Serafim Batzoglou | Academic Influence

Serafim Batzoglou's AcademicInfluence.com Rankings

Serafim Batzoglou

Computer Science

#2146

World Rank

#2229

Historical Rank

Database

#5972

World Rank

#6191

Historical Rank

computer-science Degrees

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Computer Science

Serafim Batzoglou's Degrees

PhD Computer Science Stanford University
Masters Computer Science Stanford University
Bachelors Computer Science Stanford University

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Why Is Serafim Batzoglou Influential?

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According to Wikipedia, Serafim Batzoglou is Chief Data Officer at Seer Inc. Prior to that he was Chief Data Officer at insitro, VP of computational genomics at Illumina, and professor of computer science at Stanford University between 2001 and 2016. His lab focused on computational genomics with special interest in developing algorithms, machine learning methods, and systems for the analysis of large scale genomic data. He has also been involved with the Human Genome Project and ENCODE.

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Serafim Batzoglou'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)
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project (2007) (5196)
The ENCODE (ENCyclopedia Of DNA Elements) Project (2004) (2194)
An integrated encyclopedia of DNA elements in the human genome (2012) (2080)
Genome sequence of the Brown Norway rat yields insights into mammalian evolution (2004) (2053)
Evolution of genes and genomes on the Drosophila phylogeny (2007) (1992)
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia (2012) (1701)
A User's Guide to the Encyclopedia of DNA Elements (ENCODE) (2011) (1467)
Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++ (2010) (1405)
Architecture of the human regulatory network derived from ENCODE data (2012) (1393)
Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae (2005) (1321)
Distribution and intensity of constraint in mammalian genomic sequence. (2005) (1275)
ProbCons: Probabilistic consistency-based multiple sequence alignment. (2005) (1166)
LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. (2003) (1131)
Predicting Splicing from Primary Sequence with Deep Learning (2019) (895)
Genome-Wide Analysis of Transcription Factor Binding Sites Based on ChIP-Seq Data (2008) (760)
ARACHNE: a whole-genome shotgun assembler. (2002) (686)
Linking disease associations with regulatory information in the human genome (2012) (645)
CONTRAfold: RNA secondary structure prediction without physics-based models (2006) (491)
Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learning (2016) (462)
Human and mouse gene structure: comparative analysis and application to exon prediction (2000) (412)
Glocal alignment: finding rearrangements during alignment (2003) (401)
Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer (2018) (398)
Multiple sequence alignment. (2006) (396)
Graemlin: general and robust alignment of multiple large interaction networks. (2006) (355)
Extensive Variation in Chromatin States Across Humans (2013) (346)
What is the expectation maximization algorithm? (2008) (336)
Application of independent component analysis to microarrays (2003) (290)
Mutations in early follicular lymphoma progenitors are associated with suppressed antigen presentation (2015) (286)
Bacterial flora-typing with targeted, chip-based Pyrosequencing (2007) (246)
Predicting the clinical impact of human mutation with deep neural networks (2018) (227)
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. (2007) (221)
Fast and sensitive multiple alignment of large genomic sequences (2003) (188)
Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements (2012) (184)
Fast and scalable inference of multi-sample cancer lineages (2014) (175)
Eukaryotic regulatory element conservation analysis and identification using comparative genomics. (2004) (168)
Autoimmune Disease Classification by Inverse Association with SNP Alleles (2009) (162)
Characterization of evolutionary rates and constraints in three Mammalian genomes. (2004) (146)
Quantitative estimates of sequence divergence for comparative analyses of mammalian genomes. (2003) (139)
Whole-Genome Sequencing and Assembly with High-Throughput, Short-Read Technologies (2007) (136)
Analysis of Cell Fate from Single-Cell Gene Expression Profiles in C. elegans (2009) (132)
The many faces of sequence alignment (2005) (131)
MotifCut: regulatory motifs finding with maximum density subgraphs (2006) (125)
Short read alignment with populations of genomes (2013) (116)
Automated whole-genome multiple alignment of rat, mouse, and human. (2004) (108)
A serial founder effect model for human settlement out of Africa (2009) (106)
Erratum: Initial sequencing and analysis of the human genome: International Human Genome Sequencing Consortium (Nature (2001) 409 (860-921)) (2001) (106)
CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction (2007) (105)
DNA methylation landscapes in advanced prostate cancer (2020) (98)
Automatic Parameter Learning for Multiple Network Alignment (2008) (98)
Network enhancement as a general method to denoise weighted biological networks (2018) (96)
CONTRAlign: Discriminative Training for Protein Sequence Alignment (2006) (95)
Genome-wide reconstruction of complex structural variants using read clouds (2016) (90)
High-quality genome sequences of uncultured microbes by assembly of read clouds (2018) (90)
Multi-omic tumor data reveal diversity of molecular mechanisms that correlate with survival (2018) (89)
Genome evolution during progression to breast cancer (2013) (89)
Automatic Parameter Learning for Multiple Local Network Alignment (2009) (88)
A max-margin model for efficient simultaneous alignment and folding of RNA sequences (2008) (87)
Local rules for protein folding on a triangular lattice and generalized hydrophobicity in the HP model (1997) (82)
Effect of genetic divergence in identifying ancestral origin using HAPAA. (2008) (80)
Evolutionary constraint facilitates interpretation of genetic variation in resequenced human genomes. (2010) (80)
SIMLR: a tool for large-scale single-cell analysis by multi-kernel learning (2017) (66)
Synthetic long read sequencing reveals the composition and intraspecies diversity of the human microbiome (2015) (63)
Read clouds uncover variation in complex regions of the human genome (2015) (58)
Integrated Protein Interaction Networks for 11 Microbes (2006) (52)
Phylo-VISTA: interactive visualization of multiple DNA sequence alignments (2004) (52)
Multiple alignment of protein sequences with repeats and rearrangements (2006) (50)
Inference of Tumor Phylogenies with Improved Somatic Mutation Discovery (2013) (50)
Current progress in network research: toward reference networks for key model organisms (2007) (49)
Erratum: Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer (Cell (2018) 174(3) (758–769.e9), (S0092867418308420) (10.1016/j.cell.2018.06.039)) (2018) (48)
PROBCONS: Probabilistic Consistency-Based Multiple Alignment of Amino Acid Sequences (2004) (48)
The DNA methylation landscape of advanced prostate cancer (2020) (44)
Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer (2018) (44)
Local rules for protein folding on a triangular lattice and generalized hydrophobicity in the HP model. (1997) (41)
AGenDA: homology-based gene prediction (2003) (39)
A suite of web-based programs to search for transcriptional regulatory motifs (2004) (38)
Training Conditional Random Fields for Maximum Labelwise Accuracy (2006) (36)
Genetic and Computational Identification of a Conserved Bacterial Metabolic Module (2008) (33)
Strain-resolved microbiome sequencing reveals mobile elements that drive bacterial competition on a clinical timescale (2018) (32)
Genome assembly from synthetic long read clouds (2016) (29)
Identification of promoter regions in the human genome by using a retroviral plasmid library-based functional reporter gene assay. (2003) (29)
Sequencing a genome by walking with clone-end sequences: a mathematical analysis. (1999) (28)
Ancestry Inference in Complex Admixtures via Variable-Length Markov Chain Linkage Models (2012) (26)
Microbial Typing by Machine Learned DNA Melt Signatures (2017) (26)
A graph-based motif detection algorithm models complex nucleotide dependencies in transcription factor binding sites (2006) (25)
A machine-compiled database of genome-wide association studies (2019) (24)
Parente2: a fast and accurate method for detecting identity by descent (2015) (23)
A hybrid cloud read aligner based on MinHash and kmer voting that preserves privacy (2017) (23)
A Classifier-based approach to identify genetic similarities between diseases (2009) (22)
A computational model for RNA multiple structural alignment (2004) (21)
A dictionary based approach for gene annotation (1999) (19)
Reconstruction of genealogical relationships with applications to Phase III of HapMap (2011) (18)
Cell-lineage heterogeneity and driver mutation recurrence in pre-invasive breast neoplasia (2015) (18)
alignment ProbCons : Probabilistic consistency-based multiple sequence data (2005) (15)
Computational biology and bioinformatics. (2014) (15)
Vicus: Exploiting local structures to improve network-based analysis of biological data (2017) (14)
De novo assembly of microbial genomes from human gut metagenomes using barcoded short read sequences (2017) (14)
Physical Mapping with Repeated Probes: The Hypergraph Superstring Problem (1999) (14)
Using multiple alignments to improve seeded local alignment algorithms (2005) (14)
Alignment of Genomic DNA LAGAN and Multi-LAGAN : Efficient Tools for Large-Scale Multiple (2003) (13)
Algorithmic challenges in mammalian whole‐genome assembly (2005) (13)
Chaining Algorithms for Alignment of Draft Sequence (2004) (12)
A dictionary-based approach for gene annotation. (1999) (11)
Privacy-Preserving Read Mapping Using Locality Sensitive Hashing and Secure Kmer Voting (2016) (11)
Automated cellular annotation for high-resolution images of adult Caenorhabditis elegans (2013) (11)
Reveel: large-scale population genotyping using low-coverage sequencing data (2014) (10)
ICA-based Clustering of Genes from Microarray Expression Data (2003) (9)
HAPDeNovo: a haplotype-based approach for filtering and phasing de novo mutations in linked read sequencing data (2017) (9)
Protein Folding in the Hydrophobic-Polar Model on the 3D Triangular Lattice (1996) (9)
Detection of Hidden Intertextuality in the Scientific Publications (2012) (8)
GATTACA: Lightweight Metagenomic Binning with Compact Indexing of Kmer Counts and MinHash-based Panel Selection (2017) (8)
Phylo-VISTA: An Interactive Visualization Tool for Multiple DNA Sequence Alignments (2003) (8)
Current Progress in Static and Dynamic Modeling of Biological Networks (2010) (7)
Recent Developments in Computational Gene Recognition (1998) (7)
Constraint and divergence of global gene expression in the mammalian embryo (2015) (7)
Toward an Individual Approach to Methadone Therapy of Heroin Addicts (2006) (7)
Culture-free generation of microbial genomes from human and marine microbiomes (2018) (7)
An Accurate Method for Inferring Relatedness in Large Datasets of Unphased Genotypes via an Embedded Likelihood-Ratio Test (2013) (6)
Fast Metagenomic Binning via Hashing and Bayesian Clustering (2018) (6)
Engineered nanoparticles enable deep proteomics studies at scale by leveraging tunable nano–bio interactions (2022) (6)
An Effective Filter for IBD Detection in Large Data Sets (2014) (5)
Unsupervised Learning from Noisy Networks with Applications to Hi-C Data (2016) (5)
Enhanced Competition at the Nano–Bio Interface Enables Comprehensive Characterization of Protein Corona Dynamics and Deep Coverage of Proteomes (2022) (5)
Network enhancement as a general method to denoise weighted biological networks (2018) (5)
Meltos: multi-sample tumor phylogeny reconstruction for structural variants (2019) (5)
Prediction of Self-Assembly of Energetic Tiles and Dominos: Experiments, Mathematics and Software (2000) (4)
Chromosome-level de novo assembly of the pig-tailed macaque genome using linked-read sequencing and HiC proximity scaffolding (2019) (4)
TreeRefiner: a tool for refining a multiple alignment on a phylogenetic tree (2005) (4)
The Human OligoGenome Resource: a database of oligonucleotide capture probes for resequencing target regions across the human genome (2011) (4)
Author Correction: Predicting the clinical impact of human mutation with deep neural networks (2018) (3)
Editorial (2014) (3)
Finding Regulatory Motifs with Maximum Density Subgraphs (2006) (3)
Computational genomics: mapping, comparison, and annotation of genomes (2000) (3)
Enhanced competitive protein exchange at the nano-bio interface enables ultra-deep coverage of the human plasma proteome (2022) (2)
Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network (2021) (2)
Peptide-centric analyses of human plasma enable increased resolution of biological insights into non-small cell lung cancer relative to protein-centric analysis (2022) (1)
Proceedings of the 13th Annual International Conference on Research in Computational Molecular Biology (2009) (1)
The landscape of tolerated genetic variation in humans and primates (2023) (1)
Effects of Genetic Divergence in Identifying Ancestral Origin Using HAPAA (2008) (1)
modENCODE consortia ChIP-seq guidelines and practices of the ENCODE and Material Supplemental (2012) (1)
Method Application of independent component analysis to microarrays (2003) (1)
Protein Structure Prediction II (2006) (0)
Gene Regulation - Session Introduction (2003) (0)
Sequence Alignment Continued Sequence Alignment Continued 1 Previous Lecture Review Needleman-wunsch with Affine Gaps Linear-space Alignment Algorithm (2005) (0)
Scribe: Vignesh Ganapathy 1/26/2006 -1 - Cs262 Computational Genomics Lecture 6: Hidden Markov Models (contd.) Professor Serafim Batzoglou Geometric Distribution of State Duration (2006) (0)
Discovering biological processes from microarray data using independent component analysis Extended Abstract (2003) (0)
human genome Linking disease associations with regulatory information in the Material Supplemental (2012) (0)
Author Correction: Predicting the clinical impact of human mutation with deep neural networks (2018) (0)
Abstract PD05-09: Whole-genome progression of breast cancer from early neoplasia to invasive carcinoma (2012) (0)
Population Genotype Calling from Low-coverage Sequencing Data (2017) (0)
Tumor Phylogeny Reconstruction for Structural Variants (2018) (0)
GATTACA: Lightweight Metagenomic Binning Using Kmer Counting (2017) (0)
ISMB 2010 Organization (2010) (0)
Strain-resolved microbiome sequencing reveals mobile elements that drive bacterial competition on a clinical timescale (2020) (0)
Editorial (2004) (0)
Goedel's Incompleteness Theorem (2021) (0)
A machine-compiled database of genome-wide association studies (2019) (0)
Special Issue Papers The many faces of sequence (2005) (0)
Clustering reveals ubiquitous heterogeneity and asymmetry of genomic signals at functional elements (2013) (0)
Cell-lineage heterogeneity and driver mutation recurrence in pre-invasive breast neoplasia (2015) (0)
Functionally distinct BMP1 isoforms show an opposite pattern of abundance in plasma from non-small cell lung cancer subjects and controls (2023) (0)
Research in Computational Molecular Biology (2009) (0)
Genome evolution during progression to breast cancer Material (2013) (0)
Author Correction: Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network (2022) (0)
A Machine-Curated Database of Genome-Wide 1 Association Studies 2 (2018) (0)
Abstract 6340: Deep, unbiased and peptide-centric plasma proteomics with differential analysis of proteoforms enabling proteogenomic studies of NSCLC at scale (2022) (0)
Nanoparticle Enrichment Mass-Spectrometry Proteomics Identifies Protein Altering Variants for Precise pQTL Mapping (2023) (0)
Author Response. (2015) (0)
Abstract 6339: Deep plasma proteomics at scale enabling proteogenomic analyses in a lung cancer (NSCLC) study (2022) (0)
Abstract 2537: Application of the proteograph to the identification of differential protein isoform plasma abundance in early lung cancer vs. healthy controls (2021) (0)
Multi-omic tumor data reveal diversity of molecular mechanisms that correlate with survival (2018) (0)
Cs 262: Computational Genomics Professor Serafim Batzoglou Lecture 8: Pair Hmms and Protein Alignment Finite State Automaton for Alignment (2006) (0)
Large-scale Population Genotyping from Low-coverage Sequencing Data using a Reference Panel (2016) (0)
Evidence for intelligent (algorithm) design (2006) (0)
Lecture 16 : Protein Structure Prediction (2006) (0)
Vicus: Exploiting Local Structures to Improve Biological Network Analysis Supplementary Information (2017) (0)
Construction of Networks from Diverse Data Sources (2006) (0)
DNA Computing and Molecular Self-Assembly Area Exam (2003) (0)
Predicting the clinical impact of human mutation with deep neural networks (2018) (0)
HAPDeNovo: a haplotype-based approach for filtering and phasing de novo mutations in linked read sequencing data (2018) (0)
RECOMB Main Conference 2009 (2010) (0)
Independence of the Continuum Hypothesis: an Intuitive Introduction (2022) (0)
Abstract 6348: A cloud-scalable software suite for large-cohort proteogenomics data analysis and visualization (2022) (0)
Analyses of Mammalian Genomes Quantitative Estimates of Sequence Divergence for Comparative Material Supplemental (2003) (0)
Fast and scalable inference of multi-sample cancer lineages (2015) (0)
Sequencing a genome by walking with clone-end sequences (abstract): a mathematical analysis (2000) (0)
An Equality Theorem Prover Based on Grammar Rewriting (1996) (0)

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