Niko Beerenwinkel
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Why Is Niko Beerenwinkel Influential?
(Suggest an Edit or Addition)According to Wikipedia, Niko Beerenwinkel, Ph.D. , is a German mathematician, who is active in the field of computational biology; he is an associate professor of the ETH Zurich since April 2013. Awards Otto Hahn Medal - Max Planck Society ;Emmy Noether Fellowship - German National Science Foundation.
Niko Beerenwinkel's Published Works
Number of citations in a given year to any of this author's works
Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author
Published Works
- ROCR: visualizing classifier performance in R (2005) (2754)
- Comparative lesion sequencing provides insights into tumor evolution (2008) (771)
- Neutrophils escort circulating tumour cells to enable cell cycle progression (2019) (615)
- Eleven grand challenges in single-cell data science (2020) (553)
- Genetic Progression and the Waiting Time to Cancer (2007) (408)
- Microbiome interactions shape host fitness (2018) (317)
- Cancer Evolution: Mathematical Models and Computational Inference (2014) (284)
- ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data (2011) (279)
- Diversity and complexity of HIV-1 drug resistance: A bioinformatics approach to predicting phenotype from genotype (2002) (259)
- Geno2pheno: estimating phenotypic drug resistance from HIV-1 genotypes (2003) (256)
- Viral Population Estimation Using Pyrosequencing (2007) (243)
- Reliable detection of subclonal single-nucleotide variants in tumour cell populations (2012) (226)
- Challenges and opportunities in estimating viral genetic diversity from next-generation sequencing data (2012) (223)
- Tree inference for single-cell data (2016) (221)
- Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies (2010) (208)
- From hype to reality: data science enabling personalized medicine (2018) (203)
- The Common Gut Microbe Eubacterium hallii also Contributes to Intestinal Propionate Formation (2016) (188)
- Predicting HIV Coreceptor Usage on the Basis of Genetic and Clinical Covariates (2007) (181)
- Ultra-deep sequencing for the analysis of viral populations. (2011) (176)
- Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020 (2020) (163)
- Clonal evolution of acute myeloid leukemia revealed by high-throughput single-cell genomics (2020) (156)
- Learning multiple evolutionary pathways from cross-sectional data (2004) (142)
- 24 Hours in the Life of HIV-1 in a T Cell Line (2013) (138)
- Probabilistic Inference of Viral Quasispecies Subject to Recombination (2012) (137)
- Single-cell sequencing data reveal widespread recurrence and loss of mutational hits in the life histories of tumors (2017) (134)
- Full-length haplotype reconstruction to infer the structure of heterogeneous virus populations (2014) (123)
- Advances in understanding tumour evolution through single-cell sequencing* (2017) (116)
- Computational methods for the design of effective therapies against drug resistant HIV strains (2005) (111)
- BitPhylogeny: a probabilistic framework for reconstructing intra-tumor phylogenies (2015) (111)
- Quantifying cancer progression with conjunctive Bayesian networks (2009) (109)
- Deep Sequencing of a Genetically Heterogeneous Sample: Local Haplotype Reconstruction and Read Error Correction (2009) (105)
- The Temporal Order of Genetic and Pathway Alterations in Tumorigenesis (2011) (105)
- Trophic Interactions of Infant Bifidobacteria and Eubacterium hallii during L-Fucose and Fucosyllactose Degradation (2017) (100)
- Network-based integration of multi-omics data for prioritizing cancer genes (2018) (99)
- Viral Quasispecies Assembly via Maximal Clique Enumeration (2014) (98)
- Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research (2020) (96)
- Integrative inference of subclonal tumour evolution from single-cell and bulk sequencing data (2017) (96)
- Estimating HIV evolutionary pathways and the genetic barrier to drug resistance. (2005) (94)
- Conjunctive Bayesian networks (2006) (91)
- Mtreemix: a software package for learning and using mixture models of mutagenetic trees (2005) (89)
- HIV Haplotype Inference Using a Propagating Dirichlet Process Mixture Model (2014) (88)
- Determinants of HIV-1 reservoir size and long-term dynamics during suppressive ART (2019) (83)
- Involvement of Novel Human Immunodeficiency Virus Type 1 Reverse Transcriptase Mutations in the Regulation of Resistance to Nucleoside Inhibitors (2006) (81)
- Modeling Mutual Exclusivity of Cancer Mutations (2014) (79)
- Genome-Scale CRISPR Screening in Human Intestinal Organoids Identifies Drivers of TGF-β Resistance. (2020) (79)
- αV-class integrins exert dual roles on α5β1 integrins to strengthen adhesion to fibronectin (2017) (78)
- Recent advances in inferring viral diversity from high-throughput sequencing data. (2017) (78)
- Single-Cell RNA-Seq Reveals Transcriptional Heterogeneity in Latent and Reactivated HIV-Infected Cells. (2018) (77)
- Tenofovir Resistance and Resensitization (2003) (76)
- Detection of SARS-CoV-2 variants in Switzerland by genomic analysis of wastewater samples (2021) (72)
- Dynamics of HIV Latency and Reactivation in a Primary CD4+ T Cell Model (2014) (72)
- EPISTASIS AND SHAPES OF FITNESS LANDSCAPES (2006) (70)
- Analysis of epistatic interactions and fitness landscapes using a new geometric approach (2007) (66)
- Analysis of HIV-1 Expression Level and Sense of Transcription by High-Throughput Sequencing of the Infected Cell (2011) (66)
- Competition-colonization dynamics in an RNA virus (2010) (64)
- Estimating cancer survival and clinical outcome based on genetic tumor progression scores (2005) (64)
- Single-cell mutation identification via phylogenetic inference (2018) (62)
- Computational approaches for the identification of cancer genes and pathways (2016) (62)
- Next-Generation Sequencing of HIV-1 RNA Genomes: Determination of Error Rates and Minimizing Artificial Recombination (2013) (61)
- Predicting the response to combination antiretroviral therapy: retrospective validation of geno2pheno-THEO on a large clinical database. (2009) (60)
- Read length versus Depth of Coverage for Viral Quasispecies Reconstruction (2012) (60)
- Improved Prediction of Response to Antiretroviral Combination Therapy using the Genetic Barrier to Drug Resistance (2006) (60)
- Methods for optimizing antiviral combination therapies (2003) (59)
- Context-dependent deposition and regulation of mRNAs in P-bodies (2017) (55)
- TiMEx: a waiting time model for mutually exclusive cancer alterations (2015) (54)
- Genomic Profiling of Advanced-Stage Oral Cancers Reveals Chromosome 11q Alterations as Markers of Poor Clinical Outcome (2011) (54)
- Structure-function relationships of HDL in diabetes and coronary heart disease. (2019) (53)
- Markov models for accumulating mutations (2007) (53)
- Patients with high-grade gliomas harboring deletions of chromosomes 9p and 10q benefit from temozolomide treatment. (2005) (53)
- Spatial structure governs the mode of tumour evolution (2019) (53)
- Geno2pheno: Interpreting Genotypic HIV Drug Resistance Tests (2001) (53)
- A Hierarchical Regulatory Landscape during the Multiple Stages of EMT. (2019) (53)
- Challenges in RNA virus bioinformatics (2014) (51)
- Computational Cancer Biology: An Evolutionary Perspective (2016) (49)
- Accurate single nucleotide variant detection in viral populations by combining probabilistic clustering with a statistical test of strand bias (2013) (49)
- Evolution on distributive lattices. (2005) (48)
- Bioinformatics for precision oncology (2017) (46)
- Kinetic, energetic, and mechanical differences between dark-state rhodopsin and opsin. (2013) (45)
- Application of oncogenetic trees mixtures as a biostatistical model of the clonal cytogenetic evolution of meningiomas (2007) (43)
- Chromosomal Alterations and Gene Expression Changes Associated with the Progression of Leukoplakia to Advanced Gingivobuccal Cancer (2017) (43)
- Expression and Mutation Patterns of PBRM1, BAP1 and SETD2 Mirror Specific Evolutionary Subtypes in Clear Cell Renal Cell Carcinoma1 (2019) (42)
- Simultaneous analysis of large-scale RNAi screens for pathogen entry (2014) (42)
- V-pipe: a computational pipeline for assessing viral genetic diversity from high-throughput data (2021) (40)
- Sequencing approach to analyze the role of quasispecies for classical swine fever. (2013) (40)
- Cell selection as driving force in lung and colon carcinogenesis. (2010) (40)
- Detailed simulation of cancer exome sequencing data reveals differences and common limitations of variant callers (2017) (40)
- Predicting cancer type from tumour DNA signatures (2017) (39)
- Characterization of Novel HIV Drug Resistance Mutations Using Clustering, Multidimensional Scaling and SVM-Based Feature Ranking (2005) (39)
- A mutagenetic tree hidden Markov model for longitudinal clonal HIV sequence data. (2006) (38)
- Learning Mixtures of Localized Rules by Maximizing the Area Under the ROC Curve (2004) (38)
- Clonal hematopoiesis in donors and long-term survivors of related allogeneic hematopoietic stem cell transplantation. (2020) (37)
- Genome‐wide expression and copy number analysis identifies driver genes in gingivobuccal cancers (2012) (35)
- gespeR: a statistical model for deconvoluting off-target-confounded RNA interference screens (2015) (34)
- The BET protein FSH functionally interacts with ASH1 to orchestrate global gene activity in Drosophila (2013) (34)
- Automated Design of Synthetic Cell Classifier Circuits Using a Two-Step Optimization Strategy. (2017) (33)
- Tracing Clonal Dynamics Reveals that Two- and Three-dimensional Patient-derived Cell Models Capture Tumor Heterogeneity of Clear Cell Renal Cell Carcinoma. (2019) (32)
- The Tumor Profiler Study: integrated, multi-omic, functional tumor profiling for clinical decision support. (2021) (32)
- Single-cell copy number calling and event history reconstruction (2020) (31)
- A Framework for Inferring Fitness Landscapes of Patient-Derived Viruses Using Quasispecies Theory (2014) (30)
- Simultaneous Integration of Multi-omics Data Improves the Identification of Cancer Driver Modules. (2019) (30)
- Stable coreceptor usage of HIV in patients with ongoing treatment failure on HAART. (2006) (30)
- Quantification of the spread of SARS-CoV-2 variant B.1.1.7 in Switzerland (2021) (29)
- Waiting Time Models of Cancer Progression (2008) (29)
- Inferring genetic interactions from comparative fitness data (2017) (28)
- Clinicopathological and prognostic implications of genetic alterations in oral cancers. (2011) (28)
- The Tumor Profiler Study: Integrated, multi-omic, functional tumor profiling for clinical decision support (2020) (27)
- Construction of oncogenetic tree models reveals multiple pathways of oral cancer progression (2009) (27)
- Models of RNA virus evolution and their roles in vaccine design (2010) (27)
- Single-Molecule Sequencing Reveals Complex Genome Variation of Hepatitis B Virus during 15 Years of Chronic Infection following Liver Transplantation (2016) (27)
- Finding Dense Subgraphs in Relational Graphs (2015) (27)
- pathTiMEx: Joint Inference of Mutually Exclusive Cancer Pathways and Their Progression Dynamics (2017) (26)
- NGS-pipe: a flexible, easily extendable and highly configurable framework for NGS analysis (2017) (26)
- A Comprehensive Analysis of Primer IDs to Study Heterogeneous HIV-1 Populations. (2016) (26)
- Detection and surveillance of SARS-CoV-2 genomic variants in wastewater (2021) (25)
- Early detection and surveillance of SARS-CoV-2 genomic variants in wastewater using COJAC (2022) (25)
- The Individualized Genetic Barrier Predicts Treatment Response in a Large Cohort of HIV-1 Infected Patients (2013) (25)
- Mutational interactions define novel cancer subgroups (2017) (25)
- Ensemble outlier detection and gene selection in triple-negative breast cancer data (2018) (25)
- Evolution of HIV resistance during treatment interruption in experienced patients and after restarting a new therapy. (2005) (25)
- HIV-Haplotype Inference using a Constraint-based Dirichlet Process Mixture Model (2010) (24)
- Correction: Context-dependent deposition and regulation of mRNAs in P-bodies (2018) (24)
- High-dimensional microbiome interactions shape host fitness (2017) (22)
- Evolutionary Games with Affine Fitness Functions: Applications to Cancer (2011) (22)
- Data and text mining ROCR : visualizing classifier performance in R (2005) (22)
- Estimating Fitness of Viral Quasispecies from Next-Generation Sequencing Data. (2016) (21)
- Efficient sampling for Bayesian inference of conjunctive Bayesian networks (2012) (21)
- Identification of Constrained Cancer Driver Genes Based on Mutation Timing (2015) (21)
- Genetic polymorphisms associated with smoking behaviour predict the risk of surgery in patients with Crohn's disease (2018) (20)
- Identification and Validation of a Biomarker Signature in Patients With Resectable Pancreatic Cancer via Genome-Wide Screening for Functional Genetic Variants. (2019) (20)
- NEMix: Single-cell Nested Effects Models for Probabilistic Pathway Stimulation (2015) (20)
- Estimating the predictability of cancer evolution (2019) (20)
- Arevir: A Secure Platform for Designing Personalized Antiretroviral Therapies Against HIV (2006) (20)
- Selective Pressures of HLA Genotypes and Antiviral Therapy on Human Immunodeficiency Virus Type 1 Sequence Mutation at a Population Level (2007) (19)
- CMOST: an open-source framework for the microsimulation of colorectal cancer screening strategies (2017) (19)
- Sulforaphane Preconditioning Sensitizes Human Colon Cancer Cells towards the Bioreductive Anticancer Prodrug PR-104A (2016) (18)
- Proteo-Transcriptomic Dynamics of Cellular Response to HIV-1 Infection (2019) (18)
- Within-patient genetic diversity of SARS-CoV-2 (2020) (18)
- SwissMTB: establishing comprehensive molecular cancer diagnostics in Swiss clinics (2018) (17)
- Limb-Enhancer Genie: An accessible resource of accurate enhancer predictions in the developing limb (2017) (17)
- Unlocking capacities of genomics for the COVID-19 response and future pandemics (2022) (16)
- A Genome-Wide siRNA Screen Implicates Spire1/2 in SipA-Driven Salmonella Typhimurium Host Cell Invasion (2016) (16)
- A switch in transcription and cell fate governs the onset of an epigenetically-deregulated tumor in Drosophila (2018) (15)
- Viral Diversity Based on Next-Generation Sequencing of HIV-1 Provides Precise Estimates of Infection Recency and Time Since Infection. (2019) (15)
- Genomic variant annotation workflow for clinical applications. (2016) (15)
- Computational Model Reveals a Stochastic Mechanism behind Germinal Center Clonal Bursts (2020) (15)
- Quantifying SARS-CoV-2 spread in Switzerland based on genomic sequencing data (2020) (14)
- Learning Monotonic Genotype-Phenotype Maps (2011) (14)
- Model Selection for Mixtures of Mutagenetic Trees (2006) (14)
- HIV-1 RNAs are Not Part of the Argonaute 2 Associated RNA Interference Pathway in Macrophages (2015) (14)
- Stability of gene rankings from RNAi screens (2012) (13)
- Covering Pairs in Directed Acyclic Graphs (2013) (13)
- BMix: probabilistic modeling of occurring substitutions in PAR-CLIP data (2015) (13)
- Visualizing the Performance of Scoring Classifiers [R package ROCR version 1.0-11] (2020) (13)
- Large-scale inference of conjunctive Bayesian networks (2016) (12)
- 12 Grand Challenges in Single-Cell Data Science (2019) (12)
- Bayesian Structure Learning and Sampling of Bayesian Networks with the R Package BiDAG (2021) (12)
- Competition–colonization trade-off promotes coexistence of low-virulence viral strains (2011) (12)
- Predicting colorectal cancer risk from adenoma detection via a two-type branching process model (2020) (12)
- Exome sequencing of healthy phenotypic extremes links TROVE2 to emotional memory and PTSD (2017) (12)
- Transcriptomic responses of cancerous and noncancerous human colon cells to sulforaphane and selenium. (2014) (11)
- Dynamic models of viral replication and latency (2015) (11)
- Ectopic expression of Msx2 in mammalian myotubes recapitulates aspects of amphibian muscle dedifferentiation. (2015) (11)
- A mathematical model of the metastatic bottleneck predicts patient outcome and response to cancer treatment (2020) (11)
- Inferring modulators of genetic interactions with epistatic nested effects models (2017) (11)
- Host factor prioritization for pan-viral genetic perturbation screens using random intercept models and network propagation (2020) (11)
- Single cell network analysis with a mixture of Nested Effects Models (2018) (11)
- Binding Profiles of Chromatin-Modifying Proteins Are Predictive for Transcriptional Activity and Promoter-Proximal Pausing (2012) (10)
- Competition-colonization dynamics (2010) (10)
- Multiple Sequence Alignment System for Pyrosequencing Reads (2009) (10)
- The Evolution of Virulence in RNA Viruses under a Competition–Colonization Trade-Off (2010) (10)
- Spatial Distribution of Private Gene Mutations in Clear Cell Renal Cell Carcinoma (2021) (10)
- Drug-induced resistance evolution necessitates less aggressive treatment (2020) (10)
- Functional Analysis Identifies Damaging CHEK2 Missense Variants Associated with Increased Cancer Risk (2021) (9)
- Erratum to: gespeR: a statistical model for deconvoluting off-target-confounded RNA interference screens (2015) (9)
- V-pipe: a computational pipeline for assessing viral genetic diversity from high-throughput sequencing data (2020) (9)
- Geno2pheno is predictive of short-term virological response (2002) (9)
- Computational analysis of HIV drug resistance data (2004) (8)
- Mutagenetic tree Fisher kernel improves prediction of HIV drug resistance from viral genotype (2006) (8)
- Algebraic Statistics for Computational Biology: Mutagenetic Tree Models (2005) (8)
- Geno2pheno[coreceptor]: a Tool for Predicting Coreceptor Usage from Genotype and for Monitoring Coreceptor-associated Sequence Alterations (2005) (7)
- Improved pathway reconstruction from RNA interference screens by exploiting off-target effects (2018) (7)
- Discovery of synthetic lethal interactions from large-scale pan-cancer perturbation screens (2019) (7)
- Abdominal pain in patients with inflammatory bowel disease: association with single-nucleotide polymorphisms prevalent in irritable bowel syndrome and clinical management (2021) (7)
- BnpC: Bayesian non-parametric clustering of single-cell mutation profiles (2020) (7)
- [Epidemiology of primary drug resistance in chronically HIV-infected patients in Nordrhein-Westfalen, Germany, 2001-2005]. (2007) (7)
- Clustering time series gene expression data with TMixClust (2018) (6)
- Inferring transmission fitness advantage of SARS-CoV-2 variants of concern from wastewater samples using digital PCR, Switzerland, December 2020 through March 2021 (2022) (6)
- Exact likelihood computation in Boolean networks with probabilistic time delays, and its application in signal network reconstruction (2014) (6)
- ModulOmics: Integrating Multi-Omics Data to Identify Cancer Driver Modules (2018) (6)
- Multi-omics data integration reveals novel drug targets in hepatocellular carcinoma (2021) (6)
- Genomic variant annotation workflow for clinical applications (2016) (6)
- Recurring Amplification at 11q22.1-q22.2 Locus Plays an Important Role in Lymph Node Metastasis and Radioresistance in OSCC (2017) (6)
- Probability, statistics, and computational science. (2012) (5)
- Estimating HIV-1 Fitness Characteristics from Cross-Sectional Genotype Data (2014) (5)
- Inferring signalling dynamics by integrating interventional with observational data (2019) (5)
- Quantitative measures of within-host viral genetic diversity. (2021) (5)
- pathTiMEx: Joint Inference of Mutually Exclusive Cancer Pathways and Their Dependencies in Tumor Progression (2016) (5)
- Involvement of novel HIV-1 reverse transcriptase mutations in the highly ordered regulation of NRTI resistance (2005) (5)
- Evaluating key characteristics of ideal colorectal cancer screening modalities: the microsimulation approach. (2021) (5)
- A statistical test on single-cell data reveals widespread recurrent mutations in tumor evolution (2016) (5)
- Identifying drug resistance-associated patterns in HIV genotypes (2001) (5)
- Myeloid differentiation primary response gene (MyD) 88 signalling is not essential for intestinal fibrosis development (2017) (5)
- Statistical tests for intra-tumour clonal co-occurrence and exclusivity (2021) (5)
- The geometry of partial fitness orders and an efficient method for detecting genetic interactions (2017) (5)
- The Bourque distances for mutation trees of cancers (2020) (5)
- Intra-tumor heterogeneity and clonal exclusivity in renal cell carcinoma (2018) (4)
- Establishing standardized immune phenotyping of metastatic melanoma by digital pathology (2021) (4)
- PyBDA: a command line tool for automated analysis of big biological data sets (2019) (4)
- Correction: 24 Hours in the Life of HIV-1 in a T Cell Line (2015) (4)
- SCIΦ: Single-cell mutation identification via phylogenetic inference (2018) (4)
- Linear effects models of signaling pathways from combinatorial perturbation data (2016) (4)
- Single-cell mutation identification via phylogenetic inference (2018) (4)
- Single-cell mutation calling and phylogenetic tree reconstruction with loss and recurrence (2022) (4)
- Clonal evolution driven by superdriver mutations (2020) (4)
- SIEVE: joint inference of single-nucleotide variants and cell phylogeny from single-cell DNA sequencing data (2022) (4)
- Quantitative phenotype prediction by support vector machines (2002) (4)
- scAmpi—A versatile pipeline for single-cell RNA-seq analysis from basics to clinics (2021) (4)
- Learning epistatic gene interactions from perturbation screens (2020) (4)
- Swiss public health measures associated with reduced SARS-CoV-2 transmission using genome data (2021) (4)
- Host genomics of the HIV-1 reservoir size and its decay rate during suppressive antiretroviral treatment. (2020) (3)
- Parametric inference of recombination in HIV genomes (2005) (3)
- Publisher Correction: Clonal evolution of acute myeloid leukemia revealed by high-throughput single-cell genomics (2020) (3)
- The International Virus Bioinformatics Meeting 2020 (2020) (3)
- Addressing the Computational Challenges of Personalized Medicine (Dagstuhl Seminar 17472) (2017) (3)
- Hierarchy of TGFβ/SMAD, Hippo/YAP/TAZ, and Wnt/β-catenin signaling in melanoma phenotype switching (2021) (3)
- Structured hierarchical models for probabilistic inference from perturbation screening data (2019) (3)
- Computational Methods for Viral Quasispecies Assembly (2021) (3)
- Discovering gene regulatory networks of multiple phenotypic groups using dynamic Bayesian networks (2021) (3)
- Host genomics of the HIV-1 reservoir size and its decay rate during suppressive antiretroviral treatment (2019) (3)
- GATA3 and MDM2 are synthetic lethal in estrogen receptor-positive breast cancers (2020) (3)
- Inferring Transmission Fitness Advantage of SARS-CoV-2 Variants of Concern in Wastewater Using Digital PCR (2021) (3)
- Viral diversity from next-generation sequencing of HIV-1 samples provides precise estimates of infection recency and time since infection (2019) (3)
- Joint copy number and mutation phylogeny reconstruction from single-cell amplicon sequencing data (2022) (3)
- Estimating the dynamics and dependencies of accumulating mutations with applications to HIV drug resistance. (2015) (3)
- Computing the Genetic Barrier (2004) (3)
- ISMB/ECCB 2017 proceedings (2017) (3)
- Tree models for the evolution of drug resistance (2003) (3)
- Additional Mutations in HIV-1 Reverse Transcriptase are Involved in the Highly Ordered Regulation of NRTI Resistance (2005) (3)
- Bayesian non-parametric clustering of single-cell mutation profiles (2020) (2)
- Bayesian reconstruction of transmission trees from genetic sequences and uncertain infection times (2020) (2)
- The geometry of partial fitness orders and an efficient method for detecting genetic interactions (2018) (2)
- Advancing genomic epidemiology by addressing the bioinformatics bottleneck: Challenges, design principles, and a Swiss example (2022) (2)
- Joint Inference of Repeated Evolutionary Trajectories and Patterns of Clonal Exclusivity or Co-occurrence from Tumor Mutation Trees (2021) (2)
- Calling subclonal mutations with deepSNV (2015) (2)
- Multiparametric Circulating Tumor Cell Analysis to Select Targeted Therapies for Breast Cancer Patients (2021) (2)
- Comparing mutational pathways to lopinavir resistance in HIV-1 subtypes B versus C (2020) (2)
- Bayesian reconstruction of HIV transmission trees from viral sequences and uncertain infection times (2018) (2)
- ITN—VIROINF: Understanding (Harmful) Virus-Host Interactions by Linking Virology and Bioinformatics (2021) (2)
- Heritability of the HIV-1 reservoir size and decay under long-term suppressive ART (2020) (2)
- The Fractional Birth Process with Power-Law Immigration (2020) (2)
- Multi-omics subtyping of hepatocellular carcinoma patients using a Bayesian network mixture model (2021) (2)
- Joint inference of exclusivity patterns and recurrent trajectories from tumor mutation trees (2023) (1)
- Systematic identification of novel cancer genes through analysis of deep shRNA perturbation screens (2019) (1)
- Identifying cancer pathway dysregulations using differential causal effects (2021) (1)
- Author response: Inferring genetic interactions from comparative fitness data (2017) (1)
- netprioR: a probabilistic model for integrative hit prioritisation of genetic screens (2019) (1)
- Wastewater monitoring of SARS-CoV-2 shows high correlation with COVID-19 case numbers and allowed early detection of the first confirmed B.1.1.529 infection in Switzerland: results of an observational surveillance study. (2022) (1)
- Perturbing resistance: a network perspective (2016) (1)
- PLOS Computational Biology 2016 Reviewer and Editorial Board Thank You (2017) (1)
- Determination of the optimal cut-offs for predicting the phenotype of nine different HIV drug-resistance algorithms (2002) (1)
- LifeTime and improving European healthcare through cell-based interceptive medicine (2020) (1)
- Supervised and Unsupervised Approaches for Analyzing Covariation and Phenotypic Impact of HIV Drug Resistance Mutations (2005) (1)
- Author Correction: Clonal evolution of acute myeloid leukemia revealed by high-throughput single-cell genomics (2021) (1)
- Geno2pheno: a new machine learning approach to predicting phenotypic drug resistance from genotype (2001) (1)
- A statistical test for clonal exclusivity in tumour evolution (2021) (1)
- Discovery of antimicrobials by massively parallelized growth assays (Mex) (2022) (1)
- Simultaneous analysis of large-scale RNAi screens for pathogen entry (2014) (1)
- PLOS Computational Biology 2017 Reviewer and Editorial Board Thank You (2018) (1)
- The drug resistance profile of tenofovir: a story of resistance and resensitization (2002) (1)
- Computational Analysis of DNA and RNA Sequencing Data Obtained from Liquid Biopsies. (2020) (1)
- TiMEx: A Waiting Time Model for Mutually Exclusive Groups of Cancer Alterations (2015) (1)
- Eleven grand challenges in single-cell data science (2020) (1)
- Inferring perturbation profiles of cancer samples (2020) (1)
- The BET protein FSH functionally interacts with ASH1 to orchestrate global gene activity in Drosophila (2013) (1)
- APSiC: Analysis of Perturbation Screens for the Identification of Novel Cancer Genes (2019) (1)
- Proteo-Transcriptomic Dynamics of Cellular Response to HIV-1 Infection (2019) (1)
- Detection and Molecular Characterization of the SARS-CoV-2 Delta Variant and the Specific Immune Response in Companion Animals in Switzerland (2023) (1)
- A Stochastic Model of Metastatic Bottleneck Predicts Patient Outcome and Therapy Response (2018) (1)
- PyBDA: a command line tool for automated analysis of big biological data sets (2019) (0)
- Statistical Challenges in Single-Cell Biology (2017) (0)
- ECCB 2012 Organization (2012) (0)
- A ug 2 00 6 Conjunctive Bayesian Networks (2007) (0)
- dCas9-mediated dysregulation of gene expression in human induced pluripotent stem cells during primitive streak differentiation. (2022) (0)
- Latent epistatic interaction model identifies loci associated with human working memory (2015) (0)
- Unravelling The Structure-Function-Relationships Of High Density Lipoproteins (Hdl) By A Systems Biological Approach (2019) (0)
- Title : Single-molecule sequencing reveals complex genomic variation of hepatitis 1 B virus during 15 years of chronic infection following liver transplantation . 2 Running title : Single-molecule analysis reveals complex HBV (2016) (0)
- Genetic interactions and network reliability (2015) (0)
- Background Towards assessing therapy failure in HIV disease: estimating in vivo fitness characteristics of viral mutants by an integrated statistical-mechanistic approach (2009) (0)
- Author response: A switch in transcription and cell fate governs the onset of an epigenetically-deregulated tumor in Drosophila (2018) (0)
- The Fractional Birth Process with Power-Law Immigration (2019) (0)
- Accurate single nucleotide variant detection in viral populations by combining probabilistic clustering with a statistical test of strand bias (2013) (0)
- Expanding epidemic of recently acquired HCV in HIV-coinfected patients over a period of 10 years (2023) (0)
- Mutational interactions define novel cancer subgroups (2018) (0)
- Coherent pathway enrichment estimation by modeling inter-pathway dependencies using regularized regression (2022) (0)
- QuasiRecomb: prediction of recombinant viral quasispecies (2012) (0)
- Abstract 3984: GATA3 and MDM2 are synthetic lethal in estrogen receptor-positive breast cancers (2022) (0)
- Dynamic changes of genomic and transcriptomic tumor diversity during melanoma progression (2021) (0)
- Host Genomics of the HIV-1 Reservoir Size and Its Decay Rate During Suppressive Antiretroviral Treatment. (2020) (0)
- ISMB 2010 Organization (2010) (0)
- Chapter 2 Probability , Statistics , and Computational Science (2019) (0)
- Biallelic ELOC Inactivated Renal Cell Carcinoma: Molecular Features Supporting Classification as a Distinct Entity. (2023) (0)
- Detecting patterns of co-variation in deep-sequenced virus populations (2016) (0)
- Statistical Applications in Genetics and Molecular Biology (2010) (0)
- A highly ordered network of HIV-1 RT mutations regulates the continuous escape from antiviral drugs (2005) (0)
- Single-cell phylogenies reveal deviations from clock-like, neutral evolution in cancer and healthy tissues (2022) (0)
- Multi-omics data integration reveals novel drug targets in hepatocellular carcinoma (2021) (0)
- Probability, Statistics, and Computational Science. (2019) (0)
- Abstract 2725: The single-cell atlas of driver mutations in acute myeloid leukemia (2019) (0)
- A systems biological approach to the anti-atherogenicity of high density lipoproteins (2018) (0)
- Tree inference for single-cell data (2016) (0)
- Detecting Selection in the HIV-1 Genome during Sexual Transmission Events (2022) (0)
- Detection of isoforms and genomic alterations by high-throughput full-length single-cell RNA sequencing for personalized oncology (2022) (0)
- Program for Dagstuhl Seminar „ Addressing the Computational Challenges of Personalized Medicine (0)
- Publisher Correction: LifeTime and improving European healthcare through cell-based interceptive medicine (2021) (0)
- Results of a ten year prospective observational study on acute hepatitis C in HCV-mono- and HIV/HCV-coinfected patients (2022) (0)
- Selection as Driving Force in Lung and R on Carcinogenesis (2010) (0)
- Editorial: the influence of genetic factors in mediating the effects of tobacco smoke in IBD—Authors’ reply (2018) (0)
- C URRENT OPINION Dynamic models of viral replication and latency (2015) (0)
- What are the keys to succeeding as a computational biologist in today's research climate? (2022) (0)
- Visualization of viral populations (2013) (0)
- Deep exponential families for single-cell data analysis (2022) (0)
- – Addressing the Computational Challenges of Personalized Medicine 2 Table of Contents (2018) (0)
- Integrative inference of subclonal tumour evolution from single-cell and bulk sequencing data (2019) (0)
- Somatic point mutation and copy number alteration matrices used in Soh et al., "Predicting cancer type from tumour DNA signatures", Genome Medicine (2017) (0)
- Recurring Amplification at 11q22.1-q22.2 Locus Plays an Important Role in Lymph Node Metastasis and Radioresistance in OSCC (2017) (0)
- High-Dimensional Inference in Bayesian Networks (2021) (0)
- Discovery of Antimicrobials By Mex : Massively Parallelized Growth Assays (2021) (0)
- Geno2pheno: Genotypic HIV Drug Resistance Tests (2001) (0)
- Deconvolution of Clonal Heterogeneity in Acute Myeloid Leukemia using Single-Cell DNA Sequencing (2019) (0)
- [Current trends and research emphasis. Epidemiology, resistance testing, vaccination strategies]. (2002) (0)
- Neutrophils escort circulating tumour cells to enable cell cycle progression (2019) (0)
- Probabilistic Viral Quasispecies Assembly (2016) (0)
- Tracking SARS-CoV-2 genomic variants in wastewater sequencing data with LolliPop (2022) (0)
- A genome-wide screen for inherited genetic variants that affect survival and therapy of resectable pancreatic ductal adenocarcinoma (2018) (0)
- Combinatorial ecology in the simple fruit fly gut microbiome (2019) (0)
- Analysis of HIV-1 Expression Level and Sense of Transcription by High-Throughput Sequencing of the Infected Cell (cid:1) (2011) (0)
- Statistical Applications in Genetics and Molecular Biology Model Selection for Mixtures of Mutagenetic Trees (2011) (0)
- Erratum to: gespeR: a statistical model for deconvoluting off-target-confounded RNA interference screens (2015) (0)
- Simultaneous Integration of Multi-omics Data Improves the Identification of Cancer DriverModules Graphical (2019) (0)
- Clonal evolution driven by superdriver mutations (2020) (0)
- gespeR: a statistical model for deconvoluting off-target-confounded RNA interference screens (2015) (0)
- Phylogeny-guided single-cell mutation calling (2020) (0)
- Marginalization in Bayesian Networks: Integrating Exact and Approximate Inference (2021) (0)
- Estimating effective drug combinations against drug-resistant mutants from genotypes (2003) (0)
- A wrapper to query DGIdb using (2016) (0)
- Abstract A49: Characterizing the order of mutation acquisition in acute myeloid leukemia using large-scale single-cell sequencing (2023) (0)
- Mapping single-cell transcriptomes to copy number evolutionary trees (2021) (0)
- Practical and scalable simulations of non-Markovian stochastic processes (2022) (0)
- Author Correction: GATA3 and MDM2 are synthetic lethal in estrogen receptor-positive breast cancers (2022) (0)
- Systematic investigation of synthetic operon designs enables prediction and control of expression levels of multiple proteins (2022) (0)
- HIV Haplotype Inference Using a Propagating Dirichlet Process Mixture Model. (2013) (0)
- Computational Tools for the Analysis and Simulation of HIV Drug Resistance (2005) (0)
- High dimensional microbiome interactions shape the host fitness landscape (2018) (0)
- Ensemble outlier detection and gene selection in triple-negative breast cancer data (2018) (0)
- Probing of viral diversity by global haplotype prediction (2013) (0)
- Acknowledgment of Reviewers for 2011 (2012) (0)
- Computational Tools for the Optimization of Antiretroviral Drug Therapies (2005) (0)
- Viral quasispecies assembly from paired-end reads (2014) (0)
- BitPhylogeny: a probabilistic framework for reconstructing intra-tumor phylogenies (2015) (0)
- Genome analysis Challenges in RNA virus bioinformatics (2014) (0)
- Systems biology Inferring perturbation profiles of cancer samples (2021) (0)
- Predicting cancer type from tumour DNA signatures (2017) (0)
- Abstract IA22: Mechanisms of evasive resistance in cancer (2016) (0)
- Interaction network analysis links tumor mutations with expression patterns (2015) (0)
- Reproducibility of Bioinformatics Tools (2022) (0)
- Spatial structure governs the mode of tumour evolution (2021) (0)
- The Bourque distances for mutation trees of cancers (2021) (0)
- Discovery of antimicrobials by massively parallelized growth assays (Mex) (2022) (0)
- Principles of Systems Biology, No. 31. (2018) (0)
- PROGRESSION RISK ASSESSMENT IN PROSTATE CANCER USING A NOVEL BIOINFORMATICS BASED GENETIC MODEL (2006) (0)
- Computational Data Integration in Toxicogenomics (2015) (0)
- Geno2pheno and the Arevir database: tools for determination of clinically relevant cut-offs and prediction of viral load change from HIV-1 genotype. (2003) (0)
- S833 THE SINGLE-CELL ATLAS OF DRIVER MUTATIONS IN AML (2019) (0)
- CanSig: discovery of shared transcriptional states across cancer patients from single-cell RNA sequencing data (2023) (0)
- Exome sequencing of healthy phenotypic extremes links TROVE 2 to 1 emotional memory and PTSD 2 3 4 (2021) (0)
- Detailed simulation of cancer exome sequencing data reveals differences and common limitations of variant callers (2017) (0)
- ROS Induction Targets Persister Cancer Cells with Low Metabolic Activity in NRAS-Mutated Melanoma. (2023) (0)
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