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: amap
https://packages.ecosyste.ms/registries/pypi.org/packages/amap
Automated mouse atlas propagation
33 versions
Latest release: over 4 years ago
1 dependent package
191 downloads last month
Papers Mentioning amap 37
10.3389/fmicb.2018.01474
Distinct Oceanic Microbiomes From Viruses to Protists Located Near the Antarctic Circumpolar CurrentCited by: 24
Author(s): Flavia Flaviani, Declan C. Schroeder, Karen Lebret, Cecilia Balestreri, Andrea Highfield, Joanna L. Schroeder, Sally Thorpe, Karen Moore, Konrad Pasckiewicz, Maya C. Pfaff, Edward P. Rybicki
Software Mentions: 27
Published: about 6 years ago
10.1016/j.stem.2019.07.008
Defining the Identity and Dynamics of Adult Gastric Isthmus Stem CellsCited by: 85
Author(s): Seungmin Han, J. Lynn Fink, David J. Jörg, Eunmin Lee, Min Kyu Yum, Lemonia Chatzeli, Sebastian R. Merker, Manon Josserand, Teodora Trendafilova, Amanda Andersson-Rolf, Catherine Dabrowska, Hyunki Kim, Ronald Naumann, Ji–Hyun Lee, Nobuo Sasaki, Richard L. Mort, Onur Basak, Hans Clevers, Daniel E. Stange, Anna Philpott, Jong Kim, Benjamin D. Simons, Bon‐Kyoung Koo
Software Mentions: 17
Published: about 5 years ago
10.1186/1471-2105-13-133
Bios2mds: an R package for comparing orthologous protein families by metric multidimensional scalingCited by: 30
Author(s): Julien Pelé, Jean Michel Bécu, Hervé Abdi, Marie Chabbert
Software Mentions: 14
Published: over 12 years ago
10.1186/1756-0500-4-546
HumMeth27QCReport: an R package for quality control and primary analysis of Illumina Infinium methylation dataCited by: 20
Author(s): Francesco Mancuso, Magda Montfort, Anna Carreras, Andreu Alibés, Guglielmo Roma
Software Mentions: 11
Published: almost 13 years ago
10.1186/s12864-016-2737-8
Cogena, a novel tool for co-expressed gene-set enrichment analysis, applied to drug repositioning and drug mode of action discoveryCited by: 55
Author(s): Zhilong Jia, Ying Liu, Naiyang Guan, Xiaochen Bo, Zhi-Gang Luo, Michael R. Barnes
Software Mentions: 10
Published: over 8 years ago
10.1371/journal.pone.0150547
Permissible Home Range Estimation (PHRE) in Restricted Habitats: A New Algorithm and an Evaluation for Sea OttersCited by: 36
Author(s): L. Max Tarjan, M. Tim Tinker
Software Mentions: 9
Published: over 8 years ago
10.1186/s13058-019-1148-6
Identification of three subtypes of triple-negative breast cancer with potential therapeutic implicationsCited by: 70
Author(s): Pascal Jézéquel, Olivier Kerdraon, Hubert Hondermarck, Catherine Guérin‐Charbonnel, Hamza Lasla, Wilfried Gouraud, Jean-Luc Canon, Andrea Gombos, Florence Dalenc, Suzette Delaloge, Jérôme Lemonnier, Delphine Loussouarn, Véronique Verrièle, Mario Campone
Software Mentions: 9
Published: over 5 years ago
10.1186/s13058-015-0550-y
Gene-expression molecular subtyping of triple-negative breast cancer tumours: importance of immune responseCited by: 223
Author(s): Pascal Jézéquel, Delphine Loussouarn, Catherine Guérin‐Charbonnel, Loı̈c Campion, Antoine Vanier, Wilfried Gouraud, Hamza Lasla, Catherine Guette, Isabelle Valo, Véronique Verrièle, Mario Campone
Software Mentions: 8
Published: over 9 years ago
10.1186/s12864-015-2319-1
Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genesCited by: 3
Author(s): Youko Horiuchi, Yoshiaki Harushima, Hironori Fujisawa, Takako Mochizuki, Masahiro Fujita, Hajime Ohyanagi, Nori Kurata
Software Mentions: 8
Published: almost 9 years ago
10.1038/s41598-017-14785-z
Poly-β-hydroxybutyrate administration during early life: effects on performance, immunity and microbial community of European sea bass yolk-sac larvaeCited by: 18
Author(s): Andrea Franke, Olivia Roth, Peter De Schryver, Till Bayer, Linsey Garcia‐Gonzalez, Sven Künzel, Peter Bossier, Joanna J. Miest, Catriona Clemmesen
Software Mentions: 8
Published: almost 7 years ago
10.1371/journal.pgen.1006883
Systematic identification and characterization of regulatory elements derived from human endogenous retrovirusesCited by: 108
Author(s): Jumpei Ito, Ryota Sugimoto, Hirofumi Nakaoka, Shiro Yamada, Tetsuaki Kimura, Takahide Hayano, Ituro Inoue
Software Mentions: 8
Published: about 7 years ago
10.1186/s12920-015-0153-6
Gene-expression signature functional annotation of breast cancer tumours in function of ageCited by: 4
Author(s): Pascal Jézéquel, Zein Sharif, Hamza Lasla, Wilfried Gouraud, Catherine Guérin‐Charbonnel, Loı̈c Campion, Stéphane Chrétien, Mario Campone
Software Mentions: 7
Published: almost 9 years ago
10.1371/journal.pcbi.1002350
Single Sample Expression-Anchored Mechanisms Predict Survival in Head and Neck CancerCited by: 66
Author(s): Xinan Yang, Kelly Regan, Yong Huang, Qingbei Zhang, Jiànróng Lǐ, Tanguy Y. Seiwert, Ezra E.W. Cohen, H. Rosie Xing, Yves A. Lussier
Software Mentions: 6
Published: over 12 years ago
10.1038/sdata.2016.95
Systematic chemical-genetic and chemical-chemical interaction datasets for prediction of compound synergismCited by: 12
Author(s): Jan Wildenhain, Michaela Spitzer, Sonam Dolma, Nick Jarvik, Robert L. White, Marcia Roy, Emma Griffiths, David S. Bellows, Gerard D. Wright, Mike Tyers
Software Mentions: 6
Published: almost 8 years ago
10.1093/gigascience/giaa131
A methodological approach to correlate tumor heterogeneity with drug distribution profile in mass spectrometry imaging dataCited by: 5
Author(s): Mridula Prasad, G.J. Postma, Pietro Franceschi, Lavinia Morosi, Silvia Giordano, Francesca Falcetta, Raffaella Giavazzi, Enrico Davoli, L.M.C. Buydens, Jeroen J. Jansen
Software Mentions: 6
Published: almost 4 years ago
10.1371/journal.pone.0068414
NanoMiner — Integrative Human Transcriptomics Data Resource for Nanoparticle ResearchCited by: 20
Author(s): Lingjia Kong, Soile Tuomela, Lauri Hahne, Helena Ahlfors, Olli Yli‐Harja, Bengt Fadeel, Riitta Lahesmaa, Reija Autio
Software Mentions: 6
Published: about 11 years ago
10.3389/fimmu.2020.01636
Immune and Metabolic Signatures of COVID-19 Revealed by Transcriptomics Data ReuseCited by: 101
Author(s): Luiz Gustavo Gardinassi, Camila Oliveira Silva Souza, Helioswilton Sales‐Campos, Simone Gonçalves Fonseca
Software Mentions: 5
Published: about 4 years ago
10.18632/oncotarget.25350
High expression of nucleoporin 133 mRNA in bone marrow CD138+ cells is a poor prognostic factor in multiple myelomaCited by: 4
Author(s): Soushi Ibata, Masayoshi Kobune, Shohei Kikuchi, Masahiro Yoshida, Satoshi Miura, Hyogo Horiguchi, Kazuyuki Murase, Satoshi Iyama, Kohichi Takada, Koji Miyanishi, Junji Kato
Software Mentions: 5
Published: over 6 years ago
10.1111/j.1365-294X.2012.05756.x
Exploring local immunological adaptation of two stickleback ecotypes by experimental infection and transcriptome‐wide digital gene expression analysisCited by: 83
Author(s): Tobias L. Lenz, Christophe Eizaguirre, Björn Rotter, Martin Kalbe, Manfred Milinski
Software Mentions: 5
Published: about 12 years ago
10.1371/journal.pone.0179613
A data analysis framework for biomedical big data: Application on mesoderm differentiation of human pluripotent stem cellsCited by: 7
Author(s): Benjamin Ulfenborg, Alexander Karlsson, Maria Riveiro, Caroline Améen, Karolina Åkesson, Christian X. Andersson, Peter Sartipy, Jane Synnergren
Software Mentions: 5
Published: about 7 years ago
10.1186/1471-2164-15-749
Metagenomics reveals that detoxification systems are underrepresented in marine bacterial communitiesCited by: 22
Author(s): Johan Bengtsson‐Palme, Magnus Alm Rosenblad, Mikael Molin, Anders Blomberg
Software Mentions: 5
Published: over 10 years ago
10.1186/1755-8794-3-21
SEURAT: Visual analytics for the integrated analysis of microarray dataCited by: 63
Author(s): Alexander Gribov, Martin Sill, Sonja C. Lück, Frank G. Rücker, Konstanze Döhner, Lars Bullinger, Axel Benner, Antony Unwin
Software Mentions: 5
Published: over 14 years ago
10.1038/s41598-018-19717-z
Annual shifts of flow regime alteration: new insights from the Chaishitan Reservoir in ChinaCited by: 12
Author(s): Yongyong Zhang, Xiaoyan Zhai, Tongtiegang Zhao
Software Mentions: 5
Published: over 6 years ago
10.1038/s41598-021-91962-1
OpiumPlex is a novel microsatellite system for profiling opium poppy (Papaver somniferum L.)Cited by: 4
Author(s): Jakub Vašek, Daniela Čílová, Martina Melounová, Pavel Svoboda, Kamila Zdeňková, Eliška Čermáková, Jaroslava Ovesná
Software Mentions: 5
Published: over 3 years ago
10.3389/fmicb.2017.02179
An Integrated Insight into the Relationship between Soil Microbial Community and Tobacco Bacterial Wilt DiseaseCited by: 83
Author(s): Yang Heng, Juan Li, Yunhua Xiao, Yanling Gu, Hongwei Liu, Yili Liang, Xueduan Liu, Jin Hu, Delong Meng, Huaqun Yin
Software Mentions: 4
Published: almost 7 years ago
10.1186/s12864-016-2482-z
Overlapping cell population expression profiling and regulatory inference in C. elegansCited by: 6
Author(s): Joshua T. Burdick, Travis Walton, Elicia Preston, Amanda L. Zacharias, Arjun Raj, John I. Murray
Software Mentions: 4
Published: over 8 years ago
10.1016/j.stemcr.2019.08.014
Base-Resolution Methylome of Retinal Pigment Epithelial Cells Used in the First Trial of Human Induced Pluripotent Stem Cell-Based Autologous TransplantationCited by: 17
Author(s): Hiromitsu Araki, Fumihito Miura, Akira Watanabe, Chikako Morinaga, Fumiyo Kitaoka, Yuko Kitano, Noriko Sakai, Yu Shibata, Makoto Terada, So Goto, Shinya Yamanaka, Masayo Takahashi, Takashi Ito
Software Mentions: 4
Published: almost 5 years ago
10.1038/s41598-020-57546-1
Genomic Survey of Salt Acclimation-Related Genes in the Halophilic Cyanobacterium Euhalothece sp. Z-M001Cited by: 14
Author(s): Hee Wook Yang, Ji-Young Song, Sung Mi Cho, Hak Cheol Kwon, Cheol‐Ho Pan, Youn‐Il Park
Software Mentions: 4
Published: over 4 years ago
10.3390/genes10010027
RNA-Seq Analyses Identify Additivity as the Predominant Gene Expression Pattern in F1 Chicken Embryonic Brain and LiverCited by: 16
Author(s): Zhuo Zhu, Susan J. Lamont, Behnam Abasht
Software Mentions: 3
Published: over 5 years ago
10.1038/s41598-018-30464-z
Metabolomic changes in the mouse retina after optic nerve injuryCited by: 13
Author(s): Kota Sato, Daisuke Saigusa, Ryosuke Saito, Amane Fujioka, Yurika Nakagawa, Koji M. Nishiguchi, Taiki Kokubun, Ikuko N. Motoike, Kouichi Maruyama, Kazuko Omodaka, Yukihiro Shiga, Akira Uruno, S. Koshiba, Masayuki Yamamoto, Toru Nakazawa
Software Mentions: 3
Published: about 6 years ago
10.1371/journal.pone.0213220
miR-7977 inhibits the Hippo-YAP signaling pathway in bone marrow mesenchymal stromal cellsCited by: 20
Author(s): Masahiro Yoshida, Hyogo Horiguchi, Shohei Kikuchi, Satoshi Iyama, Hiroshi Ikeda, Akinobu Goto, Yutaka Kawano, Kazuyuki Murase, Kohichi Takada, Koji Miyanishi, Junji Kato, Masayoshi Kobune
Software Mentions: 3
Published: over 5 years ago
10.1186/s13040-018-0178-4
A multi-objective gene clustering algorithm guided by apriori biological knowledge with intensification and diversification strategiesCited by: 15
Author(s): Jorge Parraga-Alava, Márcio Dorn, Mario Inostroza-Ponta
Software Mentions: 3
Published: about 6 years ago
10.1186/s12284-021-00481-0
Resequencing of 672 Native Rice Accessions to Explore Genetic Diversity and Trait Associations in VietnamCited by: 11
Author(s): Janet Higgins, Bruno Santos, Tran Dang Khanh, Khuất Hữu Trung, Tran Duy Duong, Nguyen Thi Phuong Doai, Nguyen Truong Khoa, Dang Thi Thanh Ha, Nguyen Thuy Diep, Kieu Thi Dung, Cong Nguyen Phi, Trần Thị Thu Thủy, Nguyễn Thành Tuấn, Hoang-Dung Tran, Nguyễn Thành Trung, Hoang Thi Nam Giang, Ta Kim Nhung, Cuong Tran, Son Lang, La Tuan Nghia, Nguyễn Văn Giảng, Tran Dang Xuan, Anthony Hall, Sarah Dyer, Lê Huy Hàm, Mario Cáccamo, Jose J De Vega
Software Mentions: 3
Published: over 3 years ago
10.3389/fimmu.2021.724060
The First Chemically-Synthesised, Highly Immunogenic Anti-SARS-CoV-2 Peptides in DNA Genotyped Aotus Monkeys for Human UseCited by: 5
Author(s): Manuel Elkín Patarroyo, Manuel A. Patarroyo, Martha Patricia Alba, Laura Pabón, Marı́a Teresa Rugeles, Wbeimar Aguilar-Jiménez, Lizdany Florez, Adriana Bermúdez, Ashok K. Rout, Christian Griesinger, Carlos F. Suárez, Jorge Aza-Conde, César Reyes, Catalina Avendaño, Jhoan Samacá, Anny Camargo, Yolanda Silva, Martha Forero, Edgardo González
Software Mentions: 2
Published: about 3 years ago
10.1371/journal.pone.0223433
Clade II Candida auris possess genomic structural variations related to an ancestral strainCited by: 29
Author(s): Tsuyoshi Sekizuka, Shigekazu Iguchi, Takashi Umeyama, Yuba Inamine, Koichi Makimura, Makoto Kuroda, Yoshitsugu Miyazaki, Ken Kikuchi
Software Mentions: 2
Published: almost 5 years ago
10.1186/s13068-017-0882-1
Time-resolved transcriptome analysis and lipid pathway reconstruction of the oleaginous green microalga Monoraphidium neglectum reveal a model for triacylglycerol and lipid hyperaccumulationCited by: 30
Author(s): Daniel Jaeger, Anderson M. Winkler, Jan H. Mussgnug, Jörn Kalinowski, Alexander Goesmann, Olaf Kruse
Software Mentions: 2
Published: about 7 years ago
10.1186/1868-7083-4-22
A systematic evaluation of whole genome amplification of bisulfite-modified DNACited by: 23
Author(s): Miki Bundo, Fumiko Sunaga, Junko Ueda, Kazuhiko Kasai, Takeshi Kato, Kazuya Iwamoto
Software Mentions: 2
Published: almost 12 years ago