Publication Records

BUDINSKÁ, Eva, Martina ČARNOGURSKÁ, Tina CATELA IVKOVIĆ, Táňa MACHÁČKOVÁ, Marie BOUDNÁ, Lucie PIFKOVÁ, Ondřej SLABÝ, Beatrix BENCSIKOVA and Vlad POPOVICI. An invasion front gene expression signature for higher-risk patient selection in stage IIA MSS colon cancer. Frontiers in Oncology. LAUSANNE: FRONTIERS MEDIA SA, 2024, vol. 14, April 2024, p. 1-8. ISSN 2234-943X. Available from: https://dx.doi.org/10.3389/fonc.2024.1367231.

KOSEČKOVÁ MICENKOVÁ, Lenka, Kristýna BRODÍKOVÁ, Soňa SMETANOVÁ, Juraj BOSÁK, David ŠMAJS, Petr ANDRLA and Eva BUDINSKÁ. High colonisation by probiotic Escherichia coli A0 34/86 strain is associated with a less diverse microbiome related to children’s age. Beneficial Microbes. Wageningen Academic, 2024, vol. 15, No 1, p. 5-17. ISSN 1876-2883. Available from: https://dx.doi.org/10.1163/18762891-20220049.

PIVRNCOVÁ, Eliška, Lucie BUREŠOVÁ, Iva KOTÁSKOVÁ, Petra VÍDEŇSKÁ, Lenka ANDRÝSKOVÁ, Pavel PILER, Petr JANKŮ, Ivo BOREK, Jan BÖHM, Jana KLÁNOVÁ, Eva BUDINSKÁ and Petra BOŘILOVÁ LINHARTOVÁ. Impact of intrapartum antibiotic prophylaxis on the oral and fecal bacteriomes of children in the first week of life. Nature Scientific Reports. London: NATURE RESEARCH, 2024, vol. 14, No 1, p. 1-17. ISSN 2045-2322. Available from: https://dx.doi.org/10.1038/s41598-024-68953-z.

PARDINI, Barbara, Giulio FERRERO, Sonia TARALLO, Gaetano GALLO, Antonio FRANCAVILLA, Nicola LICHERI, Mario TROMPETTO, Giuseppe CLERICO, Carlo SENORE, Sergio PEYRE, Veronika VYMETALKOVA, Ludmila VODICKOVA, Vaclav LISKA, Ondrej VYCITAL, Miroslav LEVY, Peter MACINGA, Tomas HUCL, Eva BUDINSKÁ, Pavel VODICKA, Francesca CORDERO and Alessio NACCARATI. A Fecal MicroRNA Signature by Small RNA Sequencing Accurately Distinguishes Colorectal Cancers: Results From a Multicenter Study. Gastroenterology. Philadelphia: W B Saunders co-Elsevier Inc, 2023, vol. 165, No 3, p. 582-607. ISSN 0016-5085. Available from: https://dx.doi.org/10.1053/j.gastro.2023.05.037.

BOŘILOVÁ LINHARTOVÁ, Petra, Dávid SZÁRAZ, Sabina CERULOVÁ, Lenka BODOKYOVÁ, Ctirad MACHÁČEK, Zdeněk DANĚK, Petra BRENEROVÁ and Eva BUDINSKÁ. Bacteriome analysis of cystic fluids from odontogenic cysts – a pilot study. In 3rd International Conference on Oral Mucosal Immunity and Microbiome. 2023.

BOŘILOVÁ LINHARTOVÁ, Petra, Dávid SZÁRAZ, Sabina CERULOVÁ, Lenka BODOKYOVÁ, Ctirad MACHÁČEK, Zdeněk DANĚK and Eva BUDINSKÁ. Bacteriomes of dental plaques from teeth affected by apical periodontitis in patients with different periapical lesions: a pilot case-case study. In 3rd International Conference on Microbiology and Immunology. 2023.

SZÁRAZ, Dávid, Zdeněk DANĚK, Petr ANDRLA, Eva BUDINSKÁ, Tereza DEISSOVÁ, Daniela GACHOVÁ, Natálie MLČŮCHOVÁ, Ctirad MACHÁČEK and Petra BOŘILOVÁ LINHARTOVÁ. Cílená detekce somatických mutací u pacientů s ameloblastomem: série případů (Targeted detection of somatic mutations in patients with ameloblastoma: a case series). In ONCO Prague, 2023. 2023.

MLČŮCHOVÁ, Natálie, Terezie SLÁMOVÁ, Petra BRENEROVÁ, Tereza DEISSOVÁ, Jan BÖHM, Lumír KUNOVSKÝ, Radek KROUPA, Jiří DOLINA, Vladimír PROCHÁZKA, Tomáš GROLICH, Jitka VACULOVÁ, Petr ANDRLA, Vít NAVRÁTIL, Ondřej URBAN, Tomáš HARUŠTIAK, Robert LISCHKE, Lydie IZAKOVIČOVÁ HOLLÁ, Ondřej SLABÝ, Zdeněk KALA, Eva BUDINSKÁ and Petra BOŘILOVÁ LINHARTOVÁ. Comparison of sequencing analyses targeting the V1/V2 and V3/V4 regions in the 16S rDNA gene – analysis of bacteriome in oral swabs and esophageal tissues. In Biologické dny, 2023. 2023.

KLVAŇOVÁ, Eva, Petra VÍDEŇSKÁ, Lucie BUREŠOVÁ, Milan URÍK, Soňa SMETANOVÁ, Stanislav SMATANA, Roman PROKEŠ, Barbara LÁNÍČKOVÁ, Eva BUDINSKÁ, Jana KLÁNOVÁ and Petra BOŘILOVÁ LINHARTOVÁ. Enrichment of human nasopharyngeal bacteriome with bacteria from dust after short-term exposure to indoor environment. In Setkání biochemiků a molekulárních biologů. 2023.

KONEČNÁ, Eva, Petra VÍDEŇSKÁ, Lucie BUREŠOVÁ, Milan URÍK, Soňa SMETANOVÁ, Stanislav SMATANA, Roman PROKEŠ, Barbara LÁNÍČKOVÁ, Eva BUDINSKÁ, Jana KLÁNOVÁ and Petra BOŘILOVÁ LINHARTOVÁ. Enrichment of human nasopharyngeal bacteriome with bacteria from dust after short-term exposure to indoor environment: a pilot study. BMC Microbiology. London: BioMed Central, 2023, vol. 23, No 1, p. 1-16. ISSN 1471-2180. Available from: https://dx.doi.org/10.1186/s12866-023-02951-5.

PAČÍNKOVÁ, Anna and Vlad POPOVICI. IntOMICS: A Bayesian Framework for Reconstructing Regulatory Networks Using Multi-Omics Data. Journal of Computational Biology. Mary Ann Liebert, Inc., 2023, vol. 30, No 5, p. 569-574. ISSN 1066-5277. Available from: https://dx.doi.org/10.1089/cmb.2022.0149.

BOŘILOVÁ LINHARTOVÁ, Petra, Filip RŮŽIČKA, František JANDA, Pavla HOLOCHOVÁ, Maximilián RADA, Zdeněk POKORNÝ, Eva KUŽELOVÁ KOŠŤÁKOVÁ, Eva BUDINSKÁ, Petra RŮŽIČKOVÁ and Jana KLÁNOVÁ. Laboratoře analýzy mikrobiomu - testování nanomateriálu obsahujícího probiotikum a jeho využití v preventivní medicíně (Microbiome analysis laboratories - testing of a nanomaterial containing a probiotic and its use in preventive medicine). In MATEDAS, 2023. 2023.

BUDINSKÁ, Eva, Martina HRIVŇÁKOVÁ, Tina CATELA IVKOVIĆ, Marie BOUDNÁ, Rudolf NENUTIL, Beatrix BENCSIKOVÁ, Dagmar AL TUKMACHI, Michaela RUČKOVÁ, Lenka DUBSKÁ, Ondřej SLABÝ, Josef FEIT, Dragomir MIHNEA-PAUL, Petra BOŘILOVÁ LINHARTOVÁ, Sabine TEJPAR and Vlad POPOVICI. Molecular portraits of colorectal cancer morphological regions. eLife. CAMBRIDGE: ELIFE SCIENCES PUBL LTD, 2023, vol. 12, Nov, p. 1-20. ISSN 2050-084X. Available from: https://dx.doi.org/10.7554/eLife.86655.3.

BOUCHALOVÁ, Pavla, Jan ŠIMONÍK, Petr LAPČÍK, Lucia JANÁČOVÁ, David POTĚŠIL, Ján PODHOREC, Alice HLOBILKOVÁ, Vlad POPOVICI, Milan HORA, Alexandr POPRACH, Ondřej FIALA and Pavel BOUCHAL. Next generation proteomics identifies a potential protein marker of poor response to tyrosine kinase inhibitors in metastatic renal cell carcinoma. In Abstract Book of EACR Conference: Cellular Bases for Patient Response to Cancer Therapies, Lyon, Francie 14.-16.11.2023, P12. 2023.

GACHOVÁ, Daniela, Zdeněk DANĚK, Ctirad MACHÁČEK, Soňa SMETANOVÁ, Petr ANDRLA, Eva BUDINSKÁ and Petra BOŘILOVÁ LINHARTOVÁ. Orální bakteriom u pacientů s dlaždicobuněčným karcinomem dle stavu jejich dentice: pilotní studie (Oral bacterioma in patients with squamous cell carcinoma based on their gingival status: a pilot study). In ONCO Prague, 2023. 2023.

ŠIMONÍK, Jan, Richard ŠTEFANÍK, Pavla BOUCHALOVÁ, Petr LAPČÍK, David POTĚŠIL, Vlad POPOVICI, Ján PODHOREC, Milan HORA, Alexandr POPRACH, Ondřej FIALA and Pavel BOUCHAL. Proteotype classification of localized and metastatic renal cell carcinoma for prognosis and therapy response. In Abstract Book of BSRP - EuPA Annual Scientific Meeting, Newcastle upon Tyne, UK, 17.-20.7.2023. 2023.

ŠIMONÍK, Jan, Pavla BOUCHALOVÁ, Richard ŠTEFANÍK, Petr LAPČÍK, David POTĚŠIL, Vlad POPOVICI, Ján PODHOREC, Milan HORA, Alexandr POPRACH, Ondřej FIALA and Pavel BOUCHAL. Proteotype classification of metastatic and localized renal cell carcinomas for prognosis and therapy response. In Abstract Book of XVIII. Czech Annual Cancer Research Meeting, Olomouc, CZ, 20.-22.11.2023. 2023. ISBN 978-80-908348-2-8.

PIVRNCOVÁ, Eliška, Iva KOTÁSKOVÁ, Lucie BUREŠOVÁ, Lenka ANDRÝSKOVÁ, Pavel PILER, Petr JANKŮ, Ivo BOREK, Jana KLÁNOVÁ, Petra VÍDEŇSKÁ, Eva BUDINSKÁ and Petra BOŘILOVÁ LINHARTOVÁ. The effect of intrapartum antibiotics prophylaxis on neonatal gut and oral bacteriome. In RECETOX PhD Conference 2023. 2023.

PIVRNCOVÁ, Eliška, Iva KOTÁSKOVÁ, Lucie BUREŠOVÁ, Lenka ANDRÝSKOVÁ, Pavel PILER, Petr JANKŮ, Ivo BOREK, Jana KLÁNOVÁ, Petra VÍDEŇSKÁ, Eva BUDINSKÁ and Petra BOŘILOVÁ LINHARTOVÁ. The effect of intrapartum antibiotics prophylaxis on oral bacteriome in neonates in the first week of theri life - i pilot study. In World of Microbiome. 2023.

BOŘILOVÁ LINHARTOVÁ, Petra, Natálie MLČŮCHOVÁ, Jan BÖHM, Petra BRENEROVÁ, Vojtěch BARTOŇ, Adam MAJER, Zdeněk PAVLOVSKÝ, Lumír KUNOVSKÝ, Radek KROUPA, Jiří DOLINA, Ondřej URBAN, Vít NAVRÁTIL, Tomáš HARUŠTIAK, Robert LISCHKE, Tomáš GROLICH, Vladimír PROCHÁZKA, Lydie IZAKOVIČOVÁ HOLLÁ, Martina ZAPLETALOVÁ, Jan LOCHMAN, Ondřej SLABÝ, Eva BUDINSKÁ and Zdeněk KALA. Transcriptomic analysis of esophageal tissues and potential biomarkers for differential diagnostics of Barrett´s mucosa and esophageal adenocarcinoma. In Cancer Science, 2023. 2023.

ŠIMONÍK, Jan, Pavla BOUCHALOVÁ, Petr LAPČÍK, David POTĚŠIL, Ján PODHOREC, Lucia JANÁČOVÁ, Alice HLOBILKOVÁ, Vlad POPOVICI, Alexandr POPRACH, Milan HORA, Ondřej FIALA and Pavel BOUCHAL. Transmembrane glycoprotein GPNMB is a potential marker of poor response of metastatic renal cell carcinoma to tyrosine kinase receptor inhibitor treatment. In 9th Informal Proteomic Meeting November 30 – December 1, Mělník, Masaryk Cultural House. 2023.

BOŘILOVÁ LINHARTOVÁ, Petra, Petra BRENEROVÁ, Pavla HOLOCHOVÁ, Jana VRZALOVÁ, Vojtěch BARTOŇ, Jan BÖHM, Eva BUDINSKÁ, Petra PŘIBYLOVÁ, Petra RŮŽIČKOVÁ, Jana KLÁNOVÁ and Břetislav LIPOVÝ. Výzkumná infrastruktura RECETOX – metagenomické analýzy a hojení ran (Research infrastructure RECETOX - metagenomic analyses and wound healing). In III. Česko - Slovenský kongres mezioborové přístupy hojení ran. 2023.

BUDINSKÁ, Eva and Petra BOŘILOVÁ LINHARTOVÁ. WP2: Characterizing the internal and the external exposome in the cohort and case-series. In DISCERN Kick-off meeting, 2023. 2023.

VYKLICKÁ, Kateřina, Jan BÖHM, Petr ANDRLA, Eva BUDINSKÁ, Břetislav LIPOVÝ and Petra BOŘILOVÁ LINHARTOVÁ. 16S rDNA sequencing analysis of low-abundance samples spiked with bacterial mock community. In III. ČESKO-SLOVENSKÝ KONGRES MEZIOBOROVÉ PŘÍSTUPY V HOJENÍ RAN. 2023.

KUBASOVA, Ivana, Lucia STEMPELOVA, Aladar MADARI, Dobroslava BUJNAKOVA, Lenka KOSEČKOVÁ MICENKOVÁ and Viola STROMPFOVA. Application of Canine-Derived Enterococcus faecium DSM 32820 in Dogs with Acute Idiopathic Diarrhoea. Acta Veterinaria Beograd. Warsaw: De Gruyter Open, 2022, vol. 72, No 2, p. 167-183. ISSN 0567-8315. Available from: https://dx.doi.org/10.2478/acve-2022-0014.

BOŘILOVÁ LINHARTOVÁ, Petra, Iva KOTÁSKOVÁ, Petra ŠPLÍCHALOVÁ, Daniela GACHOVÁ, Dávid SZÁRAZ, Sabina CERULOVÁ, Ctirad MACHÁČEK, Petr ANDRLA, Jan LOCHMAN, Danuše FRIDRICHOVÁ, Zbyněk ZDRÁHAL, Petra VÍDEŇSKÁ and Zdeněk DANĚK. Comparative bacteriome analysis of tooth and cystic fluid in patients with apical periodontitis and radicular cyst – pilot study. In FEBS, 2022. 2022. Available from: https://dx.doi.org/10.1002/2211-5463.13440.

BARTOŇ, Vojtěch and Helena SKUTKOVA. Data Transformation for Clustering Utilization for Feature Detection in Mass Spectrometry. In Rojas I., Valenzuela O., Rojas F., Herrera L.J., Ortuño F. Bioinformatics and Biomedical Engineering (IWBBIO 2022) : Lecture Notes in Computer Science, vol 13347. Cham: Springer, 2022, p. 288-299. ISBN 978-3-031-07801-9. Available from: https://dx.doi.org/10.1007/978-3-031-07802-6_24.

IBRAHIM, Akkouh, Hana HŘÍBKOVÁ, Marta GRABIEC, Eva BUDINSKÁ, Attila SZABO, Tomáš KAŠPÁREK, Andreassen A. OLE, Yuh-Man SUN and Srdjan DJUROVIC. Derivation and Molecular Characterization of a Morphological Subpopulation of Human iPSC Astrocytes Reveal a Potential Role in Schizophrenia and Clozapine Response. SCHIZOPHRENIA BULLETIN. Oxford: Oxford University Press, 2022, vol. 48, No 1, p. 190-198. ISSN 0586-7614. Available from: https://dx.doi.org/10.1093/schbul/sbab092.

PIVRNCOVÁ, Eliška, Iva KOTÁSKOVÁ, Lucie BUREŠOVÁ, Hana VESPALCOVÁ, Petr ANDRLA, Stanislav SMATANA, Lenka ANDRÝSKOVÁ, Pavel PILER, Petr JANKŮ, Ivo BOREK, Jana KLÁNOVÁ, Tomáš FREIBERGER, Petra VÍDEŇSKÁ, Eva BUDINSKÁ and Petra BOŘILOVÁ LINHARTOVÁ. Effect of mode of delivery and intrapartum antibiotic prophylaxis on gut bacteriome of newborns in the first days of their life: a case-control study. In Setkání biochemiků a molekulárních biologů, 2022. 2022.

LAUKOVA, Andrea, Lubica CHRASTINOVA, Lenka KOSEČKOVÁ MICENKOVÁ, Eva BINO, Ivana KUBASOVA, Anna KANDRICAKOVA, Sona GANCARCIKOVA, Iveta PLACHA, Monika HOLODOVA, Lubomira GRESAKOVA, Zuzana FORMELOVA and Monika POGANY SIMONOVA. Enterocin M in Interaction in Broiler Rabbits with Autochthonous, Biofilm-Forming Enterococcus hirae Kr8 Strain. Probiotics and Antimicrobial Proteins. New York: Springer New York LLC, 2022, vol. 14, No 5, p. 845-853. ISSN 1867-1306. Available from: https://dx.doi.org/10.1007/s12602-022-09941-5.

SLÁMOVÁ, Terezie, Natálie MLČŮCHOVÁ, Zdeněk KALA, Zdeněk PAVLOVSKÝ, Jan BÖHM, Radek KROUPA, Jiří DOLINA, Vladimír PROCHÁZKA, Tomáš GROLICH, Jitka VACULOVÁ, Lumír KUNOVSKÝ, Petra BRENEROVÁ, Petr ANDRLA, Ondřej URBAN, Vít NAVRÁTIL, Tomáš HARUSTIAK, Robert LISCHKE, Tereza DEISSOVÁ, Jan LOCHMAN, Lydie IZAKOVIČOVÁ HOLLÁ, Ondřej SLABÝ, Eva BUDINSKÁ and Petra BOŘILOVÁ LINHARTOVÁ. Helicobacter analysis in gastric mucosa samples – comparison of two methodical approaches. In Setkání biochemiků a molekulárních biologů, 2022. 2022.

GACHOVÁ, Daniela, Zdeněk DANĚK, Ctirad MACHÁČEK, Soňa SMETANOVÁ, Petr ANDRLA, Eva BUDINSKÁ and Petra BOŘILOVÁ LINHARTOVÁ. Komparace bakteriomu z tumoru a ze sliznic dutiny ústní u pacientů s orálním dlaždicobuněčným karcinomem (Comparison of bacterioma from tumor and oral mucosa in patients with oral squamous cell carcinoma). In Biologické dny 2022. 2022.

CHOCHOLOVÁ, Eva, Eva DROZDOVÁ, Dana FIALOVÁ, Pavel ROUDNICKÝ, Zbyněk ZDRÁHAL, Barbora ZWINSOVÁ, Kateřina NOVOTNÁ, Filip PARDY, Jakub HYNŠT, Marek PEŠKA, Antonín ZŮBEK, Kateřina MRÁZOVÁ, Vladislav KRZYŽÁNEK, Michael DOUBEK and Šárka POSPÍŠILOVÁ. Metagenomic and proteomic analysis of dental calculus of abbot Gregor Johann Mendel. Folia Mendeliana : supplementum ad Acta Musei Moraviae. Moravian Museum Brno, 2022, vol. 58, No 1, p. 57-61. ISSN 0085-0748.

CHOCHOLOVÁ, Eva, Eva DROZDOVÁ, Dana FIALOVÁ, Pavel ROUDNICKÝ, Zbyněk ZDRÁHAL, Barbora ZWINSOVÁ, Kateřina NOVOTNÁ, Filip PARDY, Jakub HYNŠT, Marek PEŠKA, Antonín ZŮBEK, Kateřina MRÁZOVÁ, Vladislav KRZYŽÁNEK, Michael DOUBEK and Šárka POSPÍŠILOVÁ. Metagenomic and proteomic analysis of dental calculus of abbot Gregor Johann Mendel. In Mendel Genetics Conference 2022. 2022. ISBN 978-80-11-01750-7.

CHOCHOLOVÁ, Eva, Eva DROZDOVÁ, Dana FIALOVÁ, Martin ČERNÝ, Barbora ZWINSOVÁ, Petra VÍDEŇSKÁ, Kristýna BRZOBOHATÁ and Kateřina NOVOTNÁ. Metagenomic research of the ancient human dental calculus as a potential source for the study of rare infectious diseases. In The Biomania Student Scientific Meeting 2022. 2022. ISBN 978-80-280-0040-0.

LAUKOVÁ, Andrea, Lenka MICENKOVÁ, Ľubomíra GREŠÁKOVÁ, Michaela MAĎAROVÁ, Monika POGÁNY SIMONOVÁ, Valentína FOCKOVÁ and Jana ŠČERBOVÁ. Microbiome Associated with Slovak Raw Goat Milk, Trace Minerals, and Vitamin E Content. International Journal of Food Science. Hindawi, 2022, vol. 2022, Aug 2022, p. 1-8. ISSN 2356-7015. Available from: https://dx.doi.org/10.1155/2022/4595473.

CHOCHOLOVÁ, Eva, Eva DROZDOVÁ, Dana FIALOVÁ, Kateřina NOVOTNÁ, Pavel ROUDNICKÝ, Zbyněk ZDRÁHAL, Kateřina MRÁZOVÁ, Vladislav KRZYŽÁNEK, Barbora ZWINSOVÁ, Filip PARDY, Marek PEŠKA, Antonín ZŮBEK, Michael DOUBEK and Šárka POSPÍŠILOVÁ. Molekulárně biologická analýza zubního kamene a mumifikované tkáně Gregora Johanna Mendela (Biomolecular analysis of calculus and mummified tissue of Gregor Johann Mendel). In Genetická konference Genetické společnosti Gregora Mendela a XXIX. Genetické dny. 2022. ISBN 978-80-7302-182-5.

BOUCHALOVÁ, Pavla, Jan ŠIMONÍK, David POTĚŠIL, Petr LAPČÍK, Ján PODHOREC, Lucia JANÁČOVÁ, Milan HORA, Alice HLOBILKOVÁ, Alexandr POPRACH, Vlad POPOVICI, Ondřej FIALA and Pavel BOUCHAL. Proteiny odpovědné za špatnou terapeutickou odpověď metastatických nádorů ledvin na léčbu tyrosinkinasovými inhibitory (Proteins associated with low response to tyrosinkinase inhibitor therapy in metastatic kidney tumors). In Sborník abstrakt, přednášek a posterů, XXV. Biologické dny, Brno 5.- 6.9.2022, p. 40. 2022. ISSN 1805-9619.

MARTYNIUK, Christopher J., Amanda N. BUERGER, Hana VESPALCOVÁ, Barbora RUDZANOVÁ, Shahadur R. SOHAG, Amy T. HANLON, Pamela E. GINN, Serena L. CRAFT, Soňa SMETANOVÁ, Eva BUDINSKÁ, Joseph H. Jr. BISESI and Ondřej ADAMOVSKÝ. Sex-dependent host-microbiome dynamics in zebrafish: Implications for toxicology and gastrointestinal physiology. Comparative Biochemistry and Physiology Part D: Genomics and Proteomics. NEW YORK: ELSEVIER SCIENCE INC, 2022, vol. 42, June 2022, p. 1-9. ISSN 1744-117X. Available from: https://dx.doi.org/10.1016/j.cbd.2022.100993.

BELVONCIKOVA, Paulina, Petra ŠPLÍCHALOVÁ, Petra VÍDEŇSKÁ and Roman GARDLIK. The Human Mycobiome: Colonization, Composition and the Role in Health and Disease. Journal of Fungi. St. Alban-Anlage: MDPI, 2022, vol. 8, No 10, p. 1-26. ISSN 2309-608X. Available from: https://dx.doi.org/10.3390/jof8101046.

PAČÍNKOVÁ, Anna and Vlad POPOVICI. Using empirical biological knowledge to infer regulatory networks from multi-omics data. BMC Bioinformatics. London: BioMed Central, 2022, vol. 23, No 1, p. 1-23. ISSN 1471-2105. Available from: https://dx.doi.org/10.1186/s12859-022-04891-9.

PROCHAZKOVA, Magdalena, Eva BUDINSKÁ, Marek KUZMA, Helena PELANTOVA, Jaromir HRADECKY, Marie HECZKOVA, Nikola DASKOVA, Miriam BRATOVA, Istvan MODOS, Petra VÍDEŇSKÁ, Petra ŠPLÍCHALOVÁ, Solomon A. SOWAH, Maria KRÁLOVÁ, Marina HENIKOVA, Eliska SELINGER, Krystof KLIMA, Karel CHALUPSKY, Radislav SEDLACEK, Rikard LANDBERG, Tilman KÜHN, Jan GOJDA and Monika CAHOVA. Vegan Diet Is Associated With Favorable Effects on the Metabolic Performance of Intestinal Microbiota: A Cross-Sectional Multi-Omics Study. Frontiers in Nutrition. LAUSANNE (SWITZERLAND): Frontiers Media SA, 2022, vol. 8, January, p. 1-18. ISSN 2296-861X. Available from: https://dx.doi.org/10.3389/fnut.2021.783302.

KOTÁSKOVÁ, Iva, Vít SYROVÁTKA, Hana OBRUČOVÁ, Petra VÍDEŇSKÁ, Barbora ZWINSOVÁ, Veronika HOLÁ, Eva BLAŠTÍKOVÁ, Filip RŮŽIČKA and Tomáš FREIBERGER. Actinotignum schaalii: Relation to Concomitants and Connection to Patients’ Conditions in Polymicrobial Biofilms of Urinary Tract Catheters and Urines. Microorganisms. Basel: MDPI, 2021, vol. 9, No 3, p. 1-23. ISSN 2076-2607. Available from: https://dx.doi.org/10.3390/microorganisms9030669.

KUTILOVA, Iva, Adam VALCEK, Costas C. PAPAGIANNITSIS, Darina ČEJKOVÁ, Martina MASARIKOVA, Veronika PASKOVA, Lenka DAVIDOVA-GERZOVA, Petra VÍDEŇSKÁ, Jaroslav HRABAK, Ivan LITERÁK and Monika DOLEJSKÁ. Carbapenemase-Producing Gram-Negative Bacteria from American Crows in the United States. Antimicrobial Agents and Chemotherapy. Washington, D.C.: American Society for Microbiology, 2021, vol. 65, No 1, p. 1-6. ISSN 0066-4804. Available from: https://dx.doi.org/10.1128/AAC.00586-20.

ZWINSOVÁ, Barbora, Viacheslav PETROV, Martina HRIVŇÁKOVÁ, Stanislav SMATANA, Lenka KOSEČKOVÁ MICENKOVÁ, Natálie KAZDOVÁ, Vlad POPOVICI, Roman HRSTKA, Roman ŠEFR, Beatrix BENCSIKOVÁ, Lenka ZDRAŽILOVÁ DUBSKÁ, Veronika BRYCHTOVÁ, Rudolf NENUTIL, Petra VÍDEŇSKÁ and Eva BUDINSKÁ. Colorectal Tumour Mucosa Microbiome Is Enriched in Oral Pathogens and Defines Three Subtypes That Correlate with Markers of Tumour Progression. Cancers. MDPI, 2021, vol. 13, No 19, p. 1-25. ISSN 2072-6694. Available from: https://dx.doi.org/10.3390/cancers13194799.

DASKOVA, Nikola, Marie HECZKOVA, Istvan MODOS, Petra VÍDEŇSKÁ, Petra ŠPLÍCHALOVÁ, Helena PELANTOVA, Marek KUZMA, Jan GOJDA and Monika CAHOVA. Determination of Butyrate Synthesis Capacity in Gut Microbiota: Quantification of but Gene Abundance by qPCR in Fecal Samples. Biomolecules. BASEL: MDPI, 2021, vol. 11, No 9, p. 1-17. ISSN 2218-273X. Available from: https://dx.doi.org/10.3390/biom11091303.

HRALA, Matěj, Juraj BOSÁK, Lenka MICENKOVÁ, Jitka KŘENOVÁ, Matej LEXA, Viktória PIRKOVÁ, Zuzana TOMASTIKOVA, Ivana KOLÁČKOVÁ and David ŠMAJS. Escherichia coli Strains Producing Selected Bacteriocins Inhibit Porcine Enterotoxigenic Escherichia coli (ETEC) under both In Vitro and In Vivo Conditions. Applied and Environmental Microbiology. WASHINGTON, DC (USA): AMER SOC MICROBIOLOGY, 2021, vol. 87, No 14, p. 1-12. ISSN 0099-2240. Available from: https://dx.doi.org/10.1128/AEM.03121-20.

CHYRA, Zuzana, Tereza SEVIKOVA, Petr VOJTA, Janka PUTEROVÁ, Lucie KUBÍNOVÁ, Kateřina GROWKOVÁ, Jana FILIPOVA, Martina ZATOPKOVA, Sebastian GROSICKI, Agnieszka BARCHNICKA, Wieslaw WIKTOR-JEDRZEJCZAK, Anna WASZCZUK-GAJDA, Alexandra JUNGOVA, Aneta MIKULASOVA, Marian HAJDÚCH, Martin MOKREJŠ, Luděk POUR, Martin ŠTORK, Lubica HARVANOVA, Martin MISTRIK, Gabor MIKALA, Pawel ROBAK, Anna CZYZ, Jakub DEBSKI, Lidia USNARSKA-ZUBKIEWICZ, Artur JURCZYSZYN, Lukas STEJSKAL, Gareth MORGAN, Fedor KRYUKOV, Eva BUDINSKÁ, Michal SIMICEK, Tomas JELINEK, Matous HRDINKA and Roman HAJEK. Heterogenous mutation spectrum and deregulated cellular pathways in aberrant plasma cells underline molecular pathology of light-chain amyloidosis. haematologica. Pavia: Ferrata-Storti Foundation, 2021, vol. 106, No 2, p. 601-604. ISSN 0390-6078. Available from: https://dx.doi.org/10.3324/haematol.2019.239756.

HUA, Qing, Ondřej ADAMOVSKÝ, Hana VESPALCOVÁ, Jonna BOYDA, Jordan T. SCHMIDT, Marianne KOZUCH, Serena L. M. CRAFT, Pamela E. GINN, Stanislav SMATANA, Eva BUDINSKÁ, Maria PERSICO, Joseph H., Jr. BISESI and Christopher J. MARTYNIUK. Microbiome analysis and predicted relative metabolomic turnover suggest bacterial heme and selenium metabolism are altered in the gastrointestinal system of zebrafish (Danio rerio) exposed to the organochlorine dieldrin. Environmental Pollution. Elsevier Ltd., 2021, vol. 268, January 2021, p. 1-11. ISSN 0269-7491. Available from: https://dx.doi.org/10.1016/j.envpol.2020.115715.

LAUKOVA, Andrea, Lenka MICENKOVÁ, Monika Pogany SIMONOVA, Valentina FOCKOVA, Jana SCERBOVA, Martin TOMASKA, Emilia DVOROZNAKOVA and Miroslav KOLOSTA. Microbiome Associated with Slovak Traditional Ewe's Milk Lump Cheese. Processes. MDPI, 2021, vol. 9, No 9, p. 1-8. ISSN 2227-9717. Available from: https://dx.doi.org/10.3390/pr9091603.

JABANDŽIEV, Petr, Tatsuhiko KAKISAKA, Júlia BOHOŠOVÁ, Tereza PINKASOVÁ, Lumír KUNOVSKÝ, Ondřej SLABÝ and Ajay GOEL. MicroRNAs in Colon Tissue of Pediatric Ulcerative Pancolitis Patients Allow Detection and Prognostic Stratification. Journal of Clinical Medicine. Basel: MDPI, 2021, vol. 10, No 6, p. 1-11. ISSN 2077-0383. Available from: https://dx.doi.org/10.3390/jcm10061325.

BOHOŠOVÁ, Júlia, Jiří VAJČNER, Petr JABANDŽIEV, Hana OŠLEJŠKOVÁ, Ondřej SLABÝ and Štefánia AULICKÁ. MicroRNAs in the development of resistance to antiseizure drugs and their potential as biomarkers in pharmacoresistant epilepsy. Epilepsia. Hoboken: Wiley-Blackwell, 2021, vol. 62, No 11, p. 2573-2588. ISSN 0013-9580. Available from: https://dx.doi.org/10.1111/epi.17063.

KOLÁŘOVÁ, Hana, Jan VÍTEČEK, Anna ČERNÁ, Marek ČERNÍK, Jan PŘIBYL, Petr SKLÁDAL, David POTĚŠIL, Ivana IHNATOVÁ, Zbyněk ZDRÁHAL, Aleš HAMPL, Anna KLINKE and Lukáš KUBALA. Myeloperoxidase mediated alteration of endothelial function is dependent on its cationic charge. Free Radical Biology and Medicine. New York: Elsevier, 2021, vol. 162, January 2021, p. 14-26. ISSN 0891-5849. Available from: https://dx.doi.org/10.1016/j.freeradbiomed.2020.11.008.

ZAHRADNÍKOVÁ, Martina, Ivana IHNATOVÁ, Erika LATTOVÁ, Lukáš UHRÍK, Eliška STUCHLÍKOVÁ, Rudolf NENUTIL, Dalibor VALÍK, Monika NÁLEŽINSKÁ, Josef CHOVANEC, Zbyněk ZDRÁHAL, Bořivoj VOJTĚŠEK, Lenka HERNYCHOVÁ and Miloš NOVOTNÝ. N-Glycome changes reflecting resistance to platinum-based chemotherapy in ovarian cancer. JOURNAL OF PROTEOMICS. Elsevier, 2021, vol. 230, JAN, p. "103964", 13 pp. ISSN 1874-3919. Available from: https://dx.doi.org/10.1016/j.jprot.2020.103964.

BOSÁK, Juraj, Matěj HRALA, Lenka MICENKOVÁ and David ŠMAJS. Non-antibiotic antibacterial peptides and proteins ofEscherichia coli: efficacy and potency of bacteriocins. EXPERT REVIEW OF ANTI-INFECTIVE THERAPY. ABINGDON: TAYLOR & FRANCIS LTD, 2021, vol. 19, No 3, p. 309-322. ISSN 1478-7210. Available from: https://dx.doi.org/10.1080/14787210.2020.1816824.

AUST, Anne-Christine, Eliška BENEŠOVÁ, Veronika VIDOVÁ, Kateřina COUFALÍKOVÁ, Soňa SMETANOVÁ, Ivo BOREK, Petr JANKŮ, Eva BUDINSKÁ, Jana KLÁNOVÁ, Vojtěch THON and Zdeněk SPÁČIL. Profiling Tryptophan Catabolites of Human Gut Microbiota and Acute-Phase Protein Levels in Neonatal Dried Blood Specimens. Frontiers in Microbiology. Switzerland: Frontiers Research Foundation, 2021, vol. 12, October 2021, p. 1-16. ISSN 1664-302X. Available from: https://dx.doi.org/10.3389/fmicb.2021.665743.

MICENKOVÁ, Lenka, Juraj BOSÁK, Stanislav SMATANA, Adam NOVOTNÝ, Eva BUDINSKÁ and David ŠMAJS. Administration of the Probiotic Escherichia coli Strain A0 34/86 Resulted in a Stable Colonization of the Human Intestine During the First Year of Life. Probiotics and Antimicrobial Proteins. New York: Springer New York LLC, 2020, vol. 12, No 2, p. 343-350. ISSN 1867-1306. Available from: https://dx.doi.org/10.1007/s12602-019-09548-3.

STENVANG, Jan, Eva BUDINSKÁ, Eric VAN CUTSEM, Fred BOSMAN, Vlad POPOVICI and Nils BRUNNER. An Explorative Analysis of ABCG2/TOP-1 mRNA Expression as a Biomarker Test for FOLFIRI Treatment in Stage III Colon Cancer Patients: Results from Retrospective Analyses of the PETACC-3 Trial. Cancers. Basel: MDPI, 2020, vol. 12, No 4, p. 1-12. ISSN 2072-6694. Available from: https://dx.doi.org/10.3390/cancers12040977.

KONEČNÁ, Eva, Petra VÍDEŇSKÁ and Milan URÍK. Biologický význam a vývoj mikrobiomu horních cest dýchacích (Biological import­ance and development of upper respiratory tract microbiome). Otorhinolaryngologie a foniatrie. Praha: Mladá fronta a.s., 2020, vol. 69, No 3, p. 135-138. ISSN 1210-7867.

POPRACH, Alexandr, Miloš HOLÁNEK, Renata CHLOUPKOVÁ, Radek LAKOMÝ, Michal STANÍK, Ondřej FIALA, Bohuslav MELICHAR, Kateřina KOPECKOVA, Milada ZEMANOVA, Igor KISS, Igor PENKA, Júlia BOHOŠOVÁ and Tomáš BUCHLER. Cytoreductive Nephrectomy and Overall Survival of Patients with Metastatic Renal Cell Carcinoma Treated with Targeted Therapy-Data from the National Renis Registry. Cancers. BASEL: MDPI, 2020, vol. 12, No 10, p. 1-10. ISSN 2072-6694. Available from: https://dx.doi.org/10.3390/cancers12102911.

KOLLARCIKOVA, Miloslava, Marcela FALDYNOVA, Jitka MATIASOVICOVA, Eva JAHODAROVA, Tereza KUBASOVA, Zuzana SEIDLEROVA, Vladimir BABAK, Petra VÍDEŇSKÁ, Alois CIZEK and Ivan RYCHLIK. Different Bacteroides Species Colonise Human and Chicken Intestinal Tract. Microorganisms. Basel: MDPI, 2020, vol. 8, No 10, p. 1-14. ISSN 2076-2607. Available from: https://dx.doi.org/10.3390/microorganisms8101483.

HECHT, Helge, Sarhan MHD HASAN and Vlad POPOVICI. Disentangled Autoencoder for Cross-Stain Feature Extraction in Pathology Image Analysis. Applied Sciences. Basel: MDPI, 2020, vol. 10, No 18, p. 1-14. ISSN 2076-3417. Available from: https://dx.doi.org/10.3390/app10186427.

FEDORKO, Michal, Júlia BOHOŠOVÁ, Alexandr POPRACH and Dalibor PACÍK. Dlouhé nekódující RNA a karcinom z renálních buněk (Long non-coding RNAs and renal cell carcinoma). Klinická onkologie. Praha: Česká lékařská společnost J. E. Purkyně, 2020, vol. 33, No 5, p. 340-349. ISSN 0862-495X. Available from: https://dx.doi.org/10.14735/amko2020340.

MAREČKOVÁ, Klára, Anna PAČÍNKOVÁ, Anja KLASNJA, Jean SHIN, Lenka ANDRÝSKOVÁ, Kateřina STAŇO KOZUBÍK, Zdenka PAUSOVÁ, Milan BRÁZDIL and Tomáš PAUS. Epigenetic clock as a correlate of anxiety. NeuroImage. Oxford: Elsevier Science Ltd, 2020, vol. 28, No 2020, p. 102458-102465. ISSN 2213-1582. Available from: https://dx.doi.org/10.1016/j.nicl.2020.102458.

ADAMOVSKÝ, Ondřej, Amanda N. BUERGER, Hana VESPALCOVÁ, Shahadur R. SOHAG, Amy T. HANLON, Pamela E. GINN, Serena L. CRAFT, Stanislav SMATANA, Eva BUDINSKÁ, Maria PERSICO, Joseph H., Jr. BISESI and Christopher J. MARTYNIUK. Evaluation of Microbiome-Host Relationships in the Zebrafish Gastrointestinal System Reveals Adaptive Immunity Is a Target of Bis(2-ethylhexyl) Phthalate (DEHP) Exposure. Environmental Science & Technology. Washington, D.C.: American Chemical Society, 2020, vol. 54, No 9, p. 5719-5728. ISSN 0013-936X. Available from: https://dx.doi.org/10.1021/acs.est.0c00628.

SEDLÁČEK, Ivo, Roman PANTŮČEK, Michal ZEMAN, Pavla HOLOCHOVÁ, Ondrej ŠEDO, Eva STAŇKOVÁ, Pavel ŠVEC, Stanislava KRÁLOVÁ, Petra VÍDEŇSKÁ, Lenka MICENKOVÁ, Sah URVASHI, Suresh KORPOLE and Rup LAL. Hymenobacter terrestris sp. nov. and Hymenobacter lapidiphilus sp. nov., isolated from regoliths in Antarctica. International Journal of Systematic and Evolutionary Microbiology. London: Microbiology Society, 2020, vol. 70, No 12, p. 6364-6372. ISSN 1466-5026. Available from: https://dx.doi.org/10.1099/ijsem.0.004540.

BUDINSKÁ, Eva, Jan GOJDA, Marie HECZKOVA, Miriam BRATOVA, Helena DANKOVA, Petr WOHL, Hana BASTOVA, Vera LANSKA, Martin KOSTOVCIK, Milan DASTYCH, Michal SENKYRIK, Jarmila KRIZOVA, Milos MRAZ, Jaromir HRADECKY, Jana HAJSLOVA, Martin LENICEK, Katerina PODZIMKOVA, Karel CHALUPSKY, Rastislav SEDLACEK and Monika CAHOVA. Microbiome and Metabolome Profiles Associated With Different Types of Short Bowel Syndrome: Implications for Treatment. Journal of Parenteral and Enteral Nutrition. Hoboken: Wiley, 2020, vol. 44, No 1, p. 105-118. ISSN 0148-6071. Available from: https://dx.doi.org/10.1002/jpen.1595.

LATTOVÁ, Erika, Jana SKŘIČKOVÁ, Jitka HAUSNEROVÁ, Lukáš FROLA, Leoš KŘEN, Ivana IHNATOVÁ, Zbyněk ZDRÁHAL, J. BRYANT and M. POPOVIC. N-Glycan profiling of lung adenocarcinoma in patients at different stages of disease. MODERN PATHOLOGY. NEW YORK: NATURE PUBLISHING GROUP, 2020, vol. 33, No 6, p. 1146-1156. ISSN 0893-3952. Available from: https://dx.doi.org/10.1038/s41379-019-0441-3.

JABANDŽIEV, Petr, Tereza PINKASOVÁ, Lumír KUNOVSKÝ, Jan PAPEŽ, Martin JOUZA, Bára KARLÍNOVÁ, Martina NOVÁČKOVÁ, Milan URÍK, Štefánia AULICKÁ, Ondřej SLABÝ, Júlia BOHOŠOVÁ, Kateřina BAJEROVÁ, Milan BAJER and Ajay GOEL. Regional Incidence of Inflammatory Bowel Disease in a Czech Pediatric Population: 16 Years of Experience (2002–2017). Journal of Pediatric Gastroenterology and Nutrition. Philadelphia: LIPPINCOTT WILLIAMS & WILKINS, 2020, vol. 70, No 5, p. 586-592. ISSN 0277-2116. Available from: https://dx.doi.org/10.1097/MPG.0000000000002660.

JANÁČOVÁ, Lucia, Petr LAPČÍK, Anna POSPÍŠILOVÁ, David POTĚŠIL, Jan PŘIBYL, Roman HRSTKA, Eva BUDINSKÁ, Petr MÜLLER and Pavel BOUCHAL. Rola katechol-O-metyltransferázy u estrogén-receptor pozitívnych nádorov prsníka (The role of catechol-O-methyltransferase in estrogen-receptor-positive breast tumours). In Neformální proteomický webinář, 27.11.2020, in Book of Abstracts, p. 9. 2020. 2020.

FLORES-TORNERO, Maria, Frank VOGLER, Marek MUTWIL, David POTĚŠIL, Ivana IHNATOVÁ, Zbyněk ZDRÁHAL, Stefanie SPRUNCK and Thomas DRESSELHAUS. Transcriptomic and Proteomic Insights into Amborella trichopoda Male Gametophyte Functions. Plant Physiology. American Society of Plant Physiologists, 2020, vol. 184, No 4, p. 1640-1657. ISSN 0032-0889. Available from: https://dx.doi.org/10.1104/pp.20.00837.

DAILLERE, Romain, Lisa DEROSA, Melodie BONVALET, Nicola SEGATA, Bertrand ROUTY, Manuela GARIBOLDI, Eva BUDINSKÁ, I. Jolanda M. DE VRIES, Alessio Gordon NACCARATI, Valerie ZITVOGEL, Carlos CALDAS, Lars ENGSTRAND, Sibylle LOILBL, Jacques FIESCHI, Lucie HEINZERLING, Guido KROEMER and Laurence ZITVOGEL. Trial watch : the gut microbiota as a tool to boost the clinical efficacy of anticancer immunotherapy. Oncoimmunology. Philadelphia: Taylor & Francis, 2020, vol. 9, No 1, p. 1-8. ISSN 2162-402X. Available from: https://dx.doi.org/10.1080/2162402X.2020.1774298.

BARTOŇ, Vojtěch, Markéta NYKRÝNOVÁ and Helena ŠKUTKOVÁ. Watershed Segmentation for Peak Picking in Mass Spectrometry Data. Online. In International Work-Conference on Bioinformatics and Biomedical Engineering. Berlin: Springer, 2020, p. 494-502. ISBN 978-3-030-45384-8. Available from: https://dx.doi.org/10.1007/978-3-030-45385-5_44.

SMITALOVÁ, Dagmar, Tomáš LOJA, Martin ČULEN, Zdeňka HERUDKOVÁ, Eva BUDINSKÁ, Jiří MAYER, Zdeněk RÁČIL and Marianna ROMŽOVÁ. Analysis of gene expression in CD26+ CML leukemic stem cell population. In 10th International Conference Analytical Cytometry, Hotel Jizerka, Seč-Ústupky. 2019.

SELINGEROVA, I., Eva BUDINSKÁ, Barbora ZWINSOVÁ, B. MAZALOVA, B. BENCSIKOVA, D. VALIK and L.Z. DUBSKA. Anti-alpha gal antibodies in the context of blood group and stool and tumour-adjacent microbiome in colorectal cancer patients. In Immuno-Oncology Congress of the European-Society-for-Medical-Oncology (ESMO). 2019. ISSN 0923-7534.

BOUCHAL, Pavel, Olga T. SCHUBERT, Jakub FAKTOR, Lenka ČÁPKOVÁ, Hana IMRICHOVÁ, Karolína ZOUFALOVÁ, Vendula PÁRALOVÁ, Roman HRSTKA, Yansheng S. LIU, Holger A. EBHARDT, Eva BUDINSKÁ, Rudolf NENUTIL and Ruedi AEBERSOLD. Breast Cancer Classification Based on Proteotypes Obtained by SWATH Mass Spectrometry. Cell Reports. CAMBRIDGE: Cell Press, 2019, vol. 28, No 3, p. "832"-"843.e7", 20 pp. ISSN 2211-1247. Available from: https://dx.doi.org/10.1016/j.celrep.2019.06.046.

PAČÍNKOVÁ, Anna and Vlad POPOVICI. Cross-platform Data Analysis Reveals a Generic Gene Expression Signature for Microsatellite Instability in Colorectal Cancer. Biomed Research International. New York: Hindawi Publishing Corporation, 2019, vol. 2019, vol. 2019, p. 1-9. ISSN 2314-6133. Available from: https://dx.doi.org/10.1155/2019/6763596.

LOCHMANOVÁ, Gabriela, Ivana IHNATOVÁ, Hana KUCHAŘÍKOVÁ, Sylva BRABENCOVÁ, Dagmar ZACHOVÁ, Jiří FAJKUS, Zbyněk ZDRÁHAL and Miloslava FOJTOVÁ. Different Modes of Action of Genetic and Chemical Downregulation of Histone Deacetylases with Respect to Plant Development and Histone Modifications. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES. 2019, vol. 20, No 20, p. "5093", 14 pp. ISSN 1422-0067. Available from: https://dx.doi.org/10.3390/ijms20205093.

SMITALOVÁ, Dagmar, Martin ČULEN, Zdeňka HERUDKOVÁ, Eva BUDINSKÁ, Jiří MAYER, Zdeněk RÁČIL and Marianna ROMŽOVÁ. Gene expression profiling of CD26+ leukemic stem cell population from CML patients. In 24th European Hematology Association Cogress, Amsterdam, Nizozemsko in HemaSpehere. 2019.

EDUARDO, Mariana Bustamante, Vlad POPOVICI, Sara IMBODEN, Stefan AEBI, Nadja BALLABIO, Hans Jorg ALTERMATT, Andreas GUNTHERT and Rolf JAGGI. Characterization of molecular scores and gene expression signatures in primary breast cancer, local recurrences and brain metastases. BMC Cancer. London: BioMed Central, 2019, vol. 19, June, p. 1-14. ISSN 1471-2407. Available from: https://dx.doi.org/10.1186/s12885-019-5752-8.

CHOCHOLOVÁ, Eva, Dana FIALOVÁ, Eva DROZDOVÁ, Radim SKOUPÝ, Kristýna BRZOBOHATÁ, Barbora ZWINSOVÁ, Petra VÍDEŇSKÁ and Václav CHOCHOLA. Looking at the health of past populations through the lens of human dental calculus. In The Biomania Student Scientific Meeting & EUSynBioS Symposium 2019. 2019. ISBN 978-80-210-9373-7.

CHOCHOLOVÁ, Eva, Dana FIALOVÁ, Eva DROZDOVÁ, Radim SKOUPÝ, Kristýna BRZOBOHATÁ, Barbora ZWINSOVÁ, Petra VÍDEŇSKÁ and Václav CHOCHOLA. Microbial Contamination of Ancient Human Dental Calculus Studied by Scanning Electron Microscopy and Metagenomic Approach. In 6th International Anthropological Congress of Dr. Aleš Hrdlička. 2019. ISSN 2336-4777.

KOTÁSKOVÁ, Iva, Hana OBRUČOVÁ, Barbora MALIŠOVÁ, Petra VÍDEŇSKÁ, Barbora ZWINSOVÁ, Tereza PEROUTKOVÁ, Milada DVOŘÁČKOVÁ, Petr KUMSTÁT, Pavel TROJAN, Filip RŮŽIČKA, Veronika HOLÁ and Tomáš FREIBERGER. Molecular Techniques Complement Culture-Based Assessment of Bacteria Composition in Mixed Biofilms of Urinary Tract Catheter-Related Samples. Frontiers in Microbiology. Lausanne: Frontiers Media SA, 2019, vol. 10, No 462, p. 1-15. ISSN 1664-302X. Available from: https://dx.doi.org/10.3389/fmicb.2019.00462.

BOSÁK, Juraj, Matěj HRALA, Viktória PIRKOVÁ, Lenka MICENKOVÁ, Alois CIZEK, Jiri SMOLA, Dana KUCEROVA, Zdenka VACKOVA, Eva BUDINSKÁ, Ivana KOLÁČKOVÁ and David ŠMAJS. Porcine pathogenic Escherichia coli strains differ from human fecal strains in occurrence of bacteriocin types. Veterinary Microbiology. AMSTERDAM: Elsevier, 2019, vol. 232, MAY 2019, p. 121-127. ISSN 0378-1135. Available from: https://dx.doi.org/10.1016/j.vetmic.2019.04.003.

VÍDEŇSKÁ, Petra, Kristýna ŠMERKOVÁ, Barbora ZWINSOVÁ, Vlad POPOVICI, Lenka MICENKOVÁ, Karel SEDLAR and Eva BUDINSKÁ. Stool sampling and DNA isolation kits affect DNA quality and bacterial composition following 16S rRNA gene sequencing using MiSeq Illumina platform. Scientific reports. LONDON: NATURE PUBLISHING GROUP, 2019, vol. 9, SEP 2019, p. 1-14. ISSN 2045-2322. Available from: https://dx.doi.org/10.1038/s41598-019-49520-3.

FIALOVÁ, Dana, Eva CHOCHOLOVÁ, Eva DROZDOVÁ, Kristýna BRZOBOHATÁ, Barbora ZWINSOVÁ, Petra VÍDEŇSKÁ, Václav CHOCHOLA and Bohuslav KLÍMA. Study of domestication via human dental calculus in the Early Middle Ages. In 6th International Anthropological Congress of Dr. Aleš Hrdlička. 2019. ISSN 2336-4777.

JIRSOVA, Zuzana, Marie HECZKOVA, Helena DANKOVA, Hana MALINSKA, Petra VÍDEŇSKÁ, Hana VESPALCOVÁ, Lenka MICENKOVÁ, Lenka BARTONOVA, Eva STICOVA, Alena LODEREROVA, Lucia PREFERTUSOVA, Alena SEKERKOVA, Jaromir HRADECKY and Monika CAHOVA. The Effect of Butyrate-Supplemented Parenteral Nutrition on Intestinal Defence Mechanisms and the Parenteral Nutrition-Induced Shift in the Gut Microbiota in the Rat Model. Biomed Research International. New York: Hindawi Publishing Corporation, 2019, Neuveden, February, p. 1-14. ISSN 2314-6133. Available from: https://dx.doi.org/10.1155/2019/7084734.

ZWINSOVÁ, Barbora, Veronika BRYCHTOVÁ, Martina HRIVŇÁKOVÁ, Lenka ZDRAŽILOVÁ DUBSKÁ, Beatric BENCSIKOVÁ, Roman ŠEFR, Rudolf NENUTIL, Petra VÍDEŇSKÁ and Eva BUDINSKÁ. Vliv mikrobiomu na vznik a vývoj kolorektálního karcinomu (Role of the Microbiome in the Formation and Development of Colorectal Cancer). Klinická onkologie. Ambit Media, a.s., 2019, vol. 32, No 4, p. 261-269. ISSN 0862-495X. Available from: https://dx.doi.org/10.14735/amko2019261.

IHNATOVÁ, Ivana, Vlad POPOVICI and Eva BUDINSKÁ. A critical comparison of topology-based pathway analysis methods. Plos one. San Francisco: Public Library Science, 2018, vol. 13, No 1, p. 1-24. ISSN 1932-6203. Available from: https://dx.doi.org/10.1371/journal.pone.0191154.

TRNKOVÁ, Andrea, Kateřina ŠANCOVÁ, Martina ZAPLETALOVÁ, Jitka KAŠPAROVSKÁ, Kateřina DADÁKOVÁ, Ludmila KŘÍŽOVÁ, Jan LOCHMAN, Sylvie HADROVÁ, Ivana IHNATOVÁ and Tomáš KAŠPAROVSKÝ. Determination of in vitro isoflavone degradation in rumen fluid. Journal of Dairy Science. New York: Elsevier Science Inc., 2018, vol. 101, No 6, p. 5134-5144. ISSN 0022-0302. Available from: https://dx.doi.org/10.3168/jds.2017-13610.

VRBOVÁ, Markéta, Petra DOROCIAKOVÁ, Roman VYŠKOVSKÝ, Lubica MURINOVA PALKOVICOVA, Peter ČIŽNÁR, Katarina RAUSOVA, Scott J. N. MCNABB, Eva REICHRTOVA, Eva BUDINSKÁ and Vojtěch THON. Dynamics of allergy development during the first 5 years of life. European journal of pediatrics. New York: Springer, 2018, vol. 177, No 9, p. 1317-1325. ISSN 0340-6199. Available from: https://dx.doi.org/10.1007/s00431-018-3188-9.

GARLÍKOVÁ, Zuzana, Ana Catarina SILVA, Anas RABATA, David POTĚŠIL, Ivana IHNATOVÁ, Jana DUMKOVÁ, Zuzana KOLEDOVÁ, Zbyněk ZDRÁHAL, Vladimír VINARSKÝ, Aleš HAMPL, Perpétua PINTO-DO-Ó and Diana Santos NASCIMENTO. Generation of a Close-to-Native In Vitro System to Study Lung Cells-Extracellular Matrix Crosstalk. TISSUE ENGINEERING PART C-METHODS. New Rochelle: Mary Ann Liebert, 2018, vol. 24, No 1, p. 1-13. ISSN 1937-3384. Available from: https://dx.doi.org/10.1089/ten.tec.2017.0283.

ZWINSOVÁ, Barbora, Jan OPPELT, Petra VÍDEŇSKÁ and Eva BUDINSKÁ. Identifikace mikrobiomu kolorektálního karcinomu z RNAseq dat nádorové tkáně a jeho korelace s klinickými proměnnými a molekulárními podtypy. In Brněnské onkologické dny. 2018. ISSN 0862-495X.

TOKAN, Viktor, Janka PUTEROVÁ, Matej LEXA and Eduard KEJNOVSKÝ. Quadruplex DNA in long terminal repeats in maize LTR retrotransposons inhibits the expression of a reporter gene in yeast. BMC Genomics. BioMed Central, 2018, vol. 19, 06 03 2018, p. 184-194. ISSN 1471-2164. Available from: https://dx.doi.org/10.1186/s12864-018-4563-7.

POPOVICI, Vlad, Fred BOSMAN and Eva BUDINSKÁ. Recognising molecular subtypes of colon cancer from virtual slides. In 30th European Congress of Pathology. 2018. ISSN 0945-6317.

FORSYTHE, Nicholas, Alaa REFAAT, Arman JAVADI, Hajrah KHAWAJA, Jessica-Anne WEIR, Heba EMAM, Wendy L. ALLEN, Frank BURKAMP, Vlad POPOVICI, Puthen V. JITHESH, Claudio ISELLA, Melissa J. LABONTE, Ian G. MILLS, Patrick G. JOHNSTON and Sandra VAN SCHAEYBROECK. The Unfolded Protein Response: A Novel Therapeutic Target for Poor Prognostic BRAF Mutant Colorectal Cancer. Molecular Cancer Therapeutics. PHILADELPHIA: American Association for Cancer Research, 2018, vol. 17, No 6, p. 1280-1290. ISSN 1535-7163. Available from: https://dx.doi.org/10.1158/1535-7163.MCT-17-0603.

BYSTRÝ, Vojtěch, Tomáš REIGL, Adam KREJČÍ, Martin DEMKO, Barbora HANÁKOVÁ, Andrea GRIONI, Henrik KNECHT, Max SCHLITT, Peter DREGER, Leopold SELLNER, Dietrich HERRMANN, Marine PINGEON, Myriam BOUDJOGHRA, Jos RIJNTJES, Christiane POTT, Anton W. LANGERAK, Patricia J. T. A. GROENEN, Frederic DAVI, Monika BRUGGEMANN and Nikos DARZENTAS. ARResT/Interrogate: an interactive immunoprofiler for IG/TR NGS data. Bioinformatics. Oxford: Oxford University Press, 2017, vol. 33, No 3, p. 435-437. ISSN 1367-4803. Available from: https://dx.doi.org/10.1093/bioinformatics/btw634.

BOUCHAL, Pavel, Olga T SCHUBERT, Jakub FAKTOR, Lenka ČÁPKOVÁ, Hana IMRICHOVÁ, Karolína ZOUFALOVÁ, Yansheng LIU, H Alexander EBHARDT, Eva BUDINSKÁ, Rudolf NENUTIL and Ruedi AEBERSOLD. Breast cancer classification based on proteotypes obtained by SWATH-MS. In 16th Human Proteome Organisation World Congress. 2017.

KOTÁSKOVÁ, Iva, Petra VÍDEŇSKÁ, Hana OBRUČOVÁ, Barbora ZWINSOVÁ, Barbora MALIŠOVÁ, Veronika HOLÁ and Tomáš FREIBERGER. Comparison of Culture and Sequencing-Based Assessment of Bacterial Consortia Composition in Biofilms of Catheters. In ASM Microbe 2017, New Orleans. 2017.

KOTÁSKOVÁ, Iva, Petra VÍDEŇSKÁ, Hana OBRUČOVÁ, Barbora ZWINSOVÁ, Barbora MALIŠOVÁ, Veronika HOLÁ and Tomáš FREIBERGER. Comparison of Culture and Sequencing-Based Assessment of Bacterial Consortia Composition in Biofilms of Catheters. In ASM Microbe 2017. 2017.

KOTÁSKOVÁ, Iva, Barbora ZWINSOVÁ, Petra VÍDEŇSKÁ, Veronika HOLÁ and Tomáš FREIBERGER. Comparison of ready-to-use bioinformatic tools for 16S rRNA amplicon next-generation sequencing data analysis. In International Conference on Clinical Metagenomics, Ženeva. 2017.

PANIAGUA CORREAS, Candelas Maria, Anna BÍLKOVÁ, Philip Anthony P. JACKSON, Siarhei DABRAVOLSKI, Willi Sascha RIBER, Vojtěch DIDI, Josef HOUSER, Nora GIGLI-BISCEGLIA, Michaela WIMMEROVÁ, Eva BUDINSKÁ, Thorsten HAMANN and Jan HEJÁTKO. Dirigent proteins in plants: modulating cell wall metabolism during abiotic and biotic stress exposure. Journal of Experimental Botany. Oxford: OXFORD UNIV PRESS, 2017, vol. 68, No 13, p. 3287-3301. ISSN 0022-0957. Available from: https://dx.doi.org/10.1093/jxb/erx141.

FIEDOROVÁ, Kristýna, Juraj BOSÁK, Barbora ZWINSOVÁ, Matej LEXA, Jiří LITZMAN, Tomáš FREIBERGER and David ŠMAJS. Gastrointestinal microbiome in patients with primary immune deficiencies. In Food, Microbiota and Immunity, Třešť. 2017.

POPOVICI, Vlad, Aleš KŘENEK and Eva BUDINSKÁ. Identification of "BRAF-Positive" Cases Based on Whole-Slide Image Analysis. Biomed Research International. New York: HINDAWI LTD, 2017, Neuveden, April, p. nestránkováno, 7 pp. ISSN 2314-6133. Available from: https://dx.doi.org/10.1155/2017/3926498.

POPOVICI, Vlad, Eva BUDINSKÁ, Ladislav DUŠEK, Michal KOZUBEK and Fred BOSMAN. Image-based surrogate biomarkers for molecular subtypes of colorectal cancer. Bioinformatics. Oxford: Oxford University Press, 2017, vol. 33, No 13, p. 2002-2009. ISSN 1367-4803. Available from: https://dx.doi.org/10.1093/bioinformatics/btx027.

BYRNE, Annette T., Denis G. ALFEREZ, Fréderic AMANT, Daniela ANNIBALI, Joaquín ARRIBAS, Andrew V. BIANKIN, Alejandra BRUNA, Eva BUDINSKÁ, Carlo CALDAS, David K. CHANG, Robert B. CLARKE, Hans CLEVERS, George COUKOS, Virginie DANGLES-MARIE, S. Gail ECKHARDT, Eva GONZALEZ-SUAREZ, Els HERMANS, Manuel HIDALGO, Monica A. JARZABEK, Steven de JONG, Jos JONKERS, Kristel KEMPER, Luisa LANFRANCONE, Gunhild Mari MAELANDSMO, Elisabetta MARANGONI, Jean-Christophe MARINE, Enzo MEDICO, Jens Henrik NORUM, Héctor G. PALMER, Daniel S. PEEPER, Pier Giuseppe PELICCI, Alejandro PIRIS-GIMENEZ, Sergio ROMAN-ROMAN, Oscar M. RUEDA, Joan SEOANE, Violeta SERRA, Laura SOUCEK, Dominique VANHECKE, Alberto VILLANUEVA, Emilie VINOLO, Andrea BERTOTTI and Livio TRUSOLINO. Interrogating open issues in cancer precision medicine with patient-derived xenografts. NATURE REVIEWS CANCER. London: Nature Publishing Group, 2017, vol. 17, No 4, p. 254-268. ISSN 1474-175X. Available from: https://dx.doi.org/10.1038/nrc.2016.140.

BRABENCOVÁ, Sylva, Ivana IHNATOVÁ, David POTĚŠIL, Miloslava FOJTOVÁ, Jiří FAJKUS, Zbyněk ZDRÁHAL and Gabriela LOCHMANOVÁ. Variations of Histone Modification Patterns: Contributions of Inter-plant Variability and Technical Factors. Frontiers in Plant Science. Frontiers Research Foundation, 2017, vol. 8, No 2084, p. 1-12. ISSN 1664-462X. Available from: https://dx.doi.org/10.3389/fpls.2017.02084.

BOUCHAL, Pavel, Josef MARYÁŠ, Michaela GALOCZOVÁ, Jakub FAKTOR, Monika DVOŘÁKOVÁ, Roumeliotis THEODOROS, Karolína ZOUFALOVÁ, Lenka ČÁPKOVÁ, Hana IMRICHOVÁ, Eva BUDINSKÁ, Spiros D. GARBIS, Bořivoj VOJTĚŠEK and Rudolf NENUTIL. A novel panel of proteins associated with lymph node metastasis in low-grade breast cancer. In Annual Swiss Proteomics Meeting, Brig, Switzerland, 21.-22.4.2016. 2016.

BOUCHAL, Pavel, Jakub FAKTOR, Lenka ČÁPKOVÁ, Eva BUDINSKÁ and Rudolf NENUTIL. Aplikace SWATH-MS v nádorovém výzkumu. In Setkání uživatelů hmotnostní spektrometrie SCIEX, Praha, 14.6.2016. 2016.

SEDLÁŘ, Karel, Petra VÍDEŇSKÁ, Helena SKUTKOVA, Ivan RYCHLIK and Ivo PROVAZNIK. Bipartite Graphs for Visualization Analysis of Microbiome Data. EVOLUTIONARY BIOINFORMATICS. AUCKLAND: LIBERTAS ACAD, 2016, vol. 12, April, p. 17-23. ISSN 1176-9343. Available from: https://dx.doi.org/10.4137/EBO.S38546.

DIDI, Vojtěch, Jana VAŠÍČKOVÁ, Radek JUPA, Mariana BENITEZ KEINRAD, Tereza DOBISOVÁ, Anna BÍLKOVÁ, Eva BUDINSKÁ, Radim ČEGAN, Roman HOBZA, Shawn MANSFIELD, Vít GLOSER and Jan HEJÁTKO. Cytokinins control cell differentiation via regulation of secondary cell wall master switches NST1 and NST3. In Norwegian Plant Biology 2016. 2016.

NYGÅRD, Sune Boris, Ben VAINER, Signe Lykke NIELSEN, Fred BOSMAN, Sabine TEJPAR, Arnaud ROTH, Mauro DELORENZI, Nils BRÜNNER and Eva BUDINSKÁ. DNA Topoisomerase I Gene Copy Number and mRNA Expression Assessed as Predictive Biomarkers for Adjuvant Irinotecan in Stage II/III Colon Cancer. Clinical Cancer Research. Philadelphia: American Association for Cancer Research Inc., 2016, vol. 22, No 7, p. 1621-1631. ISSN 1078-0432. Available from: https://dx.doi.org/10.1158/1078-0432.CCR-15-0561.

BUDINSKÁ, Eva, Fred BOSMAN and Vlad POPOVICI. Experiments in Molecular Subtype Recognition Based on Histopathology Images. Online. In 2016 IEEE 13TH INTERNATIONAL SYMPOSIUM ON BIOMEDICAL IMAGING (ISBI). NEW YORK: IEEE, 2016, p. 1168-1172. ISBN 978-1-4799-2350-2. Available from: https://dx.doi.org/10.1109/ISBI.2016.7493474.

HANÁKOVÁ, Barbora, Jan OPPELT and Eva BUDINSKÁ. Identification of subtype specific microbiome from tumour tissue RNAseq data in colorectal cancer. In 15th European Conference on Computational Biology. 2016.

POPOVICI, Vlad, Eva BUDINSKÁ, Lenka ČÁPKOVÁ, Daniel SCHWARZ, Ladislav DUŠEK, Josef FEIT and Rolf JAGGI. Joint analysis of histopathology image features and gene expression in breast cancer. BMC Bioinformatics. London: BioMed Central, 2016, vol. 17, No 209, p. 1-9. ISSN 1471-2105. Available from: https://dx.doi.org/10.1186/s12859-016-1072-z.

WILSON, R, MR MIDDLETON, J HOULDEN, Schaeybroeck S VAN, CD ROLFO, E ELEZ, J TAIEB, T ANDRE, A BARDELLI, P LAURENT-PUIG, J TABERNERO, M PEETERS, T MAUGHAN, C ROBERTS, S LOVE, M LAWLER, M SALTO-TELLEZ, M GRAYSON, Vlad POPOVICI and Nicolantonio F DI. MErCuRIC1: A phase 1a study of MEK1/2 inhibitor PD-0325901 with cMET inhibitor crizotinib in patients with advanced solid tumours. 2016. Available from: https://dx.doi.org/10.1093/annonc/mdw370.28.

JANEČKOVÁ, Veronika, Ivana JEŽÍŠKOVÁ, Tereza TLAMKOVÁ, Eva BUDINSKÁ, Z. KOSAŘOVÁ, Martin ČULEN, A. FOLTA, Petr CETKOVSKÝ, P. ŽÁK, Tomáš SZOTKOWSKI, P. JINDRA and Zdeněk RÁČIL. Mutační analýza pacientů s akutní myeloidní leukémií – optimalizace hodnocení sekvenačních dat a předběžné výsledky národní studie. In XXX. Olomoucké hematologické dny. 2016.

MAXWELL, P, Favero J DEL, MA FUCHS, J TABERNERO, T MAUGHAN, M MIDDLETON, R ADDAMS, C ROLFO, B HENNESSEY, P LAURENT-PUIG, A BARDELLI, T ANDRE, Vlad POPOVICI, P JOHNSTONE, R WILSON, M LAWLER, Schaeybroeck S VAN and MS TELLEZ. Validation of a MEK/MET-specific NGS panel for early phase trial interrogation. Cancer Research. PHILADELPHIA: AMER ASSOC CANCER RESEARCH, 2016, vol. 76, p. "Amer Assoc Canc Res"-"3", 4 pp. ISSN 0008-5472. Available from: https://dx.doi.org/10.1158/1538-7445.AM2016-1396.

DOBIÁŠOVÁ, Hana, Petra VÍDEŇSKÁ and Monika DOLEJSKÁ. yy Complete Sequences of IncU Plasmids Harboring Quinolone Resistance Genes qnrS2 and aac(6 ')-Ib-cr in Aeromonas spp. from Ornamental Fish. Antimicrobial Agents and Chemotherapy. Washington: American Society for Microbiology, 2016, vol. 60, No 1, p. 653-657. ISSN 0066-4804. Available from: https://dx.doi.org/10.1128/AAC.01773-15.

BOUCHAL, Pavel, Monika DVOŘÁKOVÁ, Theodoros ROUMELIOTIS, Zbyněk BORTLÍČEK, Ivana IHNATOVÁ, Iva PROCHÁZKOVÁ, JTC HO, Josef MARYÁŠ, Hana IMRICHOVÁ, Eva BUDINSKÁ, Rostislav VYZULA, Spiros D, GARBIS, Bořivoj VOJTĚŠEK and Rudolf NENUTIL. Combined proteomics and transcriptomics identifies carboxypeptidase B1 and NF-kappa B associated proteins as putative biomarkers of metastasis in low grade breast cancer. In European Cancer Congress 2015, Vienna, Austria, 25.-29.9.2015 - European Journal of Cancer, Vol. 51, S3. Oxford: Elsevier Science Inc., 2015. s. S24-S25, 2 s. 2015. ISSN 0959-8049.

BOUCHAL, Pavel, Monika DVOŘÁKOVÁ, Theodoros ROUMELIOTIS, Zbyněk BORTLÍČEK, Ivana IHNATOVÁ, Iva PROCHÁZKOVÁ, JTC HO, Josef MARYÁŠ, Hana IMRICHOVÁ, Eva BUDINSKÁ, Rostislav VYZULA, SD GARBIS, Bořivoj VOJTĚŠEK and Rudolf NENUTIL. Combined Proteomics and Transcriptomics Identifies Carboxypeptidase B1 and Nuclear Factor kappa B (NF-kappa B) Associated Proteins as Putative Biomarkers of Metastasis in Low Grade Breast Cancer. MOLECULAR & CELLULAR PROTEOMICS. BETHESDA: AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC, 2015, vol. 14, No 7, p. 1814-1830. ISSN 1535-9476. Available from: https://dx.doi.org/10.1074/mcp.M114.041335.

JENSEN, Niels F., Jjan STENVANG, Mette K. BECK, Barbora HANÁKOVÁ, Kirstine C. BELLING, Khoa N. DO, Birgitte VIUFF, Sune B. NYGARD, Ramneek GUPTA, Mads H. RASMUSSEN, Line S. TARPGAARD, Tine P. HANSEN, Eva BUDINSKÁ, Per PFEIFFER, Fred BOSMAN, Sabine TEJPAR, Arnaud ROTH, Mauro DELORENZI, Claus L. ANDERSEN, Maria U. RØMER, Nils BRÜNNER and José M.A. MOREIRA. Establishment and characterization of models of chemotherapy resistance in colorectal cancer: Towards a predictive signature of chemoresistance. Molecular oncology. Oxford: Elsevier Science Inc., 2015, vol. 9, No 6, p. 1169-1185. ISSN 1574-7891. Available from: https://dx.doi.org/10.1016/j.molonc.2015.02.008.

ZANELLA, Eugenia R., Francesco GALIMI, Francesco SASSI, Giorgia MIGLIARDI, Francesca COTTINO, Simonetta M. LETO, Barbara LUPO, Jessica ERRIQUEZ, Claudio ISELLA, Paolo M. COMOGLIO, Enzo MEDICO, Sabine TEJPAR, Eva BUDINSKÁ, Livio TRUSOLINO and Andrea BERTOTTI. IGF2 is an actionable target that identifies a distinct subpopulation of colorectal cancer patients with marginal response to anti-EGFR therapies. SCIENCE TRANSLATIONAL MEDICINE. WASHINGTON: AMER ASSOC ADVANCEMENT SCIENCE, 2015, vol. 7, No 272, p. "272ra12", 13 pp. ISSN 1946-6234. Available from: https://dx.doi.org/10.1126/scitranslmed.3010445.

SCHAEYBROECK, Van, S ROLFO, CD ELEZ, E KELLY, S HOULDEN, J COLLINS, L LOVE, S ANDRE, T LAWLER, M Di NICOLANTONIO, F GRAYSON, Vlad POPOVICI, VC BARDELLI, A LAURENT-PUIG, P SALTO-TELLEZ, M MAUGHAN, T TABERNERO, J PEETERS, M WILSON, RH MIDDLETON and MR. MErCuRIC1: A Phase I study of MEK1/2 inhibitor PD-0325901 with cMET inhibitor crizotinib in RASMT and RASWT (with aberrant c-MET) metastatic colorectal cancer (mCRC) patients. Journal of clinical oncology. 2318 MILL ROAD, STE 800, ALEXANDRIA, VA: AMER SOC CLINICAL ONCOLOGY, 2015, vol. 33, No 15, p. "Amer Soc Clin Oncol"-"0", 1 pp. ISSN 0732-183X. Available from: https://dx.doi.org/10.1200/jco.2015.33.15_suppl.tps3632.

IHNATOVÁ, Ivana and Eva BUDINSKÁ. ToPASeq: an R package for topology-based pathway analysis of microarray and RNA-Seq data. BMC Bioinformatics. London: BioMed Central, 2015, vol. 16, No 350, p. 1-8. ISSN 1471-2105. Available from: https://dx.doi.org/10.1186/s12859-015-0763-1.

SCHIMEK, Michael G., Eva BUDINSKÁ, Karl G. KUGLER, Vendula ŠVENDOVÁ, Jie DING and Shili LIN. TopKLists: a comprehensive R package for statistical inference, stochastic aggregation, and visualization of multiple omics ranked lists. STATISTICAL APPLICATIONS IN GENETICS AND MOLECULAR BIOLOGY. BERLIN: WALTER DE GRUYTER GMBH, 2015, vol. 14, No 3, p. 311-316. ISSN 2194-6302. Available from: https://dx.doi.org/10.1515/sagmb-2014-0093.

BOUCHAL, Pavel, Josef MARYÁŠ, Monika DVOŘÁKOVÁ, Theodoros ROUMELIOTIS, Jenny HO, Jakub FAKTOR, Lenka ČÁPKOVÁ, Hana IMRICHOVÁ, Eva BUDINSKÁ, S D GARBIS, Bořivoj VOJTĚŠEK and Rudolf NENUTIL. Vyhledávání a validace potenciálních biomarkerů metastazování u nádorů prsu typu luminal A (Discovery and validation of potential biomarkers of metastasis in luminal A breast cancer). In Neformální proteomické setkání. 2015.

BOUCHAL, Pavel, Monika DVOŘÁKOVÁ, Theodoros ROUMELIOTIS, Zbyněk BORTLÍČEK, Ivana IHNATOVÁ, Iva STRUHÁROVÁ, Eva BUDINSKÁ, Spiros D. GARBIS, Bořivoj VOJTĚŠEK and Rudolf NENUTIL. A novel panel of proteins correlating with lymph node metastasis of low-grade breast cancer as identified by combined proteomics and transcriptomics approach. 2014.

BELMONT, Peter J., Eva BUDINSKÁ, Ping JIANG, Mark J. SINNAMON, Erin COFFEE, Jatin ROPER, Tao XIE, Paul A. REJTO, Sahra DERKITS, Owen J. SANSOM, Mauro DELORENZI, Sabine TEJPAR, Kenneth E. HUNG and Eric S. MARTIN. Cross-species analysis of genetically engineered mouse models of MAPK-driven colorectal cancer identifies hallmarks of the human disease. Disease models & mechanisms. Cambridge: Company of Biologists Ltd., 2014, vol. 7, No 6, p. 613-623. ISSN 1754-8403. Available from: https://dx.doi.org/10.1242/dmm.013904.

MISSIAGLIA, E., B. JACOBS, G. D´ARIO, A.F. DI NARZO, C. SONESON, Eva BUDINSKÁ, Vlad POPOVICI, L. VECCHIONE, S. GERSTER, P. YAN, Arnaud ROTH, D. KLINGBIEL, F.T. BOSMAN, M. DELORENZI and S. TEJPAR. Distal and proximal colon cancers differ in terms of molecular, pathological, and clinical features. Annals of Oncology. Oxford: Oxford University Press, 2014, vol. 25, No 10, p. 1995-2001, 8 pp. ISSN 0923-7534. Available from: https://dx.doi.org/10.1093/annonc/mdu275.

HIDALGO, Manuel, Frederic AMANT, Andrew V. BIANKIN, Eva BUDINSKÁ, Annete T. BYRNE, Carlos CALDAS, Robert B. CLARKE, Steven de JONG, Jos JONKERS, Gundhild Mari MAELANDSMO, Sergio ROMAN-ROMAN, Joan SEOANE, Livio TRUSOLINO and Alberto VILLANUEVA. Patient-Derived Xenograft Models: An Emerging Platform for Translational Cancer Research. Cancer Discovery. Philadelphia: American Association for Cancer Research Inc., 2014, vol. 4, No 9, p. 998-1013. ISSN 2159-8274. Available from: https://dx.doi.org/10.1158/2159-8290.CD-14-0001.

NARZO, Antonio Fabio Di, Sabine TEJPAR, Simona ROSSI, Pu YAN, Vlad POPOVICI, Pratyaksha WIRAPATI, Eva BUDINSKÁ, Tao XIE, Heather ESTRELLA, Adam PAVLICEK, Mao MAO, Martin ERIC, Weinrich SCOTT, Fred T BOSMAN, Arnaud ROTH and Mauro DELORENZI. Test of Four Colon Cancer Risk-Scores in Formalin Fixed Paraffin Embedded Microarray Gene Expression Data. Journal of the National Cancer Institute. Bethesda: National Cancer Institute, 2014, vol. 106, No 10, p. 1-8. ISSN 0027-8874. Available from: https://dx.doi.org/10.1093/jnci/dju247.

ASBAH, Layka Abbasi, Iria VAZQUEZ, Loredana VECCHIONE, Eva BUDINSKÁ, Veerle DE VRIENDT, Maria Francesca BAIETTI, Mikhail STEKLOV, Bart JACOBS, Nicholas HOE, Sharat SINGH, Naga-Sailaja IMJETI, Pascale ZIMMERMANN, Anna SABLINA and Sabine TEJPAR. The tyrosine phosphatase PTPRO sensitizes colon cancer cells to anti-EGFR therapy through activation of SRC-mediated EGFR signaling. Oncotarget. New York: Impact Journals, 2014, vol. 5, No 20, p. 10070-10083. ISSN 1949-2553.

BOUCHAL, Pavel, Jakub FAKTOR, Josef MARYÁŠ, Monika DVOŘÁKOVÁ, Lucia KNOPFOVÁ, Iva STRUHÁROVÁ, Eva BUDINSKÁ, Spiros D. GARBIS, Bořivoj VOJTĚŠEK and Rudolf NENUTIL. A novel panel of proteins correlating with lymph node metastasis of low-grade breast cancer: Towards functional characterization and clinical validation. 2013.

POPOVICI, Vlad, Eva BUDINSKÁ, Arnaud ROTH, Fred BOSMAN, Sabine TEJPAR and Mauro DELORENZI. BRAF and KRAS mutations as additional risk factors in the context of clinical parameters of patients with colorectal cancer. In American Society for Clinical Oncology Annual Meeting 2013. 2013.

BUDINSKÁ, Eva, Andrea JANOTOVÁ, sabine TEJPAR, Vlad POPOVICI, Giovanni D’ARIO, Nicolas LAPIQUE, Sikora KATARZYNA OTYLIA, Di Narzo ANTONIO FABIO, Yan PU, Hodgson JOHN GRAEME, Weinrich SCOTT, Bosman FRED, Roth ARNAUD and Delorenzi MAURO. Colorectal cancer heterogeneity from a gene expression perspective. In AACR 2013 Annual Meeting. 2013.

BUDINSKÁ, Eva, Jenny WILDING, Vlad POPOVICI, Edoardo MISSIAGLIA, Arnaud ROTH, Fred BOSMAN, Mauro DELORENZI, Walter BODMER and Sabine TEJPAR. Connecting gene expression subtypes of colorectal cancer (CRC) with cell lines and drug resistance. In ASCO Annual Meeting. 2013.

POPOVICI, Vlad, Eva BUDINSKÁ, Fred T BOSMAN, Sabine TEJPAR, Arnaud D ROTH and Mauro DELORENZI. Context-dependent interpretation of the prognostic value of BRAF and KRAS mutations in colorectal cancer. BMC Cancer. LONDON: BIOMED CENTRAL LTD, 2013, vol. 13, No 439, p. 1-7. ISSN 1471-2407. Available from: https://dx.doi.org/10.1186/1471-2407-13-439.

VRIENDT, Veerle De, Wendy De ROOCK, Antonio Fabio Di NARZO, Sun TIAN, Bart BIESMANS, Bart JACOBS, Eva BUDINSKÁ, Xavier SAGAERT, Simona ROSSI, Giovanni D´ARIO, Mauro DELORENZI, Iris SIMON, Loredana VECCHIONE and Sabine TEJPAR. DUSP 4 expression identifies a subset of colorectal cancer tumors that differ in MAPK activation, regardless of the genotype. Biomarkers. Spojené státy americké: INFORMA HEALTHCARE, 2013, vol. 18, No 6, p. 516-524. ISSN 1354-750X. Available from: https://dx.doi.org/10.3109/1354750X.2013.819038.

BUDINSKÁ, Eva, Vlad POPOVICI, Sabine TEJPAR, D Ario GIOVANNI, Nicolas LAPIQUE, Katarzyna Otylia SIKORA, Antonio Fabio DI NARZO, Pu YAN, John Graeme HODGSON, Scott WEINRICH, Fred BOSMAN, Arnaud ROTH and Mauro DELORENZI. Gene expression patterns unveil a new level of molecular heterogeneity in colorectal cancer. JOURNAL OF PATHOLOGY. HOBOKEN: WILEY-BLACKWELL, 2013, vol. 231, No 1, p. 63-76. ISSN 0022-3417. Available from: https://dx.doi.org/10.1002/path.4212.

VECCHIONE, Loredana, Valentina GAMBINO, Giovanni D'ARIO, Tian SUN, Iris SIMON, Vlad POPOVICI, Mauro DELORENZI, Rene BERNARDS and Sabine TEJPAR. Identification of synthetic lethal interactions with the BRAF oncogene in colorectal cancer. In AACR Annual Meeting. 2013.

KRYUKOV, Fedor, Pavel NĚMEC, Elena DEMENTYEVA, Lenka KUBICZKOVÁ, Ivana IHNATOVÁ, Eva BUDINSKÁ, Jiří JARKOVSKÝ, Sabina ŠEVČÍKOVÁ, Petr KUGLÍK and Roman HÁJEK. Molecular heterogeneity and centrosome-associated genes in multiple myeloma. Leukemia & Lymphoma. London: Taylor & Francis, 2013, vol. 54, No 9, p. 1982-1988. ISSN 1042-8194. Available from: https://dx.doi.org/10.3109/10428194.2013.764416.

VYBÍHAL, Václav, Tomáš SVOBODA, V PROCHÁZKA, Petr BENDA, George HANOUN, K SVOBODA, Pavel FADRUS, Eva BUDINSKÁ and Šárka BOHATÁ. Srovnání laparotomie a laparoskopie při implantaci peritoneální části shuntu v léčbě hydrocefalu. In Výroční kongres České neurochirurgické společnosti - Kniha abstrakt. 2013.

VINOLO, Emilie, Elisabetta MARANGONI, Violeta SERRA, Frederic AMANT, Andrea BERTOTTI, Andrew V BIANKIN, Anne-Lise BØRRESEN-DALE, Alejandra BRUNA, Eva BUDINSKÁ, Annette BYRNE, Carlos CALDAS, David CHANG, Robert CLARKE, Els HERMANS, Manuel HIDALGO, Steven de JONG, Jos Jonkers Pedro LÓPEZ, Gunhild Mari MÆLANDSMO, Vlad POPOVICI, Sergio ROMAN-ROMAN, Joan SEOANE, Livio TRUSOLINO and Alberto VILLANUEVA. The EurOPDX consortium: Sharing patient tumor-derived xenografts for collaborative multicentric preclinical trials. In AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics. 2013. Available from: https://dx.doi.org/10.1158/1535-7163.TARG-13-A8.

IHNATOVÁ, Ivana and Eva BUDINSKÁ. Topology Incorporating Pathway Analysis of Expression Data: An Evaluation of Existing Methods. In ITAT 2014. 2013.

XIE, Tao, Giovanni D’ ARIO, John R. LAMB, Eric MARTIN, Kai WANG, Sabine TEJPAR, Mauro DELORENZI, Fred T. BOSMAN, Arnaud D. ROTH, Yan PU, Bougel STEPHANIE, Di Narzo ANTONIO FABIO, Vlad POPOVICI, Eva BUDINSKÁ, Mao MAO, Scott L. WEINRICH, Rejto PAUL A. and J. Graeme HODGSON. A Comprehensive Characterization of Genome-Wide Copy Number Aberrations in Colorectal Cancer Reveals Novel Oncogenes and Patterns of Alterations. PLoS One. San Francisco: Public Library of Science, 2012, vol. 2012. ISSN 1932-6203.

TIAN, Sun, Paul ROEPMAN, Vlad POPOVICI, Magali MICHAUT, Ian MAJEWSKI, Ramon SALAZAR, Cristina SANTOS, Robert ROSENBERG, Ulrich NITSCHE, Wilma E MESKER, Sjoerd BRUIN, Sabine TEJPAR, Mauro DELORENZI, Rene BERNARDS and Iris SIMON. A robust genomic signature for the detection of colorectal cancer patients with microsatellite instability phenotype and high mutation frequency. JOURNAL OF PATHOLOGY. HOBOKEN: WILEY-BLACKWELL, 2012, vol. 228, No 4, p. 586-595. ISSN 0022-3417. Available from: https://dx.doi.org/10.1002/path.4092.

SCHIMEK, Michael G., Alena MYSICKOVA and Eva BUDINSKÁ. An Inference and Integration Approach for the Consolidation of Ranked Lists. COMMUNICATIONS IN STATISTICS-SIMULATION AND COMPUTATION. PHILADELPHIA: TAYLOR & FRANCIS INC, 2012, vol. 41, No 7, p. 1152-1166. ISSN 0361-0918. Available from: https://dx.doi.org/10.1080/03610918.2012.625843.

ANGHEL, Silvia I., Rafael CORREA-ROCHAL, Eva BUDINSKÁ, Kayluz F. BOLIGANL, Shahnaz ABRAHAM, Sara COLOMBETTI, Lionel FONTAO, Agnese MARIOTTI, Donata RIMOLDI, Ghanem E. GHANEM, David E. FISHER, Frederic LÉVY, Mauro DELORENZI and Vincent PIGUET. Breast cancer suppressor candidate-1 (BCSC-1) is a melanoma tumor suppressor that down regulates MITF. Pigment Cell & Melanoma Research. HOBOKEN: WILEY-BLACKWELL, 2012, vol. 25, No 4, p. 482-487. ISSN 1755-1471. Available from: https://dx.doi.org/10.1111/j.1755-148X.2012.01018.x.

KRYUKOV, Fedor, Pavel NĚMEC, Elena Vladimirovna DEMENTYEVA, Lenka KUBICZKOVÁ, Ivana IHNATOVÁ, Eva BUDINSKÁ, Jiří JARKOVSKÝ, Sabina ŠEVČÍKOVÁ, Petr KUGLÍK and Roman HÁJEK. Determining of molecular signature for centrosome abnormalities in multiple myeloma. In 17th Congress of the European Hematology Association, Amsterdam. 2012. ISSN 0390-6078.

BUDINSKÁ, Eva, Vlad POPOVICI, Katarzyna Otylia SIKORA, Nicolas LAPIQUE, Sabine TEJPAR, John Graeme HODGSON, Scott WEINRICH, Arnaud ROTH, Fred BOSMAN and Mauro DELORENZI. Identification and validation of gene expression subtypes in a large set of colorectal cancer samples. Journal of clinical oncology. United States: American Society of Clinical Oncology, 2012, vol. 30, No 15, 1 pp. ISSN 0732-183X.

POPOVICI, Vlad, Eva BUDINSKÁ, Sabine TEJPAR, Scott WEINRICH, Heather ESTRELLA, Graeme HODGSON, Eric VAN CUTSEM, Tao XIE, Fred BOSMAN, Arnaud ROTH and Mauro DELORENZI. Identification of a Poor-Prognosis BRAF-Mutant Like Population of Patients With Colon Cancer. Journal of Clinical Oncology, 30(12):12BB-1295, 2012. Journal of Clinical Oncology. 2012, 30(12), p. 1288-1295.

V, De Vriendt, Karel SIKORA, Van den Bosch B, Vlad POPOVICI, M DELORENZI and S TEJPAR. Identification of the BRAF-like Signature Predictive of Response Towards MEK Inhibition by Pimasertib (MSC1936369B) in Colorectal Cancer Cell Lines. European Journal of Cancer. Oxford, UK: ELSEVIER, 2012, vol. 48, p. 134-135. ISSN 0959-8049.

PILÁTOVÁ, Kateřina, Tereza FROSTOVÁ, Monika DOLEJSKÁ, Eva BUDINSKÁ, Jaroslav ŠTĚRBA and Lenka ZDRAŽILOVÁ DUBSKÁ. Mass spectrometry in identification of antibiotic resistance. In 2nd European Joint Congress of EFLM and UEMS "Laboratory Medicine at the Clinical Interface" 2012. 2012. ISSN 1330-0962.

BOUCHAL, Pavel, Monika DVOŘÁKOVÁ, Theodoros ROUMELIOTIS, Zbyněk BORTLÍČEK, Ivana IHNATOVÁ, Jenny HO, Iva STRUHÁROVÁ, Eva BUDINSKÁ, Rostislav VYZULA, Spiros D. GARBIS, Bořivoj VOJTĚŠEK and Rudolf NENUTIL. Molecular players in lymph node metastasis of low grade breast cancer: From proteomics-based target discovery to functional characterization. 2012.

BOUCHAL, Pavel, Monika DVOŘÁKOVÁ, Theodoros ROUMELIOTIS, Iva STRUHÁROVÁ, Eva BUDINSKÁ, Zbyněk BORTLÍČEK, Juraj LENČO, Spiros D. GARBIS, Rudolf NENUTIL and Bořivoj VOJTĚŠEK. Molekulární mechanismy metastazování u low-grade karcinomů prsu: Od proteomického profilování k funkční charakterizaci. In XXIII. Biochemický sjezd. Brno, 26.-29.8. 2012. p. 86. 2012.

ZDRAŽILOVÁ DUBSKÁ, Lenka, Dalibor VALÍK, Eva BUDINSKÁ, Tomáš FRGALA, Libuše BAČÍKOVÁ and Regina DEMLOVÁ. NKT-like Cells are Expanded in Solid Tumour Patients. Klinická onkologie. Praha: Česká lékařská společnost J.E.Purkyně, 2012, vol. 2012, No 2, p. 2S21-2S25, 5 pp. ISSN 0862-495X.

VYBÍHAL, Václav, Tomáš SVOBODA, Vladimír PROCHÁZKA, Petr BENDA, George HANOUN, Martin SMRČKA, Zdeněk KALA, Eva BUDINSKÁ and Šárka BOHATÁ. Srovnání laparotomické a laparoskopické techniky při implantaci peritoneální části shuntu v terapii hydrocefalu (Comparison of laparotomic and laparoscopic techniques for implantation of the peritoneal part of the shunt in the treatment of hydrocephalus). Rozhledy v chirurgii. Praha: Česká lékařská společnost J.E.Purkyně, 2012, vol. 91, No 6, p. 305-310. ISSN 0035-9351.

DUŠEK, Ladislav, Ondřej MÁJEK, Tomáš PAVLÍK, Jan MUŽÍK, Jana KOPTÍKOVÁ and Eva BUDINSKÁ. Analýza mnohorozměrných dat ve věku personalizované medicíny: trendy a dostupnost pro klinickou praxi (Multidimensional data analysis in age of personalized medicine: trends and availability in clinical practice). Lékař a technika. 2011, vol. 41, No 1, p. 5-14. ISSN 0301-5491.

CORREA-ROCHA, R, SI ANGHEL, Eva BUDINSKÁ, KF BOLIGAN, S ABRAHAM, S COLOMBETTI, L FONTAO, A MARIOTTI, D RIMOLDI, GE GHANEM, DE FISHER, L BRACCO, F LEVY, M DELORENZI and V PIGUET. Global analysis of transcription reveals BCSC-1 as a melanoma tumor suppressor that downregulates MITF. In Annual Meeting of the British-Society-for-Investigative-Dermatology. 2011.

PICARD, Franck, Emily LEBARBIER, Eva BUDINSKÁ and Stephane ROBIN. Joint segmentation of multivariate Gaussian processes using mixed linear models. Computational Statistics & Data Analysis. ELSEVIER, 2011, vol. 55, No 2, p. 1160-1170. ISSN 0167-9473. Available from: https://dx.doi.org/10.1016/j.csda.2010.09.015.

POPOVICI, Vlad, Eva BUDINSKÁ and Mauro DELORENZI. Rgtsp: a generalized top scoring pairs package for class prediction. Bioinformatics. 2011, vol. 27, No 12, p. 1729–1730. ISSN 1367-4803. Available from: https://dx.doi.org/10.1093/bioinformatics/btr233.

BUDINSKÁ, Eva, Zbyněk BORTLÍČEK and Ladislav DUŠEK. Současné trendy v analýze genomických dat (Current trends in genomic data analysis). Lékař a technika. 2011, vol. 2011. ISSN 0301-5491.

VAŠÍKOVÁ, Alžbeta, Monika BELIČKOVÁ, Eva BUDINSKÁ and Jaroslav ČERMÁK. A distinct expression of various gene subsets in CD34+ cells from patients with early and advanced myelodysplastic syndrome. Leukemia Research. 2010, vol. 34, No 12, p. 1566-1572. ISSN 0145-2126.

BOUCHAL, Pavel, Monika MUDROCHOVÁ, Zbyněk BORTLÍČEK, Theodoros ROUMELIOTIS, Eva BUDINSKÁ, Dominika VÁŇOVÁ, Lenka HERNYCHOVÁ, Iva STRUHÁROVÁ, Roman HRSTKA, Petr MÜLLER, Alexander SCHERL, Spiros D. GARBIS, Rudolf NENUTIL and Bořivoj VOJTĚŠEK. Biomarker discovery in low-grade breast cancer: An integrated, proteomics-based approach. In Abstract book of "3rd joint meeting on the role of p53, MDM2, AGR2/3 and ubiquitin/chaperone system in tumour biology". 2010. ISBN 978-80-86793-16-0.

BOUCHAL, Pavel, Monika MUDROCHOVÁ, Eva BUDINSKÁ, Zbyněk BORTLÍČEK, Iva STRUHÁROVÁ, Lenka HERNYCHOVÁ, Theodoros ROUMELIOTIS, Spiros D. GARBIS, Roman HRSTKA, Petr MÜLLER, Rudolf NENUTIL and Bořivoj VOJTĚŠEK. Biomarkers of lymph node metastasis in low-grade breast cancer: An integrated, proteomics-based approach. In XXII. Biochemický zjazd: The Book of Abstracts. 2010. ISBN 978-80-88866-83-1.

JEDLIČKOVÁ, Hana, Miloslav HLUBINKA, Tomáš PAVLÍK, Věra SEMRÁDOVÁ, Eva BUDINSKÁ and Zdeněk VLAŠÍN. Bullous pemphigoid and internal diseases: A case-control study. European Journal of Dermatology. Francie: John Libbey Eurotext, 2010, vol. 20, No 1, p. 96-101. ISSN 1167-1122.

JAKUBCOVÁ, Radka, Jakub FOUKAL, Karel BENDA, Eva BUDINSKÁ, Mojmír MOULIS and David ŠÁLEK. Contrast-enhanced ultrasound of peripheral lymph nodes. In European Congress of Radiology, Vienna, Austria. 2010. Available from: https://dx.doi.org/10.1594/ecr2010/C-2442.

VAVŘÍKOVÁ, Markéta, Daniel BARTUŠEK, Vlastimil VÁLEK, Jakub HUSTÝ and Eva BUDINSKÁ. Dependence of the clinical symptoms on the ultrasound findings by patients with celiac disease – prospective study. In European congress of gastroenterology. 2010.

BARTUŠEK, Daniel, Markéta VAVŘÍKOVÁ, Hana PETRÁŠOVÁ, Vlastimil VÁLEK, Jiří DOLINA and Eva BUDINSKÁ. Determination of accuracy of the transit time with respect to defecography in the diagnosis of anorectal dysfunction: use in practice. In European Congress of Abdominal and Gastrointestinal Radiology 2010. 2010.

TEJPAR, S, Vlad POPOVICI, M DELORENZI, Eva BUDINSKÁ, H ESTRELLA, Maria Leonor LIMAO OLIVEIRA, S WEINRICH, P YAN, Cutsem E VAN and A ROTH. MUTANT KRAS AND BRAF GENE EXPRESSION PROFILES IN COLORECTAL CANCER: RESULTS OF THE TRANSLATIONAL STUDY ON THE PETACC 3-EORTC 40993-SAKK 60-00 TRIAL. Annals of Oncology. Lugano: OXFORD UNIV PRESS, 2010, vol. 21, p. 17. ISSN 0923-7534.

TEJPAR, Sabine, Vlad POPOVICI, Mauro DELORENZI, Eva BUDINSKA, Heather ESTRELLA, M MAO, Scott WEINRICH, P YAN, Eric VAN CUTSEM and Arnaud ROTH. MUTANT KRAS AND BRAF GENE EXPRESSION PROFILES IN COLORECTAL CANCER: RESULTS OF THE TRANSLATIONAL STUDY ON THE PETACC 3-EORTC 40993-SAKK 60-00 TRIAL. In 12th World Congress on Gastrointestinal Cancer. 2010. ISSN 0145-2126.

POPOVICI, Vlad, Eva BUDINSKA and Mauro DELORENZI. Networks of generalized top scoring pairs for robust phenotype classification. In 9th European Conference on Computational Biology, Ghent, Belgie. 2010.

BUDINSKA, Eva, Mauro DELORENZI, Wendy DE ROOCK, Bart JACOBS, Steven WALKER, Claire WILSON, Timothy DAVISON, Richard D. KENNEDY and Sabine TEJPAR. New insights to gene expression signatures from primary FFPE tumors for the prediction of response to cetuximab in KRAS and BRAF wild-type colorectal cancer (CRC). 2010.

VAVŘÍKOVÁ, Markéta, Daniel BARTUŠEK, Vlastimil VÁLEK, Jakub HUSTÝ, Jaroslav UTĚŠENÝ, Jiří DOLINA and Eva BUDINSKÁ. Spleen size in patients with celiac disease - prospective study. In European congress of radiology. 2010.

BOUCHAL, Pavel, Iva STRUHÁROVÁ, Eva BUDINSKÁ, Ondrej ŠEDO, Tereza VYHLÍDALOVÁ, Zbyněk ZDRÁHAL, Rob VAN SPANNING and Igor KUČERA. Unraveling an FNR based regulatory circuit in Paracoccus denitrificans using a proteomics-based approach. Biochimica et Biophysica Acta - Proteins and Proteomics. Amsterdam, The Netherlands: Elsevier, 2010, vol. 1804, No 6, p. 1309-1316. ISSN 1570-9639. Available from: https://dx.doi.org/10.1016/j.bbapap.2010.01.016.

BUDINSKA, Eva, Vlad POPOVICI and Mauro DELORENZI. Unveiling heterogeneity of stage II and stage III colorectal cancer by defining molecular subtypes. In 9th European Conference on Computational Biology, Ghent, Belgie. 2010.

SCHIMEK, Michael and Eva BUDINSKA. Visualization Techniques for the Integration of Rank Data. In COMPSTAT 2010. Proceedings in Computational Statistics. Heidelberg: Physica, 2010, p. 1637 - 1644. ISBN 978-3-7908-2603-6.

BUDINSKA, Eva, Otakar FOJT and Ladislav DUŠEK. Bioinformatics in Genomics and Proteomics Data. 2009.

BUDINSKA, Eva and Zbyněk BORTLÍČEK. E-learning in genomic and proteomic data analysis. 2009.

BESZÉDESOVÁ, Natália, Eva BUDINSKÁ and Šárka SKORKOVSKÁ. Funkčná integrita neurosenzorickej sietnice u diabetikov 2. typu (Functional integrity of neural retina in 2. type diabetics). Česká a slovenská oftalmologie. 2009, vol. 65, No 4, p. 124-30, 7 pp. ISSN 1211-9059.

SCHIMEK, Michael G., Eva BUDINSKÁ, S LIN and Alena MYSICKOVA. Inference, aggregation and graphics for top-k rank lists. In useR! Abstracts. Rennes, France, 2009.

SCHIMEK, Michael G., Eva BUDINSKÁ and Alena MYSICKOVA. Integration of top-k list information inferred from paired rankings. In Proceedings of the 6th St. Petersburg Workshop on Simulation. St. Petersburg, 2009, p. 541-546. ISBN 978-5-9651-0354-6.

BUDINSKÁ, Eva, Eva GELNAROVÁ and Michael G. SCHIMEK. MSMAD: a computationally efficient method for the analysis of noisy array CGH data. Bioinformatics. Oxford University Press, 2009, vol. 25, No 6, p. 703-713. ISSN 1367-4803.

LAKOMÝ, Radek, Kristína GREPLOVÁ, Radomír PILNÝ, Eva BUDINSKÁ, Dalibor VALÍK, Alexandr POPRACH, Radim NĚMEČEK and Rostislav VYZULA. Profily nízkomolekulárního proteomového spektra získané pomocí hmotnostní spektrometrie SELDI-TOF v sérech pacientů s diseminovaným maligním melanomem: pilotní studie (Profiles of Low-Molecular Proteome Spectrum Obtained through SELDI-TOF Mass Spectrometry in the Sera of Patients with Metastatic Malignant Melanoma: Pilot Study). Klinická onkologie. Brno, 2009, vol. 22, No 5, p. 228-232. ISSN 0862-495X.

BOUCHAL, Pavel, Iva STRUHÁROVÁ, Eva BUDINSKÁ, Ondrej ŠEDO, Tereza VYHLÍDALOVÁ, Zbyněk ZDRÁHAL, Rob VAN SPANNING and Igor KUČERA. The study on Fnr-type transcription regulators functions in bacterium Paracoccus denitrificans using proteomics, transcriptomics and bioinformatics tools. In FEBS JOURNAL. Conference Information: 34th Congress of the Federation-of-European-Biochemical-Societies. 2009. ISSN 1742-464X.

BOUCHAL, Pavel, Iva STRUHÁROVÁ, Eva BUDINSKÁ, Ondrej ŠEDO, Tereza VYHLÍDALOVÁ, Zbyněk ZDRÁHAL, Rob VAN SPANNING and Igor KUČERA. Unraveling a FNR-based regulatory circuit in bacterium Paracoccus denitrificans using proteomics, transcriptomic and bioinformatic approaches. In 2009 SPS Scientific Meeting: "Proteome Dynamics: Protein Quantification in Time and Space". 2009.

JAKUBCOVÁ, Radka, Jakub FOUKAL, Eva BUDINSKÁ and Lenka ŠMARDOVÁ. Využití kontrastního ultrazvukového vyšetření v diferenciální diagnostice lymfadenopatií - první zkušenosti (Contrast-enhanced ultrasound in differential diagnosis of lymphadenopathy - first experiences). Česká radiologie. Praha: Galén, 2009, vol. 63, No 1, p. 48-55. ISSN 1210-7883.

GREPLOVÁ, Kristína, Radomír PILNÝ, Eva BUDINSKÁ, Lenka DUBSKÁ, Radek LAKOMÝ, Rostislav VYZULA, Bořivoj VOJTĚŠEK and Dalibor VALÍK. When one chip is not enough: Augmenting the validity of SELDI-TOF proteomic profiles of clinical specimens. Lab on a Chip. 2009, vol. 2009, No 9, p. 1014 - 1017. ISSN 1473-0197.

ŠEBKOVÁ, Alena, Daniela KARASOVÁ, Magdaléna CRHÁNOVÁ, Eva BUDINSKÁ and Ivan RYCHLÍK. aro Mutations in Salmonella enterica Cause Defects in Cell Wall and Outer Membrane Integrity. JOURNAL OF BACTERIOLOGY. American Society for Microbiology, 2008, vol. 190, No 9, p. 3155-3160. ISSN 0021-9193. Available from: https://dx.doi.org/10.1128/JB.00053-08.

BROŽKOVÁ, Kristýna, Eva BUDINSKÁ, Pavel BOUCHAL, Lenka HERNYCHOVÁ, Dana KNOFLÍČKOVÁ, Dalibor VALÍK, Rostislav VYZULA, Bořivoj VOJTĚŠEK and Rudolf NENUTIL. Surface-enhanced laser desorption/ionization time-of-flight proteomic profiling of breast carcinomas identifies clinicopathologically relevant groups of patients similar to previously defined clusters from cDNA expression. Breast Cancer Research. London, Great Britain: Biomed Central Ltd., 2008, vol. 10, No 3, p. R48, 11 pp. ISSN 1465-5411. Available from: https://dx.doi.org/10.1186/bcr2101.