Fereydoun Hormozdiari

发表

Not All Scale-Free Networks Are Born Equal: The Role of the Seed Graph in PPI Network Evolution

Süleyman Cenk Sahinalp, Natasa Przulj, Petra Berenbrink, 2006, Systems Biology and Computational Proteomics.

How bioinformatics and open data can boost basic science in countries and universities with limited resources

Eleazar Eskin, Pavel Pevzner, Serghei Mangul, 2019, Nature Biotechnology.

Discovery of tandem and interspersed segmental duplications using high throughput sequencing

Can Alkan, Fereydoun Hormozdiari, Arda Soylev, 2018, bioRxiv.

Towards Improved Assessment of Functional Similarity in Large-Scale Screens: A Study on Indel Length

Artem Cherkasov, Alexander Schönhuth, Süleyman Cenk Sahinalp, 2010, J. Comput. Biol..

Nebula: ultra-efficient mapping-free structural variant genotyper

Fereydoun Hormozdiari, Parsoa Khorsand, F. Hormozdiari, 2019, bioRxiv.

The Relation between Indel Length and Functional Divergence: A Formal Study

Artem Cherkasov, Alexander Schönhuth, Süleyman Cenk Sahinalp, 2008, WABI.

Meltos: multi-sample tumor phylogeny reconstruction for structural variants

Iman Hajirasouliha, Serafim Batzoglou, Victoria Popic, 2019, Bioinform..

Comrad: detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data

Faraz Hach, Iman Hajirasouliha, Colin Collins, 2011, Bioinform..

Discovery of tandem and interspersed segmental duplications using high-throughput sequencing

Can Alkan, Fereydoun Hormozdiari, Arda Soylev, 2019, Bioinform..

Biomolecular network motif counting and discovery by color coding

Noga Alon, Iman Hajirasouliha, Süleyman Cenk Sahinalp, 2008, ISMB.

Relationship between insertion/deletion (indel) frequency of proteins and essentiality

Artem Cherkasov, Fereydoun Hormozdiari, Michael Hsing, 2007, BMC Bioinformatics.

The Effect of Insertions and Deletions on Wirings in Protein-Protein Interaction Networks: A Large-Scale Study

Artem Cherkasov, Alexander Schönhuth, Süleyman Cenk Sahinalp, 2009, J. Comput. Biol..

Structural variation discovery: the easy, the hard and the ugly

Fereydoun Hormozdiari, F. Hormozdiari, 2011 .

Quantifying Systemic Evolutionary Changes by Color Coding Confidence-Scored PPI Networks

Martin Ester, Iman Hajirasouliha, Alexander Schönhuth, 2009, WABI.

Dense Graphlet Statistics of Protein Interaction and Random Networks

Martin Ester, Alexander Schönhuth, Süleyman Cenk Sahinalp, 2009, Pacific Symposium on Biocomputing.

PERSONAL GENOMICS – Session Introduction

Can Alkan, Maricel G. Kann, Fereydoun Hormozdiari, 2009 .

deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data

Süleyman Cenk Sahinalp, Malachi Griffith, Sohrab P. Shah, 2011, PLoS Comput. Biol..

Combinatorial Algorithms for Structural Variation Detection in High Throughput Sequenced Genomes

Süleyman Cenk Sahinalp, Can Alkan, Fereydoun Hormozdiari, 2009, RECOMB.

Not All Scale-Free Networks Are Born Equal: The Role of the Seed Graph in PPI Network Evolution

Süleyman Cenk Sahinalp, Natasa Przulj, Petra Berenbrink, 2006, Systems Biology and Computational Proteomics.

The Second Decade of the International Conference on Research in Computational Molecular Biology (RECOMB)

Paul Medvedev, Carl Kingsford, Fabio Vandin, 2016, RECOMB.

DENSE GRAPHLET STATISTICS OF PROTEIN INTERACTION NETWORKS AND RANDOM NETWORKS

Martin Ester, Fereydoun Hormozdiari, Recep Colak, 2008 .

Simultaneous Structural Variation Discovery in Multiple Paired-End Sequenced Genomes

Iman Hajirasouliha, Süleyman Cenk Sahinalp, Andrew McPherson, 2011, RECOMB.

Protein protein interaction network comparison and emulation

Fereydoun Hormozdiari, F. Hormozdiari, 2006 .

Proteome Network Emulating Models

Martin Ester, Iman Hajirasouliha, Phuong Dao, 2012 .

Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery

Faraz Hach, Iman Hajirasouliha, Süleyman Cenk Sahinalp, 2010, Bioinform..

mrsFAST: a cache-oblivious algorithm for short-read mapping

Faraz Hach, Inanc Birol, Can Alkan, 2010, Nature Methods.

Optimal pooling for genome re-sequencing with ultra-high-throughput short-read technologies

Inanç Birol, Iman Hajirasouliha, Süleyman Cenk Sahinalp, 2008, ISMB.

Detection and characterization of novel sequence insertions using paired-end next-generation sequencing

Inanç Birol, Iman Hajirasouliha, Süleyman Cenk Sahinalp, 2010, Bioinform..

Kevlar: a mapping-free framework for accurate discovery of de novo variants

Daniel S. Standage, Fereydoun Hormozdiari, C. Titus Brown, 2019 .

High-resolution comparative analysis of great ape genomes

David Haussler, Fred H. Gage, Andy Wing Chun Pang, 2018, Science.

A high-quality human reference panel reveals the complexity and distribution of genomic structural variants

Alexander Schönhuth, Victor Guryev, Tobias Marschall, 2016, Nature communications.

Genomic Patterns of De Novo Mutation in Simplex Autism

Len A. Pennacchio, Michael C. Zody, Archana Raja, 2017, Cell.

Great ape genetic diversity and population history

Arcadi Navarro, Thomas Mailund, Jaume Bertranpetit, 2013, Nature.

Kevlar: A Mapping-Free Framework for Accurate Discovery of De Novo Variants

Daniel S. Standage, Fereydoun Hormozdiari, C. Titus Brown, 2019, bioRxiv.

Multi-platform discovery of haplotype-resolved structural variation in human genomes

Li Ding, Amina Noor, Ali Bashir, 2018, Nature Communications.

Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzee.

Arcadi Navarro, Jay Shendure, Can Alkan, 2011, Genome research.

Characteristics of de novo structural changes in the human genome

Alexander Schönhuth, Edwin Cuppen, Victor Guryev, 2015, Genome research.

Consortium, G.P A map of human genome variation from population-scale sequencing. Nature 467, 1061-1073

Ken Chen, Joshua M. Korn, Afidalina Tumian, 2010 .

A high-quality reference panel reveals the complexity and distribution of structural genome changes in a human population

Morris A. Swertz, Jasmijn A. Baaijens, Victor Guryev, 2016, bioRxiv.

The genome sequencing of an albino Western lowland gorilla reveals inbreeding in the wild

Arcadi Navarro, Jaume Bertranpetit, Can Alkan, 2013, BMC Genomics.

Toolkit for automated and rapid discovery of structural variants.

Can Alkan, Fereydoun Hormozdiari, Arda Soylev, 2017, Methods.

The discovery of integrated gene networks for autism and related disorders

Elhanan Borenstein, Fereydoun Hormozdiari, Evan E Eichler, 2015, Genome research.

TAD fusion score: discovery and ranking the contribution of deletions to genome structure

Fereydoun Hormozdiari, Linh Huynh, F. Hormozdiari, 2019, Genome Biology.