G-SAIP: Graphical Sequence Alignment Through Parallel Programming in the Post-Genomic Era

Establishment of an eHAP1 human haploid cell line hybrid reference genome assembled from short and long reads

(2020) William D. Law et al.   GENOMICS

GPU accelerated sequence alignment with traceback for GATK HaplotypeCaller

(2019) Shanshan Ren et al.   BMC GENOMICS

Retrotransposons in Plant Genomes: Structure, Identification, and Classification through Bioinformatics and Machine Learning

(2019) Simon Orozco-Arias et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Large scale evaluation of differences between network-based and pairwise sequence-alignment-based methods of dendrogram reconstruction

(2019) Daniel Gamermann et al.   PLoS One

FlexiDot: Highly customizable, ambiguity-aware dotplots for visual sequence analyses

(2018) Kathrin M Seibt et al.   BIOINFORMATICS

Versatile genome assembly evaluation with QUAST-LG

(2018) Alla Mikheenko et al.   BIOINFORMATICS

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Earth BioGenome Project: Sequencing life for the future of life

(2018) Harris A. Lewin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

D-GENIES: dot plot large genomes in an interactive, efficient and simple way

(2018) Floréal Cabanettes et al.   PeerJ

10KP: A phylodiverse genome sequencing plan

(2018) Shifeng Cheng et al.   GigaScience

A fast adaptive algorithm for computing whole-genome homology maps

(2018) Chirag Jain et al.   BIOINFORMATICS

BGSA: A Bit-Parallel Global Sequence Alignment Toolkit for Multi-core and Many-core Architectures

(2018) Jikai Zhang et al.   BIOINFORMATICS

CRlncRC: a machine learning-based method for cancer-related long noncoding RNA identification using integrated features

(2018) Xuan Zhang et al.   BMC Medical Genomics

HPC-Based Probabilistic Analysis of LV Networks With EVs: Impacts and Control

(2017) Andreas T. Procopiou et al.   IEEE Transactions on Smart Grid

A De Novo Genome Sequence Assembly of the Arabidopsis thaliana Accession Niederzenz-1 Displays Presence/Absence Variation and Strong Synteny

(2016) Boas Pucker et al.   PLoS One

Integrating alignment-based and alignment-free sequence similarity measures for biological sequence classification

(2015) Ivan Borozan et al.   BIOINFORMATICS

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

Algebraic Dynamic Programming over general data structures

(2015) Christian zu Siederdissen et al.   BMC BIOINFORMATICS

The Release 6 reference sequence of theDrosophila melanogastergenome

(2015) Roger A. Hoskins et al.   GENOME RESEARCH

HBLAST: Parallelised sequence similarity – A Hadoop MapReducable basic local alignment search tool

(2015) Aisling O’Driscoll et al.   JOURNAL OF BIOMEDICAL INFORMATICS

PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences

(2015) Siavash Mirarab et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

High Performance computing improvements on bioinformatics consistency-based multiple sequence alignment tools

(2015) Miquel Orobitg et al.   PARALLEL COMPUTING

A comparison of algorithms for the pairwise alignment of biological networks

(2014) Connor Clark et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Big Data Bioinformatics

(2014) Casey S. Greene et al.   JOURNAL OF CELLULAR PHYSIOLOGY

The chloroplast view of the evolution of polyploid wheat

(2014) Piotr Gornicki et al.   NEW PHYTOLOGIST

Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies

(2014) David B Neale et al.   GENOME BIOLOGY

HPC-CLUST: distributed hierarchical clustering for large sets of nucleotide sequences

(2013) João F. Matias Rodrigues et al.   BIOINFORMATICS

The MaSuRCA genome assembler

(2013) Aleksey V. Zimin et al.   BIOINFORMATICS

A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers

(2012) Michael Quail et al.   BMC GENOMICS

The bonobo genome compared with the chimpanzee and human genomes

(2012) Kay Prüfer et al.   NATURE

The sequence and analysis of a Chinese pig genome

(2012) Xiaodong Fang et al.   GigaScience

The Sequence Read Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

r2cat: synteny plots and comparative assembly

(2009) P. Husemann et al.   BIOINFORMATICS

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

Genome Sequence, Comparative Analysis, and Population Genetics of the Domestic Horse

(2009) C. M. Wade et al.   SCIENCE

Lineage-Specific Biology Revealed by a Finished Genome Assembly of the Mouse

(2009) Deanna M. Church et al.   PLOS BIOLOGY

TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops

(2008) I. Milne et al.   BIOINFORMATICS

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Microbiology in the post-genomic era

(2008) Duccio Medini et al.   NATURE REVIEWS MICROBIOLOGY

MPI for Python: Performance improvements and MPI-2 extensions

(2007) Lisandro Dalcín et al.   JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING