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: treeview
https://packages.ecosyste.ms/registries/pypi.org/packages/treeview
Folder Strucutre Visualizer
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Latest release: over 5 years ago
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Papers Mentioning treeview 45
10.1002/ece3.3906
Influence of northern limit range on genetic diversity and structure in a widespread North American tree, sugar maple (<i>Acer saccharum</i>Marshall)Cited by: 11
Author(s): Noémie Graignic, Francine Tremblay, Yves Bergeron
Software Mentions: 7
Published: almost 7 years ago
10.3390/cancers12041028
Changes in the Expression of Pre-Replicative Complex Genes in hTERT and ALT Pediatric Brain TumorsCited by: 8
Author(s): Aurora Idilli, Francesca Pagani, Emanuela Kerschbamer, Francesco Berardinelli, Manuel Bernabé, María L. Cayuela, Silvano Piazza, Pietro Luigi Poliani, Emilio Cusanelli, Marina Mione
Software Mentions: 6
Published: over 4 years ago
10.1002/ece3.3175
Biogeography and systematics of endemic island damselflies: The <i>Nesobasis</i> and <i>Melanesobasis</i> (Odonata: Zygoptera) of FijiCited by: 10
Author(s): Christopher D. Beatty, Melissa Sánchez Herrera, Jeffrey H. Skevington, Arash Rashed, Hans Van Gossum, Scott Kelso, Thomas N. Sherratt
Software Mentions: 5
Published: about 7 years ago
10.1371/journal.pone.0143128
RNA-Seq Analysis Reveals MAPKKK Family Members Related to Drought Tolerance in MaizeCited by: 30
Author(s): Liu Ya, Miaoyi Zhou, Zhaoxu Gao, Wen Ren, Fan Yang, Hang He, Jiuran Zhao
Software Mentions: 5
Published: almost 9 years ago
10.1371/journal.pone.0084212
Genome Wide Expression Profiling during Spinal Cord Regeneration Identifies Comprehensive Cellular Responses in ZebrafishCited by: 74
Author(s): Subhra Prakash Hui, Dhriti Sengupta, Serene Gek Ping Lee, Triparna Sen, Sudip Kundu, Sinnakaruppan Mathavan, Sukla Ghosh
Software Mentions: 4
Published: almost 11 years ago
10.1371/journal.pone.0027965
Involvement of Histone Acetylation of Sox17 and Foxa2 Promoters during Mouse Definitive Endoderm Differentiation Revealed by MicroRNA ProfilingCited by: 26
Author(s): Shijun Fu, Fei Qi, Hua Jiang, Shannon Chuai, Song Shi, Wen Cheng Xiong, Lei Jiang, Chris X. Lu, Peter Atadja, En Li, Jianyong Shou
Software Mentions: 4
Published: almost 13 years ago
10.1002/1878-0261.12029
T-cell immunoglobulin mucin 3 blockade drives an antitumor immune response in head and neck cancerCited by: 61
Author(s): Jian-Feng Liu, Si‐Rui Ma, Liang Mao, Lin‐Lin Bu, Guang‐Tao Yu, Yicun Li, Cong-Fa Huang, Wei‐Wei Deng, Ashok B. Kulkarni, Wenfeng Zhang, Zhi‐Jun Sun
Software Mentions: 4
Published: almost 8 years ago
10.1111/j.1747-0285.2009.00832.x
On the Origins of Enzyme Inhibitor Selectivity and Promiscuity: A Case Study of Protein Kinase Binding to StaurosporineCited by: 71
Author(s): Duangrudee Tanramluk, Adrian Schreyer, William R. Pitt, Tom L. Blundell
Software Mentions: 3
Published: over 15 years ago
10.3389/fpls.2014.00364
High atomic weight, high-energy radiation (HZE) induces transcriptional responses shared with conventional stresses in addition to a core “DSB†response specific to clastogenic treatmentsCited by: 14
Author(s): Victor Missirian, Phillip A. Conklin, Kevin M. Culligan, Neil D. Huefner, Anne Britt
Software Mentions: 3
Published: over 10 years ago
10.1002/1878-0261.12505
Increased expression of the <scp>HDAC</scp>9 gene is associated with antiestrogen resistance of breast cancersCited by: 30
Author(s): Aurélien Linarès, Saïd Assou, Marion Lapierre, Erwan Thouënnon, Céline Duraffourd, Carole Fromaget, Abdelhay Boulahtouf, Tian Gao, Jiafu Ji, Özgür Şahin, Éric Badia, Nathalie Boulle, Vincent Cavaillès
Software Mentions: 3
Published: over 5 years ago
10.1186/1751-0473-6-3
WebGimm: An integrated web-based platform for cluster analysis, functional analysis, and interactive visualization of resultsCited by: 5
Author(s): Vineet K Joshi, Johannes M. Freudenberg, Zhen Hu, Mario Medvedovic
Software Mentions: 3
Published: almost 14 years ago
10.1186/s12870-019-2166-3
Transcriptomic and proteomic analysis reveals mechanisms of low pollen-pistil compatibility during water lily cross breedingCited by: 10
Author(s): Caixia Sun, Fadi Chen, Nianjun Teng, Yue-Mei Yao, Xi Shan, Zhigang Dai
Software Mentions: 3
Published: almost 5 years ago
10.1002/1878-0261.12493
Biochemical pathways mediated by <scp>KLK</scp>6 protease in breast cancerCited by: 10
Author(s): Georgios Pampalakis, Eleni Zingkou, Konstantinos G. Sidiropoulos, Eleftherios P. Diamandis, Vassilis Zoumpourlis, George M. Yousef, Georgia Sotiropoulou
Software Mentions: 3
Published: about 5 years ago
10.1186/s12864-015-1461-0
GRACOMICS: software for graphical comparison of multiple results with omics dataCited by: 7
Author(s): Minseok Seo, Joon Yoon, Taesung Park
Software Mentions: 3
Published: over 9 years ago
10.1371/journal.pcbi.1002968
RFECS: A Random-Forest Based Algorithm for Enhancer Identification from Chromatin StateCited by: 199
Author(s): Nisha Rajagopal, Wei Xie, Yan Li, Uli Wagner, Wei Wang, J Stamatoyannopoulos, Jason Ernst, M Kellis, Bing Ren
Software Mentions: 3
Published: over 11 years ago
10.1186/1471-2164-14-914
Divergent transcription is associated with promoters of transcriptional regulatorsCited by: 91
Author(s): Cyrille Lepoivre, Mohamed Belhocine, Aurélie Bergon, Aurélien Griffon, Miriam Yammine, Laurent Vanhille, Joaquin Zacarías-Cabeza, Marc Garibal, Frank‐Thomas Koch, Muhammad Ahmad Maqbool, Romain Fenouil, Béatrice Loriod, Hélène Holota, Marta Gut, Jean Imbert, Jean-Christophe Andrau, Denis Puthier, Salvatore Spicuglia
Software Mentions: 3
Published: almost 11 years ago
10.1186/1471-2407-7-61
Identification of a robust gene signature that predicts breast cancer outcome in independent data setsCited by: 37
Author(s): James E. Korkola, Ekaterini Blaveri, Sandy DeVries, Dan H. Moore, E. Shelley Hwang, Yunn Yi Chen, Anne L. Estep, Karen Chew, Ronald H. Jensen, Frederic M. Waldman
Software Mentions: 3
Published: over 17 years ago
10.1111/1751-7915.12265
Characterization of uronate dehydrogenases catalysing the initial step in an oxidative pathwayCited by: 18
Author(s): André Pick, Jochen Schmid, Volker Sieber
Software Mentions: 3
Published: over 9 years ago
10.1371/journal.pone.0000945
Transcriptional Program Induced by Wnt Protein in Human Fibroblasts Suggests Mechanisms for Cell Cooperativity in Defining Tissue MicroenvironmentsCited by: 76
Author(s): Zach Klapholz-Brown, Graham G. Walmsley, Ysbrand Nusse, Roel Nusse, Patrick O. Brown
Software Mentions: 2
Published: about 17 years ago
10.1186/1471-2164-11-435
Protein phosphatase complement in rice: genome-wide identification and transcriptional analysis under abiotic stress conditions and reproductive developmentCited by: 153
Author(s): Amarjeet Singh, Jitender Giri, Sanjay Kapoor, Akhilesh K. Tyagi, Girdhar K. Pandey
Software Mentions: 2
Published: over 14 years ago
10.1111/eva.12174
Relative contributions of neutral and non‐neutral genetic differentiation to inform conservation of steelhead trout across highly variable landscapesCited by: 47
Author(s): Andrew P. Matala, Michael W. Ackerman, Matthew R. Campbell, Shawn R. Narum
Software Mentions: 2
Published: over 10 years ago
10.1002/2211-5463.12391
Salivary proteome profiling of oral squamous cell carcinoma in a Hungarian populationCited by: 18
Author(s): Éva Csősz, Bernadett Márkus, Zsuzsanna Darula, Katalin F. Medzihradszky, Judit Nemes, Erna Szabó, József Tözsér, Csongor Kiss, Ildikó Márton
Software Mentions: 2
Published: over 6 years ago
10.1002/2211-5463.12538
Establishment and characterization of a novel vincristine‐resistant diffuse large B‐cell lymphoma cell line containing the 8q24 homogeneously staining regionCited by: 6
Author(s): Shohei Mizuno, Ichiro Hanamura, Akinobu Ota, Sivasundaram Karnan, Jo Kanasugi, Ayano Nakamura, Souichi Takasugi, Kaori Uchino, Tomohiro Horio, Mineaki Goto, Satona Murakami, Mayuko Gotou, Hiroaki Yamamoto, Masaya Watarai, Masato Shikami, Yoshitaka Hosokawa, Hiroshi Miwa, Masafumi Taniwaki, Ryuzo Ueda, Masakazu Nitta, Akiyoshi Takami
Software Mentions: 2
Published: almost 6 years ago
10.3389/fmicb.2019.01221
Sphingomonas sp. Cra20 Increases Plant Growth Rate and Alters Rhizosphere Microbial Community Structure of Arabidopsis thaliana Under Drought StressCited by: 87
Author(s): Yang Luo, Fang Wang, Yongji Huang, Meng Zhou, Jiyun Gao, Taozhe Yan, Hongmei Sheng, Lu An
Software Mentions: 2
Published: over 5 years ago
10.1038/s41598-017-11449-w
Integration of deep transcriptome and proteome analyses of salicylic acid regulation high temperature stress in Ulva proliferaCited by: 28
Author(s): Meihua Fan, Xue Sun, Nianjun Xu, Zhi Liao, Yahe Li, Jianxin Wang, Yingping Fan, Cui Da-lian, Peng Li, Zengliang Miao
Software Mentions: 2
Published: about 7 years ago
10.1186/1471-2164-5-94
Prognostic meta-signature of breast cancer developed by two-stage mixture modeling of microarray dataCited by: 118
Author(s): Ronglai Shen, Debashis Ghosh, Arul M. Chinnaiyan
Software Mentions: 2
Published: almost 20 years ago
10.1371/journal.pone.0179706
Mitochondrial DNA markers reveal high genetic diversity and strong genetic differentiation in populations of Dendrolimus kikuchii Matsumura (Lepidoptera: Lasiocampidae)Cited by: 16
Author(s): Qiu-Lei Men, Guo-Xi Xue, Dan Mu, Qiong Hu, Minyi Huang
Software Mentions: 1
Published: over 7 years ago
10.1186/1471-2148-8-288
Molecular evolution of bovine Toll-like receptor 2 suggests substitutions of functional relevanceCited by: 70
Author(s): O. Jann, Dirk Werling, Jung Su Chang, David M. Haig, Elizabeth J. Glass
Software Mentions: 1
Published: almost 17 years ago
10.1186/s12864-017-4376-0
The variome of pneumococcal virulence factors and regulatorsCited by: 29
Author(s): Gustavo Gámez, Andrés Felipe Hoyos Castro, Alejandro Gómez-Mejía, M Jorge Iván Gallego, Alejandro Bedoya, Maurício Camargo, Sven Hammerschmidt
Software Mentions: 1
Published: almost 7 years ago
10.1186/1471-2164-6-120
Duplication and positive selection among hominin-specific PRAME genesCited by: 64
Author(s): Zoë Birtle, Leo Goodstadt, Chris P. Ponting
Software Mentions: 1
Published: about 19 years ago
10.1186/1471-2229-12-119
Discovery and functional characterization of two diterpene synthases for sclareol biosynthesis in Salvia sclarea(L.) and their relevance for perfume manufactureCited by: 132
Author(s): Anne M. Caniard, Philipp Zerbe, Sylvain Legrand, Allison Cohade, Nadine Valot, Jean‐Louis Magnard, Jörg Bohlmann, Laurent Legendre
Software Mentions: 1
Published: over 12 years ago
10.1186/1752-0509-5-S3-S11
Exploring virus relationships based on virus-host protein-protein interaction networkCited by: 5
Author(s): Feng Xu, Chen Zhao, Yuhua Li, Jiang Li, Youping Deng, Tieliu Shi
Software Mentions: 1
Published: almost 13 years ago
10.1242/bio.028191
Pharmacologic inhibition of phospholipase C in the brain attenuates early memory formation in the honeybee (<i>Apis mellifera</i>L.)Cited by: 6
Author(s): Shota Suenami, Shiori Iino, Takeo Kubo
Software Mentions: 1
Published: almost 7 years ago
10.1155/2019/8597953
lncRNA Expression Reveals the Potential Regulatory Roles in Hepatocyte Proliferation during Rat Liver RegenerationCited by: 9
Author(s): Haijing Bai, Wei Jin, Jiuxin Guo, Yi Ding, Cuifang Chang, Xueqiang Guo, Yajuan Song, Jingbo Zhang, Chi Xu
Software Mentions: 1
Published: almost 5 years ago
10.1186/bcr1517
Intrinsic molecular signature of breast cancer in a population-based cohort of 412 patientsCited by: 246
Author(s): Stefano Calza, Per Hall, Gert Auer, Judith Bjöhle, Sigrid Klaar, Ulrike Kronenwett, Edison T. Liu, Lance D. Miller, Alexander Ploner, Johanna Smeds, Jonas Bergh, Yudi Pawitan
Software Mentions: 1
Published: over 18 years ago
10.1186/1476-511X-11-28
Variation of chemical composition of essential oils in wild populations of Thymus algeriensis Boiss. et Reut., a North African endemic SpeciesCited by: 64
Author(s): Nacim Zouari, Imen Ayadi, Nahed Fakhfakh, Ahmed Rebai, Sami Zouari
Software Mentions: 1
Published: over 12 years ago
10.1002/1878-0261.12583
Integrin α5 subunit is required for the tumor supportive role of fibroblasts in colorectal adenocarcinoma and serves as a potential stroma prognostic markerCited by: 23
Author(s): Ling Lu, Ruting Xie, Rong Wei, Chunmiao Cai, Dexi Bi, Dingzi Yin, Hu Liu, Jiayi Zheng, Youhua Zhang, Feifei Song, Yaohui Gao, Linhua Tan, Qing Wei, Huanlong Qin
Software Mentions: 1
Published: about 5 years ago
10.1371/journal.pcbi.0020048
Protein Family Expansions and Biological ComplexityCited by: 205
Author(s): Christine Vogel, Cyrus Chothia
Software Mentions: 1
Published: over 18 years ago
10.1371/journal.pone.0057140
Computational Analysis of siRNA Recognition by the Ago2 PAZ Domain and Identification of the Determinants of RNA-Induced Gene SilencingCited by: 30
Author(s): Mahmoud Kandeel, Yukio Kitade
Software Mentions: 1
Published: over 11 years ago
10.1111/acel.12422
Specific protein homeostatic functions of small heat‐shock proteins increase lifespanCited by: 41
Author(s): Michel J. Vos, Serena Carra, Bart Kanon, Floris Bosveld, Karin Klauke, Ody C. M. Sibon, Harm H. Kampinga
Software Mentions: 1
Published: almost 9 years ago
10.1371/journal.pone.0015986
A Novel Soluble Immune-Type Receptor (SITR) in Teleost Fish: Carp SITR Is Involved in the Nitric Oxide-Mediated Response to a Protozoan ParasiteCited by: 18
Author(s): Carla M. S. Ribeiro, Steve Bird, Geert Raes, Gholamreza Hassanzadeh Ghassabeh, Virgil E.J.C. Schijns, Maria J. S. L. Pontes, H.F.J. Savelkoul, G.F. Wiegertjes
Software Mentions: 1
Published: almost 14 years ago
10.1002/ece3.4071
<i>Daphnia</i>diversity on the Tibetan Plateau measured by DNA taxonomyCited by: 20
Author(s): Lei Xu, Qian Lin, Shufa Xu, Yangliang Gu, Juzhi Hou, Yongqin Liu, Henri J. Dumont, Bo‐Ping Han
Software Mentions: 1
Published: over 6 years ago
10.1002/2211-5463.12553
Δ12 fatty acid desaturase gene from <i>Geotrichum candidum</i> in cheese: molecular cloning and functional characterizationCited by: 8
Author(s): Xue Luo, Haisu Shi, Rina Wu, Junrui Wu, Yu Pi, Yan Zheng, Xiqing Yue
Software Mentions: 1
Published: almost 6 years ago
10.3389/fpls.2014.00678
Evidence for lateral gene transfer (LGT) in the evolution of eubacteria-derived small GTPases in plant organellesCited by: 27
Author(s): I Nengah Suwastika, Masatsugu Denawa, Saki Yomogihara, Chak Han Im, Woo Young Bang, Ryosuke L. Ohniwa, Jeong Dong Bahk, Kunio Takeyasu, Takashi Shiina
Software Mentions: 1
Published: almost 10 years ago
10.1371/journal.ppat.0040026
NetB, a New Toxin That Is Associated with Avian Necrotic Enteritis Caused by Clostridium perfringensCited by: 510
Author(s): Anthony L. Keyburn, John D. Boyce, Paola K. Vaz, Trudi Leanne Bannam, Mark Ford, Dane Parker, Antonio Di Rubbo, Julian I. Rood, Robert J. Moore
Software Mentions: 1
Published: almost 17 years ago