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MPI-INF D3 Publications

MPI-INF D3 Publications

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Adams, David
Altucci, Lucia
Antonarakis, Stylianos E
Ballesteros, Juan
Beck, Stephan
Bird, Adrian
Bock, Christoph
Boehm, Bernhard
Campo, Elias
Caricasole, Andrea
Dahl, Fredrik
Dermitzakis, Emmanouil T
Enver, Tariq
Esteller, Manel
Estivill, Xavier
Ferguson-Smith, Anne
Fitzgibbon, Jude
Flicek, Paul
Giehl, Claudia
Graf, Thomas
Grosveld, Frank
Guigó, Roderic
Gut, Ivo
Helin, Kristian
Jarvius, Jonas
Küppers, Ralf
Lehrach, Hans
Lengauer, Thomas
Lernmark, Åke
Leslie, David
Loeffler, Markus
Macintyre, Elizabeth
Mai, Antonello
Martens, Joost H A
Minucci, Saverio
Ouwehand, Willem H
Pelicci, Pier Giuseppe
Pendeville, Hèléne
Porse, Bo
Rakyan, Vardhman
Reik, Wolf
Schrappe, Martin
Schübeler, Dirk
Seifert, Martin
Siebert, Reiner
Simmons, David
Soranzo, Nicole
Spicuglia, Salvatore
Stratton, Michael
Stunnenberg, Hendrik G
Tanay, Amos
Torrents, David
Valencia, Alfonso
Vellenga, Edo
Vingron, Martin
Walter, Jörn
Willcocks, Spike
BLUEPRINT to decode the epigenetic signature written in blood
In: Nature Biotechnology [30], 224-226
Alcaraz, Nicolas
Kucuk, Hande
Weile, Jochen
Wipat, Anil
Baumbach, Jan
KeyPathwayMiner - Detecting case-specific biological pathways by using expression data
In: Internet Mathematics [7], 299-313
Baumbach, JanIntegrative computational biology
In: Integrative Biology [4], 713-714
Beggel, Bastian
Neumann-Fraune, Maria
Doering, Matthias
Lawyer, Glenn
Kaiser, Rolf
Verheyen, Jens
Lengauer, Thomas
Genotyping hepatitis B virus dual infections using population-based sequence data
In: Journal of General Virology [9], 1899-1907
Bhattacharyya, Malay
Feuerbach, Lars
Bhadra, Tapas
Bandyopadhyay, Sanghamitra
MicroRNA Transcription Start Site Prediction with Multi-objective Feature Selection
In: Statistical Applications in Genetics and Molecular Biology [11], 6.1-6.25
Bock, ChristophAnalysing and interpreting DNA methylation data
In: Nature Reviews Genetics [13], 705-719
Bock, Christoph
Lengauer, Thomas
Epigenom-Karten erstellen und nutzen
In: BIOspektrum [18], 138-141
Bock, Christoph
Lengauer, Thomas
Managing drug resistance in cancer: lessons from HIV therapy
In: Nature Reviews Cancer [12], 494-501
Bogojeska, Jasmina
Lengauer, Thomas
Hierarchical Bayes Model for Predicting Effectiveness of HIV Combination Therapies
In: Statistical Applications in Genetics and Molecular Biology [11], 11.1-11.19
Bozek, Katarzyna
Eckhardt, Manon
Sierra, Saleta
Kaiser, Rolf
Kräusslich, Hans-Georg
Müller, Barbara
Lengauer, Thomas
An expanded model of HIV cell entry phenotype based on multi-parameter single-cell data
In: Retrovirology [9], 60.1-60.15
Calvanese, Vincenzo
Fernandez, Agustín F.
Urdinguio, Rocío G.
Suarez-Álvarez, Beatriz
Mangas, Cristina
Pérez-García, Vicente
Bueno, Clara
Montes, Rosa
Ramos-Mejía, Verónica
Martínez-Camblor, Pablo
Ferrero, Cecilia
Assenov, Yassen
Bock, Christoph
Menendez, Pablo
Carrera, Ana Clara
Lopez-Larrea, Carlos
Fraga, Mario F.
A promoter DNA demethylation landscape of human hematopoietic differentiation
In: Nucleic Acids Research [40], 116-131
Dietzen, Matthias
Zotenko, Elena
Hildebrandt, Andreas
Lengauer, Thomas
On the Applicability of Elastic Network Normal Modes in Small-Molecule Docking
In: Journal of Chemical Information and Modeling [52], 844-856
Doncheva, Nadezhda T
Assenov, Yassen
Domingues, Francisco S.
Albrecht, Mario
Topological analysis and interactive visualization of biological networks and protein structures
In: Nature Protocols [7], 670-685
Doncheva, Nadezhda T
Kacprowski, Tim
Albrecht, Mario
Recent approaches to the prioritization of candidate disease genes
In: Wiley Interdisciplinary Reviews: Systems Biology and Medicine [4], 429-442
Fernandez, Agustin F.
Assenov, Yassen
Martin-Subero, Jose Ignacio
Balint, Balazs
Siebert, Reiner
Taniguchi, Hiroaki
Yamamoto, Hiroyuki
Hidalgo, Manuel
Tan, Aik-Choon
Galm, Oliver
Ferrer, Isidre
Sanchez-Cespedes, Montse
Villanueva, Alberto
Carmona, Javier
Sanchez-Mut, Jose V.
Berdasco, Maria
Moreno, Victor
Capella, Gabriel
Monk, David
Ballestar, Esteban
Ropero, Santiago
Martinez, Ramon
Sanchez-Carbayo, Marta
Prosper, Felipe
Agirre, Xabier
Fraga, Mario F.
Gran˜a, Osvaldo
Perez-Jurado, Luis
Mora, Jaume
Puig, Susana
Prat, Jaime
Badimon, Lina
Puca, Annibale A.
Meltzer, Stephen J.
Lengauer, Thomas
Bridgewater, John
Bock, Christoph
Esteller, Manel
A DNA methylation fingerprint of 1628 human samples
In: Genome Research [22], 407-419
Garai, Ágnes
Zeke, András
Gógl, Gergo
Töro, Imre
Fördos, Ferenc
Blankenburg, Hagen
Bárkai, Tünde
Varga, János
Alexa, Anita
Emig, Dorothea
Albrecht, Mario
Reményi, Attila
Specificity of linear motifs that bind to a common mitogen-activated protein kinase docking groove
In: Science Signaling [5], ra74,1-ra74,14
Halachev, K.
Bast, H.
Albrecht, F.
Lengauer, Thomas
Bock, Christoph
EpiExplorer: live exploration and global analysis of large epigenomic datasets
In: Genome Biology [13], R96,1-R96,14
Heger, Eva
Thielen, Alexander
Gilles, Ramona
Obermeier, Martin
Lengauer, Thomas
Kaiser, Rolf
Trapp, Susanna
APOBEC3G/F a one possible driving source for co-receptor switch of the human immunodeficiency virus-1
In: Medical Microbiology and Immunology [201], 7-16
Lawyer, Glenn
Schülter, Eugen
Kaiser, Rolf
Reuter, Stefan
Oette, Mark
Lengauer, Thomas
Attachment IconEndogenous or exogenous spreading of HIV-1 in Nordrhein-Westfalen, Germany, investigated by phylodynamic analysis of the RESINA Study cohort
In: Medical Microbiology and Immunology [201], 259-269
Lengauer, ThomasBioinformatical Assistance of Selecting Anti-HIV Therapies: Where Do We Stand?
In: Intervirology [55], 108-112
Lengauer, Thomas
Bock, Christoph
Managing drug resistance in cancer: lessons from HIV therapy
In: Nature Reviews Cancer [12], 494-501
Mekhubad, Shila
Bock, Christoph
de Boer, A. Sophie
Kiskinis, Evangelos
Meissner, Alexander
Eggan, Kevin
Erosion of dosage compensation impacts human iPSC disease modeling
In: Cell Stem Cell [10], 595-609
Mikeska, Thomas
Bock, Christoph
Do, Hongdo
Dobrovic, Alexander
DNA methylation biomarkers in cancer: Progress towards clinical implementation
In: Expert Reviews of Molecular Diagnostics [12], 473-487
Obermeier, Martin
Pironti, Alejandro
Berg, Thomas
Braun, Patrick
Däumer, Martin
Eberle, Josef
Ehret, Robert
Kaiser, Rolf
Kleinkauf, Niels
Korn, Klaus
Kücherer, Claudia
Müller, Harm
Noah, Christian
Stürmer, Martin
Thielen, Alexander
Wolf, Eva
Walter, Hauke
HIV-GRADE: A Publicly Available, Rules-Based Drug Resistance Interpretation Algorithm Integrating Bioinformatic Knowledge
In: Intervirology [55], 102-107
Oette, Mark
Schulter, Eugen
Rosen-Zvi, Michal
Peres, Yardena
Zazzi, Maurizio
Sonnerborg, Anders
Struck, Daniel
Altmann, Andre
Kaiser, Rolf
Efficacy of antiretroviral therapy switch in HIV-infected patients: A 10-year analysis of the EuResist cohort
In: Intervirology [55], 160-166
Pauling, Josch
Röttger, Richard
Neuner, Andreas
Salgado, Heladia
Collado-Vides, Julio
Kalaghatgi, Prabhav
Azevedo, Vasco
Tauch, Andreas
Pühler, Alfred
Baumbach, Jan
On the trail of EHEC/EAEC - unraveling the gene regulatory networks of human pathogenic Escherichia coli bacteria
In: Integrative Biology [4], 728-733
Pauling, Josch
Röttger, Richard
Tauch, Andreas
Azevedo, Vasco
Baumbach, Jan
CoryneRegNet 6.0 - Updated database content, new analysis methods and novel features focusing on community demands
In: Nucleic Acids Research [40], D610-D614
Pfeifer, Nico
Lengauer, Thomas
Improving coreceptor usage prediction in the clinic using hints from next generation sequencing data
In: Bioinformatics [28], i589-i595
Pfeifer, Nico
Lengauer, Thomas
Attachment IconImproving HIV coreceptor usage prediction in the clinic using hints from next-generation sequencing data
In: Bioinformatics [28], i589-i595
Ramírez, Fidel
Lawyer, Glenn
Albrecht, Mario
Novel search method for the discovery of functional relationships
In: Bioinformatics [28], 269-276
Reuter, Stefan
Oette, Mark
Kaiser, Rolf
Lengauer, Thomas
Fätkenheuer, Gerd
Rockstroh, Jürgen
Knechten, Heribert
Häussinger, Dieter
Risk factors associated with older age in treatment-naive HIV-positive patients
In: Intervirology [55], 147-153
Röttger, Richard
Rueckert, Ulrich
Taubert, Jan
Baumbach, Jan
How Little Do We Actually Know? - On the Size of Gene Regulatory Networks.
In: IEEE/ACM transactions on computational biology and bioinformatics [9], 1293-1300
Rost, Burkhard
Gaasterland, Terry
Lengauer, Thomas
Linial, Michal
Markel, Scott
McKay, B. J. Morrison
Schneider, Reinhard
Horton, Paul
Kelso, Janet
Paving the future: finding suitable ISMB venues
In: Bioinformatics [28], 2556-2559
Setty, YakiMulti-scale computational modeling of developmental biology
In: Bioinformatics [28], 2022-2028
Simmer, Femke
Brinkman, Arie B.
Assenov, Yassen
Matarese, Filomena
Kaan, Anita
Sabatino, Lina
Villanueva, Alberto
Huertas, Dori
Esteller, Manel
Lengauer, Thomas
Bock, Christoph
Colantuoni, Vittorio
Altucci, Lucia
Stunnenberg, Henk G.
Comparative genome-wide DNA methylation analysis of colorectal tumor and matched normal tissues
In: Epigenetics [7], 1355-1367
Thielen, Alexander
Lengauer, Thomas
Geno2pheno[454]: A Web Server for the Prediction of HIV-1 Coreceptor Usage from Next-Generation Sequencing Data
In: Intervirology [55], 113-117
Welsch, Christoph
Schweizer, Sabine
Shimakami, Testsuro
Domingues, Francisco S.
Kim, Seungtaek
Lemon, Stanley, M.
Antes, Iris
Ketoamide Resistance and Hepatitis C Virus Fitness in Val55 Variants
of the NS3 Serine Protease
In: Antimicrobial Agents and Chemotherapy [56], 1907-1915
Welsch, Christoph
Shimakami, Tetsuro
Hartmann, Christoph
Yang, Yan
Domingues, Francisco S.
Lengauer, Thomas
Zeuzem, Stefan
Lemon, Stanley M.
Peptidomimetic Escape Mechanisms Arise via Genetic Diversity in the Ligand-Binding Site of the Hepatitis C Virus NS3/4A Serine Protease
In: Gastroenterology [142], 654-663
Xi, Yuanxin
Bock, Christoph
Müller, Fabian
Sun, Deqiang
Meissner, Alexander
Li, Wei
RRBSMAP: a fast, accurate and user-friendly alignment tool for reduced representation bisulfite sequencing
In: Bioinformatics [28], 430-432
Zazzi, Maurizio
Incardona, Francesca
Rosen-Zvi, Michal
Prosperi, Mattia
Lengauer, Thomas
Altmann, Andre
Sonnerborg, Anders
Lavee, Tamar
Schülter, Eugen
Kaiser, Rolf
Predicting Response to Antiretroviral Treatment by Machine Learning:
The EuResist Project
In: Intervirology [55], 123-127
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