pypi: make | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0232822

SimSurvey: An R package for comparing the design and analysis of surveys by simulating spatially-correlated populations
Cited by: 5
Author(s): Paul M. Regular, Gregory J. Robertson, Keith P. Lewis, Jonathan Babyn, Brian Healey, Fran Mowbray
Software Mentions: 17
Published: over 4 years ago

10.1186/s12864-016-3278-x

Plastid: nucleotide-resolution analysis of next-generation sequencing and genomics data
Cited by: 131
Author(s): Joshua G. Dunn, Jonathan S. Weissman
Software Mentions: 14
Published: about 8 years ago

10.12688/wellcomeopenres.16430.2

Polysomal mRNA Association and Gene Expression in Trypanosoma brucei
Cited by: 0
Author(s): Michele Tinti, Anna Kelner-Mirôn, Lizzie J. Marriott, Michael A. J. Ferguson
Software Mentions: 11
Published: about 3 years ago

10.1186/s40168-019-0745-z

Specific gut microbiome members are associated with distinct immune markers in pediatric allogeneic hematopoietic stem cell transplantation
Cited by: 57
Author(s): Anna Cäcilia Ingham, Katrine Kielsen, Malene Skovsted Cilieborg, Ole Lund, Susan Holmes, Frank Møller Aarestrup, Klaus Müller, Sünje Johanna Pamp
Software Mentions: 9
Published: about 5 years ago

10.1371/journal.pone.0220926

Gut microbiome shifts with urbanization and potentially facilitates a zoonotic pathogen in a wading bird
Cited by: 50
Author(s): Maureen H. Murray, Emily W. Lankau, Anjelika D. Kidd, Catharine N. Welch, Taylor Ellison, Henry Adams, Erin K. Lipp, Sonia M. Hernández
Software Mentions: 8
Published: over 4 years ago

10.1186/s40168-019-0687-5

Evolution of the gut microbiome following acute HIV-1 infection
Cited by: 61
Author(s): Muntsa Rocafort, Marc Noguera‐Julian, Javier Rivera, Lucía Pastor, Yolanda Guillén, Jost Langhorst, Mariona Parera, Inácio Mandomando, Jorge Carrillo, Víctor Urrea, C. Rodríguez, María Casadellà, M. Luz Calle, Bonaventura Clotet, Julià Blanco, Denise Naniche, Roger Paredes
Software Mentions: 6
Published: over 5 years ago

10.1038/s41396-021-00931-z

Fine-scale metabolic discontinuity in a stratified prokaryote microbiome of a Red Sea deep halocline
Cited by: 8
Author(s): Grégoire Michoud, David Kamanda Ngugi, Alan Barozzi, Giuseppe Merlino, María Ll. Calleja, António Delgado Huertas, Xosé Anxelu G. Morán, Daniele Daffonchio
Software Mentions: 6
Published: over 3 years ago

10.1038/s41598-017-01498-6

An optimal distance cutoff for contact-based Protein Structure Networks using side-chain centers of mass
Cited by: 64
Author(s): Juan Salamanca Viloria, Maria Francesca Allega, Matteo Lambrughi, Elena Papaleo
Software Mentions: 6
Published: over 7 years ago

10.1038/srep21969

Culex quinquefasciatus larval microbiomes vary with instar and exposure to common wastewater contaminants
Cited by: 27
Author(s): Marcus J. Pennington, Sean M. Prager, William E. Walton, John T. Trumble
Software Mentions: 6
Published: over 8 years ago

10.1371/journal.pone.0125393

Biochar in Co-Contaminated Soil Manipulates Arsenic Solubility and Microbiological Community Structure, and Promotes Organochlorine Degradation
Cited by: 45
Author(s): Samuel Gregory, Christopher Anderson, Marta Camps Arbestain, Patrick J. Biggs, Austen R. D. Ganley, Justin M. O’Sullivan, Michael T. McManus
Software Mentions: 5
Published: over 9 years ago

10.12688/f1000research.5773.3

ActivePapers: a platform for publishing and archiving computer-aided research
Cited by: 11
Author(s): Konrad Hinsen
Software Mentions: 5
Published: over 9 years ago

10.3389/fimmu.2019.03014

Bacterial Exposure Mediates Developmental Plasticity and Resistance to Lethal Vibrio lentus Infection in Purple Sea Urchin (Strongylocentrotus purpuratus) Larvae
Cited by: 12
Author(s): Nicholas W Schuh, Tyler J. Carrier, Catherine S. Schrankel, Adam M. Reitzel, Andreas Heyland, Jonathan P. Rast
Software Mentions: 5
Published: almost 5 years ago

10.3389/fmicb.2020.589898

Dietary Lipid:Protein Ratio and n-3 Long-Chain Polyunsaturated Fatty Acids Alters the Gut Microbiome of Atlantic Salmon Under Hypoxic and Normoxic Conditions
Cited by: 31
Author(s): David Huyben, Beeke K. Roehe, Michaël Bekaert, Bente Ruyter, Brett Glencross
Software Mentions: 5
Published: almost 4 years ago

10.1128/AEM.02992-18

Characterizing the Key Agents in a Disease-Suppressed Soil Managed by Reductive Soil Disinfestation
Cited by: 33
Author(s): Liang Liang Liu, Xinqi Huang, Jun Zhao, Jinbo Zhang, Zucong Cai
Software Mentions: 5
Published: over 5 years ago

10.3389/fmicb.2016.00434

Restructuring of Epibacterial Communities on Fucus vesiculosus forma mytili in Response to Elevated pCO2 and Increased Temperature Levels
Cited by: 26
Author(s): Birte Mensch, Sven C. Neulinger, Angelika Graiff, Andreas Pansch, Sven Künzel, Martin Fischer, Ruth A. Schmitz
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pgen.1005954

Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding
Cited by: 102
Author(s): Shubha Vij, Heiner Kuhl, Irina M. Kuznetsova, Aleksey Komissarov, Andrey A. Yurchenko, Peter van Heusden, Siddharth Singh, Natascha May Thevasagayam, Sai Rama Sridatta Prakki, K. Purushothaman, Jolly M. Saju, Junhui Jiang, Stanley Kimbung Mbandi, Mario Jonas, Amy Tong, Sarah Mwangi, Doreen Lau, Si Yan Ngoh, Woei Chang Liew, Xueyan Shen, Lawrence S. Hon, James Drake, Matthew Boitano, Richard J. Hall, Chen-Shan Chin, Ramkumar Lachumanan, Jonas Korlach, Vladimir A. Trifonov, Мarsel R. Kabilov, Alexey E. Tupikin, Darrell Green, Simon Moxon, Tyler Garvin, Fritz J. Sedlazeck, Gregory W. Vurture, G. Gopikrishna, Vinaya Kumar Katneni, Tansyn H. Noble, Vinod Scaria, Sridhar Sivasubbu, Dean R. Jerry, Stephen J. O’Brien, Michael C. Schatz, Tamás Dalmay, Stephen W. Turner, Si Lok, Alan Christoffels, László Orbán
Software Mentions: 4
Published: over 8 years ago

10.1186/s12859-017-1554-7

SFREEMAP - A simulation-free tool for stochastic mapping
Cited by: 3
Author(s): Diego Pasqualin, Marcos S. Barbeitos, Fabiano Silva
Software Mentions: 4
Published: almost 8 years ago

10.1093/gigascience/gix042

Kronos: a workflow assembler for genome analytics and informatics
Cited by: 5
Author(s): Mohammad Jafar Taghiyar, Jamie Rosner, Diljot Grewal, Bruno M. Grande, Radhouane Aniba, Jasleen K. Grewal, Paul C. Boutros, Ryan D. Morin, Ali Bashashati, Sohrab P. Shah
Software Mentions: 4
Published: over 7 years ago

10.3389/fmicb.2016.00579

Metagenomics Reveals Pervasive Bacterial Populations and Reduced Community Diversity across the Alaska Tundra Ecosystem
Cited by: 61
Author(s): Eric R. Johnston, Luis M. Rodriguez-R, Chengwei Luo, Mengting Yuan, Liyou Wu, Zhili He, Edward A. G. Schuur, Yiqi Luo, James M. Tiedje, Jizhong Zhou, Konstantinos T. Konstantinidis
Software Mentions: 4
Published: over 8 years ago

10.12688/wellcomeopenres.11635.2

exampletestr—An easy start to unit testing R packages
Cited by: 2
Author(s): Rory Nolan, Sergi Padilla‐Parra
Software Mentions: 4
Published: over 7 years ago

10.3389/fninf.2017.00063

Running Neuroimaging Applications on Amazon Web Services: How, When, and at What Cost?
Cited by: 15
Author(s): Tara M. Madhyastha, Natalie Koh, Trevor K. M. Day, Moisés Hernández-Fernández, Austin Kelley, Daniel J. Peterson, S.Thiraviya Regina Rajan, Karl A. Woelfer, Jonathan Wolf, Thomas J. Grabowski
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.pone.0020450

Modeling Symmetric Macromolecular Structures in Rosetta3
Cited by: 191
Author(s): Frank DiMaio, Andrew Leaver‐Fay, Philip Bradley, David Baker, Ingemar André
Software Mentions: 3
Published: over 13 years ago

10.1371/journal.pone.0085611

Saliva from Obese Individuals Suppresses the Release of Aroma Compounds from Wine
Cited by: 87
Author(s): Paola Piombino, Alessandro Genovese, Sabrina Esposito, Luigi Moio, Pier Paolo Cutolo, Angela Chambery, Valeria Severino, Elisabetta Moneta, Daniel P. Smith, Sarah M. Owens, Jack A. Gilbert, Danilo Ercolini
Software Mentions: 3
Published: almost 11 years ago

10.1186/1751-0473-3-12

CRANKITE: A fast polypeptide backbone conformation sampler
Cited by: 17
Author(s): Alexei A. Podtelezhnikov, David L. Wild
Software Mentions: 3
Published: over 16 years ago

10.3389/fmicb.2016.01407

Biostimulation of Indigenous Microbial Community for Bioremediation of Petroleum Refinery Sludge
Cited by: 106
Author(s): Jayeeta Sarkar, Sufia K. Kazy, Abhishek Gupta, Avishek Dutta, Balaram Mohapatra, Ajoy Roy, Paramita Bera, Adinpunya Mitra, Pinaki Sar
Software Mentions: 3
Published: about 8 years ago

10.1186/s12859-020-3408-y

AllEnricher: a comprehensive gene set function enrichment tool for both model and non-model species
Cited by: 16
Author(s): Zhenmin Du, Qi Hu, Xinxing Liu, Kai Zou, Emmanuel Konadu Sarkodie, Xueduan Liu, Fei Gao
Software Mentions: 3
Published: over 4 years ago

10.1093/braincomms/fcab083

Defining functional variants associated with Alzheimer’s disease in the induced immune response
Cited by: 13
Author(s): Janet Harwood, Ganna Leonenko, Rebecca Sims, Valentina Escott‐Price, Julie Williams, Peter Holmans
Software Mentions: 3
Published: over 3 years ago

10.7717/peerj.5382

A meta-analysis reveals the environmental and host factors shaping the structure and function of the shrimp microbiota
Cited by: 79
Author(s): Fernanda Cornejo‐Granados, Luigui Gallardo-Becerra, Miriam Leonardo-Reza, Juan Pablo Ochoa‐Romo, Adrián Ochoa-Leyva
Software Mentions: 3
Published: over 6 years ago

10.1186/s12859-015-0677-y

Coevolutionary analyses require phylogenetically deep alignments and better null models to accurately detect inter-protein contacts within and between species
Cited by: 13
Author(s): Aram Avila-Herrera, Katherine S. Pollard
Software Mentions: 3
Published: about 9 years ago

10.1186/s40478-016-0338-z

A comprehensive next generation sequencing-based virome assessment in brain tissue suggests no major virus - tumor association
Cited by: 54
Author(s): Michael J. Strong, Eugene Blanchard, Zhen Lin, Cindy A. Morris, Melody Baddoo, Christopher M. Taylor, Marcus L. Ware, Erik K. Flemington
Software Mentions: 3
Published: over 8 years ago

10.1186/s12711-019-0487-1

Genotyping by low-coverage whole-genome sequencing in intercross pedigrees from outbred founders: a cost-efficient approach
Cited by: 38
Author(s): Yanjun Zan, Thibaut Payen, Mette Lillie, Christa F. Honaker, P. B. Siegel, Örjan Carlborg
Software Mentions: 2
Published: over 5 years ago

10.1093/aobpla/ply064

Understanding biogeographical patterns in the western Balkan Peninsula using environmental niche modelling and geostatistics in polymorphic Edraianthus tenuifolius
Cited by: 8
Author(s): Peter Glasnović, Martina Temunović, Dmitar Lakušić, Tamara Rakić, Valentina Brečko Grubar, Boštjan Surina
Software Mentions: 2
Published: about 6 years ago

10.1186/s12876-019-1156-0

Deficiency of Gankyrin in the small intestine is associated with augmented colitis accompanied by altered bacterial composition of intestinal microbiota
Cited by: 3
Author(s): Toshiharu Sakurai, Hiroki Nishiyama, Tatsuo Nagai, Susumu Goto, Hiroyuki Ogata, Masatoshi Kudo
Software Mentions: 2
Published: almost 5 years ago

10.3390/biom9100535

MS-Based Approaches Enable the Structural Characterization of Transcription Factor/DNA Response Element Complex
Cited by: 9
Author(s): Lukáš Slavata, Josef Chmelı́k, Daniel Kavan, Růžena Filandrová, Jan Fiala, Michal Rosůlek, Hynek Mrázek, Zdeněk Kukačka, Karel Vališ, Petr Man, Michael Miller, William D. McIntyre, Daniele Fabris, Petr Novák
Software Mentions: 2
Published: about 5 years ago

10.1016/j.ymeth.2013.10.015

Hyb: A bioinformatics pipeline for the analysis of CLASH (crosslinking, ligation and sequencing of hybrids) data
Cited by: 72
Author(s): Anthony J. Travis, Jonathan Moody, Aleksandra Helwak, David Tollervey, Grzegorz Kudla
Software Mentions: 2
Published: almost 11 years ago

10.7717/peerj.6526

TarSynFlow, a workflow for bacterial genome comparisons that revealed genes putatively involved in the probiotic character of<i>Shewanella putrefaciens</i>strain Pdp11
Cited by: 3
Author(s): Pedro Seoane, Silvana Tapia‐Paniagua, Rocío Bautista, Elena Alcaide, Consuelo Esteve, Eduardo Martínez‐Manzanares, M.C. Balebona, M. Gonzalo Claros, Miguel A. Moriñigo
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pbio.1002506

A Practical Guide for Improving Transparency and Reproducibility in Neuroimaging Research
Cited by: 109
Author(s): Krzysztof J. Gorgolewski, Russell A. Poldrack
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pcbi.1007291

Patient Dossier: Healthcare queries over distributed resources
Cited by: 2
Author(s): Miguél Vázquez, Alfonso Valencia
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pcbi.1003714

A Multiscale Approach to Modelling Drug Metabolism by Membrane-Bound Cytochrome P450 Enzymes
Cited by: 40
Author(s): Richard Lonsdale, Sarah L. Rouse, Mark S. P. Sansom, Adrian J. Mulholland
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0095664

Anomalous Small Angle X-Ray Scattering Simulations: Proof of Concept for Distance Measurements for Nanoparticle-Labelled Biomacromolecules in Solution
Cited by: 9
Author(s): Valerie J. Pinfield, David J. Scott
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0068429

Invasion Is a Community Affair: Clandestine Followers in the Bacterial Community Associated to Green Algae, Caulerpa racemosa, Track the Invasion Source
Cited by: 58
Author(s): Tânia Aires, Ester A. Serrão, Gary A. Kendrick, Carlos M. Duarte, Sophie Arnaud–Haond
Software Mentions: 2
Published: over 11 years ago

10.1002/ece3.5534

Diel patterning in the bacterial community associated with the sea anemone <i>Nematostella vectensis</i>
Cited by: 16
Author(s): Whitney B. Leach, Tyler J. Carrier, Adam M. Reitzel
Software Mentions: 2
Published: over 5 years ago

10.3389/fmicb.2019.02938

Goethite Reduction by a Neutrophilic Member of the Alphaproteobacterial Genus Telmatospirillum
Cited by: 22
Author(s): Emma J. Gagen, Julian Zaugg, Gene W. Tyson, Gordon Southam
Software Mentions: 2
Published: almost 5 years ago

10.3389/fmicb.2021.673553

Microbial Communities on Plastic Polymers in the Mediterranean Sea
Cited by: 53
Author(s): Annika Vaksmaa, Katrin Knittel, Alejandro Abdala Asbun, Maaike Goudriaan, Andreas Ellrott, Harry J. Witte, Ina Vollmer, Florian Meirer, Christian Lott, Miriam Weber, Julia C. Engelmann, Helge Niemann
Software Mentions: 2
Published: over 3 years ago

10.1038/s41598-017-11805-w

Microbiome of Pacific Whiteleg shrimp reveals differential bacterial community composition between Wild, Aquacultured and AHPND/EMS outbreak conditions
Cited by: 177
Author(s): Fernanda Cornejo‐Granados, Alonso A. López-Zavala, Luigui Gallardo-Becerra, Alfredo Mendoza-Vargas, F. Sánchez, Rodrigo Vichido, Luis G. Brieba, Marı́a Teresa Viana, Rogerio R. Sotelo‐Mundo, Adrián Ochoa-Leyva
Software Mentions: 2
Published: about 7 years ago

10.1186/1751-0473-5-10

DOG-SPOT database for comprehensive management of dog genetic research data
Cited by: 1
Author(s): Julie A. S. Powell, Jeremy J. Allen, Nathan B. Sutter
Software Mentions: 2
Published: almost 14 years ago

10.2196/13780

Generative Participatory Design Methodology to Develop Electronic Health Interventions: Systematic Literature Review
Cited by: 53
Author(s): Pieter Vandekerckhove, Marleen de Mul, Wichor M. Bramer, Antoinette de Bont
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0006711

Visualization of Shared Genomic Regions and Meiotic Recombination in High-Density SNP Data
Cited by: 34
Author(s): Elisha D.O. Roberson, Jonathan Pevsner
Software Mentions: 1
Published: over 15 years ago

10.1186/s13567-015-0274-0

The vaginal microbiome is stable in prepubertal and sexually mature Ellegaard Göttingen Minipigs throughout an estrous cycle
Cited by: 30
Author(s): Emma Lorenzen, Eglė Kudirkiene, Nicole Gutman, Anette Blak Grossi, Jørgen Steen Agerholm, Karin Erneholm, Christina Skytte, Marlene Danner Dalgaard, Anders Miki Bojesen
Software Mentions: 1
Published: about 9 years ago

10.1038/srep37800

Amino acid substitutions V63I or A37S/I61T/V63I/V100A in the PA N-terminal domain increase the virulence of H7N7 influenza A virus
Cited by: 25
Author(s): Meng Hu, Hin Chu, Ke Zhang, K. N. Singh, Cun Li, Shuofeng Yuan, Billy K. C. Chow, Wenjun Song, Jie Zhou, Bo‐Jian Zheng
Software Mentions: 1
Published: almost 8 years ago

10.1186/1471-2105-11-S6-S28

IView: introgression library visualization and query tool
Cited by: 3
Author(s): Christopher A. Bottoms, Sherry Flint-García, Michael D. McMullen
Software Mentions: 1
Published: about 14 years ago

10.1186/1471-2105-14-243

4273π: Bioinformatics education on low cost ARM hardware
Cited by: 22
Author(s): Daniel Barker, David Ferrier, Peter W.H. Holland, John B. O. Mitchell, Heleen Plaisier, Michael G. Ritchie, Steven D. Smart
Software Mentions: 1
Published: over 11 years ago

10.1038/s41598-018-33524-6

Daily HIV pre-exposure prophylaxis (PrEP) with tenofovir disoproxil fumarate-emtricitabine reduced Streptococcus and increased Erysipelotrichaceae in rectal microbiota
Cited by: 21
Author(s): Michael P. Dubé, Sung Yong Park, Heather Ross, Tanzy Love, Sheldon R. Morris, Ha Youn Lee
Software Mentions: 1
Published: about 6 years ago

10.1038/s41598-019-48935-2

A trade-off for covalent and intercalation binding modes: a case study for Copper (II) ions and singly modified DNA nucleoside
Cited by: 1
Author(s): Jean‐Marie Mouesca, Hania Ahouari, Sarath Chandra Dantu, Giuseppe Sicoli
Software Mentions: 1
Published: about 5 years ago

10.3390/jimaging6010001

Morphing a Stereogram into Hologram
Cited by: 3
Author(s): Enrique Canessa, Livio Tenze
Software Mentions: 1
Published: almost 5 years ago

10.1186/1471-2105-10-233

A realistic assessment of methods for extracting gene/protein interactions from free text
Cited by: 59
Author(s): Renata Kabiljo, Andrew B. Clegg, Adrian J. Shepherd
Software Mentions: 1
Published: over 15 years ago

10.1186/s13063-018-2984-x

Functional brain activation changes associated with practice in delaying smoking among moderate to heavy smokers: study protocol and rationale of a randomized trial (COPE)
Cited by: 0
Author(s): Andrew T. Fox, Delwyn Catley, Kimber P. Richter, Edward F. Ellerbeck, Morgan G. Brucks, Vlad B. Papa, Laura E. Martin
Software Mentions: 1
Published: about 6 years ago

10.3390/genes10040299

Commensal and Pathogenic Members of the Dental Calculus Microbiome of Badia Pozzeveri Individuals from the 11th to 19th Centuries
Cited by: 8
Author(s): Tasha M. Santiago-Rodríguez, Antonio Fornaciari, Gino Fornaciari, Stefania Luciani, Isolina Marota, Giuseppe Vercellotti, Gary A. Toranzos, Valentina Giuffra, Raúl J. Cano
Software Mentions: 1
Published: over 5 years ago

10.3389/fncir.2018.00112

Prenatal Irradiation-Induced Hippocampal Abnormalities in Rats Evaluated Using Manganese-Enhanced MRI
Cited by: 5
Author(s): Shigeyoshi Saito, Kazuhiko Sawada, Ichio Aoki
Software Mentions: 1
Published: almost 6 years ago

10.1186/2047-217X-2-3

AXIOME: automated exploration of microbial diversity
Cited by: 46
Author(s): Michael D. J. Lynch, Andre P. Masella, Michael W. Hall, Andrea K. Bartram, Josh D. Neufeld
Software Mentions: 1
Published: over 11 years ago

Projects: pypi: make

Papers Mentioning make 60