B., Salim K., Ragas P., Ram A.F.J., Kudla B., Jarry B., Punt P.J. & Hondel C.A.M.J.J. van den (2004), Development of a system for integrative and stable transformation of the zygomycete Rhizopus oryzae by Agrobacterium-mediated DNA transfer, Molecular Genetics and Genomics 271: 499-510.
- Michielse C.B., Ram A.F.J., Hooykaas P.J.J. & Hondel C.A.M.J.J. van den (2004), Role of bacterial virulence proteins in Agrobacterium-mediated transformation of Aspergillus awamori, Fungal Genetics and Biology 41(5): 571-578.
- Michielse C.B., Ram A.F.J. & Hondel C.A.M.J.J. van den (2004), The Aspergillus nidulans amdS gene as a marker for the identification of multicopy T-DNA integration events in Agrobacterium-mediated transformation of Aspergillus awamori, Current Genetics 45: 399-403.
- Michielse C.B., Ram A.F.J., Hooykaas P.J.J. & Hondel C.A.M.J.J. van den (2004), Agrobacterium-mediated transformation of Aspergillus awamori in the absence of full-length VirD2, VirC2, or VirE2 leads to insertion of aberrant T-DNA structures, Journal of Bacteriology 186(7): 2038-2045.
- Takken F.L., Wijk R. van, Michielse C.B., Houterman P.M., Ram A.F.J. & Cornelissen B.J. (2004), A one-step method to convert vectors into binary vectors suited for Agrobacterium-mediated transformation, Current Genetics 45: 242-248.
- Ram A.F.J., Arentshorst M., Damveld R.A., Kuyk P.A. van, Klis F.M. & Hondel C.A.M.J.J. van den (2004), The cell wall stress response in Aspergillus niger involves increased expression of the glutamine: fructose-6-phosphate amidotransferase-encoding gene (gfaA) and increased deposition of chitin in the cell wall , Microbiology 150(10): 3315-3326.
- Lagopodi A., Ram A.F.J., Lamers G.E.M., Punt P.J., Hondel C.A.M.J.J. van den, Lugtenberg E.J.J. & Bloemberg G.V. (2002), Novel aspects of tomato root colonization and infection by Fusarium oxysporum f. sp. radicislycopersici revealed by confocal laser scanning microscopic analysis using the green fluorescent protein as a marker, Molecular Plant-Microbe Interactions 15(2): 172-179.
- Bordon C.L., Khalaj V., Ram A.F.J., Archer D.B., Brookman J.L., Trinci A.P.J., Jeenes D.J., Doonan J.H., Wells B., Punt P.J., Hondel C.A.M.J.J. van den & Robson G.D. (2000), Glucoamylase: green fluorescent protein fusions to monitor protein secretion in Aspergillus niger, Microbiology 146(2): 415-426.
- Berkel M.A. van, Rieger M., Heesen S. te, Ram A.F.J., Ende H van den, Aebi M. & Klis F.M. (1999), The S. cerevisiae CWH8 gene is required for full levels of dolichol-linked oligosaccharides in the endoplasmic reticulum and for efficient N-glycosylation, Glycobiology 9:3: 243-253.
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