Philipp Bucher
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Philipp Buchercomputer-science Degrees
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Computer Science
Philipp Bucher's Degrees
- PhD Computer Science ETH Zurich
- Masters Computer Science ETH Zurich
- Bachelors Computer Science ETH Zurich
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(Suggest an Edit or Addition)Philipp Bucher'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
- The PROSITE database, its status in 1997 (1997) (1570)
- The PROSITE database, its status in 2002 (2002) (1525)
- The PROSITE database, its status in 1999 (1999) (1157)
- Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences. (1990) (1141)
- ESTScan: A Program for Detecting, Evaluating, and Reconstructing Potential Coding Regions in EST Sequences (1999) (1130)
- The InterPro database, an integrated documentation resource for protein families, domains and functional sites (2001) (1061)
- PROSITE: A Documented Database Using Patterns and Profiles as Motif Descriptors (2002) (927)
- A superfamily of conserved domains in DNA damage‐ responsive cell cycle checkpoint proteins (1997) (789)
- The InterPro Database, 2003 brings increased coverage and new features (2003) (742)
- The CARD domain: a new apoptotic signalling motif. (1997) (547)
- Recent improvements to the PROSITE database (2004) (467)
- DNA Binding Specificity of Different STAT Proteins (2001) (424)
- The UBA domain: a sequence motif present in multiple enzyme classes of the ubiquitination pathway. (1996) (395)
- Methods and algorithms for statistical analysis of protein sequences. (1992) (385)
- InterPro: An Integrated Documentation Resource for Protein Families, Domains and Functional Sites (2002) (376)
- The FHA domain: a putative nuclear signalling domain found in protein kinases and transcription factors. (1995) (362)
- KRAB–Zinc Finger Proteins and KAP1 Can Mediate Long-Range Transcriptional Repression through Heterochromatin Spreading (2010) (309)
- A Flexible Motif Search Technique Based on Generalized Profiles (1996) (304)
- The PROSITE database, its status in 1995 (1996) (302)
- A conserved domain is present in different families of vesicular fusion proteins: a new superfamily. (1997) (300)
- Classification of human astrocytic gliomas on the basis of gene expression: a correlated group of genes with angiogenic activity emerges as a strong predictor of subtypes. (2003) (293)
- Compilation and analysis of eukaryotic POL II promoter sequences. (1986) (293)
- The PCI domain: a common theme in three multiprotein complexes. (1998) (291)
- Numerous potentially functional but non-genic conserved sequences on human chromosome 21 (2002) (256)
- Searching for regulatory elements in human noncoding sequences. (1997) (244)
- A Generalized Profile Syntax for Biomolecular Sequence Motifs and its Function in Automatic Sequence Interpretation (1994) (233)
- High-throughput SELEX–SAGE method for quantitative modeling of transcription-factor binding sites (2002) (232)
- The Eukaryotic Promoter Database: expansion of EPDnew and new promoter analysis tools (2014) (212)
- PROSITE: recent developments. (1994) (211)
- A Human Homolog of Yeast Est1 Associates with Telomerase and Uncaps Chromosome Ends When Overexpressed (2003) (208)
- Single-cell PCR analysis of TCR repertoires selected by antigen in vivo: a high magnitude CD8 response is comprised of very few clones. (1996) (205)
- Shotgun sequencing of the human transcriptome with ORF expressed sequence tags. (2000) (194)
- The discoidin domain family revisited: New members from prokaryotes and a homology‐based fold prediction (1998) (187)
- The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms (2016) (175)
- The Eukaryotic Promoter Database EPD (1998) (164)
- InterPro--an integrated documentation resource for protein families, domains and functional sites. (2000) (157)
- The Eukaryotic Promoter Database (EPD) (2000) (156)
- EPD in its twentieth year: towards complete promoter coverage of selected model organisms (2005) (149)
- Modeling sequencing errors by combining Hidden Markov models (2003) (140)
- Genome-wide prediction of matrix attachment regions that increase gene expression in mammalian cells (2007) (138)
- SNP2TFBS – a database of regulatory SNPs affecting predicted transcription factor binding site affinity (2016) (135)
- EPD and EPDnew, high-quality promoter resources in the next-generation sequencing era (2012) (135)
- Chromatin three-dimensional interactions mediate genetic effects on gene expression (2019) (124)
- Improving the sensitivity of the sequence profile method (1994) (120)
- The Eukaryotic Promoter Database, EPD: new entry types and links to gene expression data (2002) (117)
- Elf-1 and Stat5 bind to a critical element in a new enhancer of the human interleukin-2 receptor alpha gene (1996) (116)
- Sea urchin histone mRNA termini are located in gene regions downstream from putative regulatory sequences (1980) (112)
- UCNEbase—a database of ultraconserved non-coding elements and genomic regulatory blocks (2012) (100)
- The Eukaryotic Promoter Database EPD: the impact of in silico primer extension (2004) (95)
- PWMScan: a fast tool for scanning entire genomes with a position-specific weight matrix (2018) (90)
- ChIP-Seq Data Reveal Nucleosome Architecture of Human Promoters (2007) (89)
- Regulatory elements and expression profiles. (1999) (85)
- A model of Cdc25 phosphatase catalytic domain and Cdk-interaction surface based on the presence of a rhodanese homology domain. (1998) (83)
- Long-range heterogeneity at the 3' ends of human mRNAs. (2002) (82)
- SMiLE-seq identifies binding motifs of single and dimeric transcription factors (2017) (82)
- A consensus motif in the RFX DNA binding domain and binding domain mutants with altered specificity (1996) (81)
- Experimental analysis and computer prediction of CTF/NFI transcription factor DNA binding sites. (2000) (81)
- Telomere Maintenance in Fission Yeast Requires an Est1 Ortholog (2003) (81)
- Indexing Strategies for Rapid Searches of Short Words in Genome Sequences (2007) (77)
- Statistical methods and insights for protein and DNA sequences. (1991) (75)
- Mouse interleukin-2 receptor alpha gene expression. Interleukin-1 and interleukin-2 control transcription via distinct cis-acting elements. (1995) (73)
- The rsp5‐domain is shared by proteins of diverse functions (1995) (69)
- APDB: a novel measure for benchmarking sequence alignment methods without reference alignments (2003) (65)
- The Transcription Factor Rfx3 Regulates β-Cell Differentiation, Function, and Glucokinase Expression (2010) (64)
- Natural DNA sequences can form left-handed helices in low salt solution under conditions of topological constraint. (1982) (64)
- Opposing chromatin remodelers control transcription initiation frequency and start site selection (2019) (64)
- Similarities and differences of polyadenylation signals in human and fly (2006) (60)
- Long Distance Control of MHC Class II Expression by Multiple Distal Enhancers Regulated by Regulatory Factor X Complex and CIITA1 (2004) (59)
- A cSNP map and database for human chromosome 21. (2001) (57)
- The frizzled motif: in how many different protein families does it occur? (1998) (57)
- RNA Profiling and Chromatin Immunoprecipitation-Sequencing Reveal that PTF1a Stabilizes Pancreas Progenitor Identity via the Control of MNX1/HLXB9 and a Network of Other Transcription Factors (2012) (53)
- ZFN-Site searches genomes for zinc finger nuclease target sites and off-target sites (2011) (53)
- A Sequence Similarity Search Algorithm Based on a Probabilistic Interpretation of an Alignment Scoring System (1996) (53)
- Can Survival Prediction Be Improved By Merging Gene Expression Data Sets? (2009) (52)
- Nuclear factor I revealed as family of promoter binding transcription activators (2011) (52)
- Nineteen additional unpredicted transcripts from human chromosome 21. (2002) (51)
- MER41 Repeat Sequences Contain Inducible STAT1 Binding Sites (2010) (50)
- Evaluation of computer tools for the prediction of transcription factor binding sites on genomic DNA (1998) (50)
- The SIB Swiss Institute of Bioinformatics’ resources: focus on curated databases (2015) (47)
- Identification of CIITA Regulated Genetic Module Dedicated for Antigen Presentation (2008) (47)
- Elf-1 and Stat5 bind to a critical element in a new enhancer of the human interleukin-2 receptor alpha gene (1997) (45)
- The Eukaryotic Promoter Database (EPD): recent developments (1999) (42)
- Detection and benchmarking of somatic mutations in cancer genomes using RNA-seq data (2018) (41)
- Stealth Proteins: In Silico Identification of a Novel Protein Family Rendering Bacterial Pathogens Invisible to Host Immune Defense (2005) (41)
- CleanEx: a database of heterogeneous gene expression data based on a consistent gene nomenclature (2004) (40)
- Quantile distributions of amino acid usage in protein classes. (1992) (40)
- Identification of evolutionarily conserved regulatory elements in the mouse Fgf8 locus (2006) (40)
- trEST, trGEN and Hits: access to databases of predicted protein sequences (2001) (39)
- ChIPnorm: A Statistical Method for Normalizing and Identifying Differential Regions in Histone Modification ChIP-seq Libraries (2012) (35)
- Occurrence of oligopurine.oligopyrimidine tracts in eukaryotic and prokaryotic genes. (1991) (34)
- Transcription of a cloned Xenopus laevis H4 histone gene in the homologous frog oocyte system depends on an evolutionary conserved sequence motif in the -50 region. (1983) (33)
- Signal search analysis server (2003) (32)
- Predicting transcription factor site occupancy using DNA sequence intrinsic and cell-type specific chromatin features (2016) (32)
- Signal search analysis: a new method to localize and characterize functionally important DNA sequences (1984) (31)
- HTPSELEX—a database of high-throughput SELEX libraries for transcription factor binding sites (2005) (31)
- Molecular Models for the two Discoidin Domains of Human Blood Coagulation Factor V (1998) (30)
- CCAAT box revisited: bidirectionality, location and context. (1988) (30)
- Memory TCR repertoires analyzed long-term reflect those selected during the primary response. (1996) (30)
- A gene-rich, transcriptionally active environment and the pre-deposition of repressive marks are predictive of susceptibility to KRAB/KAP1-mediated silencing (2011) (28)
- Classification of selectively constrained DNA elements using feature vectors and rule-based classifiers. (2014) (28)
- The secreted protease Adamts18 links hormone action to activation of the mammary stem cell niche (2020) (28)
- Insights gained from a comprehensive all-against-all transcription factor binding motif benchmarking study (2020) (27)
- BlastR—fast and accurate database searches for non-coding RNAs (2011) (27)
- The ChIP-Seq tools and web server: a resource for analyzing ChIP-seq and other types of genomic data (2016) (27)
- Correlation analysis of amino acid usage in protein classes. (1992) (26)
- Nuclear Factor I genomic binding associates with chromatin boundaries (2013) (25)
- Significant similarity and dissimilarity in homologous proteins. (1992) (25)
- Genomic context analysis reveals dense interaction network between vertebrate ultraconserved non-coding elements (2012) (24)
- Proof of concept for microarray-based detection of DNA-binding oncogenes in cell extracts (2005) (24)
- The Eukaryotic Promoter Database (2002) (22)
- A quantitative, single-cell PCR analysis of an antigen-specific TCR repertoire selected during an in vivo CD8 response: direct evidence for a wide range of clone sizes with uniform tissue distribution. (1999) (22)
- Promoter Rearrangements Cause Species-specific Hepatic Regulation of the Glyoxylate Reductase/Hydroxypyruvate Reductase Gene by the Peroxisome Proliferator-activated Receptor α* (2005) (22)
- Influence of Rotational Nucleosome Positioning on Transcription Start Site Selection in Animal Promoters (2016) (21)
- Comparative T cell receptor repertoire selection by antigen after adoptive transfer: a glimpse at an antigen-specific preimmune repertoire. (2000) (18)
- Evidence for selective evolution in codon usage in conserved amino acid segments of human alphaherpesvirus proteins (1991) (18)
- Nucleosome eviction from MHC class II promoters controls positioning of the transcription start site (2009) (17)
- EPD in 2020: enhanced data visualization and extension to ncRNA promoters (2019) (17)
- trome, trEST and trGEN: databases of predicted protein sequences (2004) (17)
- Common genetic variants associated with Parkinson’s disease display widespread signature of epigenetic plasticity (2019) (16)
- Intraductal xenografts show lobular carcinoma cells rely on their own extracellular matrix and LOXL1 (2021) (16)
- Probabilistic partitioning methods to find significant patterns in ChIP-Seq data (2014) (15)
- Splicy: a web-based tool for the prediction of possible alternative splicing events from Affymetrix probeset data (2007) (15)
- Vertebrate conserved non coding DNA regions have a high persistence length and a short persistence time (2007) (14)
- Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support (2014) (13)
- Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach (2013) (13)
- Study of cell differentiation by phylogenetic analysis using histone modification data (2014) (12)
- Mmsearch: a Motif Arrangement Language and Search Program (2001) (12)
- MGA repository: a curated data resource for ChIP-seq and other genome annotated data (2017) (11)
- DNA formed by reassociation of complementary single-stranded circles from natural DNA is shown to contain left- and right-handed double helices. (1983) (10)
- SEView: a Java applet for browsing molecular sequence data (1998) (10)
- Individuality of Ag-selected and preimmune TCR repertoires (2001) (10)
- Characterization of a new tissue-specific transcription factor binding to the simian virus 40 enhancer TC-II (NF-kappa B) element (1992) (10)
- Practicality and Time Complexity of a Sparsified RNA Folding Algorithm (2012) (10)
- Contraceptive progestins with androgenic properties stimulate breast epithelial cell proliferation (2021) (10)
- Intra- and inter-chromosomal chromatin interactions mediate genetic effects on regulatory networks (2017) (9)
- A Conserved IL-2 Responsive Enhancer in the IL-2Rα Gene (1997) (9)
- Computational analysis of transcriptional regulatory elements: a field in flux (1996) (9)
- Chemically induced mouse liver tumors are resistant to treatment with atorvastatin (2014) (9)
- Estrogen receptor positive breast cancers have patient specific hormone sensitivities and rely on progesterone receptor (2022) (8)
- Mouse Interleukin-2 Receptor Gene Expression (1995) (8)
- Compilation andanalysis ofeukaryotic POLIIpromoter sequences (1986) (8)
- MADAP, a flexible clustering tool for the interpretation of one-dimensional genome annotation data (2007) (7)
- Principles of ChIP-seq Data Analysis Illustrated with Examples (2017) (7)
- A maximum-likelihood approach for building cell-type trees by lifting (2016) (6)
- CleanEx: new data extraction and merging tools based on MeSH term annotation (2008) (6)
- A conserved IL-2 responsive enhancer in the IL-2R alpha gene. (1997) (6)
- The Cis-Acting Elements Controlling Mouse IL-2Rα Transcription (1995) (5)
- Simulation of TATA Box Sequences in Eukaryotes (1997) (5)
- On Nussinov's compilation of eukaryotic transcription initiation sites. (1987) (4)
- Phylogenetic Analysis of Cell Types Using Histone Modifications (2013) (4)
- Algorithms in Bioinformatics, 6th International Workshop, WABI 2006, Zurich, Switzerland, September 11-13, 2006, Proceedings (2006) (3)
- Erratum: Elf-1 and Stat5 bind to a critical element in a new enhancer of the human interleukin-2 receptor α gene (Molecular and Cellular Biology 16:12 (6831)) (1997) (3)
- Non-food production of Jerusalem artichoke (Helianthus tuberosus) and possibilities of its energetic utilization. (2012) (2)
- Motif recognition in Biomolecular sequences (1999) (1)
- Insights gained from a comprehensive all-against-all transcription factor binding motif benchmarking study (2020) (1)
- Nuclear Factor I genomic binding associates with chromatin boundaries (2013) (1)
- Transcription factor binding and nucleosome positioning are alternative pathways for transcription start site selection in eukaryotic promoters (2014) (1)
- SPar-K: a method to partition NGS signal data (2019) (1)
- DATA ON EUKARYOTIC PROMOTERS AS DESCRIBED IN THE EPD DATABASE (1997) (1)
- Influence of rotational nucleosome positioning on transcription start site selection in animals promoters (2016) (1)
- Gene Feature Identification (1999) (1)
- SMiLE-seq: Selective Microfluidics-based Ligand Enrichment followed by sequencing (2017) (1)
- Computational identification and experimental characterization of preferred downstream positions in human core promoters (2021) (1)
- Study of cell differentiation by phylogenetic analysis using histone modification data (2014) (1)
- Automatic Procedures for Compilation of Promoter sequences and their Evaluation based on Signal Content and Positional Distributions (2003) (1)
- [Description of eukaryotic promoters in the EPD database]. (1997) (1)
- CleanEx : a Gene Expression Reference Database (2003) (0)
- Differentiation trees for cell developmental history based on histone modifications (2013) (0)
- Characterization of a New Tissue-Specific Factor Binding to the Simian Virus 40 TC-II (NF-FB) Element Transcription Enhancer (0)
- Optimizing generalized profiles for enhanced discrimination of biomolecular sequences (2000) (0)
- The ChIP-Seq tools and web server: a resource for analyzing ChIP-seq and other types of genomic data (2016) (0)
- Short-lived AUF1 p42-binding mRNAs of RANKL and BCL6 have two distinct instability elements each (2018) (0)
- altered specificity . domain and binding domain mutants with A consensus motif in the RFX DNA binding (1996) (0)
- receptor alpha gene. new enhancer of the human interleukin-2 Elf-1 and Stat5 bind to a critical element in a (2012) (0)
- Rapid and selective surveillance of Arabidopsis thaliana genome annotations with Centrifuge (2005) (0)
- Computational Biology: Annotated Glossary of Terms (2004) (0)
- Methods for discovery and characterization of DNA sequence motifs (2009) (0)
- Proceedings of the 6th international conference on Algorithms in Bioinformatics (2006) (0)
- Computational Biology: annotated glossary of terms (appendix 1). (2004) (0)
- Predicting transcription factor site occupancy using DNA sequence intrinsic and cell-type specific chromatin features (2016) (0)
- The secreted protease Adamts18 links hormone action to activation of the mammary stem cell niche (2020) (0)
- Abstract 2993: Intraductal xenografts model ERα-positive invasive lobular carcinoma of the breast (2021) (0)
- A mouse MHC class I-restricted response against HLA-CW3 is of high magnitude but, paradoxically, involves relatively few clones (1996) (0)
- The Breast Cancer Epigenomics Track Hub (2022) (0)
- 17 3583-3589 PROSITE : recent developments (2017) (0)
- The cis-acting elements controlling mouse IL-2R alpha transcription. (1995) (0)
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