Publications

 

This is a listing of published papers (PubMed, Google Scholar, ORCID). Articles marked with * appeared with the note “These authors contributed equally”. Scroll to the bottom of the list for articles that appeared as part of conference proceedings.

Journal Papers

  1. Sepideh Sadaghiani, Bernard Ng, Andre Altmann, Jean-Baptiste Poline, Tobias Banaschewski, Arun L.W. Bokde, Uli Bromberg, Christian Büchel, Erin Burke Quinlan, Patricia Conrod, Sylvane Desrivières, Herta Flor, Vincent Frouin, Hugh Garavan, Penny Gowland, Jürgen Gallinat, Andreas Heinz, Bernd Ittermann, Jean-Luc Martinot, Marie-Laure Paillère Martinot, Hervé Lemaitre, Frauke Nees, Dimitri Papadopoulos Orfanos, Tomáš Paus, Luise Poustka, Sabina Millenet, Juliane H. Fröhner, Michael N. Smolka, Henrik Walter, Robert Whelan, Gunter Schumann, Valerio Napolioni and Michael Greicius
    Overdominant effect of a CHRNA4 polymorphism on cingulo-opercular network activity and cognitive control
    Journal of Neuroscience, 2017, (in press)  doi: 10.1523/JNEUROSCI.0991-17.2017
  2. Andre Altmann*, Manuel S Schröter*, Victor I Spoormaker, Sara A Kiem, Denis Jordan, Rüdiger Ilg, Ed T Bullmore, Michael D Greicius, Michael Czisch, Philipp G Sämann
    Validation of non-REM sleep stage decoding from resting state fMRI using linear support vector machines
    NeuroImage, 2016, 125, 544-555. doi: 10.1016/j.neuroimage.2015.09.072
  3. Janine Arloth*, Daniel M Bader*, Simone Röh, Andre Altmann
    Re-Annotator: Annotation Pipeline for Microarray Probe Sequences
    PLoS ONE, 2015, 10(10): e0139516. doi:10.1371/journal.pone.0139516 [preprint @ bioRxiv]
  4. Andre Altmann, Bernard Ng, Susan Landau, William Jagust, Michael D Greicius
    Regional Brain Hypometabolism Is Unrelated to Regional Amyloid Plaque Burden
    Brain, 2015, 138 (12), 3743-3746. doi: 10.1093/brain/awv278
  5. Jonas Richiardi*, Andre Altmann*, Anna-Clare Milazzo, Catie Chang, M. Mallar Chakravarty, Tobias Banaschewski, Gareth J. Barker, Arun L.W. Bokde, Uli Bromberg, Christian Büchel, Patricia Conrod, Mira Fauth-Bühler, Herta Flor, Vincent Frouin, Jürgen Gallinat, Hugh Garavan, Penny Gowland, Andreas Heinz, Hervé Lemaître, Karl F. Mann, Jean-Luc Martinot, Frauke Nees, Tomáš Paus, Zdenka Pausova, Marcella Rietschel, Trevor W. Robbins, Michael N. Smolka, Rainer Spanagel, Andreas Ströhle, Gunter Schumann, Mike Hawrylycz, Jean-Baptiste Poline, Michael D. Greicius and the IMAGEN consortium
    Correlated gene expression supports synchronous activity in brain networks
    Science, 2015, 348 (6240),1241-1244. doi: 10.1126/science.1255905
  6. Janine Arloth, Ryan Bogdan, Peter Weber, Goar Frishman, Andreas Menke, Klaus V Wagner, Georgia Balsevich, Mathias V. Schmidt, Nazanin Karbalai, Darina Czamara, Andre Altmann, Dietrich Trümbach, Wolfgang Wurst, Divya Mehta, Manfred Uhr, Torsten Klengel, Angelika Erhardt, Caitlin E. Carey, Emily Drabant Conley, Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium (PGC), Andreas Ruepp, Bertram Müller-Myhsok, Ahmad R. Hariri, and Elisabeth B. Binder
    Genetic Differences in the Immediate Transcriptome Response to Stress Predict Risk-Related Brain Function and Psychiatric Disorders
    Neuron, 2015, 86(5):1189-1202. http://dx.doi.org/10.1016/j.neuron.2015.05.034
  7. Julia Brenndörfer, André Altmann, Regina Widner-Andrä, Benno Pütz, Darina Czamara, Erik Tilch, Tony Kam-Thong, Peter Weber, Monika Rex-Haffner, Thomas Bettecken, Andrea Bultmann, Bertram Müller-Myhsok, Elisabeth E Binder, Rainer Landgraf, Ludwig Czibere
    Connecting Anxiety and Genomic Copy Number Variation: a Genome-Wide Analysis in Mice
    PLoS ONE, 2015, 10(5):e0128465. doi: 10.1371/journal.pone.0128465.
  8. Andre Altmann, Lu Tian, Victor W Henderson, Michael D Greicius
    Sex modifies APOE-related risk of developing Alzheimer’s Disease
    Annals of Neurology, 2014, 75:563–573. doi: 10.1002/ana.24135
  9. Christiana Labermaier, Christine Kohl, Jakob Hartmann, Christian Devigny, Andre Altmann, Peter Weber, Janine Arloth, Carina Quast, Klaus V Wagner, Sebastian H Scharf, Ludwig Czibere, Regina Widner-Andrä, Julia Brenndörfer, Rainer Landgraf, Felix Hausch, Ken A Jones, Marianne B Müller, Manfred Uhr, Florian Holsboer, Elisabeth B Binder, Mathias V Schmidt
    A polymorphism in the crhr1 gene determines stress vulnerability in male mice
    Endocrinology, 2014, 155(7):2492–2499. doi: 10.1210/en.2013-1986
  10. Leo Unger, Andre Altmann, Michael D Greicius
    Apolipoprotein E, Gender, and Alzheimer’s Disease: An Overlooked, but Potent and Promising Interaction
    Brain Imaging and Behavior, 2014, 8(2):262-73. doi:10.1007/s11682-013-9272-x
  11. Carina Quast, Serena Cuboni, Daniel Bader, André Altmann, Peter Weber, Janine Arloth, Simone Röh, Tanja Brückl, Marcus Ising, Anna Kopczak, Angelika Erhardt, Felix Hausch, Susanne Lucae, Elisabeth Binder
    Functional coding variants in SLC6A15, a possible risk gene for major depression
    PLoS ONE, 2013, 8(7):e68645. doi:10.1371/journal.pone.0068645
  12. Divya Mehta, Torsten Klengel, Karen N Conneely, Alicia K Smith, Andre Altmann, Thaddeus W Pace, Monika Rex-Haffner, Anne Loeschner, Mariya Gonik, Kristina B Mercer, Bekh Bradley, Bertram Müller-Myhsok, Kerry J. Ressler, Elisabeth Binder
    Childhood maltreatment is associated with distinct genomic and epigenetic profiles in posttraumatic stress disorder
    PNAS, 2013, 110(20): 8302–7. doi: 10.1073/pnas.1217750110.
  13. Andre Altmann, Carina Quast, Peter Weber
    Detecting Rare Variants for Psychiatric Disorders Using Next Generation Sequencing: A Methods Primer
    Current Psychiatry Reports, 2012, 15:333. doi: 10.1007/s11920-012-0333-4
  14. Benno Puetz, Tony Kam-Thong, Nazanin Karbalai, Andre Altmann, Bertram Mueller-Myhsok
    Cost-effective GPU-Grid for Genome-wide Epistasis Calculations
    Methods of Information in Medicine, 2013, 53:93-97. doi: 10.3414/ME11-02-0049
  15. Andre Altmann, Peter Weber, Daniel Bader, Michael Preuss, Elisabeth B Binder, Bertram Mueller-Myhsok
    A Beginners Guide To SNP Calling From High-Throughput DNA-Sequencing Data
    Human Genetics, 2012, 131(10):1541-1554. doi: 10.1007/s00439-012-1213-z
  16. Carina Quast, Andre Altmann, Janine Arloth, Daniel Bader, Angela Heck, Hildegard Pfister, Bertram Mueller-Myhsok, Angelika Erhardt, Elisabeth B Binder
    Rare variants in TMEM132D in a case-control sample for panic disorder
    Am J Med Genet Part B, 2012, 159B(8):896-907. doi: 10.1002/ajmg.b.32096
  17. Tony Kam-Thong*, Chloe-Agathe Azencott*, Lawrence Cayton, Benno Puetz, Andre Altmann, Nazanin Karbalai, Philipp G Saemann, Bernhard Schoelkopf, Bertram Mueller-Myhsok+, Karsten M. Borgwardt+
    GLIDE: GPU-Based Linear Regression for Detection of Epistasis
    Hum Hered, 2012, 73:220-236. doi: 10.1159/000341885
  18. Mark Oette, Eugen Schülter, Michal Rosen-Zvi, Yardena Peres, Maurizio Zazzi, Anders Sönnerborg, Daniel Struck, Andre Altmann, Rolf Kaiser, the EuResist Network Study Group
    Efficacy of Antiretroviral Therapy Switch in HIV-Infected Patients: A 10-Year Analysis of the EuResist Cohort
    Intervirology, 2012, 55:160–166. doi:10.1159/000332018
  19. Maurizio Zazzi, Francesca Incardona, Michal Rosen-Zvi, Mattia Prosperi, Thomas Lengauer, Andre Altmann, Anders Sönnerborg, Tamar Lavee, Eugen Schülter, Rolf Kaiser
    Predicting Response to Antiretroviral treatment by Machine Learning: The EuResist Project
    Intervirology, 2012, 55:123–127. doi:10.1159/000332008
  20. Glenn Lawyer, Andre Altmann, Alexander Thielen, Maurizio Zazzi, Anders Sönnerborg, Thomas Lengauer
    HIV-1 mutational pathways under multidrug therapy
    AIDS Research and Therapy, 2011, 8:26. doi:10.1186/1742-6405-8-26
  21. Hiroto Saigo*, Andre Altmann*, Jasmina Bogojeska, Fabian Müller, Sebastian Nowozin, Thomas Lengauer
    Learning from past treatments and their outcome improves prediction of in vivo response to anti-HIV therapy
    Statistical Applications in Genetics and Molecular Biology, 2011, 10(1), art6. doi:10.2202/1544-6115.1604
  22. Mattia CF Prosperi, Michal Rosen-Zvi, Andre Altmann, Maurizio Zazzi, Simona Di Giambenedetto, Rolf Kaiser, Eugen Schülter, Daniel Struck, Peter Sloot, David A. van de Vijver, Anne-Mieke Vandamme, Anders Sönnerborg, for the EuResist and Virolab study groups
    Antiretroviral Therapy Optimisation without Genotype Resistance Testing: A Perspective on Treatment History Based Models
    PLoS ONE, 2010, 5:10, e13753. doi:10.1371/journal.pone.0013753
  23. Jasmina Bogojeska, Steffen Bickel, Andre Altmann, Thomas Lengauer
    Dealing with sparse data in predicting outcomes of HIV combination therapies
    Bioinformatics, 2010, 26:17, 2085-2092. doi:10.1093/bioinformatics/btq361
  24. Maurizio Zazzi, Rolf Kaiser, Anders Sönnerborg, Daniel Struck, Andre Altmann, Mattia Prosperi, Michal Rosen-Zvi, Andrea Petroczi, Yardena Peres, Eugen Schülter, Charles Boucher, Francoise Brun-Vezinet, Richard Harigan, Lynn Morris, Martin Obermeier, Carlo Federico Perno, Robert Shafer, Anne-Mieke Vandamme, Kristel van Laethem, Annemarie Wensing, Thomas Lengauer, Francesca Incardona
    Prediction of Response to Antiretroviral Therapy by Human Experts and by the EuResist Data-Driven Expert System (the EVE Study)
    HIV Medicine, 2010. doi:10.1111/j.1468-1293.2010.00871.x
  25. Andre Altmann*, Laura Tolosi*, Oliver Sander, Thomas Lengauer
    Permutation importance: a corrected feature importance measure
    Bioinformatics, 2010, 26:10, 1340-1347. doi:10.1093/bioinformatics/btq134
    Pre-Print PDF Supplementary material Source Code
  26. Hendrik Weisser, Andre Altmann, Saleta Sierra, Francesca Incardona, Daniel Struck, Anders Sönnerborg, Rolf Kaiser, Maurizio Zazzi, Monika Tschochner, Hauke Walter, Thomas Lengauer
    Only slight impact of predicted replicative capacity for therapy response prediction
    PLoS ONE, 2010, 5:2, e9044. doi:10.1371/journal.pone.0009044
  27. Thomas Lengauer, Andre Altmann, Alexander Thielen, Rolf Kaiser
    Chasing the AIDS virus
    Communications of the ACM, 2010, 53:3, 66-74. doi:10.1145/1666420.1666440
  28. Thomas Lengauer, Andre Altmann, Alexander Thielen
    Bioinformatische Unterstützung der Auswahl von HIV-Therapien
    Informatik-Spektrum, 2009, 32:4, 320-331. doi:10.1007/s00287-009-0352-7
  29. Nadine Sichtig, Saleta Sierra, Rolf Kaiser, Martin Däumer, Stefan Reuter, Eugen Schülter, Andre Altmann, Gerd Fätkenheuer, Ulf Dittmer, Herbert Pfister, Stefan Esser
    Evolution of Raltegravir Resistance During Therapy
    Journal of Antimicrobial Chemotherapy, 2009, 64, 25-32. doi:10.1093/jac/dkp153
  30. Mattia CF Prosperi, Andre Altmann, Michal Rosen-Zvi, Ehud Aharoni, Gabor Borgulya, Fulop Bazso, Anders Sönnerborg, Yarenda Peres, Eugen Schülter, Daniel Struck, Giovanni Ulivi, Francesca Incardona, Anne-Mieke Vandamme, Jürgen Vercauteren and Maurizio Zazzi for the EuResist and Virolab study groups
    Investigation of Expert Rule Bases, Logistic Regression, and Non-Linear Machine Learning Techniques for Predicting Response to Antiretroviral Treatment
    Antiviral Thearapy, 2009, 14: 433-442.
  31. Andre Altmann*, Tobias Sing*, Hans Vermeiren, Bart Winters, Elke Van Craenenbroeck, Koen Van der Borght, Soo-Yon Rhee, Robert W Shafer, Eugen Schülter, Rolf Kaiser, Yardena Peres, Anders Sönnerborg, W Jeffrey Fessel, Francesca Incardona, Maurizio Zazzi, Lee Bacheler, Herman Van Vlijmen, Thomas Lengauer
    Advantages of Predicted Phenotypes and Statistical Learning Models in Inferring Virological Response to Antiretroviral Therapy from HIV Genotype
    Antiviral Thearapy, 2009, 14: 273-283.
  32. Andre Altmann, Martin Däumer, Niko Beerenwinkel, Yardena Peres, Eugen Schülter, Joachim Büch, Soo-Yon Rhee, Anders Sönnerborg, Jeffrey Fessel, Robert W Shafer, Maurizio Zazzi, Rolf Kaiser and Thomas Lengauer
    Predicting response to combination antiretroviral therapy: retrospective validation of geno2pheno-THEO on a large clinical database
    Journal of Infectious Diseases, 2009, 199(7), 999-1006.
  33. Andre Altmann, Michal Rosen-Zvi , Mattia Prosperi, Ehud Aharoni, Hani Neuvirth, Anders Sönnerborg, Eugen Schülter, Joachim Büch, Daniel Struck, Yardena Peres, Francesca Incardona, Rolf Kaiser, Maurizio Zazzi and Thomas Lengauer
    Comparison of Classifier Fusion Methods for Predicting Response to Anti HIV-1 Therapy
    PLoS ONE, 2008, 3(10): e3470.
  34. Jasmina Bogojeska, Adrian Alexa, Andre Altmann, Thomas Lengauer and Jörg Rahnenführer
    Rtreemix: an R package for estimating evolutionary pathways and genetic progression scores
    Bioinformatics, 2008, 24 (20): 2391.
  35. Andre Altmann, Niko Beerenwinkel, Tobias Sing, Igor Savenkov, Martin Däumer, Rolf Kaiser, Soo-Yon Rhee, W Jeffrey Fessel, Robert W Shafer and Thomas Lengauer
    Improved prediction of response to antiretroviral combination therapy using the genetic barrier to drug resistance
    Antiviral Therapy, 2007, 12 (2):169-178.

Conference Papers

  1. Marco Lorenzi, Boris Gutman, Paul M Thompson, Daniel C Alexander, Sebastien Ourselin, Andre Altmann
    Secure multivariate large-scale multi-centric analysis through on-line learning: an imaging genetics case study
    12th International Symposium on Medical Information Processing and Analysis (SIPAIM 2016), 2016. doi: 10.1117/12.2256799
  2. Marco Lorenzi, Boris Gutman, Derrek P Hibar, Andre Altmann, Neda Jahanashad, Paul M Thompson, Sebastien Ourselin
    Partial Least Squares Modelling For Imaging-Genetics in Alzheimer’s Disease: Plausibility and Generalization
    International Symposium on Biomedical Imaging (ISBI 2016), 2016. doi: 10.1109/ISBI.2016.7493396
  3. Bernard Ng, Anna-Claire Milazzo, Andre Altmann
    Node-based Gaussian Graphical Model for Identifying Discriminative Brain Regions from Connectivity Graphs
    Machine Learning in Medical Imaging, Lecture Notes in Computer Science, 2015, 9352:44-51. doi:10.1007/978-3-319-24888-2_6
    Best Paper Award!
  4. Andre Altmann, Bernard Ng
    Joint Feature Extraction from Functional Connectivity Graphs with Multi-task Feature Learning
    PRNI 2015, 2015. doi:10.1109/PRNI.2015.17
  5. Jonas Richiardi, Andre Altmann, Michael Greicius
    Two test statistics for cross-modal graph community significance [pdf]
    PRNI 2013, 2013. doi:10.1109/PRNI.2013.27
  6. Andre Altmann, Peter Weber, Carina Quast, Monika Rex-Haffner, Elisabeth B Binder, Bertram Müller-Myhsok
    vipR: variant identification in pooled DNA using R
    Bioinformatics, 2011, 27 (13):i77-84. doi:10.1093/bioinformatics/btr205
  7. Juliane Perner , Andre Altmann and Thomas Lengauer
    Semi-Supervised Learning for Improving Prediction of HIV Drug Resistance
    Lecture Notes in Informatics (Proceedings of GCB2009, 2009
  8. Michal Rosen-Zvi , Andre Altmann, Mattia Prosperi, Ehud Aharoni, Hani Neuvirth, Anders Sönnerborg, Eugen Schülter, Daniel Struck, Yardena Peres, Francesca Incardona, Rolf Kaiser, Maurizio Zazzi and Thomas Lengauer
    Selecting anti-HIV therapies based on a variety of genomic and clinical factors
    Bioinformatics, 2008, 24 (13):i399-406.

Preprints

  1. Janine Arloth, Daniel M Bader, Simone Röh, Andre Altmann
    Re-Annotator: Annotation Pipeline for Microarrays
    bioRxiv, 2015, doi:10.1101/019596

Book Chapters

  1. Andre Altmann, Peter Weber
    Targeted Re-Sequencing in Psychiatric Disorders
    in Applied Neurogenomics, Series: Neuromethods, Vol. 97, Springer 2015 Editor: Jain, Kewal K.

Theses

  1. Andre Altmann
    Bioinformatical Approaches to Ranking of anti-HIV Therapies and Planning of Treatment Schedules
    PhD Thesis, Saarland University, Saarbrücken, Germany, 2010.
  2. Andre Altmann
    Lattice Rescoring and Log-Linear System Combination
    Diploma Thesis, RWTH Aaachen, Aachen, Germany, 2005.
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