Sean Eddy
#25,808
Most Influential Person Now
American computational biologist
Sean Eddy's AcademicInfluence.com Rankings
Sean Eddybiology Degrees
Biology
#972
World Rank
#1687
Historical Rank
#517
USA Rank
Bioinformatics
#13
World Rank
#13
Historical Rank
#6
USA Rank
Computational Biology
#24
World Rank
#24
Historical Rank
#10
USA Rank
Sean Eddycomputer-science Degrees
Computer Science
#2278
World Rank
#2374
Historical Rank
#1023
USA Rank
Informatics
#5
World Rank
#5
Historical Rank
#3
USA Rank
Database
#285
World Rank
#298
Historical Rank
#136
USA Rank
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Biology Computer Science
Sean Eddy's Degrees
- PhD Biophysics University of Colorado Boulder
- Bachelors Biology University of Washington
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Why Is Sean Eddy Influential?
(Suggest an Edit or Addition)According to Wikipedia, Sean Roberts Eddy is Professor of Molecular & Cellular Biology and of Applied Mathematics at Harvard University. Previously he was based at the Janelia Research Campus from 2006 to 2015 in Virginia. His research interests are in bioinformatics, computational biology and biological sequence analysis. projects include the use of Hidden Markov models in HMMER, Infernal Pfam and Rfam.
Sean Eddy'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
- Initial sequencing and analysis of the human genome. (2001) (15222)
- Pfam: the protein families database (2013) (12454)
- tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. (1997) (9661)
- The Pfam protein families database (2005) (7519)
- Profile hidden Markov models (1998) (5137)
- The Pfam protein families database: towards a more sustainable future (2015) (4710)
- Initial sequencing and comparative analysis of the mouse genome. (2002) (4609)
- Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids (1998) (4580)
- What is dynamic programming? (2004) (4351)
- Accelerated Profile HMM Searches (2011) (4214)
- HMMER web server: interactive sequence similarity searching (2011) (3963)
- The Pfam protein families database in 2019 (2018) (3247)
- The Pfam protein families database (2004) (2565)
- Pfam: clans, web tools and services (2005) (2262)
- Hidden Markov models. (1996) (1984)
- A uniform system for microRNA annotation. (2003) (1825)
- Infernal 1.1: 100-fold faster RNA homology searches (2013) (1800)
- Rfam: an RNA family database (2003) (1446)
- Rfam: annotating non-coding RNAs in complete genomes (2004) (1419)
- Non–coding RNA genes and the modern RNA world (2001) (1360)
- Infernal 1.0: inference of RNA alignments (2009) (1257)
- Pfam: A comprehensive database of protein domain families based on seed alignments (1997) (1221)
- A new generation of homology search tools based on probabilistic inference. (2009) (1132)
- HMMER web server: 2018 update (2018) (989)
- Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions (2013) (925)
- Rfam 12.0: updates to the RNA families database (2014) (895)
- Rfam: updates to the RNA families database (2008) (861)
- RNA sequence analysis using covariance models. (1994) (851)
- Hidden Markov model speed heuristic and iterative HMM search procedure (2010) (799)
- A dynamic programming algorithm for RNA structure prediction including pseudoknots. (1998) (785)
- Pfam: multiple sequence alignments and HMM-profiles of protein domains (1998) (784)
- Rfam 11.0: 10 years of RNA families (2012) (772)
- HMMER web server: 2015 update (2015) (721)
- Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families (2017) (719)
- Automated de novo identification of repeat sequence families in sequenced genomes. (2002) (710)
- Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain (2015) (541)
- Noncoding RNA gene detection using comparative sequence analysis (2001) (538)
- Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins (1999) (532)
- nhmmer: DNA homology search with profile HMMs (2013) (531)
- Pack-MULE transposable elements mediate gene evolution in plants (2004) (525)
- Multiple Alignment Using Hidden Markov Models (1995) (520)
- The Distributed Annotation System (2001) (483)
- A computational screen for methylation guide snoRNAs in yeast. (1999) (472)
- An active DNA transposon family in rice (2003) (441)
- Computational identification of noncoding RNAs in E. coli by comparative genomics (2001) (433)
- The DNA sequence of human chromosome 7 (2003) (425)
- Rfam: Wikipedia, clans and the “decimal” release (2010) (413)
- The Dfam database of repetitive DNA families (2015) (410)
- Homologs of small nucleolar RNAs in Archaea. (2000) (348)
- Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs (2000) (325)
- ATV: display and manipulation of annotated phylogenetic (2001) (316)
- Kissing complex RNAs mediate interaction between the Fragile-X mental retardation protein KH2 domain and brain polyribosomes. (2005) (311)
- Query-Dependent Banding (QDB) for Faster RNA Similarity Searches (2007) (310)
- A Probabilistic Model of Local Sequence Alignment That Simplifies Statistical Significance Estimation (2008) (304)
- The Pfam protein families database (2009) (296)
- RSEARCH: Finding homologs of single structured RNA sequences (2003) (295)
- Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction (2004) (293)
- Maximum Discrimination Hidden Markov Models of Sequence Consensus (1995) (278)
- Where did the BLOSUM62 alignment score matrix come from? (2004) (274)
- Rfam 14: expanded coverage of metagenomic, viral and microRNA families (2020) (265)
- A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure (2002) (265)
- Computational Genomics of Noncoding RNA Genes (2002) (260)
- A statistical test for conserved RNA structure shows lack of evidence for structure in lncRNAs (2016) (251)
- Changes in gene expression associated with developmental arrest and longevity in Caenorhabditis elegans. (2001) (237)
- A simple algorithm to infer gene duplication and speciation events on a gene tree (2001) (226)
- Structural rna homology search and alignment using covariance models (2009) (223)
- RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs (2002) (217)
- The Pfam protein families database. (2004) (204)
- Dfam: a database of repetitive DNA based on profile hidden Markov models (2012) (202)
- What is a hidden Markov model? (2004) (201)
- Noncoding RNA genes identified in AT-rich hyperthermophiles (2002) (194)
- The language of RNA: a formal grammar that includes pseudoknots (2000) (193)
- The Oxytricha trifallax Macronuclear Genome: A Complex Eukaryotic Genome with 16,000 Tiny Chromosomes (2013) (192)
- Prepublication data sharing (2009) (190)
- Biological sequence analysis: Background on probability (1998) (172)
- The Pfam Protein Families Database (2002) (166)
- How do RNA folding algorithms work? (2004) (164)
- Noncoding RNA genes. (1999) (153)
- The C-value paradox, junk DNA and ENCODE (2012) (142)
- Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints (2006) (142)
- A genetic, genomic, and computational resource for exploring neural circuit function (2018) (132)
- A Model of the Statistical Power of Comparative Genome Sequence Analysis (2005) (131)
- Cell type–specific genomics of Drosophila neurons (2012) (129)
- Epigenomic landscapes of retinal rods and cones (2016) (121)
- Computational analysis of conserved RNA secondary structure in transcriptomes and genomes. (2014) (109)
- Erratum: Initial sequencing and analysis of the human genome: International Human Genome Sequencing Consortium (Nature (2001) 409 (860-921)) (2001) (106)
- Computational identification of non-coding RNAs in Saccharomyces cerevisiae by comparative genomics. (2003) (104)
- Biological sequence analysis: Preface (1998) (100)
- Generation and annotation of the DNA sequences of human chromosomes 2 and 4 (2005) (98)
- Sharing Publication-Related Data and Materials: Responsibilities of Authorship in the Life Sciences1 (2003) (98)
- The ENCODE project: Missteps overshadowing a success (2013) (95)
- A range of complex probabilistic models for RNA secondary structure prediction that includes the nearest-neighbor model and more. (2012) (94)
- Many, but not all, lineage-specific genes can be explained by homology detection failure (2020) (73)
- The Pfam protein families database (2007) (72)
- The phage T4 nrdB intron: a deletion mutant of a version found in the wild. (1991) (69)
- Probabilistic Phylogenetic Inference with Insertions and Deletions (2008) (67)
- Members of the immunoglobulin superfamily in bacteria (1996) (67)
- Autogenous translational operator recognized by bacteriophage T4 DNA polymerase. (1990) (66)
- What is Bayesian statistics? (2004) (66)
- HMMER User's Guide - Biological sequence analysis using profile hidden Markov models (1998) (64)
- Representation learning of genomic sequence motifs with convolutional neural networks (2018) (61)
- Estimating the power of sequence covariation for detecting conserved RNA structure (2019) (54)
- C. elegans noncoding RNA genes. (2005) (52)
- Circular box C/D RNAs in Pyrococcus furiosus. (2004) (49)
- Identification and Characterization of a Class of MALAT1-like Genomic Loci. (2017) (46)
- Fast filtering for RNA homology search (2011) (38)
- Computational identification of functional RNA homologs in metagenomic data (2013) (37)
- Artificial mobile DNA element constructed from the EcoRI endonuclease gene. (1992) (33)
- Computational analysis of RNAs. (2006) (31)
- “Antedisciplinary” Science (2005) (30)
- A Member of the Immunoglobulin Superfamily in Bacteriophage T4 (2004) (30)
- Inferring Sequence-Structure Preferences of RNA-Binding Proteins with Convolutional Residual Networks (2018) (27)
- A survey of nematode SmY RNAs (2009) (27)
- Parameterizing sequence alignment with an explicit evolutionary model (2015) (26)
- Combinatorial DNA Rearrangement Facilitates the Origin of New Genes in Ciliates (2015) (25)
- Remote homology search with hidden Potts models (2020) (23)
- Archaeal Guide RNAs Function in rRNA Modification in the Eukaryotic Nucleus (2002) (22)
- A tool for identification of genes expressed in patterns of interest using the Allen Brain Atlas (2009) (22)
- Local RNA structure alignment with incomplete sequence (2009) (21)
- Group I introns are widespread in archaea (2018) (19)
- Sequence analysis Infernal 1 . 0 : inference of RNA alignments (2009) (18)
- Transcription Factors That Convert Adult Cell Identity Are Differentially Polycomb Repressed (2013) (18)
- Mixing genome annotation methods in a comparative analysis inflates the apparent number of lineage-specific genes (2022) (17)
- Gene Evolution: Getting Something from Nothing (2017) (17)
- Exploiting Oxytricha trifallax nanochromosomes to screen for non-coding RNA genes (2011) (15)
- Multiple-alignment and -sequence searches (1998) (13)
- A computational screen for alternative genetic codes in over 250,000 genomes (2021) (12)
- Genome Sequence of Additional Caenorhabditis species : Enhancing the Utility of C . elegans as a Model Organism (2003) (11)
- Biological sequence analysis: Markov chains and hidden Markov models (1998) (11)
- Total Information Awareness for Worm Genetics (2006) (9)
- Free circular introns with an unusual branchpoint in neuronal projections (2019) (9)
- Constructing benchmark test sets for biological sequence analysis using independent set algorithms (2021) (8)
- Unrestricted free access works and must continue (2003) (7)
- The Caenorhabditis Elegans Genome Project (1994) (6)
- Rna structural alignment using stochastic context-free grammars (2004) (6)
- Response to Tavares et al., “Covariation analysis with improved parameters reveals conservation in lncRNA structures” (2020) (6)
- Biological sequence analysis: Building phylogenetic trees (1998) (5)
- Biological sequence analysis: Pairwise alignment (1998) (5)
- Homology searches for structural RNAs: from proof of principle to practical use (2015) (4)
- Open Revolution (2009) (3)
- 19 RNA: The Shape of Things to Come (1993) (3)
- Biological sequence analysis: Profile HMMs for sequence families (1998) (3)
- Biological sequence analysis: Probabilistic approaches to phylogeny (1998) (3)
- Biological sequence analysis: RNA structure analysis (1998) (3)
- Biological sequence analysis: Pairwise alignment using HMMs (1998) (3)
- Multiple alignment and multiple sequence based searches (1998) (2)
- RNA structure alignment on a massively parallel computer (1995) (1)
- Improved HMMERHEAD for Better Sensitivity (2007) (1)
- Shotgun coverage of human genome computing (1999) (1)
- Biological sequence analysis: Multiple sequence alignment methods (1998) (1)
- Codetta: predicting the genetic code from nucleotide sequence (2022) (1)
- Biological sequence analysis: Introduction (1998) (1)
- Is the Pope the Pope? (1996) (1)
- Genetics. Total information awareness for worm genetics. (2006) (1)
- Broadening Pfam Protein Sequence Annotations (2009) (0)
- Correction: Constructing Benchmark Test Sets for Biological Sequence Analysis Using Independent Set Algorithms (2023) (0)
- Handout for the Phylogenetics Lecture (2017) (0)
- [Invited Lecture] Genome sequence analysis and profile hidden Markov models (1998) (0)
- Inside the black boxes Computer methods for macromolecular sequence analysis (Methods in enzymology vol. 266) (1997) (0)
- BIOL 495S/ CS 490B/ MATH 490B/ STAT 490B (2002) (0)
- Sequence analysis Local RNA structure alignment with incomplete sequence (2009) (0)
- Resource Identification and Charact erization of a Class of MALAT 1-like Genomic Loci Graphical Abstract Highlights (2017) (0)
- wild.The phage T4 nrdB intron: a deletion mutant of a version found in the (2007) (0)
- Statistical models called hidden Markov models are a recurring theme in computational biology. What are hidden Markov models, and why are they so useful for so many different problems? (2004) (0)
- Running title : Covariance models of RNA RNA Sequence Analysis Using Covariance Models (1998) (0)
- Author response: Epigenomic landscapes of retinal rods and cones (2015) (0)
- Comparison of key ciliate macronuclear genomes. (2013) (0)
- A computational screen for 1 alternative genetic codes in over 2 250 , 000 genomes 3 (2021) (0)
- Comparative genomics of Oxytricha and related spirotrichous ciliates : Minimal eukaryotic genome architectures (2007) (0)
- The human genome project: Deciphering the blueprint of heredity: edited by Necla Grant Cooper, University Science Press, 1994. £27.95 (vii + 360 pages) ISBN 0 935702 29 6 (1995) (0)
- RNA Families A survey of nematode SmY RNAs (0)
- HIDDEN MARKOV MODELS AND LARGE-SCALE GENOMEANALYSISSean (1997) (0)
- Biological sequence analysis: Bibliography (1998) (0)
- Parameterizing sequence alignment with an explicit evolutionary model (2015) (0)
- Biological sequence analysis: Transformational grammars (1998) (0)
- Molecular genetics in silico (1996) (0)
- Probabilities and probabilistic models (2002) (0)
- ORFeus: A Computational Method to Detect Programmed Ribosomal Frameshifts and Other Non-Canonical Translation Events (2023) (0)
- Genomic Analysis of Noncoding RNAs (2003) (0)
- Title : Cortical neuron cell types develop highly divergent epigenetic configurations (2014) (0)
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What Schools Are Affiliated With Sean Eddy?
Sean Eddy is affiliated with the following schools:
