My Bibliography

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Altmann A, Beerenwinkel N, Sing T, Savenkov I, Doumer M, Kaiser R, Rhee SY, Fessel WJ, Shafer RW, Lengauer T. Improved prediction of response to antiretroviral combination therapy using the genetic barrier to drug resistance. Antivir Ther. 2007;12(2):169-78. PubMed PMID: 17503659.

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Rosen-Zvi M, Altmann A, Prosperi M, Aharoni E, Neuvirth H, Sönnerborg A, Schülter E, Struck D, Peres Y, Incardona F, Kaiser R, Zazzi M, Lengauer T. Selecting anti-HIV therapies based on a variety of genomic and clinical factors. Bioinformatics. 2008 Jul 1;24(13):i399-406. doi: 10.1093/bioinformatics/btn141. PubMed PMID: 18586740; PubMed Central PMCID: PMC2718619.

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Bogojeska J, Alexa A, Altmann A, Lengauer T, Rahnenführer J. Rtreemix: an R package for estimating evolutionary pathways and genetic progression scores. Bioinformatics. 2008 Oct 15;24(20):2391-2. doi: 10.1093/bioinformatics/btn410. Epub 2008 Aug 20. PubMed PMID: 18718947; PubMed Central PMCID: PMC2562010.

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Altmann A, Rosen-Zvi M, Prosperi M, Aharoni E, Neuvirth H, Schülter E, Büch J, Struck D, Peres Y, Incardona F, Sönnerborg A, Kaiser R, Zazzi M, Lengauer T. Comparison of classifier fusion methods for predicting response to anti HIV-1 therapy. PLoS One. 2008;3(10):e3470. doi: 10.1371/journal.pone.0003470. Epub 2008 Oct 21. PubMed PMID: 18941628; PubMed Central PMCID: PMC2565127.

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Prosperi MC, Altmann A, Rosen-Zvi M, Aharoni E, Borgulya G, Bazso F, Sönnerborg A, Schülter E, Struck D, Ulivi G, Vandamme AM, Vercauteren J, Zazzi M. Investigation of expert rule bases, logistic regression, and non-linear machine learning techniques for predicting response to antiretroviral treatment. Antivir Ther. 2009;14(3):433-42. PubMed PMID: 19474477.

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Altmann A, Sing T, Vermeiren H, Winters B, Van Craenenbroeck E, Van der Borght K, Rhee SY, Shafer RW, Schülter E, Kaiser R, Peres Y, Sönnerborg A, Fessel WJ, Incardona F, Zazzi M, Bacheler L, Van Vlijmen H, Lengauer T. Advantages of predicted phenotypes and statistical learning models in inferring virological response to antiretroviral therapy from HIV genotype. Antivir Ther. 2009;14(2):273-83. PubMed PMID: 19430102.

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Altmann A, Däumer M, Beerenwinkel N, Peres Y, Schülter E, Büch J, Rhee SY, Sönnerborg A, Fessel WJ, Shafer RW, Zazzi M, Kaiser R, Lengauer T. Predicting the response to combination antiretroviral therapy: retrospective validation of geno2pheno-THEO on a large clinical database. J Infect Dis. 2009 Apr 1;199(7):999-1006. doi: 10.1086/597305. PubMed PMID: 19239365.

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Sichtig N, Sierra S, Kaiser R, Däumer M, Reuter S, Schülter E, Altmann A, Fätkenheuer G, Dittmer U, Pfister H, Esser S. Evolution of raltegravir resistance during therapy. J Antimicrob Chemother. 2009 Jul;64(1):25-32. doi: 10.1093/jac/dkp153. Epub 2009 May 14. PubMed PMID: 19447792.

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Weisser H, Altmann A, Sierra S, Incardona F, Struck D, Sönnerborg A, Kaiser R, Zazzi M, Tschochner M, Walter H, Lengauer T. Only slight impact of predicted replicative capacity for therapy response prediction. PLoS One. 2010 Feb 3;5(2):e9044. doi: 10.1371/journal.pone.0009044. PubMed PMID: 20140263; PubMed Central PMCID: PMC2815793.

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Altmann A, Toloşi L, Sander O, Lengauer T. Permutation importance: a corrected feature importance measure. Bioinformatics. 2010 May 15;26(10):1340-7. doi: 10.1093/bioinformatics/btq134. Epub 2010 Apr 12. PubMed PMID: 20385727.

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Bogojeska J, Bickel S, Altmann A, Lengauer T. Dealing with sparse data in predicting outcomes of HIV combination therapies. Bioinformatics. 2010 Sep 1;26(17):2085-92. doi: 10.1093/bioinformatics/btq361. Epub 2010 Jul 12. PubMed PMID: 20624779.

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Prosperi MC, Rosen-Zvi M, Altmann A, Zazzi M, Di Giambenedetto S, Kaiser R, Schülter E, Struck D, Sloot P, van de Vijver DA, Vandamme AM, Sönnerborg A. Antiretroviral therapy optimisation without genotype resistance testing: a perspective on treatment history based models. PLoS One. 2010 Oct 29;5(10):e13753. doi: 10.1371/journal.pone.0013753. PubMed PMID: 21060792; PubMed Central PMCID: PMC2966424.

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Saigo H, Altmann A, Bogojeska J, Müller F, Nowozin S, Lengauer T. Learning from past treatments and their outcome improves prediction of in vivo response to anti-HIV therapy. Stat Appl Genet Mol Biol. 2011;10:Article 6. doi: 10.2202/1544-6115.1604. Epub 2011 Jan 14. PubMed PMID: 21291416.

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Zazzi M, Kaiser R, Sönnerborg A, Struck D, Altmann A, Prosperi M, Rosen-Zvi M, Petroczi A, Peres Y, Schülter E, Boucher CA, Brun-Vezinet F, Harrigan PR, Morris L, Obermeier M, Perno CF, Phanuphak P, Pillay D, Shafer RW, Vandamme AM, van Laethem K, Wensing AM, Lengauer T, Incardona F. Prediction of response to antiretroviral therapy by human experts and by the EuResist data-driven expert system (the EVE study). HIV Med. 2011 Apr;12(4):211-8. doi: 10.1111/j.1468-1293.2010.00871.x. Epub 2010 Aug 19. PubMed PMID: 20731728.

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Altmann A, Weber P, Quast C, Rex-Haffner M, Binder EB, Müller-Myhsok B. vipR: variant identification in pooled DNA using R. Bioinformatics. 2011 Jul 1;27(13):i77-84. doi: 10.1093/bioinformatics/btr205. PubMed PMID: 21685105; PubMed Central PMCID: PMC3117388.

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Lawyer G, Altmann A, Thielen A, Zazzi M, Sönnerborg A, Lengauer T. HIV-1 mutational pathways under multidrug therapy. AIDS Res Ther. 2011 Jul 27;8:26. doi: 10.1186/1742-6405-8-26. PubMed PMID: 21794106; PubMed Central PMCID: PMC3162516.

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Oette M, Schülter E, Rosen-Zvi M, Peres Y, Zazzi M, Sönnerborg A, Struck D, Altmann A, Kaiser R. Efficacy of antiretroviral therapy switch in HIV-infected patients: a 10-year analysis of the EuResist Cohort. Intervirology. 2012;55(2):160-6. doi: 10.1159/000332018. Epub 2012 Jan 24. PubMed PMID: 22286887.

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Zazzi M, Incardona F, Rosen-Zvi M, Prosperi M, Lengauer T, Altmann A, Sonnerborg A, Lavee T, Schülter E, Kaiser R. Predicting response to antiretroviral treatment by machine learning: the EuResist project. Intervirology. 2012;55(2):123-7. doi: 10.1159/000332008. Epub 2012 Jan 24. Review. PubMed PMID: 22286881.

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Kam-Thong T, Azencott CA, Cayton L, Pütz B, Altmann A, Karbalai N, Sämann PG, Schölkopf B, Müller-Myhsok B, Borgwardt KM. GLIDE: GPU-based linear regression for detection of epistasis. Hum Hered. 2012;73(4):220-36. doi: 10.1159/000341885. Epub 2012 Sep 4. PubMed PMID: 22965145.

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Altmann A, Weber P, Bader D, Preuss M, Binder EB, Müller-Myhsok B. A beginners guide to SNP calling from high-throughput DNA-sequencing data. Hum Genet. 2012 Oct;131(10):1541-54. doi: 10.1007/s00439-012-1213-z. Epub 2012 Aug 11. Review. PubMed PMID: 22886560.

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Quast C, Altmann A, Weber P, Arloth J, Bader D, Heck A, Pfister H, Müller-Myhsok B, Erhardt A, Binder EB. Rare variants in TMEM132D in a case-control sample for panic disorder. Am J Med Genet B Neuropsychiatr Genet. 2012 Dec;159B(8):896-907. doi: 10.1002/ajmg.b.32096. Epub 2012 Aug 22. PubMed PMID: 22911938.

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Altmann A, Quast C, Weber P. Detecting rare variants for psychiatric disorders using next generation sequencing: a methods primer. Curr Psychiatry Rep. 2013 Jan;15(1):333. doi: 10.1007/s11920-012-0333-4. PubMed PMID: 23250814.

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Pütz B, Kam-Thong T, Karbalai N, Altmann A, Müller-Myhsok B. Cost-effective GPU-grid for genome-wide epistasis calculations. Methods Inf Med. 2013;52(1):91-5. doi: 10.3414/ME11-02-0049. Epub 2012 Dec 7. PubMed PMID: 23223640.

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Mehta D, Klengel T, Conneely KN, Smith AK, Altmann A, Pace TW, Rex-Haffner M, Loeschner A, Gonik M, Mercer KB, Bradley B, Müller-Myhsok B, Ressler KJ, Binder EB. Childhood maltreatment is associated with distinct genomic and epigenetic profiles in posttraumatic stress disorder. Proc Natl Acad Sci U S A. 2013 May 14;110(20):8302-7. doi: 10.1073/pnas.1217750110. Epub 2013 Apr 29. PubMed PMID: 23630272; PubMed Central PMCID: PMC3657772.

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Quast C, Cuboni S, Bader D, Altmann A, Weber P, Arloth J, Röh S, Brückl T, Ising M, Kopczak A, Erhardt A, Hausch F, Lucae S, Binder EB. Functional coding variants in SLC6A15, a possible risk gene for major depression. PLoS One. 2013;8(7):e68645. doi: 10.1371/journal.pone.0068645. Print 2013. PubMed PMID: 23874702; PubMed Central PMCID: PMC3712998.

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Altmann A, Tian L, Henderson VW, Greicius MD. Sex modifies the APOE-related risk of developing Alzheimer disease. Ann Neurol. 2014 Apr;75(4):563-73. doi: 10.1002/ana.24135. Epub 2014 Apr 14. PubMed PMID: 24623176; PubMed Central PMCID: PMC4117990.

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Ungar L, Altmann A, Greicius MD. Apolipoprotein E, gender, and Alzheimer's disease: an overlooked, but potent and promising interaction. Brain Imaging Behav. 2014 Jun;8(2):262-73. doi: 10.1007/s11682-013-9272-x. Review. PubMed PMID: 24293121; PubMed Central PMCID: PMC4282773.

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Labermaier C, Kohl C, Hartmann J, Devigny C, Altmann A, Weber P, Arloth J, Quast C, Wagner KV, Scharf SH, Czibere L, Widner-Andrä R, Brenndörfer J, Landgraf R, Hausch F, Jones KA, Müller MB, Uhr M, Holsboer F, Binder EB, Schmidt MV. A polymorphism in the Crhr1 gene determines stress vulnerability in male mice. Endocrinology. 2014 Jul;155(7):2500-10. doi: 10.1210/en.2013-1986. Epub 2014 Apr 28. PubMed PMID: 24773341.

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Brenndörfer J, Altmann A, Widner-Andrä R, Pütz B, Czamara D, Tilch E, Kam-Thong T, Weber P, Rex-Haffner M, Bettecken T, Bultmann A, Müller-Myhsok B, Binder EE, Landgraf R, Czibere L. Connecting Anxiety and Genomic Copy Number Variation: A Genome-Wide Analysis in CD-1 Mice. PLoS One. 2015;10(5):e0128465. doi: 10.1371/journal.pone.0128465. eCollection 2015. PubMed PMID: 26011321; PubMed Central PMCID: PMC4444327.

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Arloth J, Bogdan R, Weber P, Frishman G, Menke A, Wagner KV, Balsevich G, Schmidt MV, Karbalai N, Czamara D, Altmann A, Trümbach D, Wurst W, Mehta D, Uhr M, Klengel T, Erhardt A, Carey CE, Conley ED, Ruepp A, Müller-Myhsok B, Hariri AR, Binder EB. Genetic Differences in the Immediate Transcriptome Response to Stress Predict Risk-Related Brain Function and Psychiatric Disorders. Neuron. 2015 Jun 3;86(5):1189-202. doi: 10.1016/j.neuron.2015.05.034. PubMed PMID: 26050039; PubMed Central PMCID: PMC4490780.

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Richiardi J, Altmann A, Milazzo AC, Chang C, Chakravarty MM, Banaschewski T, Barker GJ, Bokde AL, Bromberg U, Büchel C, Conrod P, Fauth-Bühler M, Flor H, Frouin V, Gallinat J, Garavan H, Gowland P, Heinz A, Lemaître H, Mann KF, Martinot JL, Nees F, Paus T, Pausova Z, Rietschel M, Robbins TW, Smolka MN, Spanagel R, Ströhle A, Schumann G, Hawrylycz M, Poline JB, Greicius MD. BRAIN NETWORKS. Correlated gene expression supports synchronous activity in brain networks. Science. 2015 Jun 12;348(6240):1241-4. doi: 10.1126/science.1255905. Epub 2015 Jun 11. PubMed PMID: 26068849; PubMed Central PMCID: PMC4829082.

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Arloth J, Bader DM, Röh S, Altmann A. Re-Annotator: Annotation Pipeline for Microarray Probe Sequences. PLoS One. 2015;10(10):e0139516. doi: 10.1371/journal.pone.0139516. eCollection 2015. PubMed PMID: 26426330; PubMed Central PMCID: PMC4591122.

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Altmann A, Ng B, Landau SM, Jagust WJ, Greicius MD. Regional brain hypometabolism is unrelated to regional amyloid plaque burden. Brain. 2015 Dec;138(Pt 12):3734-46. doi: 10.1093/brain/awv278. Epub 2015 Sep 29. PubMed PMID: 26419799; PubMed Central PMCID: PMC4806718.

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Altmann A, Schröter MS, Spoormaker VI, Kiem SA, Jordan D, Ilg R, Bullmore ET, Greicius MD, Czisch M, Sämann PG. Validation of non-REM sleep stage decoding from resting state fMRI using linear support vector machines. Neuroimage. 2016 Jan 15;125:544-555. doi: 10.1016/j.neuroimage.2015.09.072. Epub 2015 Oct 24. PubMed PMID: 26596551.

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Sadaghiani S, Ng B, Altmann A, Poline JB, Banaschewski T, Bokde ALW, Bromberg U, Büchel C, Burke Quinlan E, Conrod P, Desrivières S, Flor H, Frouin V, Garavan H, Gowland P, Gallinat J, Heinz A, Ittermann B, Martinot JL, Paillère Martinot ML, Lemaitre H, Nees F, Papadopoulos Orfanos D, Paus T, Poustka L, Millenet S, Fröhner JH, Smolka MN, Walter H, Whelan R, Schumann G, Napolioni V, Greicius M. Overdominant Effect of a CHRNA4 Polymorphism on Cingulo-Opercular Network Activity and Cognitive Control. J Neurosci. 2017 Oct 4;37(40):9657-9666. doi: 10.1523/JNEUROSCI.0991-17.2017. Epub 2017 Sep 6. PubMed PMID: 28877969; PubMed Central PMCID: PMC6596609.