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: lima
https://packages.ecosyste.ms/registries/pypi.org/packages/lima
Lightweight Marshalling of Python 3 Objects.
4 versions
Latest release: over 9 years ago
1,355 downloads last month
Papers Mentioning lima 40
10.3390/diagnostics10020066
Identification of Key Biomarkers in Bladder Cancer: Evidence from a Bioinformatics AnalysisCited by: 22
Author(s): Chuan Zhang, Mandy Berndt‐Paetz, Jochen Neuhaus
Software Mentions: 12
Published: almost 5 years ago
10.1534/g3.120.401612
A Reference Genome Sequence for Giant SequoiaCited by: 53
Author(s): Alison Dawn Scott, Aleksey V. Zimin, Daniela Puiu, Rachael E. Workman, Monica Britton, Sumaira Zaman, Madison Caballero, Andrew C. Read, Adam J. Bogdanove, Emily E. Burns, Jill L. Wegrzyn, Winston Timp, Steven L. Salzberg, David B. Neale
Software Mentions: 11
Published: about 4 years ago
10.3390/ijms21218148
Utilizing PacBio Iso-Seq for Novel Transcript and Gene Discovery of Abiotic Stress Responses in Oryza sativa L.Cited by: 25
Author(s): Stephanie Schaarschmidt, Axel Fischer, Lovely Mae F Lawas, Rejbana Alam, Endang M. Septiningsih, Julia Bailey‐Serres, Krishna Jagadish, Bruno Huettel, Dirk K. Hincha, Ellen Zuther
Software Mentions: 11
Published: about 4 years ago
10.1128/AEM.00880-20
Community Structure of Arbuscular Mycorrhizal Fungi in Soils of Switchgrass Harvested for BioenergyCited by: 7
Author(s): Alden C. Dirks, Randall D. Jackson
Software Mentions: 10
Published: about 4 years ago
10.1534/g3.120.401309
CeMbio - The<i>Caenorhabditis elegans</i>Microbiome ResourceCited by: 71
Author(s): Philipp Dirksen, Adrien Assié, Johannes Zimmermann, Fan Zhang, Adina-Malin Tietje, Sarah Arnaud Marsh, Marie‐Anne Félix, Michael Y. Shapira, Christoph Kaleta, Hinrich Schulenburg, Buck S. Samuel
Software Mentions: 10
Published: about 4 years ago
10.1186/s12864-020-07123-7
Illuminating the dark side of the human transcriptome with long read transcript sequencingCited by: 76
Author(s): Richard Kuo, Yuanyuan Cheng, Runxuan Zhang, John W. Brown, Jacqueline Smith, Alan Archibald, David W. Burt
Software Mentions: 8
Published: about 4 years ago
10.1093/g3journal/jkab189
Long-read transcriptome and other genomic resources for the angiosperm <i>Silene noctiflora</i>Cited by: 7
Author(s): Alissa M. Williams, Michael W. Itgen, Amanda K. Broz, Olivia G. Carter, Daniel B Sloan
Software Mentions: 6
Published: over 3 years ago
10.1371/journal.pbio.3000091
Non-proteolytic ubiquitin modification of PPARγ by Smurf1 protects the liver from steatosisCited by: 16
Author(s): Kun Yan Zhu, Yi Tang, Xuan Xu, Hien Dang, Liu-Ya Tang, Xiang Wang, Xin Wei Wang, Ying E. Zhang
Software Mentions: 5
Published: almost 6 years ago
10.1186/s12864-020-6769-8
High-resolution profile of transcriptomes reveals a role of alternative splicing for modulating response to nitrogen in maizeCited by: 20
Author(s): Yuancong Wang, Jing Xu, Min Ge, Lei Ning, Meng-Mei Hu, Han Zhao
Software Mentions: 5
Published: over 4 years ago
10.3389/fgene.2021.656334
A de novo Full-Length mRNA Transcriptome Generated From Hybrid-Corrected PacBio Long-Reads Improves the Transcript Annotation and Identifies Thousands of Novel Splice Variants in Atlantic SalmonCited by: 15
Author(s): Sigmund Ramberg, Bjørn Høyheim, Tone-Kari K Østbye, Rune Andreassen
Software Mentions: 5
Published: over 3 years ago
10.1186/s12864-021-07558-6
The draft genome of the specialist flea beetle Altica viridicyanea (Coleoptera: Chrysomelidae)Cited by: 5
Author(s): Huai‐Jun Xue, Yiwei Niu, Kari A. Segraves, Rui Nie, Ya Jing Hao, Li Li Zhang, Xin Cheng, Xuewen Zhang, Wen Zhu Li, Run Sheng Chen, Xing Yang
Software Mentions: 4
Published: over 3 years ago
10.3389/fphar.2021.646701
Aripiprazole as a Candidate Treatment of COVID-19 Identified Through Genomic AnalysisCited by: 22
Author(s): Benedicto Crespo‐Facorro, Miguel Ruiz‐Veguilla, Javier Vázquez-Bourgon, Ana C. Sánchez-Hidalgo, Nathalia Garrido-Torres, José Miguel Cisneros, Carlos Prieto, Jesús Sainz
Software Mentions: 4
Published: over 3 years ago
10.1186/s13059-021-02369-0
Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptomeCited by: 23
Author(s): Robin-Lee Troskie, Yohaann Jafrani, Tim R. Mercer, Adam D. Ewing, Geoffrey J. Faulkner, Seth W. Cheetham
Software Mentions: 4
Published: over 3 years ago
10.3389/fmicb.2021.625857
Fermented Soybean Meal Replacement in the Diet of Lactating Holstein Dairy Cows: Modulated Rumen Fermentation and Ruminal MicrofloraCited by: 11
Author(s): Wang Zuo, Yuannian Yu, Xinyao Li, Hongyan Xiao, Peihua Zhang, Weijun Shen, Fachun Wan, Jianhua He, Shaoxun Tang, Zhiliang Tan, Duanqin Wu, Hui Yao
Software Mentions: 3
Published: almost 4 years ago
10.3390/microorganisms9081769
B7 Family Molecule VSIG4 Regulates Intestinal Anti-Enterohemorrhagic Escherichia coli Immunity by Altering Gut Flora DiversityCited by: 2
Author(s): Zi He, Jiajia Li, Saisai Gong, Li Xing, Ye Sun, Jianxin Wang, Tao Li, Nianzhi Ning, Liangyan Zhang, Wenjing Yu, Di Luo, Hui Wang
Software Mentions: 3
Published: about 3 years ago
10.3390/microorganisms9091843
Influence of Tall Fescue Epichloë Endophytes on Rhizosphere Soil MicrobiomeCited by: 9
Author(s): Kishan Mahmud, Kendall Lee, Nicholas S. Hill, Anaas Mergoum, Ali Missaoui
Software Mentions: 3
Published: about 3 years ago
10.1093/gigascience/giaa050
High-quality chromosome-scale assembly of the walnut (Juglans regia L.) reference genomeCited by: 64
Author(s): Annarita Marrano, Monica Britton, Paulo A. Zaini, Aleksey V. Zimin, Rachael E. Workman, Daniela Puiu, Luca Bianco, Erica A. Di Pierro, Brian Allen, Sandeep Chakraborty, Michela Troggio, Charles A. Leslie, Winston Timp, Abhaya M. Dandekar, Steven L. Salzberg, David B. Neale
Software Mentions: 3
Published: over 4 years ago
10.1371/journal.ppat.1009431
High-throughput, single-copy sequencing reveals SARS-CoV-2 spike variants coincident with mounting humoral immunity during acute COVID-19Cited by: 29
Author(s): Sung Hee Ko, Elham Bayat Mokhtari, Prakriti Mudvari, Sydney Stein, Christopher D. Stringham, Danielle A. Wagner, Sabrina Ramelli, Marcos J. Ramos‐Benitez, Jeffrey R Strich, Richard T. Davey, Tongqing Zhou, John Misasi, Peter D. Kwong, Daniel S. Chertow, Nancy J. Sullivan, Eli Boritz
Software Mentions: 3
Published: over 3 years ago
10.1038/s41598-021-86068-7
Long read, isoform aware sequencing of mouse nucleus accumbens after chronic cocaine treatmentCited by: 3
Author(s): Molly Estill, Efrain Ribeiro, Nancy Francoeur, Melissa Smith, Robert Sebra, Szu-Ying Yeh, Ashley M. Cunningham, Eric J. Nestler, Li Shen
Software Mentions: 3
Published: over 3 years ago
10.1101/2021.02.21.432184
High-Throughput, Single-Copy Sequencing Reveals SARS-CoV-2 Spike Variants Coincident with Mounting Humoral Immunity during Acute COVID-19Cited by: 4
Author(s): Sung Hee Ko, Elham Bayat Mokhtari, Prakriti Mudvari, Sydney Stein, Christopher D. Stringham, Danielle A. Wagner, Sabrina Ramelli, Marcos J. Ramos‐Benitez, Jeffrey R Strich, Richard T. Davey, Tongqing Zhou, John Misasi, Peter D. Kwong, Daniel S. Chertow, Nancy J. Sullivan, Eli Boritz
Software Mentions: 3
Published: over 3 years ago
10.1186/s13287-018-0950-x
New insights into the genic and metabolic characteristics of induced pluripotent stem cells from polycystic ovary syndrome womenCited by: 15
Author(s): Zheying Min, Qian Gao, Xiumei Zhang, Yong Fan, Tao Tan, Rong Li, Yue Zhao, Yang Yu
Software Mentions: 2
Published: over 6 years ago
10.1186/s12920-021-01085-9
Identification of seven novel ferroptosis-related long non-coding RNA signatures as a diagnostic biomarker for acute myeloid leukemiaCited by: 15
Author(s): Zhiyuan Zheng, Wei Wu, Zehang Lin, Shuhan Liu, Qiaoqian Chen, Xiandong Jiang, Yu Xue, Lin Dong
Software Mentions: 2
Published: about 3 years ago
10.3390/toxins13070504
Effect of Different Species of Prorocentrum Genus on the Japanese Oyster Crassostrea gigas Proteomic ProfileCited by: 1
Author(s): Miguel Ángel Matus-Hernández, Norma Yolanda Hernández Saavedra
Software Mentions: 2
Published: over 3 years ago
10.3389/fcimb.2020.00117
Comparative Metagenome-Assembled Genome Analysis of “Candidatus Lachnocurva vaginae”, Formerly Known as Bacterial Vaginosis-Associated Bacterium−1 (BVAB1)Cited by: 44
Author(s): Johanna B. Holm, Michael France, Bing Ma, Elias McComb, Courtney K. Robinson, Aditya Mehta, Luke J. Tallon, Rebecca M. Brotman, Jacques Ravel
Software Mentions: 2
Published: over 4 years ago
10.1186/s12915-021-00994-6
Comparison of 15 dinoflagellate genomes reveals extensive sequence and structural divergence in family Symbiodiniaceae and genus SymbiodiniumCited by: 52
Author(s): Raúl A. González‐Pech, Timothy G. Stephens, Yibi Chen, Amin R. Mohamed, Yuanyuan Cheng, Surya Shah, Katherine E. Dougan, Michael D. A. Fortuin, Rémi Lagorce, David W. Burt, Debashish Bhattacharya, Mark A. Ragan, Cheong Xin Chan
Software Mentions: 2
Published: over 3 years ago
10.3389/fgene.2021.670727
CFH and CFHR Copy Number Variations in C3 Glomerulopathy and Immune Complex-Mediated Membranoproliferative GlomerulonephritisCited by: 9
Author(s): Rossella Piras, Matteo Breno, Elisabetta Valoti, Marta Alberti, Paraskevas Iatropoulos, Caterina Mele, Elena Bresin, Roberta Donadelli, Paola Cuccarolo, Richard J.H. Smith, Ariela Benigni, Giuseppe Remuzzi, Marina Noris
Software Mentions: 2
Published: over 3 years ago
10.1186/s12915-020-00782-8
Genomes of the dinoflagellate Polarella glacialis encode tandemly repeated single-exon genes with adaptive functionsCited by: 50
Author(s): Timothy G. Stephens, Raúl A. González‐Pech, Yuanyuan Cheng, Amin R. Mohamed, David W. Burt, Debashish Bhattacharya, Mark A. Ragan, Cheong Xin Chan
Software Mentions: 2
Published: over 4 years ago
10.1038/s41598-020-57507-8
Enhanced STAT3 phosphorylation and PD-L1 expression in myeloid dendritic cells indicate impaired IL-27Ralpha signaling in type 1 diabetesCited by: 13
Author(s): Zuzana Paračková, Petra Vrabcová, Irena Zentsová, Jana Kayserová, I. Richtrova, Luděk Sojka, Kateřina Štechová, Zdenĕk Šumnı́k, Anna Šedivá
Software Mentions: 1
Published: almost 5 years ago
10.1186/s40064-015-1124-2
Selective forces acting during multi-domain protein evolution: the case of multi-domain globinsCited by: 7
Author(s): Joana Projecto-Garcia, Didier Jollivet, Jean Mary, François H. Lallier, Stephen W. Schaeffer, Stéphane Hourdez
Software Mentions: 1
Published: over 9 years ago
10.3390/toxins8060159
Early Genotoxic and Cytotoxic Effects of the Toxic Dinoflagellate Prorocentrum lima in the Mussel Mytilus galloprovincialisCited by: 24
Author(s): María Verónica Prego-Faraldo, Vanessa Valdiglesias, Blanca Laffón, Josefina Méndez, José M. Eirín‐López
Software Mentions: 1
Published: over 8 years ago
10.3390/toxins8100272
The Mechanism of Diarrhetic Shellfish Poisoning Toxin Production in Prorocentrum spp.: Physiological and Molecular PerspectivesCited by: 53
Author(s): Thomas Chun-Hung Lee, Fiona Long-Yan Fong, Kin Chung Ho, Fred Lee
Software Mentions: 1
Published: about 8 years ago
10.3390/e23060654
Dynamical Localization Simulated on Actual Quantum HardwareCited by: 8
Author(s): Andrea Pizzamiglio, Su Yeon Chang, Maria Bondani, Simone Montangero, Dario Gerace, Giuliano Benenti
Software Mentions: 1
Published: over 3 years ago
10.3390/microorganisms9020274
Impacts of Low Temperature and Ensiling Period on the Bacterial Community of Oat Silage by SMRTCited by: 26
Author(s): Xiaomei Li, Fei Chen, Xuekai Wang, Lin Sun, Linna Guo, Yi Xiong, Wenjie Yuan, Hongxu Zhou, Shangang Jia, Yang Fang, Ke Ni
Software Mentions: 1
Published: almost 4 years ago
10.3389/fmicb.2019.01753
Occurrence and Characterization of mcr-1-Positive Escherichia coli Isolated From Food-Producing Animals in Poland, 2011–2016Cited by: 54
Author(s): Magdalena Zając, Paweł Sztromwasser, Valeria Bortolaia, Pimlapas Leekitcharoenphon, Lina Cavaco, Anna Ziętek-Barszcz, René S. Hendriksen, Dariusz Wasyl
Software Mentions: 1
Published: over 5 years ago
10.1128/MRA.00847-21
Complete Circular Genome Sequences of Brachyspira hyodysenteriae Isolates of the Four Different Sequence Types Causing Swine Dysentery in SwitzerlandCited by: 1
Author(s): Ana B. García-Martín, Sarah Schmitt, Friederike Zeeh, Vincent Perreten
Software Mentions: 1
Published: about 3 years ago
10.3390/md19020063
Cinnamaldehyde Could Reduce the Accumulation of Diarrhetic Shellfish Toxins in the Digestive Gland of the Mussel Perna viridis under Laboratory ConditionsCited by: 3
Author(s): Guo-Fang Duan, Yang Liu, Lina Zhang, Hongye Li, Jie‐Sheng Liu, Wei‐Dong Yang
Software Mentions: 1
Published: almost 4 years ago
10.3390/md18120647
Improved Isolation Procedures for Okadaic Acid Group Toxins from Shellfish (Mytilus edulis) and Microalgae (Prorocentrum lima)Cited by: 8
Author(s): Jane Kilcoyne, Stephen Burrell, Cíara Nulty, Rafael Salas, Elliott J. Wright, Isabelle Rajotte, Christopher O. Miles
Software Mentions: 1
Published: almost 4 years ago
10.1186/s13059-021-02406-y
SMOOTH-seq: single-cell genome sequencing of human cells on a third-generation sequencing platformCited by: 37
Author(s): Xiaoying Fan, Cheng Yang, Wen Li, Xiuzhen Bai, Xin Zhou, Haoling Xie, Lu Wen, Fuchou Tang
Software Mentions: 1
Published: over 3 years ago
10.3390/ijms22052616
Robust Detection of Somatic Mosaicism and Repeat Interruptions by Long-Read Targeted Sequencing in Myotonic Dystrophy Type 1Cited by: 18
Author(s): Antoine Mangin, Laure de Pontual, Yu‐Chih Tsai, L. Monteil, Mathilde Nizon, Pierre Boisseau, Sandra Mercier, Janet Ziegle, John Harting, Cheryl Heiner, Geneviève Gourdon, Stéphanie Tomé
Software Mentions: 1
Published: over 3 years ago
10.1038/s41597-020-00686-w
Transcriptome sequencing of cochleae from constant-frequency and frequency-modulated echolocating batsCited by: 4
Author(s): Lu Ma, Haijian Sun, Xiuguang Mao
Software Mentions: 1
Published: about 4 years ago