Ecosyste.ms: Papers

10.1186/s40168-019-0658-x

Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments
Cited by: 124
Author(s): Erik L. Clarke, Louis J. Taylor, Chunyu Zhao, Andrew Jesse Connell, Jung‐Jin Lee, Bryton Fett, Frederic D. Bushman, Kyle Bittinger
Software Mentions: 11
Published: over 5 years ago

10.1371/journal.pone.0253010

Community evolution on Stack Overflow
Cited by: 11
Author(s): Iraklis Moutidis, Hywel T. P. Williams
Software Mentions: 10
Published: over 3 years ago

10.1093/gigascience/giaa072

Sequence Compression Benchmark (SCB) database—A comprehensive evaluation of reference-free compressors for FASTA-formatted sequences
Cited by: 19
Author(s): Kirill Kryukov, Mahoko Takahashi Ueda, So Nakagawa, Tadashi Imanishi
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pone.0201483

HSRA: Hadoop-based spliced read aligner for RNA sequencing data
Cited by: 11
Author(s): Roberto R. Expósito, Jorge González-Domínguez, Juan Touriño
Software Mentions: 5
Published: over 6 years ago

10.1186/1748-7188-8-25

Data compression for sequencing data
Cited by: 84
Author(s): Sebastian Deorowicz, Szymon Grabowski
Software Mentions: 5
Published: almost 12 years ago

10.3389/fmicb.2013.00291

FunGene: the functional gene pipeline and repository
Cited by: 451
Author(s): Jordan A. Fish, Benli Chai, Qiong Wang, Yanni Sun, C. Titus Brown, James M. Tiedje, James R. Cole
Software Mentions: 5
Published: almost 12 years ago

10.7717/peerj.3720

Atropos: specific, sensitive, and speedy trimming of sequencing reads
Cited by: 168
Author(s): John P. Didion, Marcel Martin, Francis S. Collins
Software Mentions: 5
Published: about 7 years ago

10.1186/s12859-018-2279-y

Matataki: an ultrafast mRNA quantification method for large-scale reanalysis of RNA-Seq data
Cited by: 8
Author(s): Yasunobu Okamura, Kengo Kinoshita
Software Mentions: 4
Published: over 6 years ago

10.1038/sdata.2018.154

Single cell genomes of Prochlorococcus, Synechococcus, and sympatric microbes from diverse marine environments
Cited by: 73
Author(s): Paul M. Berube, Steven J. Biller, Thomas Hackl, Brandon M. Satinsky, Jamie W. Becker, Rogier Braakman, Sara B. Collins, Libusha Kelly, Jessie W Berta-Thompson, Allison Coe, Kristin Bergauer, Heather A. Bouman, Thomas J. Browning, Daniele De Corte, Christel Hassler, Yotam Hulata, Jeremy E. Jacquot, Elizabeth W. Maas, Thomas Reinthaler, Eva Sintes, Taichi Yokokawa, Debbie Lindell, Ramunas Stepanauskas, Sallie W. Chisholm
Software Mentions: 4
Published: about 6 years ago

10.1093/gigascience/giy125

A benchmark study of k-mer counting methods for high-throughput sequencing
Cited by: 43
Author(s): Swati Manekar, S. R. Sathe
Software Mentions: 4
Published: about 6 years ago

10.1186/1471-2105-9-242

Compressing DNA sequence databases with coil
Cited by: 17
Author(s): W. Timothy J. White, Michael D. Hendy
Software Mentions: 3
Published: over 16 years ago

10.1093/bib/bbw101

A bioimage informatics platform for high-throughput embryo phenotyping
Cited by: 9
Author(s): James M. Brown, Neil R. Horner, Thomas N. Lawson, Tanja Fiegel, Simon Greenaway, Hugh W. Morgan, Natalie Ring, Luís Santos, Duncan Sneddon, Lydia Teboul, Jennifer Vibert, Gagarine Yaikhom, Henrik Westerberg, Ann‐Marie Mallon
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.pone.0167822

On the Reconstruction of Text Phylogeny Trees: Evaluation and Analysis of Textual Relationships
Cited by: 7
Author(s): Guilherme D. Marmerola, Marina Atsumi Oikawa, Zanoni Dias, Siome Goldenstein, Anderson Rocha
Software Mentions: 3
Published: almost 8 years ago

10.1186/s13742-015-0058-5

A quantitative assessment of the Hadoop framework for analyzing massively parallel DNA sequencing data
Cited by: 15
Author(s): Alexey Siretskiy, T. Sundqvist, Mikhail Voznesenskiy, Ola Spjuth
Software Mentions: 3
Published: over 9 years ago

10.1186/s12859-020-03658-4

Performance evaluation of lossy quality compression algorithms for RNA-seq data
Cited by: 1
Author(s): Rongshan Yu, Wenxian Yang, Wang Shun
Software Mentions: 3
Published: over 4 years ago

10.3389/fnins.2013.00074

Abrupt changes in the patterns and complexity of anterior cingulate cortex activity when food is introduced into an environment
Cited by: 14
Author(s): Barak F. Caracheo, Eldon Emberly, Shirin Hadizadeh, James M. Hyman, Jeremy K. Seamans
Software Mentions: 3
Published: almost 12 years ago

10.1186/gb-2007-8-5-r69

Towards the uniform distribution of null P values on Affymetrix microarrays
Cited by: 29
Author(s): Anthony A. Fodor, Timothy L. Tickle, Christine Richardson
Software Mentions: 2
Published: almost 18 years ago

10.1186/1471-2105-11-514

Data structures and compression algorithms for high-throughput sequencing technologies
Cited by: 45
Author(s): Kenneth Daily, Paul Rigor, Scott Christley, Xiaohui Xie, Pierre Baldi
Software Mentions: 2
Published: about 14 years ago

10.1186/1471-2105-15-S15-S10

Compression of next-generation sequencing quality scores using memetic algorithm
Cited by: 12
Author(s): Jian Zhou, Zhen Ji, Zexuan Zhu, Shan He
Software Mentions: 2
Published: almost 10 years ago

10.1186/s12859-016-0932-x

MetaCRAM: an integrated pipeline for metagenomic taxonomy identification and compression
Cited by: 12
Author(s): Minji Kim, Xiejia Zhang, Jonathan G. Ligo, Farzad Farnoud, Venugopal V. Veeravalli, Olgica Milenković
Software Mentions: 2
Published: almost 9 years ago

10.1186/1471-2105-5-147

Cited by: 314
Author(s): Hao Chen, Burt M. Sharp
Software Mentions: 2
Published: almost 21 years ago

10.1093/bioinformatics/bty632

Dynamic compression schemes for graph coloring
Cited by: 23
Author(s): Harun Mustafa, Ingo Schilken, Mikhail Karasikov, Carsten Eickhoff, Gunnar Rätsch, André Kahles
Software Mentions: 2
Published: over 6 years ago

10.1093/bioinformatics/btu170

Trimmomatic: a flexible trimmer for Illumina sequence data
Cited by: 39,409
Author(s): Anthony Bolger, Marc Lohse, Björn Usadel
Software Mentions: 2
Published: over 10 years ago

10.7717/peerj.243

PhyloSift: phylogenetic analysis of genomes and metagenomes
Cited by: 541
Author(s): Aaron E. Darling, Guillaume Jospin, Eric Lowe, F. A. Matsen, Holly M. Bik, Jonathan A. Eisen
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0014373

Sequence Alignment, Mutual Information, and Dissimilarity Measures for Constructing Phylogenies
Cited by: 26
Author(s): Orion Penner, Peter Grassberger, Maya Paczuski
Software Mentions: 2
Published: almost 14 years ago

10.1371/journal.pone.0119306

Prediction of Protein Structural Features from Sequence Data Based on Shannon Entropy and Kolmogorov Complexity
Cited by: 16
Author(s): Robert P. Bywater
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0081414

SRComp: Short Read Sequence Compression Using Burstsort and Elias Omega Coding
Cited by: 10
Author(s): Jeremy John Selva, Xin Chen
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0116082

MAFCO: A Compression Tool for MAF Files
Cited by: 3
Author(s): Luís M. O. de Matos, António J. R. Neves, Diogo Pratas, Armando J. Pinho
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0059190

Compression of FASTQ and SAM Format Sequencing Data
Cited by: 175
Author(s): James K. Bonfield, Matthew V. Mahoney
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0079871

Compression of Structured High-Throughput Sequencing Data
Cited by: 34
Author(s): Fabien Campagne, Kevin C. Dorff, Nyasha Chambwe, James T. Robinson, Jill P. Mesirov
Software Mentions: 2
Published: about 11 years ago

10.3390/e21020215

The Choice of an Appropriate Information Dissimilarity Measure for Hierarchical Clustering of River Streamflow Time Series, Based on Calculated Lyapunov Exponent and Kolmogorov Measures
Cited by: 10
Author(s): Dragutin T. Mihailović, Emilija Nikolić-Đorić, Slavica Malinović‐Milićević, Vijay P. Singh, Anja Mihailović, Tatijana Stŏsíc, Borko Stošić, Nusret Drešković
Software Mentions: 2
Published: over 5 years ago

10.3389/fimmu.2018.00976

VDJServer: A Cloud-Based Analysis Portal and Data Commons for Immune Repertoire Sequences and Rearrangements
Cited by: 56
Author(s): Scott Christley, Walter Scarborough, Eddie Salinas, William Rounds, Inimary T. Toby, John Fonner, Mikhail K. Levin, Min Kim, Stephen Mock, Christopher Jordan, Jared Ostmeyer, Adam Buntzman, Florian Rubelt, Marco L. Davila, Nancy Monson, Richard H. Scheuermann, Lindsay G. Cowell
Software Mentions: 2
Published: over 6 years ago

10.1186/1758-2946-3-13

PubChem3D: Similar conformers
Cited by: 28
Author(s): Evan Bolton, Sunghwan Kim, Stephen H. Bryant
Software Mentions: 2
Published: over 13 years ago

10.3390/s151229785

A Primer on Autonomous Aerial Vehicle Design
Cited by: 5
Author(s): Hugo Herman Godelieve Coppejans, Hermanus Carel Myburgh
Software Mentions: 2
Published: almost 9 years ago

10.1128/mSystems.00020-16

MetaPalette: a <i>k</i> -mer Painting Approach for Metagenomic Taxonomic Profiling and Quantification of Novel Strain Variation
Cited by: 56
Author(s): David Koslicki, Daniel Falush
Software Mentions: 2
Published: over 8 years ago

10.1155/2012/271758

Application of Multiprotocol Medical Imaging Communications and an Extended DICOM WADO Service in a Teleradiology Architecture
Cited by: 4
Author(s): George V. Koutelakis, George Anastassopoulos, Dimitrios Lymberopoulos
Software Mentions: 2
Published: almost 13 years ago

10.3390/s21155160

Energy and Performance Analysis of Lossless Compression Algorithms for Wireless EMG Sensors
Cited by: 7
Author(s): Giorgio Biagetti, Paolo Crippa, Laura Falaschetti, Ali Mansour, Claudio Turchetti
Software Mentions: 1
Published: over 3 years ago

10.1186/s13029-019-0073-5

MZPAQ: a FASTQ data compression tool
Cited by: 2
Author(s): Achraf El Allali, Mariam Arshad
Software Mentions: 1
Published: over 5 years ago

10.7554/eLife.66175

Mice in a labyrinth show rapid learning, sudden insight, and efficient exploration
Cited by: 37
Author(s): Matthew Rosenberg, Tony Zhang, Pietro Perona, Markus Meister
Software Mentions: 1
Published: over 3 years ago

10.1186/1471-2164-15-195

Western corn rootworm (Diabrotica virgifera virgifera) transcriptome assembly and genomic analysis of population structure
Cited by: 24
Author(s): Lex E. Flagel, Raman Bansal, Randall A. Kerstetter, Mao Chen, Matthew Carroll, Ronald D. Flannagan, Thomas L. Clark, Barry S. Goldman, Andy Michel
Software Mentions: 1
Published: over 10 years ago

10.1186/1471-2164-13-302

Duplicate gene evolution, homoeologous recombination, and transcriptome characterization in allopolyploid cotton
Cited by: 87
Author(s): Lex E. Flagel, Jonathan F. Wendel, Joshua A. Udall
Software Mentions: 1
Published: over 12 years ago

10.3389/fphys.2017.00113

Fetal Heart Rate Analysis for Automatic Detection of Perinatal Hypoxia Using Normalized Compression Distance and Machine Learning
Cited by: 5
Author(s): Óscar Barquero-Pérez, Ricardo Santiago-Mozos, José María Lillo-Castellano, Beatriz García-Viruete, Rebeca Goya–Esteban, Antonio J. Caamaño, José Luis Rojo-Álvarez, Carlos Martín-Caballero
Software Mentions: 1
Published: over 7 years ago

10.1186/gb-2005-6-5-r47

Cited by: 263
Author(s): Ilya G. Goldberg, Chris Allan, Jean‐Marie Burel, Doug Creager, Andrea Falconi, Harry Hochheiser, Josiah Johnston, Jeff Mellen, Peter K. Sorger, Jason R. Swedlow
Software Mentions: 1
Published: almost 20 years ago

10.1186/1471-2105-7-263

Automatic generation of gene finders for eukaryotic species
Cited by: 29
Author(s): Kasper Munch, Anders Krogh
Software Mentions: 1
Published: over 18 years ago

10.1186/2047-217X-2-5

Sequence squeeze: an open contest for sequence compression
Cited by: 14
Author(s): Richard Holland, Nick Lynch
Software Mentions: 1
Published: over 11 years ago

10.1186/s12859-017-1588-x

LW-FQZip 2: a parallelized reference-based compression of FASTQ files
Cited by: 21
Author(s): Zhi Huang, Zhenkun Wen, Qingjin Deng, Yingli Chu, Yiwen Sun, Zexuan Zhu
Software Mentions: 1
Published: over 7 years ago

10.7717/peerj-cs.404

Accelerated implementation for testing IID assumption of NIST SP 800-90B using GPU
Cited by: 1
Author(s): Kim Yewon, Yongjin Yeom
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pone.0173038

IOPA: I/O-aware parallelism adaption for parallel programs
Cited by: 0
Author(s): Tao Liu, Yi Liu, Qian Chen, Depei Qian
Software Mentions: 1
Published: over 7 years ago

10.1186/s12859-018-2162-x

Live neighbor-joining
Cited by: 10
Author(s): Guilherme P. Telles, Graziela S. Araújo, Maria Emília M. T. Walter, Marcelo M. Brigido, Nalvo F. Almeida
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0204883

Why twenty amino acid residue types suffice(d) to support all living systems
Cited by: 6
Author(s): Robert P. Bywater
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0224806

LFastqC: A lossless non-reference-based FASTQ compressor
Cited by: 10
Author(s): Sultan Al Yami, Chun-Hsi Huang
Software Mentions: 1
Published: about 5 years ago

10.1186/s12859-016-1214-3

VDJML: a file format with tools for capturing the results of inferring immune receptor rearrangements
Cited by: 10
Author(s): Inimary T. Toby, Mikhail K. Levin, Edward A. Salinas, Scott Christley, Sanchita Bhattacharya, Felix Breden, Adam Buntzman, Brian Corrie, John Fonner, Namita Gupta, Uri Hershberg, Nishanth Marthandan, Aaron M. Rosenfeld, William Rounds, Florian Rubelt, Walter Scarborough, Jamie K. Scott, Mohamed Uduman, Jason A. Vander Heiden, Richard H. Scheuermann, Nancy Monson, Steven H. Kleinstein, Lindsay G. Cowell
Software Mentions: 1
Published: about 8 years ago

10.7717/peerj.2584

VSEARCH: a versatile open source tool for metagenomics
Cited by: 5,816
Author(s): Torbjørn Rognes, Tomáš Flouri, Ben Nichols, Christopher Quince, Frédéric Mahé
Software Mentions: 1
Published: about 8 years ago

10.3390/mi10060411

Fine-Grained Power Gating Using an MRAM-CMOS Non-Volatile Flip-Flop
Cited by: 5
Author(s): Jaeyoung Park, Young Uk Yim
Software Mentions: 1
Published: over 5 years ago

10.1107/S1600577520007353

Impact of lossy compression of X-ray projections onto reconstructed tomographic slices
Cited by: 0
Author(s): Federica Marone, Jakob Vogel, Marco Stampanoni
Software Mentions: 1
Published: over 4 years ago

10.1186/s13104-016-1900-2

AdapterRemoval v2: rapid adapter trimming, identification, and read merging
Cited by: 1,078
Author(s): Mikkel Schubert, Stinus Lindgreen, Ludovic Orlando
Software Mentions: 1
Published: almost 9 years ago

10.1186/1748-7188-6-23

ReCoil - an algorithm for compression of extremely large datasets of dna data
Cited by: 35
Author(s): Vladimir Yanovsky
Software Mentions: 1
Published: about 13 years ago

10.2196/13559

Development and Implementation of the Portable Operating Room Tracker App With Vital Signs Streaming Infrastructure: Operational Feasibility Study
Cited by: 6
Author(s): Matthias Görges, Nicholas West, Chris Petersen, J. Mark Ansermino
Software Mentions: 1
Published: over 5 years ago