Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: pypi: make
https://packages.ecosyste.ms/registries/pypi.org/packages/make
Create project layout from jinja2 templates.
10 versions
Latest release: about 4 years ago
4 dependent packages
11,442 downloads last month
Papers Mentioning make 60
10.1371/journal.pone.0232822
SimSurvey: An R package for comparing the design and analysis of surveys by simulating spatially-correlated populationsCited 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 dataCited by: 131
Author(s): Joshua G. Dunn, Jonathan S. Weissman
Software Mentions: 14
Published: almost 8 years ago
10.12688/wellcomeopenres.16430.2
Polysomal mRNA Association and Gene Expression in Trypanosoma bruceiCited 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 transplantationCited 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 birdCited 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 infectionCited 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 haloclineCited 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 massCited 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 contaminantsCited 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 DegradationCited 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 researchCited 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) LarvaeCited 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 ConditionsCited 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 DisinfestationCited 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 LevelsCited 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 ScaffoldingCited 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 mappingCited by: 3
Author(s): Diego Pasqualin, Marcos S. Barbeitos, Fabiano Silva
Software Mentions: 4
Published: over 7 years ago
10.1093/gigascience/gix042
Kronos: a workflow assembler for genome analytics and informaticsCited 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 EcosystemCited 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 packagesCited 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 Rosetta3Cited 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 WineCited 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 samplerCited 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 SludgeCited 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 speciesCited 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 responseCited 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 microbiotaCited by: 79
Author(s): Fernanda Cornejo‐Granados, Luigui Gallardo-Becerra, Miriam Leonardo-Reza, Juan Pablo Ochoa‐Romo, Adrián Ochoa-Leyva
Software Mentions: 3
Published: about 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 speciesCited 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 associationCited 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 approachCited by: 38
Author(s): Yanjun Zan, Thibaut Payen, Mette Lillie, Christa F. Honaker, P. B. Siegel, Örjan Carlborg
Software Mentions: 2
Published: about 5 years ago
10.1093/aobpla/ply064
Understanding biogeographical patterns in the western Balkan Peninsula using environmental niche modelling and geostatistics in polymorphic Edraianthus tenuifoliusCited 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 microbiotaCited 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 ComplexCited 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) dataCited 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 Pdp11Cited 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 ResearchCited 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 resourcesCited 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 EnzymesCited 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 SolutionCited 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 SourceCited 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: about 5 years ago
10.3389/fmicb.2019.02938
Goethite Reduction by a Neutrophilic Member of the Alphaproteobacterial Genus TelmatospirillumCited 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 SeaCited 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 conditionsCited 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 dataCited 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 ReviewCited 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 DataCited by: 34
Author(s): Elisha D.O. Roberson, Jonathan Pevsner
Software Mentions: 1
Published: about 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 cycleCited 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 virusCited 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 toolCited 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 hardwareCited 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: about 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 microbiotaCited 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 nucleosideCited 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 HologramCited 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 textCited 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: almost 6 years ago
10.3390/genes10040299
Commensal and Pathogenic Members of the Dental Calculus Microbiome of Badia Pozzeveri Individuals from the 11th to 19th CenturiesCited 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 MRICited 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 diversityCited 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