cran: MCL | Projects | Ecosyste.ms: Papers

10.1093/gbe/evaa193

De Novo Gene Birth, Horizontal Gene Transfer, and Gene Duplication as Sources of New Gene Families Associated with the Origin of Symbiosis in<i>Amanita</i>
Cited by: 5
Author(s): Yen-Wen Wang, Jaqueline Hess, Jason C. Slot, Anne Pringle
Software Mentions: 1
Published: over 3 years ago

10.1093/gbe/evab024

Novel Two-Component System-Like Elements Reveal Functional Domains Associated with Restriction–Modification Systems and paraMORC ATPases in Bacteria
Cited by: 4
Author(s): Daniel Bellieny-Rabelo, Willem J S Pretorius, Lucy N. Moleleki
Software Mentions: 1
Published: over 3 years ago

10.1093/gbe/evab085

The Asgard Archaeal-Unique Contribution to Protein Families of the Eukaryotic Common Ancestor Was 0.3%
Cited by: 5
Author(s): Michael Knopp, Simon Stockhorst, Mark van der Giezen, Sriram G. Garg, Sven B. Gould
Software Mentions: 1
Published: about 3 years ago

10.1093/gbe/evab215

Plastome Structural Evolution and Homoplastic Inversions in Neo-Astragalus (Fabaceae)
Cited by: 13
Author(s): Joseph L.M. Charboneau, Richard Cronn, Aaron Liston, Martin F. Wojciechowski, Michael J. Sanderson
Software Mentions: 1
Published: over 2 years ago

10.1093/gigascience/gix116

Large-scale phylogenomic analysis resolves a backbone phylogeny in ferns
Cited by: 78
Author(s): Hui Shen, Dongmei Jin, Jiang-Ping Shu, Xin Zhou, Ming Lei, Ran Wei, Hui Shang, Hong‐Jin Wei, Rui Zhang, Li Liu, Yu‐Cheng Gu, Xian‐Chun Zhang, Yue‐Hong Yan
Software Mentions: 1
Published: over 6 years ago

10.1093/gigascience/giz119

PIRATE: A fast and scalable pangenomics toolbox for clustering diverged orthologues in bacteria
Cited by: 123
Author(s): Sion C. Bayliss, Harry A. Thorpe, Nicola M. Coyle, Samuel K. Sheppard, Edward J. Feil
Software Mentions: 1
Published: over 4 years ago

10.1093/gigascience/giz118

SwiftOrtho: A fast, memory-efficient, multiple genome orthology classifier
Cited by: 22
Author(s): Xiao Hu, Iddo Friedberg
Software Mentions: 1
Published: over 4 years ago

10.1038/s41438-020-0264-x

Al-induced proteomics changes in tomato plants over-expressing a glyoxalase I gene
Cited by: 5
Author(s): Sun X, Li H, Santosh Thapa, Reddy Sangireddy S, Xin Pei, Liu W, Ye Jiang, Shaolan Yang, Hwa Dai, Sarabjit Bhatti, Suping Zhou, Yong Yang, Tara Fish, Thannhauser Tw
Software Mentions: 1
Published: about 4 years ago

10.1371/journal.ppat.1002503

Immune Subversion and Quorum-Sensing Shape the Variation in Infectious Dose among Bacterial Pathogens
Cited by: 40
Author(s): João Alves Gama, Sophie S. Abby, Sara Vieira-Silva, Francisco Dionísio, Eduardo P. C. Rocha
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.ppat.1003670

An RxLR Effector from Phytophthora infestans Prevents Re-localisation of Two Plant NAC Transcription Factors from the Endoplasmic Reticulum to the Nucleus
Cited by: 189
Author(s): Hazel McLellan, Petra C. Boevink, Miles Armstrong, Leighton Pritchard, Sofía González Gómez, Juan Morales, Stephen C. Whisson, Jim Beynon, Paul R. J. Birch
Software Mentions: 1
Published: over 10 years ago

10.1186/1477-5956-9-S1-S14

NWE: Node-weighted expansion for protein complex prediction using random walk distances
Cited by: 21
Author(s): Osamu Maruyama, Ayaka Chihara
Software Mentions: 1
Published: over 13 years ago

10.1186/1477-5956-9-S1-S18

A binary matrix factorization algorithm for protein complex prediction
Cited by: 8
Author(s): Shikui Tu, Runsheng Chen, Lei Xu
Software Mentions: 1
Published: over 12 years ago

10.1186/1477-5956-11-S1-S2

Integrating domain similarity to improve protein complexes identification in TAP-MS data
Cited by: 6
Author(s): Bingjing Cai, Haiying Wang, Huiru Zheng, Hui Wang
Software Mentions: 1
Published: over 10 years ago

10.1186/1477-5956-11-S1-S18

Detecting overlapping protein complexes in PPI networks based on robustness
Cited by: 24
Author(s): Shuliang Wang, Fang Wu
Software Mentions: 1
Published: over 11 years ago

10.1186/1477-5956-11-S1-S20

Detecting protein complexes from active protein interaction networks constructed with dynamic gene expression profiles
Cited by: 17
Author(s): Qianghua Xiao, Jianxin Wang, Xiaoqing Peng, Fang‐Xiang Wu
Software Mentions: 1
Published: over 10 years ago

10.1186/s41039-015-0024-y

GPS sensor-based mobile learning for English: an exploratory study on self-efficacy, self-regulation and student achievement
Cited by: 16
Author(s): Jerry Chih‐Yuan Sun, Kai-Yu Chang, Yang-Hsueh Chen
Software Mentions: 1
Published: over 8 years ago

10.1038/srep13798

The identification of an integral membrane, cytochrome c urate oxidase completes the catalytic repertoire of a therapeutic enzyme
Cited by: 13
Author(s): Nicola Doniselli, Enrico Monzeglio, Alessandro Dal Palù, Angelo Merli, Riccardo Percudani
Software Mentions: 1
Published: over 8 years ago

10.1038/srep14344

Integrative analysis of human protein, function and disease networks
Cited by: 29
Author(s): Wei Liu, Aiping Wu, Matteo Pellegrini, Xiaofan Wang
Software Mentions: 1
Published: over 8 years ago

10.1038/srep17068

System-wide assembly of pathways and modules hierarchically reveal metabolic mechanism of cerebral ischemia
Cited by: 18
Author(s): Yan Zhu, Zhiyong Guo, Liangxiao Zhang, Yingying Zhang, Yinying Chen, Jingyi Nan, Buchang Zhao, Hongbin Xiao, Zhong Wang, Yongyan Wang
Software Mentions: 1
Published: over 8 years ago

10.1038/srep19149

Network-Based Comparative Analysis of Arabidopsis Immune Responses to Golovinomyces orontii and Botrytis cinerea Infections
Cited by: 35
Author(s): Zhenhong Jiang, Xiaobao Dong, Ziding Zhang
Software Mentions: 1
Published: over 8 years ago

10.1038/srep21223

Using contrast patterns between true complexes and random subgraphs in PPI networks to predict unknown protein complexes
Cited by: 28
Author(s): Quanzhong Liu, Jiangning Song, Jinyan Li
Software Mentions: 1
Published: over 8 years ago

10.1038/srep23971

Evaluation of genetic diversity among strains of the human gut commensal Bifidobacterium adolescentis
Cited by: 82
Author(s): Sabrina Duranti, Christian Milani, Gabriele Andrea Lugli, Leonardo Mancabelli, Francesca Turroni, Chiara Ferrario, Marta Mangifesta, Alice Viappiani, Borja Sánchez, Abelardo Margollés, Douwe van Sinderen, Marco Ventura
Software Mentions: 1
Published: about 8 years ago

10.1038/srep41425

Exploring the dark foldable proteome by considering hydrophobic amino acids topology
Cited by: 22
Author(s): Tristan Bitard‐Feildel, Isabelle Callebaut
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-017-01133-4

Genome-wide fitness analyses of the foodborne pathogen Campylobacter jejuni in in vitro and in vivo models
Cited by: 36
Author(s): Stefan P. W. de Vries, Shefali Gupta, Abiyad Baig, Elli A. Wright, Amy Wedley, Annette Nygaard Jensen, Lizeth LaCharme Lora, Suzanne Humphrey, Henrik Skovgård, Kareen Macleod, Elsa Pont, Dominika P. Wolanska, Joanna L’Heureux, Fredrick M. Mobegi, David George Emslie Smith, Paul Everest, Aldert Zomer, Nicola Williams, Paul Wigley, T. J. Humphrey, Duncan J. Maskell, A. Grant
Software Mentions: 1
Published: about 7 years ago

10.1038/s41598-017-03268-w

Discovering overlapped protein complexes from weighted PPI networks by removing inter-module hubs
Cited by: 13
Author(s): Ali M.A. Maddi, Ch. Eslahchi
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41598-017-08760-x

Identifying protein complexes in PPI network using non-cooperative sequential game
Cited by: 11
Author(s): Ujjwal Maulik, Srinka Basu, Sumanta Ray
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41598-017-13236-z

Genome-Guided Phylo-Transcriptomic Methods and the Nuclear Phylogenetic Tree of the Paniceae Grasses
Cited by: 28
Author(s): Jacob D. Washburn, James C. Schnable, Gavin C. Conant, Thomas P. Brutnell, Ying Shao, Yang Zhang, Martha Ludwig, Gerrit Davidse, J. Chris Pires
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-017-16270-z

Functional diversity of topological modules in human protein-protein interaction networks
Cited by: 12
Author(s): Guangming Liu, Huixin Wang, Hang Chu, Jian Yu, Xuezhong Zhou
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-018-28218-y

Analysis of atomic beam collimation by laser cooling
Cited by: 2
Author(s): Shangyan Li, Min Zhou, Xiaojun Xu
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41598-019-45198-9

Neonatal oral fluid as a transmission route for bifidobacteria to the infant gut immediately after birth
Cited by: 13
Author(s): Kazuya Toda, Ken Hisata, Tsuyoshi Satoh, Noriko Katsumata, Toshitaka Odamaki, Eri Mitsuyama, Takane Katayama, Tetsuya Kuhara, Kohzo Aisaka, Toshiaki Shimizu, Jin‐zhong Xiao
Software Mentions: 1
Published: almost 5 years ago

10.1038/s41598-019-47468-y

Detection of dynamic protein complexes through Markov Clustering based on Elephant Herd Optimization Approach
Cited by: 7
Author(s): R. Ranjani Rani, D. Ramyachitra, A. Brindhadevi
Software Mentions: 1
Published: almost 5 years ago

10.1038/s41598-019-48446-0

Network analysis of canine brain morphometry links tumour risk to oestrogen deficiency and accelerated brain ageing
Cited by: 6
Author(s): Nina Marie Rzechorzek, Olivia M. Saunders, Lucy V Hiscox, Tobias Schwarz, Katia Marioni‐Henry, David Argyle, Jeffrey J. Schoenebeck, Tom C. Freeman
Software Mentions: 1
Published: almost 5 years ago

10.1038/s41598-019-49225-7

CDAP: An Online Package for Evaluation of Complex Detection Methods
Cited by: 7
Author(s): Ali M.A. Maddi, Fatemeh Ahmadi Moughari, Mohammad Mehdi Balouchi, Changiz Eslahchi
Software Mentions: 1
Published: over 4 years ago

10.1038/s41598-020-60723-x

Phylogenomics of Rhodocyclales and its distribution in wastewater treatment systems
Cited by: 20
Author(s): Zhongjie Wang, Wenqing Li, Hao Li, Wei Zheng, Feng Guo
Software Mentions: 1
Published: over 4 years ago

10.1155/2013/169635

A Fast Map Merging Algorithm in the Field of Multirobot SLAM
Cited by: 6
Author(s): Yanli Liu, Xiaoping Fan, Heng Zhang
Software Mentions: 1
Published: over 11 years ago

10.3390/s90806150

An Efficient and Self-Adapting Localization in Static Wireless Sensor Networks
Cited by: 7
Author(s): Guodong Teng, Kun Zheng, Wei Dong
Software Mentions: 1
Published: almost 15 years ago

10.3390/s90402760

Adapting Mobile Beacon-Assisted Localization in Wireless Sensor Networks
Cited by: 31
Author(s): Guodong Teng, Kun Zheng, Wei Dong
Software Mentions: 1
Published: about 15 years ago

10.3390/s130101268

Robot Evolutionary Localization Based on Attentive Visual Short-Term Memory
Cited by: 7
Author(s): Julio Vega, Eduardo Perdices, José María Plaza
Software Mentions: 1
Published: over 11 years ago

10.3390/s18072344

Intersection and Complement Set (IACS) Method to Reduce Redundant Node in Mobile WSN Localization
Cited by: 4
Author(s): Muhammad Zar Mohd. Zaid Harith, Noorzaily Mohamed Noor, Mohd Yamani Idna Idris, Emran Mohd Tamil
Software Mentions: 1
Published: almost 6 years ago

10.3390/s19102230

A Novel Approach for Lidar-Based Robot Localization in a Scale-Drifted Map Constructed Using Monocular SLAM
Cited by: 14
Author(s): Su Wang, Yukinori Kobayashi, Ankit A. Ravankar, Abhijeet Ravankar, Takanori Emaru
Software Mentions: 1
Published: about 5 years ago

10.3390/s19153331

Reliable and Fast Localization in Ambiguous Environments Using Ambiguity Grid Map
Cited by: 14
Author(s): Gen Li, Jie Meng, Yuanlong Xie, Xiaolong Zhang, Yu Huang, Laizhu Jiang, Chao Liu
Software Mentions: 1
Published: almost 5 years ago

10.3390/s20113145

Improved LiDAR Probabilistic Localization for Autonomous Vehicles Using GNSS
Cited by: 24
Author(s): Miguel Ángel de Miguel, Fernando García, José María Armingol
Software Mentions: 1
Published: about 4 years ago

10.3390/s20154128

Robust and Efficient Indoor Localization Using Sparse Semantic Information from a Spherical Camera
Cited by: 6
Author(s): Irem Uygur, Renato Miyagusuku, Sarthak Pathak, Alessandro Moro, Atsushi Yamashita, Hajime Asama
Software Mentions: 1
Published: almost 4 years ago

10.3390/s21082859

Acceleration of Inner-Pairing Product Operation for Secure Biometric Verification
Cited by: 2
Author(s): Seong-Yun Jeon, Mun-Kyu Lee
Software Mentions: 1
Published: about 3 years ago

10.1038/s41392-021-00572-w

Small molecules in targeted cancer therapy: advances, challenges, and future perspectives
Cited by: 470
Author(s): Lei Zhong, Yueshan Li, Liang Xiong, Wenjing Wang, Ming Wu, Ting Yuan, Wei Yang, Chuanshan Tian, Miao Zhang, Tianqi Wang, Shengyong Yang
Software Mentions: 1
Published: about 3 years ago

10.1186/1742-4682-8-47

Modularity analysis based on predicted protein-protein interactions provides new insights into pathogenicity and cellular process of Escherichia coli O157:H7
Cited by: 8
Author(s): Xia Wang, Junjie Yue, Xianwen Ren, Yuelan Wang, Mingfeng Tan, Beiping Li, Long Liang
Software Mentions: 1
Published: over 12 years ago

10.1128/mBio.00671-17

Disguised as a Sulfate Reducer: Growth of the Deltaproteobacterium <i>Desulfurivibrio alkaliphilus</i> by Sulfide Oxidation with Nitrate
Cited by: 94
Author(s): Charlotte Brun Thorup, Andreas Schramm, Alyssa Findlay, Kai Finster, Lars Schreiber
Software Mentions: 1
Published: over 6 years ago

10.1128/mSphere.00631-19

Comparative Genomics Reveals a Well-Conserved Intrinsic Resistome in the Emerging Multidrug-Resistant Pathogen Cupriavidus gilardii
Cited by: 7
Author(s): Cristian Ruiz, Ashley McCarley, Manuel Luis Espejo, Kerry K. Cooper, Dana E. Harmon
Software Mentions: 1
Published: over 4 years ago

10.1038/s41396-020-00870-1

Host population diversity as a driver of viral infection cycle in wild populations of green sulfur bacteria with long standing virus-host interactions
Cited by: 16
Author(s): Maureen Berg, Danielle Goudeau, Charles N. Olmsted, Katherine D. McMahon, Senay Yitbarek, Jennifer Thweatt, Donald A. Bryant, Emiley A. Eloe‐Fadrosh, Rex R. Malmstrom, Simon Roux
Software Mentions: 1
Published: over 3 years ago

10.3390/jof7040285

Terpenoid Biosynthesis Dominates among Secondary Metabolite Clusters in Mucoromycotina Genomes
Cited by: 13
Author(s): Grzegorz Koczyk, Julia Pawłowska, Anna Muszewska
Software Mentions: 1
Published: about 3 years ago

10.1186/s13045-020-00961-8

Advances in the assessment of minimal residual disease in mantle cell lymphoma
Cited by: 14
Author(s): Da-Young Jung, Preetesh Jain, Yixin Yao, Michael Wang
Software Mentions: 1
Published: over 3 years ago

10.1186/s40425-019-0529-9

A good response of refractory mantel cell lymphoma to haploidentical CAR T cell therapy after failure of autologous CAR T cell therapy
Cited by: 10
Author(s): Tongjuan Li, Yuanyuan Zhang, Dan Peng, Xia Mao, Xiaoxi Zhou, Jianfeng Zhou
Software Mentions: 1
Published: over 5 years ago

10.1089/omi.2016.0169

Cancer Transcriptome Dataset Analysis: Comparing Methods of Pathway and Gene Regulatory Network-Based Cluster Identification
Cited by: 4
Author(s): Seungyoon Nam
Software Mentions: 1
Published: about 7 years ago

10.1186/1752-1947-7-105

Mantle cell lymphoma presenting as a pelvi-ureteric junction obstruction: a case report
Cited by: 5
Author(s): Ishvar Naranji, Rhana Hassan Zakri, T. G. Liston
Software Mentions: 1
Published: about 11 years ago

10.3390/ijms17060862

Review on Graph Clustering and Subgraph Similarity Based Analysis of Neurological Disorders
Cited by: 14
Author(s): Jaya Thomas, Dongmin Seo, Lee Sael
Software Mentions: 1
Published: about 8 years ago

10.3390/ijms17122060

Toll Like Receptor 2, 4, and 9 Signaling Promotes Autoregulative Tumor Cell Growth and VEGF/PDGF Expression in Human Pancreatic Cancer
Cited by: 42
Author(s): Tanja Grimmig, Romana Moench, Jennifer Kreckel, Stephanie Haack, Felix Rueckert, Roberta Rehder, Sudipta Tripathi, Carmen Austrália Paredes Marcondes Ribas, Anil Chandraker, Christoph T. Germer, Martin Gasser, Ana Maria Waaga-Gasser
Software Mentions: 1
Published: over 7 years ago

10.3390/ijms18091880

CytoCluster: A Cytoscape Plugin for Cluster Analysis and Visualization of Biological Networks
Cited by: 74
Author(s): Min Li, Dongyan Li, Yu Tang, Fang‐Xiang Wu, Jianxin Wang
Software Mentions: 1
Published: almost 7 years ago

10.3390/ijms20040919

Systematical Identification of Breast Cancer-Related Circular RNA Modules for Deciphering circRNA Functions Based on the Non-Negative Matrix Factorization Algorithm
Cited by: 16
Author(s): Shuyuan Wang, Peng Xia, Li Zhang, Lei Yu, Liu Hui, Qianqian Meng, Siyao Liu, Jie Li, Qian Song, Jie Wu, Weida Wang, Lei Yang, Yun Xiao, Chaohan Xu
Software Mentions: 1
Published: over 5 years ago

10.3390/ijms20133114

Molecular Inverse Comorbidity between Alzheimer’s Disease and Lung Cancer: New Insights from Matrix Factorization
Cited by: 11
Author(s): Alessandro Greco, Jon Sanchez Valle, Véra Pancaldi, Anaı̈s Baudot, Emmanuel Barillot, Michele Caselle, Alfonso Valencia, Andreï Zinovyev, Laura Cantini
Software Mentions: 1
Published: almost 5 years ago

10.3390/ijms21176338

Isolation and Characterization of the Novel Bacteriophage AXL3 against Stenotrophomonas maltophilia
Cited by: 15
Author(s): Jaclyn G. McCutcheon, Andrea Lin, Jonathan J. Dennis
Software Mentions: 1
Published: almost 4 years ago

10.18632/oncotarget.12941

Increased phosphorylation of eIF2α in chronic myeloid leukemia cells stimulates secretion of matrix modifying enzymes
Cited by: 15
Author(s): Paulina Podszywałow-Bartnicka, Anna Cmoch, Magdalena Wołczyk, Łukasz Bugajski, Marcin Tkaczyk, Michał Dadlez, Margaret Nieborowska‐Skorska, Antonis E. Koromilas, Tomasz Skórski, Katarzyna Piwocka
Software Mentions: 1
Published: over 7 years ago

10.18632/oncotarget.25146

Proteomic profiling of skeletal and cardiac muscle in cancer cachexia: alterations in sarcomeric and mitochondrial protein expression
Cited by: 35
Author(s): A. Shum, Anne Poljak, Nicholas Bentley, Nigel Turner, Timothy C. Tan, Patsie Polly
Software Mentions: 1
Published: about 6 years ago

10.1186/s12859-016-1142-2

A De-Novo Genome Analysis Pipeline (DeNoGAP) for large-scale comparative prokaryotic genomics studies
Cited by: 16
Author(s): Shalabh Thakur, David S. Guttman
Software Mentions: 1
Published: almost 8 years ago

Projects: cran: MCL

Papers Mentioning MCL 563