pypi: bash | Projects | Ecosyste.ms: Papers

10.1371/journal.pgen.1008405

Causal relationships between obesity and the leading causes of death in women and men
Cited by: 106
Author(s): Jenny C Censin, Sanne A.E. Peters, Jonas Bovijn, Teresa Ferreira, Sara L. Pulit, Reedik Mägi, Anubha Mahajan, Michael V Holmes, Cecilia M. Lindgren
Software Mentions: 14
Published: about 5 years ago

10.3389/fgene.2020.580580

Global Analysis of Transcription Start Sites in the New Ovine Reference Genome (Oar rambouillet v1.0)
Cited by: 20
Author(s): Mazdak Salavati, Alex Caulton, Richard Clark, Iveta Gažová, Timothy P. L. Smith, Kim C. Worley, Noelle E. Cockett, Alan Archibald, Shannon Clarke, Brenda M. Murdoch, Emily L. Clark
Software Mentions: 11
Published: about 4 years ago

10.1002/elsc.202000053

Implementing a digital infrastructure for the lab using a central laboratory server and the SiLA2 communication standard
Cited by: 3
Author(s): Marc Porr, F. Lange, Daniel Marquard, Laura Niemeyer, Patrick Lindner, Thomas Scheper, Sascha Beutel
Software Mentions: 8
Published: about 4 years ago

10.1371/journal.pgen.1009094

Transposon mutagenesis identifies cooperating genetic drivers during keratinocyte transformation and cutaneous squamous cell carcinoma progression
Cited by: 2
Author(s): Aziz Aiderus, Justin Y. Newberg, Liliana Guzmán-Rojas, Ana M. Contreras-Sandoval, Amanda L. Meshey, Devin J. Jones, Felipe Amaya-Manzanares, Roberto Rangel, Jerrold M. Ward, Song Choon Lee, Kenneth Ban, Keith Rogers, Susan Rogers, Luxmanan Selvanesan, Leslie A. McNoe, Neal G. Copeland, Nancy A. Jenkins, Kenneth Y. Tsai, Michael A. Black, Karen Mann, Michael B. Mann
Software Mentions: 8
Published: over 3 years ago

10.1186/s13007-019-0440-x

Comparing time series transcriptome data between plants using a network module finding algorithm
Cited by: 6
Author(s): Jiyoung Lee, Lenwood S. Heath, Ruth Grene, Song Li
Software Mentions: 7
Published: over 5 years ago

10.1371/journal.pone.0128854

ONION: Functional Approach for Integration of Lipidomics and Transcriptomics Data
Cited by: 5
Author(s): Monika Piwowar, Wiktor Jurkowski
Software Mentions: 6
Published: over 9 years ago

10.7717/peerj.1417

Tools for quantitative form description; an evaluation of different software packages for semi-landmark analysis
Cited by: 28
Author(s): Léo Botton‐Divet, Alexandra Houssaye, Anthony Herrel, Anne‐Claire Fabre, Raphaël Cornette
Software Mentions: 6
Published: about 9 years ago

10.1186/s13068-018-1036-9

Genome-resolved metagenomics of sugarcane vinasse bacteria
Cited by: 16
Author(s): Noriko A. Cassman, Késia Silva Lourenço, Janaína Braga do Carmo, Heitor Cantarella, Eiko E. Kuramae
Software Mentions: 6
Published: almost 7 years ago

10.1186/s12864-019-5914-8

DAIRYdb: a manually curated reference database for improved taxonomy annotation of 16S rRNA gene sequences from dairy products
Cited by: 36
Author(s): Marco Meola, Étienne Rifa, Noam Shani, Céline Delbès, Hélène Berthoud, Christophe Chassard
Software Mentions: 6
Published: over 5 years ago

10.1111/eva.12708

The genetic legacy of 50 years of desert bighorn sheep translocations
Cited by: 27
Author(s): Joshua P. Jahner, Marjorie D. Matocq, Jason L. Malaney, Mike Cox, Peregrine L. Wolff, Mitchell A. Gritts, Thomas L. Parchman
Software Mentions: 5
Published: about 6 years ago

10.12688/f1000research.28142.2

MIREyA: a computational approach to detect miRNA-directed gene activation
Cited by: 1
Author(s): A. N. Elizarova, Mumin Ozturk, Reto Guler, Yulia A. Medvedeva
Software Mentions: 5
Published: over 3 years ago

10.1186/s12864-018-4943-z

ATAC2GRN: optimized ATAC-seq and DNase1-seq pipelines for rapid and accurate genome regulatory network inference
Cited by: 19
Author(s): Thomas Pranzatelli, Drew G. Michael, John A. Chiorini
Software Mentions: 5
Published: over 6 years ago

10.1186/s12864-018-4750-6

Signatures of host specialization and a recent transposable element burst in the dynamic one-speed genome of the fungal barley powdery mildew pathogen
Cited by: 124
Author(s): Lamprinos Frantzeskakis, Barbara Kracher, Stefan Kusch, Makoto Yoshikawa-Maekawa, Saskia Bauer, Carsten Pedersen, Pietro D. Spanu, Takaki Maekawa, Paul Schulze‐Lefert, Ralph Panstruga
Software Mentions: 5
Published: over 6 years ago

10.1128/mSphere.00327-18

TaxAss: Leveraging a Custom Freshwater Database Achieves Fine-Scale Taxonomic Resolution
Cited by: 57
Author(s): Robin R Rohwer, Joshua J. Hamilton, Ryan J. Newton, Katherine D. McMahon
Software Mentions: 5
Published: about 6 years ago

10.1371/journal.pcbi.1008622

Using prototyping to choose a bioinformatics workflow management system
Cited by: 20
Author(s): Michael Jackson, Kostas Kavoussanakis, Eric Wallace
Software Mentions: 5
Published: almost 4 years ago

10.1371/journal.pone.0172583

Solving global shallow water equations on heterogeneous supercomputers
Cited by: 2
Author(s): Haohuan Fu, Lin Gan, Chao Yang, Wei Xue, Lanning Wang, Xinliang Wang, Xiaomeng Huang, Guangwen Yang
Software Mentions: 5
Published: almost 8 years ago

10.1371/journal.pone.0188415

Physiological effects of a novel artificially synthesized antimalarial cyclic peptide: Mahafacyclin B
Cited by: 2
Author(s): Yūkō Fujita, Panpaki Seekaki, Naoya Ogata, Kazuhiro Chiba
Software Mentions: 5
Published: about 7 years ago

10.1186/s12983-015-0109-x

Transcriptional profiling of predator-induced phenotypic plasticity in Daphnia pulex
Cited by: 33
Author(s): Andrey Rozenberg, Mrutyunjaya Parida, Florian Leese, Linda C. Weiss, Ralph Tollrian, J. Robert Manak
Software Mentions: 5
Published: over 9 years ago

10.1038/s42003-020-01382-6

Adaptation by copy number variation increases insecticide resistance in the fall armyworm
Cited by: 40
Author(s): Sylvie Gimenez, Heba Abdelgaffar, Gaëlle Le Goff, Frédérique Hilliou, Carlos A. Blanco, Sabine Hänniger, Anthony Bretaudeau, Fabrice Legeai, Nicolas Nègre, Juan Luís Jurat-Fuentes, Emmanuelle d’Alençon, Kiwoong Nam
Software Mentions: 5
Published: about 4 years ago

10.1111/eva.12659

Recent advances in conservation and population genomics data analysis
Cited by: 77
Author(s): Sarah A. Hendricks, Eric C. Anderson, Tiago Antão, Louis Bernatchez, Brenna R. Forester, Brittany A. Garner, Brian K. Hand, Paul A. Hohenlohe, Marty Kardos, Ben F. Koop, Arun Sethuraman, Robin S. Waples, Gordon Luikart
Software Mentions: 5
Published: over 6 years ago

10.1186/s12911-016-0374-4

Introduction of digital speech recognition in a specialised outpatient department: a case study
Cited by: 8
Author(s): Christoph Ahlgrim, Oliver Maenner, Manfred W. Baumstark
Software Mentions: 4
Published: about 8 years ago

10.3389/fninf.2016.00002

Using Make for Reproducible and Parallel Neuroimaging Workflow and Quality-Assurance
Cited by: 19
Author(s): Mary K. Askren, Trevor K. M. Day, Natalie Koh, Zoé Mestre, Jennifer N. Dines, Benjamin Korman, Susan J. Melhorn, Daniel J. Peterson, Matthew Peverill, Xiaoyan Qin, Swati Rane, Melissa Reilly, M. Reiter, Kelly Sambrook, Karl A. Woelfer, Thomas J. Grabowski, Tara M. Madhyastha
Software Mentions: 4
Published: almost 9 years ago

10.1128/mBio.00766-20

Codon Usage Optimization in the Prokaryotic Tree of Life: How Synonymous Codons Are Differentially Selected in Sequence Domains with Different Expression Levels and Degrees of Conservation
Cited by: 9
Author(s): José Luis López, Mauricio Javier Lozano, María Laura Fabre, Antonio Lagares
Software Mentions: 4
Published: over 4 years ago

10.7717/peerj.5984

Characterization of bacterioplankton communities and quantification of organic carbon pools off the Galapagos Archipelago under contrasting environmental conditions
Cited by: 5
Author(s): Nataly Guevara, Christiane Hassenrück, Pier Luigi Buttigieg, Astrid Gärdes
Software Mentions: 4
Published: about 6 years ago

10.3390/ijms19040961

A Whole Germline BRCA2 Gene Deletion: How to Learn from CNV In Silico Analysis
Cited by: 11
Author(s): Giovanni Luca Scaglione, Paola Concolino, Maria De Bonis, Elisa De Paolis, Angelo Minucci, Gabriella Ferrandina, Ettore Capoluongo
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12864-021-07373-z

Inferring time series chromatin states for promoter-enhancer pairs based on Hi-C data
Cited by: 2
Author(s): Henriette Miko, Yunjiang Qiu, Bjoern Gaertner, Maike Sander, Uwe Ohler
Software Mentions: 3
Published: almost 4 years ago

10.1242/dev.188631

A landmark-free morphometrics pipeline for high-resolution phenotyping: application to a mouse model of Down syndrome
Cited by: 23
Author(s): Nicolas Toussaint, Yushi Redhead, Marta Vidal‐García, Lucas Lo Vercio, Elizabeth Fisher, Benedikt Hallgrímsson, Victor L. J. Tybulewicz, Julia A. Schnabel, Jeremy Green
Software Mentions: 3
Published: almost 4 years ago

10.7717/peerj.356

The complex hybrid origins of the root knot nematodes revealed through comparative genomics
Cited by: 85
Author(s): David H. Lunt, Sujai Kumar, Georgios Koutsovoulos, Mark Blaxter
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0249773

Whole genome variation in 27 Mexican indigenous populations, demographic and biomedical insights.
Cited by: 8
Author(s): Israel Aguilar-Ordóñez, Fernando Pérez-Villatoro, Humberto Garcia‐Ortíz, Francisco Barajas‐Olmos, Judith Ballesteros-Villascán, Ram González-Buenfil, Cristóbal Fresno, Alejandro Garcíarrubio, Juan Carlos Fernández-López, Hugo Tovar, Enrique Hernández‐Lemus, Xavier Soberón, Enrique Morett
Software Mentions: 3
Published: almost 4 years ago

10.1186/1471-2164-15-955

Comparative transcriptomics reveals striking similarities between the bovine and feline isolates of Tritrichomonas foetus: consequences for in silico drug-target identification
Cited by: 34
Author(s): Victoria Morin-Adeline, Rodrigo Lomas, Denis O’Meally, Colin M. Stack, Ana Conesa, Jan Šlapeta
Software Mentions: 3
Published: about 10 years ago

10.7554/eLife.29820

Epidemiological and ecological determinants of Zika virus transmission in an urban setting
Cited by: 76
Author(s): José Lourenço, Maricélia Maia de Lima, Nuno Rodrigues Faria, Andrew Walker, Moritz U. G. Kraemer, Christian Julián Villabona-Arenas, Ben Lambert, Erenilde Marques de Cerqueira, Oliver G. Pybus, Luíz Carlos Júnior Alcântara, Mario Recker
Software Mentions: 3
Published: over 7 years ago

10.1186/s12864-020-6568-2

GenomeQC: a quality assessment tool for genome assemblies and gene structure annotations
Cited by: 48
Author(s): Nancy Manchanda, John L. Portwood, Margaret R. Woodhouse, Arun S. Seetharam, Carolyn J. Lawrence‐Dill, Carson M. Andorf, Matthew B. Hufford
Software Mentions: 3
Published: almost 5 years ago

10.1186/1471-2105-9-S4-S12

Bio-jETI: a service integration, design, and provisioning platform for orchestrated bioinformatics processes
Cited by: 45
Author(s): Tiziana Margaria, Christian Kubczak, Bernhard Steffen
Software Mentions: 3
Published: over 16 years ago

10.1186/s12876-021-01885-4

Study protocol P-MAPS: microbiome as predictor of severity in acute pancreatitis—a prospective multicentre translational study
Cited by: 2
Author(s): Christoph Ammer‐Herrmenau, Thomas Asendorf, Georg Beyer, S Buchholz, Silke Cameron, Marko Damm, Fabian Frost, Robert Henker, Robert Jaster, Veit Phillip, Marius Placzek, C. Ratei, Simon Sirtl, T. van den Berg, Molly Weingarten, Julia Woitalla, Julia Mayerle, Volker Ellenrieder, Albrecht Neeße
Software Mentions: 3
Published: over 3 years ago

10.1186/s13073-015-0167-x

JAFFA: High sensitivity transcriptome-focused fusion gene detection
Cited by: 130
Author(s): N. Davidson, Ian J. Majewski, Alicia Oshlack
Software Mentions: 3
Published: over 9 years ago

10.1007/s00702-018-1916-y

Clinical pain and functional network topology in Parkinson’s disease: a resting-state fMRI study
Cited by: 9
Author(s): Gwenda Engels, Brónagh McCoy, Annemarie Vlaar, Jan Theeuwes, Henry C. Weinstein, E.J.A. Scherder, Linda Douw
Software Mentions: 3
Published: over 6 years ago

10.1186/1471-2164-15-446

Characterization of the kidney transcriptome of the South American olive mouse Abrothrix olivacea
Cited by: 14
Author(s): Facundo Giorello, Matías Feijoo, Guillermo D’Elı́a, Lourdes Valdez, Juan C. Opazo, Valeria Varas, Daniel E. Naya, Enrique P. Lessa
Software Mentions: 3
Published: almost 11 years ago

10.3389/fninf.2014.00044

The Insight ToolKit image registration framework
Cited by: 404
Author(s): Brian B. Avants, Nicholas J. Tustison, Michael Stauffer, Gang Song, Bangyu Wu, James C. Gee
Software Mentions: 3
Published: over 10 years ago

10.1186/s12859-019-2711-y

SSS-test: a novel test for detecting positive selection on RNA secondary structure
Cited by: 12
Author(s): Maria Beatriz Walter Costa, Christian Höner zu Siederdissen, Marko Dunjić, Peter F. Stadler, Katja Nowick
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12859-014-0445-4

Evaluation and improvements of clustering algorithms for detecting remote homologous protein families
Cited by: 24
Author(s): Juliana Silva Bernardes, Fabio Rocha Jimenez Vieira, Lygia M M Costa, Gerson Zaverucha
Software Mentions: 2
Published: almost 10 years ago

10.7717/peerj.9789

Range reduction of Oblong Rocksnail,Leptoxis compacta, shapes riverscape genetic patterns
Cited by: 1
Author(s): Aaliyah D. Wright, Nicole L. Garrison, A. O. Williams, Paul D. Johnson, Nathan V. Whelan
Software Mentions: 2
Published: over 4 years ago

10.1002/pld3.52

Maize GO Annotation—Methods, Evaluation, and Review (maize‐GAMER)
Cited by: 80
Author(s): Kokulapalan Wimalanathan, Iddo Friedberg, Carson M. Andorf, Carolyn J. Lawrence‐Dill
Software Mentions: 2
Published: over 6 years ago

10.3389/fmicb.2018.00610

Gene Enrichment Analysis Reveals Major Regulators of Mycobacterium tuberculosis Gene Expression in Two Models of Antibiotic Tolerance
Cited by: 11
Author(s): William M. Matern, Dalin Rifat, Joel S. Bader, Petros C. Karakousis
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.ppat.1001037

Spliced Leader Trapping Reveals Widespread Alternative Splicing Patterns in the Highly Dynamic Transcriptome of Trypanosoma brucei
Cited by: 173
Author(s): Daniel Nilsson, Kapila Gunasekera, Jan Mani, Magne Østerås, Laurent Farinelli, Loic Bærlocher, Isabel Roditi, Torsten Ochsenreiter
Software Mentions: 2
Published: over 14 years ago

10.1038/s41598-018-30515-5

Analysis of sequencing strategies and tools for taxonomic annotation: Defining standards for progressive metagenomics
Cited by: 75
Author(s): Alejandra Escobar‐Zepeda, Elizabeth Ernestina Godoy-Lozano, Luciana Raggi, Lorenzo Segovia, Enrique Merino, Rosa Marı́a Gutièrrez-Rı́os, Katy Juarez, Alexei F. Licea-Navarro, Liliana Pardo-López, Alejandro Sánchez-Flores
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-021-92834-4

In Silico identification of a common mobile element insertion in exon 4 of RP1
Cited by: 0
Author(s): Dongju Won, Joo-Yeon Hwang, Yeeun Shim, Suk Ho Byeon, Junwon Lee, Christopher S. Lee, Min Kim, Hyun Taek Lim, Jong Rak Choi, Seung Tae Lee, Jinu Han
Software Mentions: 2
Published: over 3 years ago

10.3390/s20092737

Explora: Interactive Querying of Multidimensional Data in the Context of Smart Cities
Cited by: 8
Author(s): Leandro Ordóñez-Ante, Gregory Van Seghbroeck, Tim Wauters, Bruno Volckaert, Filip De Turck
Software Mentions: 2
Published: over 4 years ago

10.1016/j.jlr.2021.100105

A novel compound heterozygous leptin receptor mutation causes more severe obesity than in Lepr mice
Cited by: 3
Author(s): C Berger, Henrike O. Heyne, Tina Heiland, Sebastian Dommel, Corinna Höfling, Esther Guiu‐Jurado, Jana E. Lorenz, Steffen Rößner, Michael Dannemann, Janet Kelso, Peter Kovacs, Matthias Blüher, Nora Klöting
Software Mentions: 2
Published: almost 4 years ago

10.3390/ijms21155567

Cell Sheets from Adipose Tissue MSC Induce Healing of Pressure Ulcer and Prevent Fibrosis via Trigger Effects on Granulation Tissue Growth and Vascularization
Cited by: 15
Author(s): Natalya Alexandrushkina, Peter Nimiritsky, Roman Eremichev, В. С. Попов, Mikhail Arbatskiy, Н В Данилова, П.Г. Мальков, Zhanna Akopyan, В. А. Ткачук
Software Mentions: 2
Published: over 4 years ago

10.1083/jcb.202010003

Parameter-free molecular super-structures quantification in single-molecule localization microscopy
Cited by: 11
Author(s): Mattia Marenda, Elena Lazarova, Sebastian van de Linde, Nick Gilbert, Davide Michieletto
Software Mentions: 1
Published: almost 4 years ago

10.7717/peerj.203

ezRAD: a simplified method for genomic genotyping in non-model organisms
Cited by: 182
Author(s): Robert J. Toonen, Jonathan B. Puritz, Zac H. Forsman, Jonathan L. Whitney, Iria Fernández-Silva, Kimberly R. Andrews, Christopher E. Bird
Software Mentions: 1
Published: about 11 years ago

10.1016/j.xpro.2021.100550

Protocol for detecting introgressed archaic variants with SPrime
Cited by: 5
Author(s): Ying Zhou, Sharon R. Browning
Software Mentions: 1
Published: over 3 years ago

10.1038/srep26234

Controllability of protein-protein interaction phosphorylation-based networks: Participation of the hub 14-3-3 protein family
Cited by: 11
Author(s): Marina Uhart, Gabriel Flores, Diego Martín Bustos
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-018-25020-8

Improved strategy for the curation and classification of kinases, with broad applicability to other eukaryotic protein groups
Cited by: 10
Author(s): Andreas J. Stroehlein, Neil D. Young, Robin B. Gasser
Software Mentions: 1
Published: over 6 years ago

10.1186/1472-6750-14-66

Screening and genetic characterization of thermo-tolerant Synechocystis sp. PCC6803 strains created by adaptive evolution
Cited by: 29
Author(s): Ulrich M. Tillich, Nick Wolter, Philipp Franke, Ulf Dühring, Marcus Frohme
Software Mentions: 1
Published: over 10 years ago

10.1038/s41598-020-66494-9

Brain transcriptomics of agonistic behaviour in the weakly electric fish Gymnotus omarorum, a wild teleost model of non-breeding aggression
Cited by: 13
Author(s): Guillermo Eastman, Guillermo Valiño, Santiago Radío, Rebecca L. Young, Laura Quintana, Harold H. Zakon, Hans A. Hofmann, José Sotelo‐Silveira, Ana C. Silva
Software Mentions: 1
Published: over 4 years ago

10.1093/brain/awab109

A Bayesian optimization approach for rapidly mapping residual network function in stroke
Cited by: 9
Author(s): Romy Lorenz, Michelle Johal, Frederick A. Dick, Adam Hampshire, Robert Leech, Fatemeh Geranmayeh
Software Mentions: 1
Published: almost 4 years ago

10.1186/s12864-019-5749-3

Comparative analyses of the variation of the transcriptome and proteome of Rhodobacter sphaeroides throughout growth
Cited by: 57
Author(s): Jochen Bathke, Anne Konzer, Bernhard Remes, Matthew McIntosh, Gabriele Klug
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pgen.1006807

Dynamics of DNA methylomes underlie oyster development
Cited by: 51
Author(s): Guillaume Rivière, Yan He, Samuele Tecchio, Elizabeth Crowell, Michaël Gras, Pascal Sourdaine, Ximing Guo, Pascal Favrel
Software Mentions: 1
Published: over 7 years ago

10.12688/f1000research.11254.1

DangerTrack: A scoring system to detect difficult-to-assess regions
Cited by: 9
Author(s): Igor Dolgalev, Fritz J. Sedlazeck, Ben Busby
Software Mentions: 1
Published: over 7 years ago

10.1002/ece3.4017

Roads to isolation: Similar genomic history patterns in two species of freshwater crabs with contrasting environmental tolerances and range sizes
Cited by: 2
Author(s): Y. C. Tay, Daniel J. J. Ng, Jun Bin Loo, Danwei Huang, Yong Cai, Darren C. J. Yeo, Rudolf Meier
Software Mentions: 1
Published: over 6 years ago

10.3390/cancers13020225

Promoterless Transposon Mutagenesis Drives Solid Cancers via Tumor Suppressor Inactivation
Cited by: 1
Author(s): Aziz Aiderus, Ana M. Contreras-Sandoval, Amanda L. Meshey, Justin Y. Newberg, Jerrold M. Ward, Deborah A. Swing, Neal G. Copeland, Nancy A. Jenkins, Karen Mann, Michael B. Mann
Software Mentions: 1
Published: almost 4 years ago

10.1534/g3.119.400970

Contingent Convergence: The Ability To Detect Convergent Genomic Evolution Is Dependent on Population Size and Migration
Cited by: 5
Author(s): James R. Whiting, Bonnie A. Fraser
Software Mentions: 1
Published: almost 5 years ago

10.1186/s13059-018-1572-4

Recurrent mutations at estrogen receptor binding sites alter chromatin topology and distal gene expression in breast cancer
Cited by: 21
Author(s): Jiekun Yang, Xiaolong Wei, Turan Tufan, Cem Kuscu, Hayrunnisa Unlu, Salman Farooq, Elif Demirtas, Bryce M. Paschal, Mazhar Adli
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0198335

A scalable method to improve gray matter segmentation at ultra high field MRI
Cited by: 29
Author(s): Omer Faruk Gulban, Marian Schneider, Ingo Marquardt, Roy A M Haast, Federico De Martino
Software Mentions: 1
Published: over 6 years ago

Projects: pypi: bash

Papers Mentioning bash 65