Martin Vingron

Q: What Schools Are Affiliated With Martin Vingron

Martin Vingron is affiliated with the following schools: University of Cologne, University of Stuttgart, University of Southern California, University of Vienna, Heidelberg University

Martin Vingron's AcademicInfluence.com Rankings

Martin Vingron

Mathematics

#3467

World Rank

#5113

Historical Rank

Algebra

#172

World Rank

#264

Historical Rank

Measure Theory

#1061

World Rank

#1363

Historical Rank

mathematics Degrees

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Mathematics

Martin Vingron's Degrees

PhD Mathematics University of Vienna

Why Is Martin Vingron Influential?

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According to Wikipedia, Martin Vingron is an Austrian mathematician working in the fields of bioinformatics and computational biology. Since 2000, he has been Director of the Max Planck Institute for Molecular Genetics. Education Vingron grew up in Vienna, and gained his Diploma in Mathematics from the University of Vienna in 1985. He later studied at Heidelberg University and the European Molecular Biology Laboratory, gaining his Dr. rer. nat. in Applied Mathematics in 1991. His thesis studied the applications of multiple sequence alignment in molecular biology.

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Martin Vingron'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

Minimum information about a microarray experiment (MIAME)—toward standards for microarray data (2001) (4145)
TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing (2002) (2613)
A gene expression map of Arabidopsis thaliana development (2005) (2507)
Variance stabilization applied to microarray data calibration and to the quantification of differential expression (2002) (2276)
Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels (2012) (1405)
Comprehensive genomic profiles of small cell lung cancer (2015) (1397)
A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome (2008) (1298)
IntAct: an open source molecular interaction database (2004) (967)
Histone modification levels are predictive for gene expression (2010) (714)
Ontologizer 2.0 - a multifunctional tool for GO term enrichment analysis and data exploration (2008) (512)
Formation of new chromatin domains determines pathogenicity of genomic duplications (2016) (509)
T cells become licensed in the lung to enter the central nervous system (2012) (370)
The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery (2016) (360)
Correspondence analysis applied to microarray data (2001) (351)
Improved detection of overrepresentation of Gene-Ontology annotations with parent-child analysis (2007) (339)
Homology of 54K protein of signal-recognition particle, docking protein and two E. coli proteins with putative GTPbinding domains (1989) (333)
BLUEPRINT to decode the epigenetic signature written in blood (2012) (320)
Plant nitric oxide synthase: a never-ending story? (2006) (318)
The Translational Landscape of the Human Heart (2019) (303)
Modeling Amino Acid Replacement (2000) (298)
A trans-acting locus regulates an anti-viral expression network and type 1 diabetes risk (2010) (290)
Sequence alignment and penalty choice. Review of concepts, case studies and implications. (1994) (252)
Frequent mutations in chromatin-remodeling genes in pulmonary carcinoids (2014) (230)
X-exome sequencing of 405 unresolved families identifies seven novel intellectual disability genes (2015) (229)
Monitoring the Switch from Housekeeping to Pathogen Defense Metabolism in Arabidopsis thaliana Using cDNA Arrays* (2002) (226)
Increase of functional diversity by alternative splicing. (2003) (217)
Predicting transcription factor affinities to DNA from a biophysical model (2007) (212)
CD74-NRG1 fusions in lung adenocarcinoma. (2014) (212)
Integrative genomic profiling of large-cell neuroendocrine carcinomas reveals distinct subtypes of high-grade neuroendocrine lung tumors (2018) (210)
Gene expression screening in Xenopus identifies molecular pathways, predicts gene function and provides a global view of embryonic patterning (1998) (209)
Transcription factor binding predictions using TRAP for the analysis of ChIP-seq data and regulatory SNPs (2011) (204)
Parameter estimation for the calibration and variance stabilization of microarray data (2003) (200)
Identification and classification of differentially expressed genes in renal cell carcinoma by expression profiling on a global human 31,500-element cDNA array. (2001) (200)
Molecular cloning of YPT1/SEC4-related cDNAs from an epithelial cell line (1990) (192)
Haplotype-resolved sweet potato genome traces back its hexaploidization history (2017) (191)
Soluble epoxide hydrolase is a susceptibility factor for heart failure in a rat model of human disease (2008) (185)
Computational Molecular Biology (1996) (181)
New evidence for genome-wide duplications at the origin of vertebrates using an amphioxus gene set and completed animal genomes. (2003) (175)
Functional dissection of the Sox9–Kcnj2 locus identifies nonessential and instructive roles of TAD architecture (2019) (175)
Prediction of alternative isoforms from exon expression levels in RNA-Seq experiments (2010) (174)
q-gram based database searching using a suffix array (QUASAR) (1999) (173)
Processing and quality control of DNA array hybridization data (2000) (164)
Rapid and accurate estimates of statistical significance for sequence data base searches. (1994) (160)
The SRF target gene Fhl2 antagonizes RhoA/MAL-dependent activation of SRF. (2004) (155)
Sequence Comparison Significance and Poisson Approximation (1994) (155)
Estimating amino acid substitution models: a comparison of Dayhoff's estimator, the resolvent approach and a maximum likelihood method. (2002) (149)
TIF‐IA, the factor mediating growth‐dependent control of ribosomal RNA synthesis, is the mammalian homolog of yeast Rrn3p (2000) (145)
Transcriptional profiling on all open reading frames of Saccharomyces cerevisiae (1998) (145)
PASTAA: identifying transcription factors associated with sets of co-regulated genes (2008) (143)
Polymer physics predicts the effects of structural variants on chromatin architecture (2018) (142)
The BTB and CNC Homology 1 (BACH1) Target Genes Are Involved in the Oxidative Stress Response and in Control of the Cell Cycle* (2011) (137)
An integrated gene annotation and transcriptional profiling approach towards the full gene content of the Drosophila genome (2003) (137)
A new subfamily of vertebrate calpains lacking a calmodulin-like domain: implications for calpain regulation and evolution. (1997) (136)
Mapping translocation breakpoints by next-generation sequencing. (2008) (135)
A fast and sensitive multiple sequence alignment algorithm (1989) (133)
Motif recognition and alignment for many sequences by comparison of dot-matrices. (1991) (130)
SVIM: structural variant identification using mapped long reads (2018) (130)
Dynamic 3D chromatin architecture contributes to enhancer specificity and limb morphogenesis (2018) (124)
Genome-Wide Array Analysis of Normal and Malformed Human Hearts (2003) (123)
Phylogenetic conservation of arylsulfatases. cDNA cloning and expression of human arylsulfatase B. (1990) (121)
The Effect of Micrococcal Nuclease Digestion on Nucleosome Positioning Data (2010) (119)
Determination of reliable regions in protein sequence alignments. (1990) (117)
ChIP-exo signal associated with DNA-binding motifs provides insight into the genomic binding of the glucocorticoid receptor and cooperating transcription factors (2015) (116)
On the Power of Profiles for Transcription Factor Binding Site Detection (2003) (116)
PROmiRNA: a new miRNA promoter recognition method uncovers the complex regulation of intronic miRNAs (2013) (111)
Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding (2017) (104)
Paracrine control of oligodendrocyte differentiation by SRF-directed neuronal gene expression (2009) (103)
Preformed chromatin topology assists transcriptional robustness of Shh during limb development (2019) (102)
Prediction of human population responses to toxic compounds by a collaborative competition (2015) (101)
Large scale hierarchical clustering of protein sequences (2005) (97)
Gene expression in kidney cancer is associated with cytogenetic abnormalities, metastasis formation, and patient survival. (2005) (95)
The SYSTERS protein sequence cluster set (2000) (95)
Genome-wide kinase-chromatin interactions reveal the regulatory network of ERK signaling in human embryonic stem cells. (2013) (90)
Weighting in sequence space: a comparison of methods in terms of generalized sequences. (1993) (89)
Primer design for large scale sequencing. (1998) (88)
Genome wide identification and classification of alternative splicing based on EST data (2004) (88)
Early vertebrate whole genome duplications were predated by a period of intense genome rearrangement. (2008) (86)
Quantifying the local reliability of a sequence alignment. (1996) (85)
Serial genomic inversions induce tissue-specific architectural stripes, gene misexpression and congenital malformations (2019) (84)
CORG: a database for COmparative Regulatory Genomics (2003) (83)
Normalization and quantification of differential expression in gene expression microarrays (2006) (82)
Optimal robust non-unique probe selection using Integer Linear Programming (2004) (82)
A polyhedral approach to RNA sequence structure alignment (1998) (81)
Modeling Read Counts for CNV Detection in Exome Sequencing Data (2011) (78)
Composition and dosage of a multipartite enhancer cluster control developmental expression of Indian hedgehog (2017) (77)
Comparative 3'UTR Analysis Allows Identification of Regulatory Clusters that Drive Eph/ephrin Expression in Cancer Cell Lines (2008) (75)
SYSTERS, GeneNest, SpliceNest: exploring sequence space from genome to protein (2002) (74)
Microarray data warehouse allowing for inclusion of experiment annotations in statistical analysis (2002) (73)
Detecting genomic indel variants with exact breakpoints in single- and paired-end sequencing data using SplazerS (2012) (72)
Towards detection of orthologues in sequence databases (1998) (72)
Dynamics of Transcription Regulation in Human Bone Marrow Myeloid Differentiation to Mature Blood Neutrophils (2018) (71)
DeBi: Discovering Differentially Expressed Biclusters using a Frequent Itemset Approach (2011) (70)
Translational regulation shapes the molecular landscape of complex disease phenotypes (2015) (69)
Gene expression profile of mouse bone marrow stromal cells determined by cDNA microarray analysis (2003) (68)
Identifying splits with clear separation: a new class discovery method for gene expression data (2001) (66)
A set-theoretic approach to database searching and clustering (1998) (66)
Hi-C Identifies Complex Genomic Rearrangements and TAD-Shuffling in Developmental Diseases. (2020) (66)
NOA1 is an essential GTPase required for mitochondrial protein synthesis (2011) (66)
Statistical Modeling of Transcription Factor Binding Affinities Predicts Regulatory Interactions (2008) (66)
Quantifying the effect of sequence variation on regulatory interactions (2010) (66)
Molecular cloning and structural analysis of genes from Zea mays (L.) coding for members of the ras-related ypt gene family. (1992) (65)
Esrrb Unlocks Silenced Enhancers for Reprogramming to Naive Pluripotency. (2018) (65)
Methylation and deamination of CpGs generate p53-binding sites on a genomic scale. (2009) (63)
Sequence-dependent nucleosome positioning. (2009) (62)
Natural variation of histone modification and its impact on gene expression in the rat genome (2014) (61)
Drosophila and vertebrate myb proteins share two conserved regions, one of which functions as a DNA‐binding domain. (1987) (60)
A systems biological approach suggests that transcriptional feedback regulation by dual‐specificity phosphatase 6 shapes extracellular signal‐related kinase activity in RAS‐transformed fibroblasts (2009) (60)
Near-optimal sequence alignment. (1996) (60)
Combinatorial Binding in Human and Mouse Embryonic Stem Cells Identifies Conserved Enhancers Active in Early Embryonic Development (2011) (59)
Improved sensitivity proteomics by postharvest alkylation and radioactive labeling of proteins (2000) (57)
Natural similarity measures between position frequency matrices with an application to clustering (2008) (56)
Nucleotide sequence of the glyceraldehyde-3-phosphate dehydrogenase gene from the mesophilic methanogenic archaebacteria Methanobacterium bryantii and Methanobacterium formicicum. Comparison with the respective gene structure of the closely related extreme thermophile Methanothermus fervidus. (1989) (56)
Control of replication initiation and heterochromatin formation in Saccharomyces cerevisiae by a regulator of meiotic gene expression. (2005) (56)
A naturally occuring insertion of a single amino acid rewires transcriptional regulation by glucocorticoid receptor isoforms (2013) (55)
Mammalian mitochondrial nitric oxide synthase: Characterization of a novel candidate (2006) (53)
Duplication-Based Measures of Difference Between Gene and Species Trees (1998) (53)
In silico identification of a core regulatory network of OCT4 in human embryonic stem cells using an integrated approach (2009) (52)
Horizontal Gene Transfers in prokaryotes show differential preferences for metabolic and translational genes (2009) (52)
SpliceNest: visualizing gene structure and alternative splicing based on EST clusters (2002) (51)
Sequences flanking the core-binding site modulate glucocorticoid receptor structure and activity (2016) (51)
The SYSTERS Protein Family Database in 2005 (2004) (50)
Finding Associations among Histone Modifications Using Sparse Partial Correlation Networks (2013) (50)
Genome-wide comparison of cyanobacterial transposable elements, potential genetic diversity indicators. (2011) (50)
CpG-depleted promoters harbor tissue-specific transcription factor binding signals—implications for motif overrepresentation analyses (2009) (50)
GeneNest: automated generation and visualization of gene indices. (2000) (50)
Analysis of microarray gene expression data (2003) (50)
Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood counts (2012) (49)
Support Vector Machines for Protein Fold Class Prediction (2003) (49)
Strengths and weaknesses of EST-based prediction of tissue-specific alternative splicing (2004) (49)
Towards Integration of Multiple Alignment and Phylogenetic Tree Construction (1997) (48)
Analysis of CREM-dependent gene expression during mouse spermatogenesis (2003) (48)
Deeply conserved chordate noncoding sequences preserve genome synteny but do not drive gene duplicate retention. (2009) (48)
T-Reg Comparator: an analysis tool for the comparison of position weight matrices (2005) (48)
An Improved Statistic for Detecting Over-Represented Gene Ontology Annotations in Gene Sets (2006) (48)
A DNA microarray for fission yeast: minimal changes in global gene expression after temperature shift (2004) (47)
An entropic characterization of protein interaction networks and cellular robustness (2006) (46)
Capn7: A highly divergent vertebrate calpain with a novel C-terminal domain (1999) (46)
A joint model of regulatory and metabolic networks (2006) (45)
Protein sequence comparison: methods and significance. (1991) (43)
Role of the chromatin landscape and sequence in determining cell type-specific genomic glucocorticoid receptor binding and gene regulation (2016) (43)
CpG Deamination Creates Transcription Factor–Binding Sites with High Efficiency (2011) (42)
Comparative promoter region analysis powered by CORG (2005) (41)
Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data (2015) (41)
Epigenomic Co-localization and Co-evolution Reveal a Key Role for 5hmC as a Communication Hub in the Chromatin Network of ESCs. (2016) (41)
TransFind—predicting transcriptional regulators for gene sets (2010) (41)
Genome-wide analysis of LXRα activation reveals new transcriptional networks in human atherosclerotic foam cells (2013) (39)
The KRAB-containing zinc-finger transcriptional regulator ZBRK1 activates SCA2 gene transcription through direct interaction with its gene product, ataxin-2. (2011) (38)
Annotating regulatory DNA based on man-mouse genomic comparison (2002) (38)
Genome-scale design of PCR primers and long oligomers for DNA microarrays. (2003) (38)
Self-correcting networks: function, robustness, and motif distributions in biological signal processing. (2008) (37)
Exonization of active mouse L1s: a driver of transcriptome evolution? (2007) (36)
Correlating protein-DNA and protein-protein interaction networks. (2003) (36)
Expression profile and transcription factor binding site exploration of imprinted genes in human and mouse (2009) (35)
The deferred path heuristic for the generalized tree alignment problem (1997) (35)
Epigenomic profiling of non-small cell lung cancer xenografts uncover LRP12 DNA methylation as predictive biomarker for carboplatin resistance (2018) (34)
The mole genome reveals regulatory rearrangements associated with adaptive intersexuality (2020) (34)
A calibrated diversity assay for nucleic acid libraries using DiStRO—a Diversity Standard of Random Oligonucleotides (2009) (33)
Breakpointer: using local mapping artifacts to support sequence breakpoint discovery from single-end reads (2012) (33)
Evolution of DNA-Binding Sites of a Floral Master Regulatory Transcription Factor (2015) (33)
ssHMM: extracting intuitive sequence-structure motifs from high-throughput RNA-binding protein data (2016) (33)
Transcriptional Autoregulatory Loops Are Highly Conserved in Vertebrate Evolution (2008) (32)
Predicting the outcome of renal transplantation (2012) (31)
Molecular phylogenetics: parallelized parameter estimation and quartet puzzling (2003) (31)
Elucidating regulatory mechanisms downstream of a signaling pathway using informative experiments (2009) (31)
histoneHMM: Differential analysis of histone modifications with broad genomic footprints (2015) (31)
Microarray data representation, annotation and storage. (2002) (30)
Computational aspects of expression data (1999) (29)
Synthetic sickness or lethality points at candidate combination therapy targets in glioblastoma (2013) (29)
Inference of interactions between chromatin modifiers and histone modifications: from ChIP-Seq data to chromatin-signaling (2014) (28)
Genome-wide H4 K16 acetylation by SAS-I is deposited independently of transcription and histone exchange (2011) (28)
Familz specific rates of protein evolution (2006) (27)
Development and application of a modified dynamic time warping algorithm (DTW-S) to analyses of primate brain expression time series (2011) (26)
Limits of homology detection by pairwise sequence comparison (2001) (26)
Integrating sequence, evolution and functional genomics in regulatory genomics (2009) (26)
Design and statistical properties of robust functional networks: a model study of biological signal transduction. (2007) (26)
Inferring the paths of somatic evolution in cancer (2014) (26)
SVIM-asm: structural variant detection from haploid and diploid genome assemblies (2020) (26)
A new interactive protein sequence alignment program and comparison of its results with widely used algorithms (1989) (25)
Linking aberrant chromatin features in chronic lymphocytic leukemia to transcription factor networks (2019) (25)
Axeldb: a Xenopus laevis database focusing on gene expression (2000) (25)
Fast and Adaptive Variable Order Markov Chain Construction (2008) (25)
Integer linear programming approaches for non-unique probe selection (2007) (24)
Reconstruction of gene networks using prior knowledge (2015) (24)
Phylogenetic information improves homology detection (2001) (24)
Inferring nucleosome positions with their histone mark annotation from ChIP data (2013) (23)
Lethality and entropy of protein interaction networks. (2005) (23)
Horizontal Gene Transfer in Aminoacyl-tRNA Synthetases Including Leucine-Specific Subtypes (2006) (23)
Functional analysis and identification of cis-regulatory elements of human chromosome 21 gene promoters (2010) (22)
Detection of interacting transcription factors in human tissues using predicted DNA binding affinity (2012) (22)
Genomic dissection of enhancers uncovers principles of combinatorial regulation and cell type-specific wiring of enhancer–promoter contacts (2018) (22)
Identification of highly specific localized sequence motifs in human ribosomal protein gene promoters. (2006) (22)
Statistics of large scale sequence searching (1997) (21)
Reconstruction of gene regulatory network related to photosynthesis in Arabidopsis thaliana (2014) (21)
On the Equivalence of Two Tree Mapping Measures (1998) (21)
A genome-wide transcriptional fingerprint of normal and malformed human hearts (2003) (21)
Evidence for Gene-Specific Rather Than Transcription Rate–Dependent Histone H3 Exchange in Yeast Coding Regions (2009) (21)
Prediction of cardiac transcription networks based on molecular data and complex clinical phenotypes. (2008) (20)
Genome-wide comparison of cyanobacterial transposable elements, potential genetic diversity indicators (2010) (20)
Theoretical analysis of alternative splice forms using computational methods (2002) (19)
SITEBLAST-rapid and sensitive local alignment of genomic sequences employing motif anchors (2005) (19)
Multiple Sequence Comparison and Consistency on Multipartite Graphs (1995) (19)
Sensitivity comparison of protein amino acid sequences. (1990) (18)
The R Package bgmm: Mixture Modeling with Uncertain Knowledge (2012) (18)
Reconstructing Domain Compositions of Ancestral Multi-domain Proteins (2006) (18)
Synthetic STARR-seq reveals how DNA shape and sequence modulate transcriptional output and noise (2018) (18)
Somatic neurofibromatosis type 1 (NF1) inactivation events in cutaneous neurofibromas of a single NF1 patient (2014) (18)
Ranbow: A fast and accurate method for polyploid haplotype reconstruction (2020) (17)
Conserved DNA sequence features underlie pervasive RNA polymerase pausing (2021) (17)
CRUP: a comprehensive framework to predict condition-specific regulatory units (2018) (17)
Weighted sequence graphs: boosting iterated dynamic programming using locally suboptimal solutions (2003) (17)
Using transcription factor binding site co-occurrence to predict regulatory regions. (2007) (16)
Comparative analysis of cell cycle regulated genes in eukaryotes. (2005) (16)
WWW access to the SYSTERS protein sequence cluster set (1999) (16)
A computational evaluation of over-representation of regulatory motifs in the promoter regions of differentially expressed genes (2010) (16)
Bioinformatics needs to adopt statistical thinking. (2001) (16)
Studying the Evolution of Promoter Sequences: A Waiting Time Problem (2010) (15)
Comparison of annotating duplication, tree mapping, and copying as methods to compare gene trees with species trees (1996) (15)
Proteome analysis based on motif statistics (2002) (15)
Statistical detection of cooperative transcription factors with similarity adjustment (2009) (15)
Identification of Guanine-Nucleotide Binding Proteins in Plants: Structural Analysis and Evolutionary Comparison of the Ras-Related Ypt-Gene Family from Zea Mays (1989) (15)
Genomic dissection of enhancers uncovers principles of combinatorial regulation and cell type-specific wiring of enhancer–promoter contacts (2018) (15)
T-STAG: resource and web-interface for tissue-specific transcripts and genes (2005) (14)
Functional inference from non-random distributions of conserved predicted transcription factor binding sites (2004) (14)
Proceedings of the seventh annual international conference on Research in computational molecular biology (2003) (14)
Single-Cell Analysis Uncovers a Vast Diversity in Intracellular Viral Defective Interfering RNA Content Affecting the Large Cell-to-Cell Heterogeneity in Influenza A Virus Replication (2020) (13)
SDip: A novel graph-based approach to haplotype-aware assembly based structural variant calling in targeted segmental duplications sequencing (2020) (13)
Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach (2013) (13)
Transcriptional profiling: is it worth the money? (2000) (13)
Haplotype Reconstruction for Diploid Populations (2005) (13)
Effects of Long-Range Correlations in DNA on Sequence Alignment Score Statistics (2007) (13)
Introducing Knowledge into Differential Expression Analysis (2010) (12)
Compound Poisson Approximation of the Number of Occurrences of a Position Frequency Matrix (PFM) on Both Strands (2008) (12)
A tandem sequence motif acts as a distance-dependent enhancer in a set of genes involved in translation by binding the proteins NonO and SFPQ (2011) (12)
Genome-wide Chromatin Profiling of Legionella pneumophila-Infected Human Macrophages Reveals Activation of the Probacterial Host Factor TNFAIP2. (2016) (12)
In silico analysis of gene expression patterns during early development of Xenopus laevis. (1999) (12)
Exploring potential target genes of signaling pathways by predicting conserved transcription factor binding sites (2003) (12)
An inventory of yeast proteins associated with nucleolar and ribosomal components (2006) (12)
The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources (2004) (11)
Corrigendum: Sequences flanking the core-binding site modulate glucocorticoid receptor structure and activity (2016) (11)
Error models for microarray intensities (2004) (11)
The haplotype-resolved genome sequence of hexaploid Ipomoea batatas reveals its evolutionary history (2016) (11)
A MicroRNA Network Controls Legionella pneumophila Replication in Human Macrophages via LGALS8 and MX1 (2020) (11)
Simultaneous alignment and annotation of cis-regulatory regions (2007) (11)
An improved compound Poisson model for the number of motif hits in DNA sequences (2017) (11)
A physical model for tiling array analysis (2007) (11)
The Distance Precision Matrix: computing networks from non-linear relationships (2016) (10)
Effect of imputation on gene network reconstruction from single-cell RNA-seq data (2021) (10)
Condition-specific target prediction from motifs and expression (2014) (10)
Transcription profiling of renal cell carcinoma. (2002) (10)
Gaussian Mixture Density Estimation Applied to Microarray Data (2003) (10)
Anatomy of fos proteins. (1988) (10)
Application of bootstrap techniques to physical mapping. (2000) (10)
Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements (2022) (10)
Molecular Phenotyping of Mouse Mutant Resources by RNA Expression Profiling (2002) (9)
An introduction to low-level analysis methods of DNA microarray data (2005) (9)
Improved Prediction of Non-methylated Islands in Vertebrates Highlights Different Characteristic Sequence Patterns (2016) (9)
Incorporating evolution of transcription factor binding sites into annotated alignments (2007) (9)
Bioinformatics needs to adopt statistical thinking - Editorial (2001) (9)
R2KS: A Novel Measure for Comparing Gene Expression Based on Ranked Gene Lists (2012) (8)
Predicting enhancers in mammalian genomes using supervised hidden Markov models (2019) (8)
Repression and 3D-restructuring resolves regulatory conflicts in evolutionarily rearranged genomes (2022) (8)
P53 Binding Sites in Transposons (2012) (8)
Esrrb Unlocks Silenced Enhancers for Reprogramming to Naive Pluripotency. (2018) (8)
Functional dissection of TADs reveals non-essential and instructive roles in regulating gene expression (2019) (8)
About the interrelation of evolutionary rate and protein age. (2006) (7)
Enhanced cortical neural stem cell identity through short SMAD and WNT inhibition in human cerebral organoids facilitates emergence of outer radial glial cells (2022) (7)
Correspondence analysis with microarray data (2003) (7)
Comparison of sequence-dependent tiling array normalization approaches (2009) (7)
Mathematical Support for Molecular Biology (1999) (7)
Stochastics of Cellular Differentiation Explained by Epigenetics: The Case of T‐Cell Differentiation and Functional Plasticity (2017) (7)
Time-Dependent Gene Network Modelling by Sequential Monte Carlo (2016) (6)
ModHMM: A Modular Supra-Bayesian Genome Segmentation Method (2019) (6)
A new statistical model to select target sequences bound by transcription factors. (2006) (6)
Prioritization of gene regulatory interactions from large-scale modules in yeast (2008) (6)
Characteristic differences between the promoters of intron-containing and intronless ribosomal protein genes in yeast (2008) (6)
Integrated annotation and analysis of genomic features reveal new types of functional elements and large-scale epigenetic phenomena in the developing zebrafish (2021) (6)
Variance Stabilization and Robust Normalization for Microarray Gene Expression Data (2002) (6)
Classifying human promoters by occupancy patterns identifies recurring sequence elements, combinatorial binding, and spatial interactions (2018) (6)
Dynamic 3D chromatin architecture contributes to enhancer specificity and limb morphogenesis (2018) (5)
coTRaCTE predicts co-occurring transcription factors within cell-type specific enhancers (2018) (5)
Bioinformatics research and education in Germany (2002) (5)
Multiple Sequence Comparison and n-Dimensional Image Reconstruction (1993) (5)
Assessing genome-wide dynamic changes in enhancer activity during early mESC differentiation by FAIRE-STARR-seq (2021) (5)
Visualizing cluster-specific genes from single-cell transcriptomics data using Association Plots. (2022) (5)
Integrative genomic profiling of large-cell neuroendocrine carcinomas reveals distinct subtypes of high-grade neuroendocrine lung tumors (2018) (5)
A trans locus causes a ribosomopathy in hypertrophic hearts that affects mRNA translation in a protein length-dependent fashion (2021) (4)
Statistical Significance of Local Alignments with Gaps (2007) (4)
Developments in CORG: a gene-centric comparative genomics resource (2006) (4)
Promoter repression and 3D-restructuring resolves divergent developmental gene expression in TADs (2021) (4)
ModHMM: A Modular Supra-Bayesian Genome Segmentation Method. (2019) (4)
RIF1 and KAP1 differentially regulate the choice of inactive versus active X chromosomes (2021) (4)
Predicting enhancers using a small subset of high confidence examples and co-training (2016) (4)
Alignment Networks and Electrical Networks (1996) (4)
Anisotropic expansion of hepatocyte lumina enforced by apical bulkheads (2021) (4)
Exact Score Distribution Computation for Similarity Searches in Ontologies (2009) (4)
8 DNA Arrays for Transcriptional Profiling (1999) (4)
The SYSTERS protein family database: Taxon-related protein family size distributions and singleton frequencies (2003) (3)
Alignment Statistics for Long-Range Correlated Genomic Sequences (2006) (3)
TADA—a machine learning tool for functional annotation-based prioritisation of pathogenic CNVs (2022) (3)
Sequence alignment and phylogeny construction (1998) (3)
This special issue comprises the papers accepted for presentationat the 19th Annual International Conference on Intelligent Systemsfor Molecular Biology, joint with the 10th European Conference onComputational Biology, an official conference of the InternationalSociety for Computational Biology. (2011) (3)
Position effects at the FGF8 locus are associated with femoral hypoplasia. (2021) (3)
Contig selection in physical mapping (2000) (3)
Ligand-Gated Ion Channels of Drosophila (1989) (3)
Low‐level Analysis of Microarray Experiments (2008) (3)
Comparative analysis of neutrophil and monocyte epigenomes (2017) (3)
Deregulation upon DNA damage revealed by joint analysis of context-specific perturbation data (2011) (3)
TADA – a Machine Learning Tool for Functional Annotation based Prioritisation of Putative Pathogenic CNVs (2020) (3)
Hi-C Identiﬁes Complex Genomic Rearrangements and TAD-Shufﬂing in Developmental Diseases (2020) (3)
Corrigendum to “Mammalian mitochondrial nitric oxide synthase: Characterization of a novel candidate” [FEBS Lett. 580 (2006) 455–462] (2007) (3)
On the specificity of carboxypeptidase N, a comparative study. (1993) (3)
AtGenExpress: Expression atlas of Arabidopsis Development (2004) (2)
Survey of brain-expressed genes in a 7.3 mb region on proximal xp involved in non-syndromic X-linked mental retardation (2003) (2)
Phylogeny meets sequence search (1999) (2)
Trans control of cardiac mRNA translation in a protein length-dependent fashion (2020) (2)
Long-read transcriptome sequencing analysis with IsoTools (2021) (2)
Annotating significant pairs of transcription factor binding sites in regulatory DNA (2004) (2)
Haplotype-based phylogenetic analysis uncovers the tetraploid progenitor of sweet potato (2021) (2)
DNA microchips: transcriptional profiling and beyond (2000) (2)
Detecting Functional Modules of Transcription Factor Binding Sites in the Human Genome (2004) (2)
Cyclic Nucleotide-gated Channels — A Family of Proteins Involved in Vertebrate Photoreception and Olfaction (1992) (2)
Detection of interacting transcription factors in human tissues using predicted DNA binding affinity (2012) (1)
Concepts for the Estimation of Amino Acid Substitution Models (2000) (1)
Association Plots: Visualizing associations in high-dimensional correspondence analysis biplots (2020) (1)
Co-option of the transcription factor SALL1 in mole ovotestis formation (2022) (1)
Classifying human promoters by occupancy patterns identifies recurring sequence elements, combinatorial binding, and spatial interactions (2018) (1)
Soluble epoxide hydrolase (Ephx2) is a susceptibility gene for heart failure in a rat model of human disease 3044 (2008) (1)
Algorithms for Phylogenetic Reconstructions (2006) (1)
An Improved Algorithm for the Macro-evolutionary Phylogeny Problem (2006) (1)
Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data (2015) (1)
Ecient Estimation of Variable Order Markov Chains (2004) (1)
Connecting the Dots: PHF13 and cohesin promote polymer-polymer phase separation of chromatin into chromosomes (2022) (1)
SEARCH FOR REGULATORY MOTIFS IN DROSOPHILA MELANOGASTER GENOME (2004) (1)
A Clustering Approach to Generalized Tree Alignment with Application to Alu Repeats (1996) (1)
TADA—a machine learning tool for functional annotation-based prioritisation of pathogenic CNVs (2022) (1)
Differentially expressed miRNAs after Legionella pneumophila infection of human macrophages (2013) (1)
Somatic neuro fi bromatosis type 1 ( NF 1 ) inactivation events in cutaneous neuro fi bromas of a single NF 1 patient (2014) (1)
The Otto Warburg International Summer School and Workshop on Networks and Regulation (2007) (1)
The BREW workshop series: a stimulating experience in PhD education (2008) (1)
Normalization strategies for microarray data analysis (2005) (1)
Integration of Hi-C with short and long-read genome sequencing reveals the structure of germline rearranged genomes (2022) (1)
Algorithms for Phylogenetic Reconstructions Lecture Notes and Exercises (2005) (1)
ISCB Honors 2021 Award Recipients Peer Bork, Barbara Engelhardt, Ben Raphael, Teresa Attwood (2021) (1)
Massively parallel sequencing in >250 families with X-linked intellectual disability (2011) (1)
A trans locus causes a ribosomopathy in hypertrophic hearts that affects mRNA translation in a protein length-dependent fashion (2021) (1)
Research in Computational Molecular Biology, 12th Annual International Conference, RECOMB 2008, Singapore, March 30 - April 2, 2008. Proceedings (2008) (1)
Hierarchical Interleaved Bloom Filter: Enabling ultrafast, approximate sequence queries (2022) (0)
A process for indgruppering of sequences into families (1998) (0)
From gene expression profiling to gene regulation (2008) (0)
2022 ISCB Accomplishments by a Senior Scientist Award: Ron Shamir (2022) (0)
Identification of cis-regulatory elements from chromosome conformation capture data. (2015) (0)
Automatic Fusion of 3D staining patterns from mouse embryo tomograms (2007) (0)
Transcriptional control in cells and tissues A 1 Expression and activation of T cell receptor dependent transcription factors in regulatory T cells (2009) (0)
Michael Waterman's Contributions to Computational Biology and Bioinformatics (2022) (0)
2022 Outstanding Contributions to ISCB Award: Reinhard Schneider (2022) (0)
Managing and Mining Genome Information: Frontiers in Bioinformatics, 30. October - 4. November 2005 (2006) (0)
05441 Abstracts Collection - Managing and Mining Genome Information: Frontiers in Bioinformatics (2005) (0)
Statistical Applications in Genetics and Molecular Biology (2003) (0)
The SYSTERS Protein Family Web Server : Shortcut from large-scale sequence information to phylogenetic information (2004) (0)
Functional analysis and co-evolutionary model of chromatin and DNA methylation networks in embryonic stem cells (2014) (0)
Resampling Methods in Physical Mapping (2002) (0)
Role of TNFAIP2 in Legionella pneumophila-induced pulmonary inflammation (2013) (0)
PROmiRNA: a new miRNA promoter recognition method uncovers the complex regulation of intronic miRNAs (2013) (0)
Alternative and classic activation of primary macrophages – a systems biology approach (2014) (0)
The Book Review Column Review of Mathematical Support for Molecular Biology (2002) (0)
Large error models for microarray intensities (2005) (0)
Transcription factor tif-ia RNA polymerase i. (2000) (0)
Haplotype-resolved sweet potato genome traces back its hexaploidization history (2017) (0)
Haplotype reconstruction for polyploid organisms (2015) (0)
Human macrophages differentially express long non-coding RNAs upon polarization (2016) (0)
Special RECOMB 2008 Issue (2009) (0)
Evolutionary dynamics of DNA-binding sites and direct target genes of a floral master regulatory transcription factor [ChIP-Seq] (2015) (0)
BMP9 and Fluid Shear Stress Regulate Endothelial Chromatin Accessibility and Expression of SMAD Low Affinity Target Genes (2022) (0)
Epigenomic and functional dynamics of human bone marrow myeloid differentiation to mature blood neutrophils (2018) (0)
Maximum Similarity: A New Formulation of Phylogenetic Reconstruction (2009) (0)
Bioconductor Project Bioconductor Project Working Papers Year Paper Error models for microarray intensities (2013) (0)
Haplotype reconstruction for sweet potato (Ipomoea Batatas [L.] Lam) (2015) (0)
Sequence Alignment and Sequence Database Search (2008) (0)
CancerEpiSys – Integrative analysis of epigenetic networks that determine the chronic lymphocytic leukemia disease state (2018) (0)
The SYSTERS Protein Family Webserver (2002) (0)
Bioinformatics (Dagstuhl Seminar 00491) (2000) (0)
Alignment and Phylogeny Construction for Biological Sequences (1998) (0)
Serial genomic inversions induce tissue-specific architectural stripes, gene misexpression and congenital malformations (2019) (0)
DNA Motif Match Statistics Without Poisson Approximation (2019) (0)
Proceedings of the German Conference on Bioinformatics, GCB 2007, September 26-28, 2007, Potsdam, Germany (2007) (0)
An Amphioxus Gene Catalogue (2001) (0)
Systematic mutation search in families with X-linked mental retardation by next-generation sequencing (2010) (0)
Towards detection of sequence orthologs (1997) (0)
Mathematical tree models for cytogenetic development in solid tumors. (2003) (0)
ISCB/SPRINGER series in computational biology (2013) (0)
CAbiNet: Joint visualization of cells and genes based on a gene-cell graph (2022) (0)
Quantifying the tissue-specific regulatory information within enhancer DNA sequences (2021) (0)
Tree fitting: an algebraic approach using profile distances (2000) (0)
Additional data file 4 (2003) (0)
Epigenomic co-localization and co-evolution reveal a key role for 5hmC as a communication hub in the chromatin network of ESCs (2015) (0)
Attacking Generalized tree Alignment by a Deferred Path Heuristic (1996) (0)
expression in the rat genome Natural variation of histone modification and its impact on gene Material Supplemental (2014) (0)
Comparative molecular modeling of the active subunit of human kininase I. (1992) (0)
pfastDNAml: Using Parallel Computing for Maximum Likelihood Phylogenetic Analysis (1998) (0)
A role for Fra1 in the control of transcriptional network reorganization following ras transformation (2009) (0)
Sparse-Group Bayesian Feature Selection Using Expectation Propagation for Signal Recovery and Network Reconstruction (2018) (0)
SVC: structured visualization of evolutionary sequence conservation (2005) (0)
Systemic characterization of macrophage phenotypes in allergic airway inflammation (2014) (0)
2022 ISCB Overton Prize: Po-Ru Loh (2022) (0)
A biophysical approach to large-scale protein-DNA binding data (2008) (0)
Polymer physics predicts the effects of structural variants on chromatin architecture (2018) (0)
Systematic mutation search in families with X-linked intellectual disability by nextgeneration sequencing (2011) (0)
Identification of potential regulatory elements in Capture-C interaction profiles (2015) (0)
Bulkhead-like apical membrane structures between hepatocytes are required for anisotropic lumen expansion and liver tissue morphogenesis (2021) (0)
Horizontal transferred T-DNA and haplotype-based phylogenetic analysis uncovers the origin of sweetpotato (2022) (0)
Esrrb Unlocks Silenced En hancers for Reprogramming to Naive Pluripotency Graphical (2018) (0)
2022 ISCB Innovator Award: Núria López-Bigas (2022) (0)
Special RECOMB 2003 Issue (2004) (0)
Prediction of protein-protein interactions using sequences of intrinsically disordered regions. (2023) (0)
Computational Regulatory Genomics (2011) (0)
ECCB 2012 Organization (2012) (0)
Genexpressionsanalyse komplexer klinischer Phänotypen mittels cDNS-Arrays (Gene Expression Profiling of Complex Clinical Phenotypes using cDNA-Arrays) (2004) (0)
Resource Epigenomic Co-localizatio n and Co-evolution Reveal a Key Role for 5 hmC as a Communication Hub in the Chromatin Network of ESCs Graphical (2016) (0)
Special RECOMB 2002 Issue (2004) (0)
Proceedings Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computional Biology 2004 (ISMB/ECCB 2004) (2004) (0)
Otto Warburg International Summer School and Workshop on Computational Systems Biology Otto Warburg International Summer School and Workshop on Computational Systems Biology (2007) (0)
Limits of homology dete tion bypairwise sequen (2001) (0)
Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements (2022) (0)
Automatic clustering of large sequence databases (1998) (0)
A new method for modeling protein evolution (1999) (0)
A RIF1/KAP1-based toggle switch stabilises the identities of the inactive and active X chromosomes during X inactivation (2020) (0)
Special Issue: Professor Michael Waterman's 80th Birthday, Part 1 (2022) (0)
05441 Executive Summary - Managing and Mining Genome Information: Frontiers in Bioinformatics (2005) (0)
Bioinformatics of Eukaryotic Gene Regulation (2006) (0)
Phylogenetic Shadowing in Primate Promoter Regions (2005) (0)
Genomic location and expression patterns of Heidelberg unique predictions (2011) (0)
histoneHMM: Differential analysis of histone modifications with broad genomic footprints (2015) (0)
Comparative promoter analysis in vertebrate genomes with the CORG workbench. (2006) (0)
A method for classifying sequences into families (1997) (0)
Maximum likelihood estimation of mathematical models for genetic development in gastrointestinal stromal tumors (2004) (0)
Predicting enhancers in mammalian genomes using supervised hidden Markov models (2019) (0)
Epigenomic profiling of non-small cell lung cancer xenografts uncover LRP12 DNA methylation as predictive biomarker for carboplatin resistance (2018) (0)
Managing and Mining Genome Information : Frontiers in Bioinformatics Dagstuhl Seminar (2006) (0)
Statistical tools for discovering pseudo-periodicities in biological sequences (2001) (0)

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