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: cran: COUNT
https://packages.ecosyste.ms/registries/cran.r-project.org/packages/COUNT
Functions, Data and Code for Count Data
11 versions
Latest release: about 8 years ago
3 dependent packages
2,879 downloads last month
Papers Mentioning COUNT 44
10.3390/genes12030444
Genome Analysis of Endotrypanum and Porcisia spp., Closest Phylogenetic Relatives of Leishmania, Highlights the Role of Amastins in Shaping PathogenicityCited by: 9
Author(s): Amanda T S Albanaz, Evgeny S. Gerasimov, Jeffrey Jon Shaw, Jovana Sádlová, Julius Lukeš, Petr Volf, Frederik Opperdoes, Alexei Y. Kostygov, Anzhelika Butenko, Vyacheslav Yurchenko
Software Mentions: 8
Published: almost 4 years ago
10.1093/gigascience/giab060
ISA API: An open platform for interoperable life science experimental metadataCited by: 13
Author(s): David Johnson, Dominique Batista, Keeva Cochrane, Robert P. Davey, Anthony Etuk, Alejandra González-Beltrán, Kenneth Haug, Massimiliano Izzo, Martin Larralde, Thomas N. Lawson, Alice Minotto, Pablo Moreno-Ger, Venkata Chandrasekhar Nainala, Claire O’Donovan, Luca Pireddu, Pierrick Roger, Felix Shaw, Christoph Steinbeck, Ralf Weber, Susanna-Assunta Sansone, Philippe Rocca-Serra
Software Mentions: 7
Published: over 3 years ago
10.1007/s40037-018-0438-5
#MedEd: exploring the relationship between altmetrics and traditional measures of dissemination in health professions educationCited by: 38
Author(s): Lauren A. Maggio, Todd C. Leroux, Holly Meyer, Anthony R. Artino
Software Mentions: 6
Published: over 6 years ago
10.1186/1471-2105-12-136
ArrayInitiative - a tool that simplifies creating custom Affymetrix CDFsCited by: 2
Author(s): Chris Overall, Denis Carr, Ehsan Tabari, Kevin J. Thompson, Juliane Weller
Software Mentions: 4
Published: over 13 years ago
10.3389/fmicb.2021.683814
Comparative Genomic Insights Into the Taxonomic Classification, Diversity, and Secondary Metabolic Potentials of Kitasatospora, a Genus Closely Related to StreptomycesCited by: 10
Author(s): Yisong Li, Meng Wang, Zhuo Sun, Bin-Bin Xie
Software Mentions: 4
Published: over 3 years ago
10.1186/s12864-021-07432-5
Comparative genomics reveals broad genetic diversity, extensive recombination and nascent ecological adaptation in Micrococcus luteusCited by: 12
Author(s): Yisong Li, Zhuo Sun, Jin-Cheng Rong, Bin-Bin Xie
Software Mentions: 4
Published: almost 4 years ago
10.1093/gbe/evaa216
<i>Portiera</i> Gets Wild: Genome Instability Provides Insights into the Evolution of Both Whiteflies and Their EndosymbiontsCited by: 12
Author(s): Diego Santos-García, Natividad Mestre-Rincon, David Ouvrard, Einat Zchori-Fein, Shai Morin
Software Mentions: 4
Published: about 4 years ago
10.1186/s12864-019-6126-y
Comparative genomics of Leishmania (Mundinia)Cited by: 24
Author(s): Anzhelika Butenko, Alexei Y. Kostygov, Jovana Sádlová, Yuliya Kleschenko, Tomáš Bečvář, Lucie Podešvová, Diego H. Macedo, David Žihala, Julius Lukeš, Paul A. Bates, Petr Volf, Frederik Opperdoes, Vyacheslav Yurchenko
Software Mentions: 4
Published: about 5 years ago
10.3389/fmicb.2020.01192
Comparative Genomic Analysis Reveals the Metabolism and Evolution of the Thermophilic Archaeal Genus MetallosphaeraCited by: 7
Author(s): Pei Wang, Liang Zhi Li, Yipeng Qin, Zong Lin Liang, Xiu Tong Li, Hua Yin, Li Jun Liu, Shuang‐Jiang Liu, Cheng‐Ying Jiang
Software Mentions: 4
Published: over 4 years ago
10.1007/s00425-015-2434-x
Uncovering novel loci for mesocotyl elongation and shoot length in indica rice through genome-wide association mappingCited by: 38
Author(s): Qing Lu, Mengchen Zhang, Xiaojun Niu, Caihong Wang, Qun Xu, Feng Yue, Shan Wang, Xiaoping Yuan, Hao Yu, Yiping Wang, Xinghua Wei
Software Mentions: 3
Published: about 9 years ago
10.3389/fmicb.2020.612257
Diversity and Genomic Characterization of a Novel Parvarchaeota Family in Acid Mine Drainage SedimentsCited by: 20
Author(s): Zhen-Hao Luo, Qi Li, Yan Lai, Hao Chen, Bin Liao, Li-Nan Huang
Software Mentions: 3
Published: about 4 years ago
10.1186/1471-2156-11-86
Discovering joint associations between disease and gene pairs with a novel similarity testCited by: 3
Author(s): Wan-Yu Lin, Wen‐Chung Lee
Software Mentions: 3
Published: about 14 years ago
10.3389/fmicb.2021.639995
Interplay of Various Evolutionary Modes in Genome Diversification and Adaptive Evolution of the Family SulfolobaceaeCited by: 2
Author(s): Rachana Banerjee, Narendrakumar M. Chaudhari, Abhishake Lahiri, Anupam Gautam, Debaleena Bhowmik, Chitra Dutta, Sujay Chattopadhyay, Daniel H. Huson, Sandip Paul
Software Mentions: 3
Published: over 3 years ago
10.1093/gbe/evu211
Phylogenomics and Evolutionary Dynamics of the Family ActinomycetaceaeCited by: 22
Author(s): Kelei Zhao, Wujiao Li, Chunlan Kang, Lianming Du, Ting Huang, Xiuyue Zhang, Min Wu, Bisong Yue
Software Mentions: 2
Published: over 10 years ago
10.1128/mBio.00350-21
Casting Light on the Adaptation Mechanisms and Evolutionary History of the Widespread SumerlaeotaCited by: 10
Author(s): Yun Fang, Yang Yuan, Jun Liu, Geng Wu, Jian Yang, Zheng-Shuang Hua, Jibin Han, Xiying Zhang, Wenjun Li, Hongchen Jiang
Software Mentions: 2
Published: over 3 years ago
10.3389/fmicb.2020.00961
Diversity and Evolutionary Dynamics of Antiphage Defense Systems in Ralstonia solanacearum Species ComplexCited by: 11
Author(s): José A. García del Castillo, Henry Secaira-Morocho, Stephanie Maldonado, Katlheen N. Sarmiento
Software Mentions: 2
Published: over 4 years ago
10.3389/fpls.2020.00484
Evolution and Functional Divergence of the Fructokinase Gene Family in PopulusCited by: 4
Author(s): Weijie Xu, Yiyang Zhao, Sisi Chen, Jianbo Xie, Deqiang Zhang
Software Mentions: 2
Published: over 4 years ago
10.1093/database/bav127
ncRNA orthologies in the vertebrate lineageCited by: 17
Author(s): Miguel Pignatelli, Albert J. Vilella, Matthieu Muffato, Leo I. Gordon, Simon White, Paul Flicek, Javier Herrero
Software Mentions: 2
Published: almost 9 years ago
10.1128/mSystems.00867-20
Insights into the Metabolism and Evolution of the Genus <i>Acidiphilium</i> , a Typical Acidophile in Acid Mine DrainageCited by: 24
Author(s): Liangzhi Li, Zhenghua Liu, Min Zhang, Delong Meng, Xueduan Liu, Pei Wang, Xiu-Tong Li, Zhen Jiang, Shuiping Zhong, Cheng‐Ying Jiang, Huaqun Yin
Software Mentions: 2
Published: about 4 years ago
10.1186/s12864-018-4531-2
Comparative genomic analysis reveals the evolution and environmental adaptation strategies of vibriosCited by: 56
Author(s): Heyu Lin, Min Yu, Xiaolei Wang, Xiaohua Zhang
Software Mentions: 2
Published: almost 7 years ago
10.1186/s12864-019-5751-9
Genomic evidence of the illumination response mechanism and evolutionary history of magnetotactic bacteria within the Rhodospirillaceae familyCited by: 7
Author(s): Yinzhao Wang, Giorgio Casaburi, Wei Lin, Ying Liu, Fengping Wang, Yongxin Pan
Software Mentions: 2
Published: over 5 years ago
10.1128/mSystems.00602-21
Comparative Genomics Provides Insights into the Genetic Diversity and Evolution of the DPANN SuperphylumCited by: 6
Author(s): Liangzhi Li, Zhenghua Liu, Zhi Zhou, Min Zhang, Delong Meng, Xueduan Liu, Ye Huang, Xiu-Tong Li, Zhen Jiang, Shuiping Zhong, Łukasz Drewniak, Zhi Yang, Qian Li, Yongjun Liu, Xiaolong Nan, Biguang Jiang, Cheng‐Ying Jiang, Huaqun Yin
Software Mentions: 1
Published: over 3 years ago
10.7554/eLife.33014
The kinetoplastid-infecting Bodo saltans virus (BsV), a window into the most abundant giant viruses in the seaCited by: 64
Author(s): Christoph Deeg, Cheryl-Emiliane T. Chow, Curtis A. Suttle
Software Mentions: 1
Published: almost 7 years ago
10.3390/ijms21218407
High Stroma T-Cell Infiltration is Associated with Better Survival in Stage pT1 Bladder CancerCited by: 10
Author(s): Suzanne Belia Hulsen, Eleonora Lippolis, Fulvia Ferrazzi, Wolfgang Otto, Luitpold Distel, Rainer Fietkau, Stefan Denzinger, Johannes Breyer, Maximilian Burger, Simone Bertz, Markus Eckstein, Annette Ebner, Arndt Hartmann, Carol-Immanuel Geppert
Software Mentions: 1
Published: about 4 years ago
10.1186/1471-2407-9-292
Distribution of immune cells in head and neck cancer: CD8+ T-cells and CD20+B-cells in metastatic lymph nodes are associated with favourable outcome in patients with oro- and hypopharyngeal carcinomaCited by: 152
Author(s): Dominik Pretscher, Luitpold Distel, Gerhard G. Grabenbauer, Michael Wittlinger, Maike Buettner, Gerald Niedobitek
Software Mentions: 1
Published: over 15 years ago
10.1186/s12885-017-3317-2
Prognostic significance of tumor infiltrating immune cells in oral squamous cell carcinomaCited by: 114
Author(s): Juan Fang, Xiaoxu Li, Dawei Ma, Xiangqi Liu, Yi‐Chen Chen, Yun Wang, Vivian Wai Yan Lui, Juan Xia, Bin Cheng, Wang Zhi
Software Mentions: 1
Published: over 7 years ago
10.1186/s12862-017-0942-y
Reconstruction of the evolution of microbial defense systemsCited by: 41
Author(s): Pere Puigbò, Kira S. Makarova, David M. Kristensen, Yuri I. Wolf, Eugene V. Koonin
Software Mentions: 1
Published: over 7 years ago
10.1186/s12864-019-6346-1
Stratified reconstruction of ancestral Escherichia coli diversificationCited by: 22
Author(s): José Marı́a González-Alba, Fernando Baquero, Rafael Cantón, Juan Carlos Galán
Software Mentions: 1
Published: about 5 years ago
10.1186/s13062-015-0102-5
Horizontally transferred genes cluster spatially and metabolicallyCited by: 13
Author(s): Alexander Dilthey, Martin J. Lercher
Software Mentions: 1
Published: about 9 years ago
10.1186/1745-6150-6-59
Extensive intron gain in the ancestor of placental mammalsCited by: 16
Author(s): Dušan Kordiš
Software Mentions: 1
Published: almost 14 years ago
10.1186/1745-6150-7-46
Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transferCited by: 135
Author(s): Yuri I. Wolf, Kira S. Makarova, Natalya Yutin, Eugene V. Koonin
Software Mentions: 1
Published: almost 13 years ago
10.1186/1743-422X-10-106
Mimiviridae: clusters of orthologous genes, reconstruction of gene repertoire evolution and proposed expansion of the giant virus familyCited by: 93
Author(s): Natalya Yutin, Philippe Colson, Didier Raoult, Eugene V. Koonin
Software Mentions: 1
Published: over 11 years ago
10.7717/peerj.8811
Predictive value of CONUT score combined with serum CA199 levels in postoperative survival of patients with pancreatic ductal adenocarcinoma: a retrospective studyCited by: 11
Author(s): Ankang Wang, Bo Sun, Min Wang, Hao Shi, Zhiwei Huang, Tao He, Qiu Li, Jiaqi Deng, Wenguang Fu, Jiang Yu
Software Mentions: 1
Published: almost 5 years ago
10.1371/journal.pgen.1004363
Predicting the Minimal Translation Apparatus: Lessons from the Reductive Evolution of MollicutesCited by: 107
Author(s): Henri Grosjean, Michelyne Breton, Pascal Sirand‐Pugnet, Florence Tardy, François Thiaucourt, Christine Citti, Aurélien Barré, Satoko Yoshizawa, Dominique Fourmy, Valérie de Crécy‐Lagard, Alain Blanchard
Software Mentions: 1
Published: over 10 years ago
10.1371/journal.pone.0071435
Characterization and Evolution of Conserved MicroRNA through Duplication Events in Date Palm (Phoenix dactylifera)Cited by: 23
Author(s): Yong Xiao, Wei Xia, Yaodong Yang, Annaliese S. Mason, Xintao Lei, Zhiying Ma
Software Mentions: 1
Published: over 11 years ago
10.1039/c7sc01052d
Learning reduced kinetic Monte Carlo models of complex chemistry from molecular dynamicsCited by: 20
Author(s): Qiong Yang, Carlos Sing‐Long, Evan J. Reed
Software Mentions: 1
Published: almost 8 years ago
10.3389/fgene.2021.618517
Evolution of Protein-Mediated Biomineralization in Scleractinian CoralsCited by: 14
Author(s): Tal Zaquin, Assaf Malik, Jeana L. Drake, Hollie M. Putnam, Tali Mass
Software Mentions: 1
Published: almost 4 years ago
10.3389/fmicb.2017.01940
Genome of Ca. Pandoraea novymonadis, an Endosymbiotic Bacterium of the Trypanosomatid Novymonas esmeraldasCited by: 25
Author(s): Alexei Y. Kostygov, Anzhelika Butenko, Anna Nenarokova, Daria Tashyreva, Pavel Flegontov, Julius Lukeš, Vyacheslav Yurchenko
Software Mentions: 1
Published: about 7 years ago
10.3389/fmicb.2020.01530
Genomic Insights of Cryobacterium Isolated From Ice Core Reveal Genome Dynamics for Adaptation in GlacierCited by: 9
Author(s): Yongqin Liu, Liang Shen, Yonghui Zeng, Tingting Xing, Bin Xu, Ninglian Wang
Software Mentions: 1
Published: over 4 years ago
10.3389/fmicb.2016.01942
Evolution and Phylogeny of Large DNA Viruses, Mimiviridae and Phycodnaviridae Including Newly Characterized Heterosigma akashiwo VirusCited by: 15
Author(s): Fumito Maruyama, Shoko Ueki
Software Mentions: 1
Published: about 8 years ago
10.1093/gbe/evx062
A Locus Encoding Variable Defense Systems against Invading DNA Identified in Streptococcus suisCited by: 15
Author(s): Masatoshi Okura, Takashi Nozawa, Takayasu Watanabe, Kazunori Murase, Ichirô Nakagawa, Daisuke Takamatsu, Makoto Osaki, Tsutomu Sekizaki, Marcelo Gottschalk, Shigeyuki Hamada, Fumito Maruyama
Software Mentions: 1
Published: over 7 years ago
10.1186/s40981-019-0282-6
Geriatric Nutritional Risk Index and Controlling Nutritional Status Score can predict postoperative 180-day mortality in hip fracture surgeriesCited by: 11
Author(s): Atsushi Kotera
Software Mentions: 1
Published: over 5 years ago
10.1038/srep23704
Genome of Leptomonas pyrrhocoris: a high-quality reference for monoxenous trypanosomatids and new insights into evolution of LeishmaniaCited by: 71
Author(s): Pavel Flegontov, Anzhelika Butenko, Sergei Firsov, Natalya Kraeva, Marek Eliáš, Mark C. Field, Dmitry A. Filatov, Olga Flegontova, Evgeny S. Gerasimov, Jana Hlaváčová, Aygul Ishemgulova, Andrew P. Jackson, Steven Kelly, Alexei Y. Kostygov, Maria D. Logacheva, Dmitri Maslov, Frederik Opperdoes, Amanda O’Reilly, Jovana Sádlová, Tereza Ševčíková, Divya Venkatesh, Čestmı́r Vlček, Petr Volf, Jan Votýpka, Kristína Záhonová, Vyacheslav Yurchenko, Julius Lukeš
Software Mentions: 1
Published: over 8 years ago
10.1038/srep36116
Evolutionary study of Yersinia genomes deciphers emergence of human pathogenic speciesCited by: 10
Author(s): Shi Tan, İlhan Tan, Mui Fern Tan, Avirup Dutta, Siew Woh Choo
Software Mentions: 1
Published: about 8 years ago