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MS-Rescue: A Computational Pipeline to Increase the Quality and Yield of Immunopeptidomics Experiments.

Andreatta M, Nicastri A, Peng X, Hancock G, Dorrell L, Ternette N, Nielsen M.

Proteomics. 2019 Feb;19(4):e1800357. doi: 10.1002/pmic.201800357. Epub 2019 Jan 18.


Footprints of antigen processing boost MHC class II natural ligand predictions.

Barra C, Alvarez B, Paul S, Sette A, Peters B, Andreatta M, Buus S, Nielsen M.

Genome Med. 2018 Nov 16;10(1):84. doi: 10.1186/s13073-018-0594-6.


Human BDNF rs6265 polymorphism as a mediator for the generalization of contextual anxiety.

Andreatta M, Neueder D, Genheimer H, Schiele MA, Schartner C, Deckert J, Domschke K, Reif A, Wieser MJ, Pauli P.

J Neurosci Res. 2019 Mar;97(3):300-312. doi: 10.1002/jnr.24345. Epub 2018 Nov 7.


Predicting HLA CD4 Immunogenicity in Human Populations.

Dhanda SK, Karosiene E, Edwards L, Grifoni A, Paul S, Andreatta M, Weiskopf D, Sidney J, Nielsen M, Peters B, Sette A.

Front Immunol. 2018 Jun 14;9:1369. doi: 10.3389/fimmu.2018.01369. eCollection 2018.


Hypervigilance during anxiety and selective attention during fear: Using steady-state visual evoked potentials (ssVEPs) to disentangle attention mechanisms during predictable and unpredictable threat.

Kastner-Dorn AK, Andreatta M, Pauli P, Wieser MJ.

Cortex. 2018 Sep;106:120-131. doi: 10.1016/j.cortex.2018.05.008. Epub 2018 May 21.


Bioinformatics Tools for the Prediction of T-Cell Epitopes.

Andreatta M, Nielsen M.

Methods Mol Biol. 2018;1785:269-281. doi: 10.1007/978-1-4939-7841-0_18.


NetH2pan: A Computational Tool to Guide MHC Peptide Prediction on Murine Tumors.

DeVette CI, Andreatta M, Bardet W, Cate SJ, Jurtz VI, Jackson KW, Welm AL, Nielsen M, Hildebrand WH.

Cancer Immunol Res. 2018 Jun;6(6):636-644. doi: 10.1158/2326-6066.CIR-17-0298. Epub 2018 Apr 3.


Computational Tools for the Identification and Interpretation of Sequence Motifs in Immunopeptidomes.

Alvarez B, Barra C, Nielsen M, Andreatta M.

Proteomics. 2018 Jun;18(12):e1700252. doi: 10.1002/pmic.201700252. Epub 2018 Feb 26. Review.


Improved methods for predicting peptide binding affinity to MHC class II molecules.

Jensen KK, Andreatta M, Marcatili P, Buus S, Greenbaum JA, Yan Z, Sette A, Peters B, Nielsen M.

Immunology. 2018 Jul;154(3):394-406. doi: 10.1111/imm.12889. Epub 2018 Feb 6.


An automated benchmarking platform for MHC class II binding prediction methods.

Andreatta M, Trolle T, Yan Z, Greenbaum JA, Peters B, Nielsen M.

Bioinformatics. 2018 May 1;34(9):1522-1528. doi: 10.1093/bioinformatics/btx820.


Reinstatement of contextual conditioned anxiety in virtual reality and the effects of transcutaneous vagus nerve stimulation in humans.

Genheimer H, Andreatta M, Asan E, Pauli P.

Sci Rep. 2017 Dec 20;7(1):17886. doi: 10.1038/s41598-017-18183-3.


Cell-Free DNA as an Earlier Predictor of Exercise-Induced Performance Decrement Related to Muscle Damage.

Andreatta MV, Curty VM, Coutinho JVS, Santos MÂA, Vassallo PF, de Sousa NF, Barauna VG.

Int J Sports Physiol Perform. 2018 Aug 1;13(7):953-956. doi: 10.1123/ijspp.2017-0421. Epub 2018 Jul 28.


Addition of chromosomal microarray and next generation sequencing to FISH and classical cytogenetics enhances genomic profiling of myeloid malignancies.

Mukherjee S, Sathanoori M, Ma Z, Andreatta M, Lennon PA, Wheeler SR, Prescott JL, Coldren C, Casey T, Rietz H, Fasig K, Woodford R, Hartley T, Spence D, Donnelan W, Berdeja J, Flinn I, Kozyr N, Bouzyk M, Correll M, Ho H, Kravtsov V, Tunnel D, Chandra P.

Cancer Genet. 2017 Oct;216-217:128-141. doi: 10.1016/j.cancergen.2017.07.010. Epub 2017 Aug 14.


NetMHCpan-4.0: Improved Peptide-MHC Class I Interaction Predictions Integrating Eluted Ligand and Peptide Binding Affinity Data.

Jurtz V, Paul S, Andreatta M, Marcatili P, Peters B, Nielsen M.

J Immunol. 2017 Nov 1;199(9):3360-3368. doi: 10.4049/jimmunol.1700893. Epub 2017 Oct 4.


Learning mechanisms underlying threat absence and threat relief: Influences of trait anxiety.

Andreatta M, Pauli P.

Neurobiol Learn Mem. 2017 Nov;145:105-113. doi: 10.1016/j.nlm.2017.09.005. Epub 2017 Sep 8.


Machine learning reveals a non-canonical mode of peptide binding to MHC class II molecules.

Andreatta M, Jurtz VI, Kaever T, Sette A, Peters B, Nielsen M.

Immunology. 2017 Oct;152(2):255-264. doi: 10.1111/imm.12763. Epub 2017 Jun 19.


NNAlign: a platform to construct and evaluate artificial neural network models of receptor-ligand interactions.

Nielsen M, Andreatta M.

Nucleic Acids Res. 2017 Jul 3;45(W1):W344-W349. doi: 10.1093/nar/gkx276.


GibbsCluster: unsupervised clustering and alignment of peptide sequences.

Andreatta M, Alvarez B, Nielsen M.

Nucleic Acids Res. 2017 Jul 3;45(W1):W458-W463. doi: 10.1093/nar/gkx248.


Don't fear 'fear conditioning': Methodological considerations for the design and analysis of studies on human fear acquisition, extinction, and return of fear.

Lonsdorf TB, Menz MM, Andreatta M, Fullana MA, Golkar A, Haaker J, Heitland I, Hermann A, Kuhn M, Kruse O, Meir Drexler S, Meulders A, Nees F, Pittig A, Richter J, Römer S, Shiban Y, Schmitz A, Straube B, Vervliet B, Wendt J, Baas JMP, Merz CJ.

Neurosci Biobehav Rev. 2017 Jun;77:247-285. doi: 10.1016/j.neubiorev.2017.02.026. Epub 2017 Mar 3. Review.


Unconventional Peptide Presentation by Major Histocompatibility Complex (MHC) Class I Allele HLA-A*02:01: BREAKING CONFINEMENT.

Remesh SG, Andreatta M, Ying G, Kaever T, Nielsen M, McMurtrey C, Hildebrand W, Peters B, Zajonc DM.

J Biol Chem. 2017 Mar 31;292(13):5262-5270. doi: 10.1074/jbc.M117.776542. Epub 2017 Feb 8.


Learning processes underlying avoidance of negative outcomes.

Andreatta M, Michelmann S, Pauli P, Hewig J.

Psychophysiology. 2017 Apr;54(4):578-590. doi: 10.1111/psyp.12822. Epub 2017 Feb 8.


GLRB allelic variation associated with agoraphobic cognitions, increased startle response and fear network activation: a potential neurogenetic pathway to panic disorder.

Deckert J, Weber H, Villmann C, Lonsdorf TB, Richter J, Andreatta M, Arias-Vasquez A, Hommers L, Kent L, Schartner C, Cichon S, Wolf C, Schaefer N, von Collenberg CR, Wachter B, Blum R, Schümann D, Scharfenort R, Schumacher J, Forstner AJ, Baumann C, Schiele MA, Notzon S, Zwanzger P, Janzing JGE, Galesloot T, Kiemeney LA, Gajewska A, Glotzbach-Schoon E, Mühlberger A, Alpers G, Fydrich T, Fehm L, Gerlach AL, Kircher T, Lang T, Ströhle A, Arolt V, Wittchen HU, Kalisch R, Büchel C, Hamm A, Nöthen MM, Romanos M, Domschke K, Pauli P, Reif A.

Mol Psychiatry. 2017 Oct;22(10):1431-1439. doi: 10.1038/mp.2017.2. Epub 2017 Feb 7.


Effects of context preexposure and delay until anxiety retrieval on generalization of contextual anxiety.

Andreatta M, Neueder D, Glotzbach-Schoon E, Mühlberger A, Pauli P.

Learn Mem. 2016 Dec 15;24(1):43-54. doi: 10.1101/lm.044073.116. Print 2017 Jan.


The Influence of Methylphenidate on Hyperactivity and Attention Deficits in Children With ADHD: A Virtual Classroom Test.

Mühlberger A, Jekel K, Probst T, Schecklmann M, Conzelmann A, Andreatta M, Rizzo AA, Pauli P, Romanos M.

J Atten Disord. 2016 May 13. pii: 1087054716647480. [Epub ahead of print]


Converging evidence for an impact of a functional NOS gene variation on anxiety-related processes.

Kuhn M, Haaker J, Glotzbach-Schoon E, Schümann D, Andreatta M, Mechias ML, Raczka K, Gartmann N, Büchel C, Mühlberger A, Pauli P, Reif A, Kalisch R, Lonsdorf TB.

Soc Cogn Affect Neurosci. 2016 May;11(5):803-12. doi: 10.1093/scan/nsv151. Epub 2016 Jan 8.


The Multi-allelic Genetic Architecture of a Variance-Heterogeneity Locus for Molybdenum Concentration in Leaves Acts as a Source of Unexplained Additive Genetic Variance.

Forsberg SK, Andreatta ME, Huang XY, Danku J, Salt DE, Carlborg Ö.

PLoS Genet. 2015 Nov 23;11(11):e1005648. doi: 10.1371/journal.pgen.1005648. eCollection 2015 Nov.


Emotion regulation in heavy smokers: experiential, expressive and physiological consequences of cognitive reappraisal.

Wu L, Winkler MH, Wieser MJ, Andreatta M, Li Y, Pauli P.

Front Psychol. 2015 Oct 13;6:1555. doi: 10.3389/fpsyg.2015.01555. eCollection 2015.


Gapped sequence alignment using artificial neural networks: application to the MHC class I system.

Andreatta M, Nielsen M.

Bioinformatics. 2016 Feb 15;32(4):511-7. doi: 10.1093/bioinformatics/btv639. Epub 2015 Oct 29.


Generalization of Contextual Fear in Humans.

Andreatta M, Leombruni E, Glotzbach-Schoon E, Pauli P, Mühlberger A.

Behav Ther. 2015 Sep;46(5):583-96. doi: 10.1016/j.beth.2014.12.008. Epub 2015 Jan 10.


Accurate pan-specific prediction of peptide-MHC class II binding affinity with improved binding core identification.

Andreatta M, Karosiene E, Rasmussen M, Stryhn A, Buus S, Nielsen M.

Immunogenetics. 2015 Nov;67(11-12):641-50. doi: 10.1007/s00251-015-0873-y. Epub 2015 Sep 29.


When does pleasure start after the end of pain? The time course of relief.

Andreatta M, Mühlberger A, Pauli P.

J Comp Neurol. 2016 Jun 1;524(8):1653-67. doi: 10.1002/cne.23872. Epub 2015 Sep 27.


Reinstatement of contextual anxiety in humans: Effects of state anxiety.

Glotzbach-Schoon E, Andreatta M, Mühlberger A, Pauli P.

Int J Psychophysiol. 2015 Dec;98(3 Pt 2):557-66. doi: 10.1016/j.ijpsycho.2015.07.013. Epub 2015 Jul 29.


A single biopsy is valid for genetic diagnosis of eosinophilic esophagitis regardless of tissue preservation or location in the esophagus.

Dellon ES, Yellore V, Andreatta M, Stover J.

J Gastrointestin Liver Dis. 2015 Jun;24(2):151-7. doi: 10.15403/jgld.2014.1121.242.bsy.


Appetitive vs. Aversive conditioning in humans.

Andreatta M, Pauli P.

Front Behav Neurosci. 2015 May 19;9:128. doi: 10.3389/fnbeh.2015.00128. eCollection 2015.


The Recent De Novo Origin of Protein C-Termini.

Andreatta ME, Levine JA, Foy SG, Guzman LD, Kosinski LJ, Cordes MH, Masel J.

Genome Biol Evol. 2015 May 21;7(6):1686-701. doi: 10.1093/gbe/evv098.


Initial and sustained brain responses to contextual conditioned anxiety in humans.

Andreatta M, Glotzbach-Schoon E, Mühlberger A, Schulz SM, Wiemer J, Pauli P.

Cortex. 2015 Feb;63:352-63. doi: 10.1016/j.cortex.2014.09.014. Epub 2014 Oct 2.


Brain activity associated with illusory correlations in animal phobia.

Wiemer J, Schulz SM, Reicherts P, Glotzbach-Schoon E, Andreatta M, Pauli P.

Soc Cogn Affect Neurosci. 2015 Jul;10(7):969-77. doi: 10.1093/scan/nsu142. Epub 2014 Nov 18.


Delay and trace fear conditioning in a complex virtual learning environment-neural substrates of extinction.

Ewald H, Glotzbach-Schoon E, Gerdes AB, Andreatta M, Müller M, Mühlberger A, Pauli P.

Front Hum Neurosci. 2014 May 27;8:323. doi: 10.3389/fnhum.2014.00323. eCollection 2014.


Medial prefrontal cortex stimulation modulates the processing of conditioned fear.

Guhn A, Dresler T, Andreatta M, Müller LD, Hahn T, Tupak SV, Polak T, Deckert J, Herrmann MJ.

Front Behav Neurosci. 2014 Feb 18;8:44. doi: 10.3389/fnbeh.2014.00044. eCollection 2014.


Quantifying Significance of MHC II Residues.

Fan Y, Lu R, Wang L, Andreatta M, Li SC.

IEEE/ACM Trans Comput Biol Bioinform. 2014 Jan-Feb;11(1):17-25. doi: 10.1109/TCBB.2013.138.


The BDNF Val66Met polymorphism modulates the generalization of cued fear responses to a novel context.

Mühlberger A, Andreatta M, Ewald H, Glotzbach-Schoon E, Tröger C, Baumann C, Reif A, Deckert J, Pauli P.

Neuropsychopharmacology. 2014 Apr;39(5):1187-95. doi: 10.1038/npp.2013.320. Epub 2013 Nov 19.


Pain predictability reverses valence ratings of a relief-associated stimulus.

Andreatta M, Mühlberger A, Glotzbach-Schoon E, Pauli P.

Front Syst Neurosci. 2013 Sep 24;7:53. doi: 10.3389/fnsys.2013.00053. eCollection 2013.


[Micronutrients intake and urinary tract tumors in Córdoba, Argentina].

Román MD, Roqué FI, Muñoz SE, Andreatta MM, Navarro A, Díaz Mdel P.

Nutr Hosp. 2013 May-Jun;28(3):943-50. doi: 10.3305/nh.2013.28.3.6449. Spanish.


Is there a negative interpretation bias in depressed patients? An affective startle modulation study.

Käse M, Dresler T, Andreatta M, Ehlis AC, Wolff B, Kittel-Schneider S, Polak T, Fallgatter AJ, Mühlberger A.

Neuropsychobiology. 2013;67(4):201-9. doi: 10.1159/000347086. Epub 2013 Apr 27.


Contextual fear conditioning in virtual reality is affected by 5HTTLPR and NPSR1 polymorphisms: effects on fear-potentiated startle.

Glotzbach-Schoon E, Andreatta M, Reif A, Ewald H, Tröger C, Baumann C, Deckert J, Mühlberger A, Pauli P.

Front Behav Neurosci. 2013 Apr 23;7:31. doi: 10.3389/fnbeh.2013.00031. eCollection 2013.


Enhanced discrimination between threatening and safe contexts in high-anxious individuals.

Glotzbach-Schoon E, Tadda R, Andreatta M, Tröger C, Ewald H, Grillon C, Pauli P, Mühlberger A.

Biol Psychol. 2013 Apr;93(1):159-66. doi: 10.1016/j.biopsycho.2013.01.011. Epub 2013 Feb 4.


Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach.

Andreatta M, Lund O, Nielsen M.

Bioinformatics. 2013 Jan 1;29(1):8-14. doi: 10.1093/bioinformatics/bts621. Epub 2012 Oct 24.


Onset and offset of aversive events establish distinct memories requiring fear and reward networks.

Andreatta M, Fendt M, Mühlberger A, Wieser MJ, Imobersteg S, Yarali A, Gerber B, Pauli P.

Learn Mem. 2012 Oct 16;19(11):518-26. doi: 10.1101/lm.026864.112.


Altered processing of emotional stimuli in migraine: an event-related potential study.

Andreatta M, Puschmann AK, Sommer C, Weyers P, Pauli P, Mühlberger A.

Cephalalgia. 2012 Nov;32(15):1101-8. doi: 10.1177/0333102412459573. Epub 2012 Sep 19.


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