Miskei, M., Horváth, A., Vendruscolo, M., Fuxreiter, M.: Sequence-Based Prediction of Fuzzy Protein Interactions.
J. Mol. Biol. 432 (7), 2289-2303, 2020.

Horváth, A., Miskei, M., Ambrus, V., Vendruscolo, M., Fuxreiter, M.: Sequence-based prediction of protein binding mode landscapes.
PLoS Comput. Biol. 16 (5), 1-19, 2020.

Ozgyin, L., Horváth, A., Hevessy, Z., Bálint, B.: Extensive epigenetic and transcriptomic variability between genetically identical human B-lymphoblastoid cells with implications in pharmacogenomics research.
Sci Rep. 9 1-16, 2019.

Horváth, A., Dániel, B., Széles, L., Cuaranta-Monroy, I., Czimmerer, Z., Ozgyin, L., Steiner, L., Kiss, M., Simándi, Z., Póliska, S., Giannakis, N., Raineri, E., Gut, I., Nagy, B., Nagy, L.: Labelled regulatory elements are pervasive features of the macrophage genome and are dynamically utilized by classical and alternative polarization signals.
Nucleic Acids Res. 47 (6), 2778-2792, 2019.

Ivády, G., Madar, L., Dzsudzsák, E., Koczok, K., Kappelmayer, J., Krulisova, V., Macek, J., Horváth, A., Balogh, I.: Analytical parameters and validation of homopolymer detection in a pyrosequencing-based next generation sequencing system.
BMC Genomics. 19 1-8, 2018.

Simándi, Z., Pájer, K., Károlyi, K., Sieler, T., Jiang, L., Kolostyák, Z., Sári, Z., Fekecs, Z., Pap, A., Patsalos, A., Contreras, G., Rehó, B., Papp, Z., Guo, X., Horváth, A., Kiss, G., Keresztessy, Z., Vámosi, G., Hickman, J., Xu, H., Dormann, D., Hortobágyi, T., Antal, M., Nógrádi, A., Nagy, L.: Arginine Methyltransferase PRMT8 Provides Cellular Stress Tolerance in Aging Motoneurons.
J. Neurosci. 38 (35), 7683-7700, 2018.

Czimmerer, Z., Horváth, A., Dániel, B., Nagy, G., Cuaranta-Monroy, I., Kiss, M., Kolostyák, Z., Póliska, S., Steiner, L., Giannakis, N., Varga, T., Nagy, L.: Dynamic transcriptional control of macrophage miRNA signature via inflammation responsive enhancers revealed using a combination of next generation sequencing-based approaches.
Biochim. Biophys. Acta. Gene Regul. Mech. 1861 (1), 14-28, 2018.

Fejes, Z., Czimmerer, Z., Szűk, T., Póliska, S., Horváth, A., Balogh, E., Jeney, V., Váradi, J., Fenyvesi, F., Balla, G., Édes, I., Balla, J., Kappelmayer, J., Nagy, B.: Endothelial cell activation is attenuated by everolimus via transcriptional and post-transcriptional regulatory mechanisms after drug-eluting coronary stenting.
PLoS One. 13 (6), 1-20, 2018.

Czimmerer, Z., Nagy, Z., Nagy, G., Horváth, A., Silye-Cseh, T., Kriston, Á., Jonás, D., Sauer, S., Steiner, L., Dániel, B., Deleuze, J., Nagy, L.: Extensive and functional overlap of the STAT6 and RXR cistromes in the active enhancer repertoire of human CD14+ monocyte derived differentiating macrophages.
Mol. Cell. Endocrinol. 471 63-74, 2018.

Ozgyin, L., Horváth, A., Bálint, B.: Lyophilized human cells stored at room temperature preserve multiple RNA species at excellent quality for RNA sequencing.
Oncotarget. 9 (59), 31312-31329, 2018.

Simándi, Z., Horváth, A., Cuaranta-Monroy, I., Sauer, S., Deleuze, J., Nagy, L.: RXR heterodimers orchestrate transcriptional control of neurogenesis and cell fate specification.
Mol. Cell. Endocrinol. 471 51-62, 2018.

Dániel, B., Nagy, G., Horváth, A., Czimmerer, Z., Cuaranta-Monroy, I., Póliska, S., Hays, T., Sauer, S., Francois-Deleuze, J., Nagy, L.: The IL-4/STAT6/PPAR[gamma] signaling axis is driving the expansion of the RXR heterodimer cistrome, providing complex ligand responsiveness in macrophages.
Nucleic Acids Res. 46 (9), 4425-4439, 2018.

Dániel, B., Nagy, G., Czimmerer, Z., Horváth, A., Hammers, D., Cuaranta-Monroy, I., Póliska, S., Tzerpos, P., Kolostyák, Z., Hays, T., Patsalos, A., Houtman, R., Sauer, S., Francois-Deleuze, J., Rastinejad, F., Bálint, B., Sweeney, H., Nagy, L.: The Nuclear Receptor PPAR[gamma] Controls Progressive Macrophage Polarization as a Ligand-Insensitive Epigenomic Ratchet of Transcriptional Memory.
Immunity. 49 (4), 615-626, 2018.

Czimmerer, Z., Dániel, B., Horváth, A., Rückerl, D., Nagy, G., Kiss, M., Peloquin, M., Budai, M., Cuaranta-Monroy, I., Simándi, Z., Steiner, L., Nagy, B., Póliska, S., Bankó, C., Bacsó, Z., Schulman, I., Sauer, S., Deleuze, J., Allen, J., Benkő, S., Nagy, L.: The Transcription Factor STAT6 Mediates Direct Repression of Inflammatory Enhancers and Limits Activation of Alternatively Polarized Macrophages.
Immunity. 48 (1), 75-90, 2018.

Horváth, A., Simándi, Z., Nagy, L.: Commentaries on Viewpoint: Loopomics: a new functional approach to life.
J. Appl. Physiol. 123 (4), 1014-1015, 2017.

Gál, A., Balicza, P., Weaver, D., Naghdi, S., Joseph, S., Várnai, P., Gyuris, T., Horváth, A., Nagy, L., Seifert, E., Molnár, M., Hajnóczky, G.: MSTO1 is a cytoplasmic pro-mitochondrial fusion protein, whose mutation induces myopathy and ataxia in humans.
EMBO Mol Med. 9 (7), 967-984, 2017.

Imre, L., Simándi, Z., Horváth, A., Fenyőfalvi, G., Nánási, P., Firouzi Niaki, E., Hegedűs, É., Bacsó, Z., Weyemi, U., Mauser, R., Ausio, J., Jeltsch, A., Bonner, W., Nagy, L., Kimura, H., Szabó, G.: Nucleosome stability measured in situ by automated quantitative imaging.
Sci Rep. 7 (1), 1-15, 2017.

Kiss, M., Czimmerer, Z., Nagy, G., Bieniasz-Krzywiec, P., Ehling, M., Pap, A., Póliska, S., Botó, P., Tzerpos, P., Horváth, A., Kolostyák, Z., Dániel, B., Szatmári, I., Mazzone, M., Nagy, L.: Retinoid X receptor suppresses a metastasis-promoting transcriptional program in myeloid cells via a ligand-insensitive mechanism.
Proc. Natl. Acad. Sci. U. S. A. 114 (40), 10725-10730, 2017.

Varga, T., Mounier, R., Horváth, A., Cuvellier, S., Dumont, F., Póliska, S., Ardjoune, H., Juban, G., Nagy, L., Chazaud, B.: Highly Dynamic Transcriptional Signature of Distinct Macrophage Subsets during Sterile Inflammation, Resolution, and Tissue Repair.
J. Immunol. 196 (11), 4771-4782, 2016.

Varga, T., Mounier, R., Patsalos, A., Gogolák, P., Peloquin, M., Horváth, A., Pap, A., Dániel, B., Nagy, G., Pintye, É., Póliska, S., Cuvellier, S., Ben Larbi, S., Sansbury, B., Spite, M., Brown, C., Chazaud, B., Nagy, L.: Macrophage PPAR[gamma], a Lipid Activated Transcription Factor Controls the Growth Factor GDF3 and Skeletal Muscle Regeneration.
Immunity. 45 (5), 1038-1051, 2016.

Simándi, Z., Horváth, A., Wright, L., Cuaranta-Monroy, I., De, L., Károlyi, K., Sauer, S., Deleuze, J., Gudas, L., Cowley, S., Nagy, L.: OCT4 Acts as an Integrator of Pluripotency and Signal-Induced Differentiation.
Mol. Cell. 63 (4), 647-661, 2016.

Simándi, Z., Horváth, A., Nagy, P., Nagy, L.: Prediction and Validation of Gene Regulatory Elements Activated During Retinoic Acid Induced Embryonic Stem Cell Differentiation.
JoVE. 2016 (112), e53978, 2016.

Czimmerer, Z., Varga, T., Kiss, M., Vázquez, C., Doan-Xuan, Q., Rückerl, D., Tattikota, S., Yan, X., Nagy, Z., Dániel, B., Póliska, S., Horváth, A., Nagy, G., Varallyay, É., Poy, M., Allen, J., Bacsó, Z., Abreu-Goodger, C., Nagy, L.: The IL-4/STAT6 signaling axis establishes a conserved microRNA signature in human and mouse macrophages regulating cell survival via miR-342-3p.
Genome Med. 8 (1), 1-22, 2016.

Rácz, R., Bereczki, J., Sramkó, G., Kosztolányi, A., Tóth, J., Póliska, S., Horváth, A., Barta, E., Barta, Z.: Isolation and Characterisation of 15 Microsatellite Loci from Lethrus apterus (Coleoptera: Geotrupidae).
Ann. Zool. Fenn. 52 (1-2), 45-50, 2015.

Simándi, Z., Czipa, E., Horváth, A., Kőszeghy, Á., Bordás, C., Póliska, S., Juhász, I., Imre, L., Szabó, G., Dezső, B., Barta, E., Sauer, S., Károlyi, K., Kovács, I., Hutóczki, G., Bognár, L., Klekner, Á., Szűcs, P., Bálint, B., Nagy, L.: PRMT1 and PRMT8 regulate retinoic acid-dependent neuronal differentiation with implications to neuropathology.
Stem Cells. 33 (3), 726-741, 2015.

Cuaranta-Monroy, I., Simándi, Z., Kolostyák, Z., Doan-Xuan, Q., Póliska, S., Horváth, A., Nagy, G., Bacsó, Z., Nagy, L.: Highly efficient differentiation of embryonic stem cells into adipocytes by ascorbic acid.
Stem Cell Res. 13 (1), 88-97, 2014.

Gyöngyösi, A., Dócs, O., Czimmerer, Z., Orosz, L., Horváth, A., Török, O., Méhes, G., Nagy, L., Bálint, B.: Measuring expression levels of small regulatory RNA molecules from body fluids and formalin-fixed, paraffin-embedded samples.
In: RNA Mapping : Methods and Protocols . Ed.: M. Lucrecia Alvarez, Mahtab Nourbakhsh, Humana Press, New York, 105-119, 2014. ISBN: 9781493910618(Print)9781493910625(Online)

Dániel, B., Nagy, G., Hah, N., Horváth, A., Czimmerer, Z., Póliska, S., Gyuris, T., Keirsse, J., Gysemans, C., Van Ginderachter, J., Bálint, B., Evans, R., Barta, E., Nagy, L.: The active enhancer network operated by liganded RXR supports angiogenic activity in macrophages.
Genes Dev. 28 (14), 1562-1577, 2014.

Czimmerer, Z., Hulvely, J., Simándi, Z., Varallyay, É., Havelda, Z., Szabó, E., Varga, A., Dezső, B., Balogh, M., Horváth, A., Domokos, B., Török, Z., Nagy, L., Bálint, B.: A versatile method to design stem-loop primer-based quantitative PCR assays for detecting small regulatory RNA molecules.
PLoS One. 8 (1), 1-10, 2013.

Meskó, B., Póliska, S., Váncsa, A., Szekanecz, Z., Palatka, K., Holló, Z., Horváth, A., Steiner, L., Zahuczky, G., Podani, J., Nagy, L.: Peripheral blood derived gene panels predict response to infliximab in rheumatoid arthritis and Crohn's disease.
Genome Med. 5 (6), 59-69, 2013.

Laczik, M., Tukacs, E., Uzonyi, B., Domokos, B., Doma, Z., Kiss, M., Horváth, A., Batta, Z., Maros-Szabó, Z., Török, Z.: Geno viewer, a SAM/BAM viewer tool.
Bioinformation. 8 (2), 107-109, 2012.