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List of works by Serafim Batzoglou

A Classifier-based approach to identify genetic similarities between diseases

scientific article published on June 2009

A dictionary based approach for gene annotation

article

A graph-based motif detection algorithm models complex nucleotide dependencies in transcription factor binding sites

scientific article published on 13 October 2006

A hybrid cloud read aligner based on MinHash and kmer voting that preserves privacy

scientific article published on 16 May 2017

A machine-compiled database of genome-wide association studies

scientific article published on 26 July 2019

A max-margin model for efficient simultaneous alignment and folding of RNA sequences

scientific article published on July 2008

A serial founder effect model for human settlement out of Africa.

scientific article

A suite of web-based programs to search for transcriptional regulatory motifs

scientific article published on July 2004

AGenDA: homology-based gene prediction

scientific article published in August 2003

ARACHNE: a whole-genome shotgun assembler

scientific article

An effective filter for IBD detection in large data sets

scientific article

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome

scientific article published in June 2007

Analysis of cell fate from single-cell gene expression profiles in C. elegans

scientific article

Ancestry Inference in Complex Admixtures via Variable-length Markov Chain Linkage Models ⬇️

scientific article published on February 19, 2013

Application of independent component analysis to microarrays

scientific article

Architecture of the human regulatory network derived from ENCODE data

scientific article (publication date: 6 September 2012)

Author Correction: Predicting the clinical impact of human mutation with deep neural networks

scientific article published on 01 February 2019

Autoimmune disease classification by inverse association with SNP alleles

scientific article

Automated cellular annotation for high-resolution images of adult Caenorhabditis elegans ⬇️

scientific article published on July 1, 2013

Automated whole-genome multiple alignment of rat, mouse, and human

scientific article published on April 2004

Automatic parameter learning for multiple local network alignment

scientific article published on August 2009

Bacterial flora-typing with targeted, chip-based Pyrosequencing

scientific article

CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction

scientific article

CONTRAfold: RNA secondary structure prediction without physics-based models

scientific article

Cell-lineage heterogeneity and driver mutation recurrence in pre-invasive breast neoplasia

scientific article published on 9 April 2015

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

scientific article

Chaining Algorithms for Alignment of Draft Sequence

Characterization of evolutionary rates and constraints in three Mammalian genomes

scientific article published on April 2004

Chromosome-level de novo assembly of the pig-tailed macaque genome using linked-read sequencing and HiC proximity scaffolding

scientific article published on 01 July 2020

Computational biology and bioinformatics

scientific article published on June 2014

Constraint and divergence of global gene expression in the mammalian embryo

scientific article published on 14 April 2015

Current progress in network research: toward reference networks for key model organisms

scientific article published on 29 August 2007

Effect of genetic divergence in identifying ancestral origin using HAPAA.

scientific article published on 18 March 2008

Eukaryotic regulatory element conservation analysis and identification using comparative genomics

scientific article published on March 2004

Evidence for intelligent (algorithm) design

scientific article (publication date: 2006)

Evolution of genes and genomes on the Drosophila phylogeny

scientific article

Evolutionary constraint facilitates interpretation of genetic variation in resequenced human genomes

scientific article

Extensive variation in chromatin states across humans

scientific article

Fast Metagenomic Binning via Hashing and Bayesian Clustering

scientific article published on 16 April 2018

Fast and scalable inference of multi-sample cancer lineages

scientific article published on 6 May 2015

Fast and sensitive multiple alignment of large genomic sequences

scientific article

Genetic and computational identification of a conserved bacterial metabolic module

scientific article

Genome assembly from synthetic long read clouds

scientific article

Genome evolution during progression to breast cancer

scientific article published on 08 April 2013

Genome sequence of the Brown Norway rat yields insights into mammalian evolution

scientific article

Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data

scientific article

Genome-wide reconstruction of complex structural variants using read clouds.

scientific article published on 17 July 2017

Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer

Genomic Hallmarks and Structural Variation in Metastatic Prostate Cancer

Glocal alignment: finding rearrangements during alignment

scientific article

Graemlin: general and robust alignment of multiple large interaction networks

scientific article

HAPDeNovo: a haplotype-based approach for filtering and phasing de novo mutations in linked read sequencing data.

scientific article

High-quality genome sequences of uncultured microbes by assembly of read clouds

scientific article published on 15 October 2018

ICA-based Clustering of Genes from Microarray Expression Data ⬇️

scientific article published in January 2004

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

scientific article published in June 2007

Identification of promoter regions in the human genome by using a retroviral plasmid library-based functional reporter gene assay

scientific article

Identifying a high fraction of the human genome to be under selective constraint using GERP++.

scientific article

Inference of tumor phylogenies with improved somatic mutation discovery

scientific article published on November 2013

Initial sequencing and analysis of the human genome

scientific article published on 15 February 2001

LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA

scientific article (publication date: April 2003)

Linking disease associations with regulatory information in the human genome

scientific article

Meltos: multi-sample tumor phylogeny reconstruction for structural variants

scientific article published on 01 February 2020

Microbial Typing by Machine Learned DNA Melt Signatures

scientific article

MotifCut: regulatory motifs finding with maximum density subgraphs

scientific article

Multi-omic tumor data reveal diversity of molecular mechanisms that correlate with survival

scientific article published in Nature Communications

Multiple alignment of protein sequences with repeats and rearrangements.

scientific article

Multiple sequence alignment.

scientific article

Mutations in early follicular lymphoma progenitors are associated with suppressed antigen presentation

scientific article

Network enhancement as a general method to denoise weighted biological networks

scientific article published in Nature Communications

Parente2: a fast and accurate method for detecting identity by descent

scientific article

Phylo-VISTA: An Interactive Visualization Tool for Multiple DNA Sequence Alignments

scholarly article published 1 April 2004

Phylo-VISTA: interactive visualization of multiple DNA sequence alignments

scientific article published on 22 January 2004

Predicting Splicing from Primary Sequence with Deep Learning

scientific article published on 17 January 2019

Predicting the clinical impact of human mutation with deep neural networks

scientific article published on 23 July 2018

ProbCons: Probabilistic consistency-based multiple sequence alignment

scientific article

Quantitative Estimates of Sequence Divergence for Comparative Analyses of Mammalian Genomes ⬇️

scientific article published on May 1, 2003

RECOMB Main Conference 2009

scientific article published on 01 March 2010

Read clouds uncover variation in complex regions of the human genome

scientific article published on 18 August 2015

Reconstruction of genealogical relationships with applications to Phase III of HapMap ⬇️

scientific article published on July 1, 2011

Reveel: large-scale population genotyping using low-coverage sequencing data

scientific article

SIMLR: A Tool for Large-Scale Genomic Analyses by Multi-Kernel Learning.

scientific article published on 19 December 2017

Sequencing a genome by walking with clone-end sequences (abstract)

Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae

scientific article

Short read alignment with populations of genomes ⬇️

scientific article published on July 1, 2013

Strain-resolved microbiome sequencing reveals mobile elements that drive bacterial competition on a clinical timescale

scientific article published on 29 May 2020

Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome

scientific article (publication date: 2016)

The DNA methylation landscape of advanced prostate cancer

scientific article published on 13 July 2020

The Human OligoGenome Resource: a database of oligonucleotide capture probes for resequencing target regions across the human genome ⬇️

scientific article published on November 18, 2011

The many faces of sequence alignment

scientific article

Training Conditional Random Fields for Maximum Labelwise Accuracy ⬇️

scientific article published in January 2007

TreeRefiner: a tool for refining a multiple alignment on a phylogenetic tree

scientific article published in January 2005

Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements

scientific article

Unsupervised Learning from Noisy Networks with Applications to Hi-C Data ⬇️

scientific article published in January 2016

Using multiple alignments to improve seeded local alignment algorithms

scientific article

Vicus: Exploiting local structures to improve network-based analysis of biological data.

scientific article published on 12 October 2017

Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learning

scientific article

What is the expectation maximization algorithm?

scientific article published in August 2008

Whole-genome sequencing and assembly with high-throughput, short-read technologies

scientific article published on 30 May 2007

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