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: skewer
https://packages.ecosyste.ms/registries/pypi.org/packages/skewer
Enumerate AWS resources and index them in ElasticSearch
1 version
Latest release: about 10 years ago
17 downloads last month
Papers Mentioning skewer 29
10.1016/j.xcrm.2020.100096
Treatment with Commonly Used Antiretroviral Drugs Induces a Type I/III Interferon Signature in the Gut in the Absence of HIV InfectionCited by: 11
Author(s): Sean M. Hughes, Claire Levy, Fernanda Calienes, Joanne D. Stekler, Urvashi Pandey, Lucia Vojtech, Alicia R. Berard, Kenzie Birse, Laura Noël‐Romas, Brian Richardson, Jackelyn B. Golden, Michael Cartwright, Ann C. Collier, Claire E. Stevens, Marcel E. Curlin, Timothy H. Holtz, Nelly Mugo, Elizabeth Irungu, Elly Katabira, Timothy Muwonge, Javier R. Lama, Jared M. Baeten, Adam Burgener, Jairam R. Lingappa, M. Juliana McElrath, Romel D. Mackelprang, Ian McGowan, Ross D. Cranston, Mark J. Cameron, Florian Hladik
Software Mentions: 21
Published: about 4 years ago
10.1099/mgen.0.000492
Quantitative analysis of the splice variants expressed by the major hepatitis B virus genotypesCited by: 13
Author(s): Chun Shen Lim, Vitina Sozzi, Margaret Littlejohn, Lilly Yuen, Nadia Warner, Brigid Betz‐Stablein, Fabio Luciani, Peter Revill, Chris M. Brown
Software Mentions: 13
Published: almost 4 years ago
10.1371/journal.ppat.1009602
Single cell analysis of host response to helminth infection reveals the clonal breadth, heterogeneity, and tissue-specific programming of the responding CD4+ T cell repertoireCited by: 5
Author(s): Ivy K. Brown, Nathan Dyjack, Mindy M. Miller, S. Harsha Krovi, Cydney Rios, Rachel A. Woolaver, Laura Harmacek, Ting-Hui Tu, Brian P. O’Connor, Thomas Danhorn, Brian Vestal, Laurent Gapin, Clemencia Pinilla, Max A. Seibold, James Scott‐Browne, Radleigh Santos, R. Lee Reinhardt
Software Mentions: 8
Published: over 3 years ago
10.1038/s41435-020-00118-0
Genomic profiling of T-cell activation suggests increased sensitivity of memory T cells to CD28 costimulationCited by: 13
Author(s): Dafni A. Glinos, Blagoje Soskic, Cayman Williams, Alan Kennedy, Luke Jostins, David M. Sansom, Gosia Trynka
Software Mentions: 7
Published: almost 4 years ago
10.1080/19490976.2021.1902771
The intestinal microbiota and metabolites in patients with anorexia nervosaCited by: 44
Author(s): Petra Procházková, Radka Roubalová, Jiří Dvořák, Jakub Kreisinger, Martin Hill, Helena Tlaskalová‐Hogenová, Petra Tomášová, Helena Pelantová, M Cermáková, Marek Kuzma, Josef Bulant, Martin Bilej, Kvido Smitka, Alena Lambertová, Petra Holanová, Hana Papežová
Software Mentions: 6
Published: almost 4 years ago
10.1186/s12862-021-01773-1
Gut microbiota in two recently diverged passerine species: evaluating the effects of species identity, habitat use and geographic distanceCited by: 5
Author(s): Jiří Reif, Lucie Schmiedová, Jakub Kreisinger, Tomáš Albrecht, Jiří Reif, Tomasz S. Osiejuk, Radka Reifová
Software Mentions: 6
Published: over 3 years ago
10.1371/journal.pcbi.1004393
Informatics for RNA Sequencing: A Web Resource for Analysis on the CloudCited by: 73
Author(s): Malachi Griffith, Jason Walker, Nicholas C. Spies, Benjamin J. Ainscough, Obi L. Griffith
Software Mentions: 6
Published: over 9 years ago
10.1371/journal.ppat.1008869
Macrophage maturation from blood monocytes is altered in people with HIV, and is linked to serum lipid profiles and activation indices: A model for studying atherogenic mechanismsCited by: 16
Author(s): Emily Bowman, Cheryl M. Cameron, Brian Richardson, Milind V. Kulkarni, Janelle Gabriel, Morgan J. Cichon, Ken M. Riedl, Yousef Mustafa, Michael Cartwright, Brandon Snyder, Subha V. Raman, David A. Zidar, Susan L. Koletar, Martin P. Playford, Nehal N. Mehta, Scott F. Sieg, Michael L. Freeman, Michael M. Lederman, Mark J. Cameron, Nicholas T. Funderburg
Software Mentions: 5
Published: about 4 years ago
10.1016/j.devcel.2018.12.026
Comparative Epigenomics Reveals that RNA Polymerase II Pausing and Chromatin Domain Organization Control Nematode piRNA BiogenesisCited by: 32
Author(s): Toni Beltran, Consuelo Barroso, T. Y. Birkle, Lewis Stevens, Hillel T. Schwartz, Paul W. Sternberg, Hélène Fradin, Kristin C. Gunsalus, Fabio Piano, Garima Sharma, Chiara Cerrato, Julie Ahringer, Enrique Martínez-Pérez, Mark Blaxter, Peter Sarkies
Software Mentions: 5
Published: over 5 years ago
10.3390/cells10081923
Overexpression and Activation of αvβ3 Integrin Differentially Affects TGFβ2 Signaling in Human Trabecular Meshwork CellsCited by: 11
Author(s): Mark S. Filla, Keith Meyer, Jennifer A. Faralli, Donna M. Peters
Software Mentions: 5
Published: over 3 years ago
10.3390/ijms21186762
Changes in Nuclear Shape and Gene Expression in Response to Simulated Microgravity Are LINC Complex-DependentCited by: 13
Author(s): Srujana Neelam, Brian Richardson, Richard Barker, Ceasar Udave, Simon Gilroy, Mark J. Cameron, Howard G. Levine, Ye Zhang
Software Mentions: 4
Published: about 4 years ago
10.1016/j.celrep.2020.108337
Human and Mouse Transcriptome Profiling Identifies Cross-Species Homology in Pulmonary and Lymph Node Mononuclear PhagocytesCited by: 37
Author(s): Sonia M. Leach, Sophie L. Gibbings, Anita Tewari, Shaikh M. Atif, Brian Vestal, Thomas Danhorn, William J. Janssen, Tor D. Wager, Claudia Jakubzick
Software Mentions: 4
Published: about 4 years ago
10.1371/journal.ppat.1009732
Germinal Center T follicular helper (GC-Tfh) cell impairment in chronic HIV infection involves c-Maf signalingCited by: 2
Author(s): Marita Chakhtoura, Mike Fang, Rafael Cubas, Margaret O'Connor, Carmen N. Nichols, Brian Richardson, Aarthi Talla, Susan Moir, Mark J. Cameron, Virginie Tardif, Elias K. Haddad
Software Mentions: 4
Published: over 3 years ago
10.1016/j.tranon.2018.04.002
Long Noncoding RNAs AC009014.3 and Newly Discovered XPLAID Differentiate Aggressive and Indolent Prostate CancersCited by: 7
Author(s): Anthony J. Cesnik, Bing Yang, Andrew Truong, Tyler Etheridge, Michele Spiniello, Maisie I. Steinbrink, Michael R. Shortreed, Brian L. Frey, David F. Jarrard, Lloyd M. Smith
Software Mentions: 4
Published: over 6 years ago
10.1371/journal.pone.0216992
Adaptive genetic variation underlies biocomplexity of Atlantic Cod in the Gulf of Maine and on Georges BankCited by: 12
Author(s): Gemma V. Clucas, Lisa A. Kerr, Steven X. Cadrin, Douglas R. Zemeckis, Graham D. Sherwood, David Goethel, Zachary T. Whitener, Adrienne I. Kovach
Software Mentions: 3
Published: over 5 years ago
10.1186/s12864-020-07037-4
Gene expression within the periaqueductal gray is linked to vocal behavior and early-onset parkinsonism in Pink1 knockout ratsCited by: 12
Author(s): Cynthia A. Kelm‐Nelson, Stephen C. Gammie
Software Mentions: 3
Published: about 4 years ago
10.7554/eLife.66063
Distinct skeletal stem cell types orchestrate long bone skeletogenesisCited by: 35
Author(s): Thomas H. Ambrosi, Rahul Sinha, Holly Steininger, Malachia Hoover, Matthew P. Murphy, Lauren S. Koepke, Yuting Wang, Wan-Jin Lu, Maurizio Morri, Norma Neff, Irving L. Weissman, Michael T. Longaker, Charles Chan
Software Mentions: 3
Published: over 3 years ago
10.1371/journal.ppat.1009861
Integrative multi-omics profiling reveals cAMP-independent mechanisms regulating hyphal morphogenesis in Candida albicansCited by: 9
Author(s): Kyung-Hee Min, Thomas F. Jannace, Haoyu Si, Krishna R. Veeramah, John D. Haley, James B. Konopka
Software Mentions: 3
Published: over 3 years ago
10.3390/ani9080523
Global Mapping of H3K4 Trimethylation (H3K4me3) and Transcriptome Analysis Reveal Genes Involved in the Response to Epidemic Diarrhea Virus Infections in PigsCited by: 12
Author(s): Haifei Wang, Yang Li, Huan Qu, Hanping Feng, Shenglong Wu, Wenbin Bao
Software Mentions: 3
Published: over 5 years ago
10.1099/mgen.0.000497
Intraspecies plasmid and genomic variation of Mycobacterium kubicae revealed by the complete genome sequences of two clinical isolatesCited by: 7
Author(s): Jo Hendrix, L. Elaine Epperson, David Durbin, Jennifer R. Honda, Michael Strong
Software Mentions: 2
Published: almost 4 years ago
10.1371/journal.pone.0231752
Retinal astrocytes transcriptome reveals Cyp1b1 regulates the expression of genes involved in cell adhesion and migrationCited by: 7
Author(s): Juliana Falero-Perez, Christine M. Sorenson, Nader Sheibani
Software Mentions: 2
Published: over 4 years ago
10.1038/srep37302
Genetic determination of the enhanced drought resistance of rice maintainer HuHan2B by pedigree breedingCited by: 8
Author(s): Haibin Wei, Fang Fěng, Qiaojun Lou, Hui Xia, Xiaoyan Ma, Yunhua Liu, Kai Xu, Yu Xing, Hanwei Mei, Lijun Luo
Software Mentions: 2
Published: about 8 years ago
10.1002/mgg3.1418
Whole genome sequencing identifies a duplicated region encompassing Xq13.2q13.3 in a large Iranian family with intellectual disabilityCited by: 0
Author(s): Sepideh Mehvari, Farzaneh Larti, Hao Hu, Zohreh Fattahi, Maryam Beheshtian, Seyedeh Sedigheh Abedini, Sanaz Arzhangi, Hans‐Hilger Ropers, Vera M. Kalscheuer, Daniel Auld, Kimia Kahrizi, Yasser Riazalhosseini, Hossein Najmabadi
Software Mentions: 2
Published: over 4 years ago
10.1038/s41598-018-28217-z
Genome-Wide Determination of Gene Essentiality by Transposon Insertion Sequencing in Yeast Pichia pastorisCited by: 23
Author(s): Jinxiang Zhu, Ruiqing Gong, Qiaoyun Zhu, Qun He, Ning Xu, Yichun Xu, Menghao Cai, Xiangshan Zhou, Yuanxing Zhang, Mian Zhou
Software Mentions: 2
Published: over 6 years ago
10.1128/genomeA.00555-15
Draft Genome Sequence of Pseudomonas syringae pv. persicae NCPPB 2254Cited by: 3
Author(s): Wenjun Zhao, Hongshan Jiang, Qian Tian, Jie Hu
Software Mentions: 1
Published: over 9 years ago
10.1186/s12864-017-3529-5
Variability among Cucurbitaceae species (melon, cucumber and watermelon) in a genomic region containing a cluster of NBS-LRR genesCited by: 16
Author(s): Jordi Morata, Pere Puigdomènech
Software Mentions: 1
Published: almost 8 years ago
10.3390/cancers11091329
Morpho-Molecular Assessment Indicates New Prognostic Aspects and Personalized Therapeutic Options in Sinonasal MelanomaCited by: 8
Author(s): Sandra N. Freiberger, G Morand, Patrick Turko, U. Wager, Reinhard Dummer, Martin Hüllner, David Holzmann, Niels J. Rupp, Mitchell P. Levesque
Software Mentions: 1
Published: about 5 years ago
10.3390/v12101093
Thapsigargin at Non-Cytotoxic Levels Induces a Potent Host Antiviral Response that Blocks Influenza A Virus ReplicationCited by: 15
Author(s): Leah Goulding, Jiayun Yang, Zhimin Jiang, Hongyu Zhang, Daniel Lea, Richard D. Emes, Tania Dottorini, Juan Pu, Jinhua Liu, Kin-Chow Chang
Software Mentions: 1
Published: about 4 years ago
10.1038/srep20200
Study design requirements for RNA sequencing-based breast cancer diagnosticsCited by: 2
Author(s): Arvind Singh Mer, Daniel Klevebring, Henrik Grönberg, Mattias Rantalainen
Software Mentions: 1
Published: almost 9 years ago