Ecosyste.ms: Papers

10.1093/bioinformatics/btz698

scds: computational annotation of doublets in single-cell RNA sequencing data
Cited by: 114
Author(s): Abha Bais, Dennis Kostka
Software Mentions: 7
Published: about 5 years ago

10.1093/gigascience/gix129

Hybrid-denovo: a de novo OTU-picking pipeline integrating single-end and paired-end 16S sequence tags
Cited by: 15
Author(s): Xianfeng Chen, Stephen Johnson, Patricio Jeraldo, Junwen Wang, Nicholas Chia, Jean Pierre A. Kocher, Jun Chen
Software Mentions: 7
Published: almost 7 years ago

10.3390/ijms22179650

Multiple Imputation Approaches Applied to the Missing Value Problem in Bottom-Up Proteomics
Cited by: 15
Author(s): Miranda L. Gardner, Michael A. Freitas
Software Mentions: 5
Published: about 3 years ago

10.1371/journal.pcbi.1005680

Interactions between the tumor and the blood systemic response of breast cancer patients
Cited by: 21
Author(s): Vanessa Dumeaux, Bjørn Fjukstad, Hans E. Fjøsne, Jan Ole Frantzen, Marit Muri Holmen, Enno Rodegerdts, Ellen Schlichting, Anne Lise Børresen-Dale, Lars Ailo Bongo, Eiliv Lund, Michael Hallett
Software Mentions: 3
Published: about 7 years ago

10.1186/s12864-020-06826-1

Genome-wide identification and comparison of differentially expressed profiles of miRNAs and lncRNAs with associated ceRNA networks in the gonads of Chinese soft-shelled turtle, Pelodiscus sinensis
Cited by: 13
Author(s): Xiao Ma, Shuangshuang Cen, Luming Wang, Chao Zhang, Limin Wu, Tian Xue, Qing Wu, Xuejun Li, Xiaoqing Wang
Software Mentions: 3
Published: over 4 years ago

10.15252/msb.202010016

hu.MAP 2.0: integration of over 15,000 proteomic experiments builds a global compendium of human multiprotein assemblies
Cited by: 60
Author(s): Kevin Drew, John B. Wallingford, Edward M. Marcotte
Software Mentions: 3
Published: over 3 years ago

10.14814/phy2.14261

A decreased abundance of clostridia characterizes the gut microbiota in eosinophilic esophagitis
Cited by: 25
Author(s): Purna C. Kashyap, Stephen Johnson, Debra M. Geno, Heather Lekatz, Crystal Lavey, Jeffrey A. Alexander, Jun Chen, David A. Katzka
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0235641

Genomic analyses of multidrug-resistant Salmonella Indiana, Typhimurium, and Enteritidis isolates using MinION and MiSeq sequencing technologies
Cited by: 14
Author(s): Chen Zhao, Dai Kuang, Xuebin Xu, Narjol González-Escalona, David L. Erickson, Eric W. Brown, Jianghong Meng
Software Mentions: 3
Published: over 4 years ago

10.1002/ece3.5445

Utilizing the density of inventory samples to define a hybrid lattice for species distribution models: DISTRIB‐II for 135 eastern U.S. trees
Cited by: 10
Author(s): Matthew P. Peters, Louis R. Iverson, Anantha Prasad, Stephen N. Matthews
Software Mentions: 3
Published: over 5 years ago

10.3390/genes8100257

Hybrid Sequencing of Full-Length cDNA Transcripts of Stems and Leaves in Dendrobium officinale
Cited by: 18
Author(s): Li He, Shuhua Fu, Zhichao Xu, Jun Yan, Jiang Xu, Hong Zhou, Jianguo Zhou, Xinlian Chen, Ying Liu, Kin Fai Au, Hui Yao
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pgen.1003485

The Genome Organization of Thermotoga maritima Reflects Its Lifestyle
Cited by: 44
Author(s): Haythem Latif, Joshua A. Lerman, Vasiliy A. Portnoy, Yekaterina Tarasova, Harish Nagarajan, Alexandra C. Schrimpe‐Rutledge, Richard D. Smith, Joshua N. Adkins, Dong Hoon Lee, Yu Qiu, Karsten Zengler
Software Mentions: 2
Published: over 11 years ago

10.3390/ijms20010148

MiR-125b-2 Knockout in Testis Is Associated with Targeting to the PAP Gene, Mitochondrial Copy Number, and Impaired Sperm Quality
Cited by: 6
Author(s): Longlong Li, Yanling Zhu, Ting Chen, Jiajie Sun, Junyi Luo, Gang Shu, Xiaotong Zhu, Qingyan Jiang, Yongliang Zhang, Qianyun Xi
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pgen.1008765

Dynamic miRNA-mRNA interactions coordinate gene expression in adult Anopheles gambiae
Cited by: 16
Author(s): Xiao Fu, Peng-Cheng Liu, George Dimopoulos, Jinsong Zhu
Software Mentions: 2
Published: over 4 years ago

10.1186/s12985-021-01612-1

Plant responses to geminivirus infection: guardians of the plant immunity
Cited by: 26
Author(s): Neha Gupta, Kiran K. Reddy, Dhriti Bhattacharyya, Supriya Chakraborty
Software Mentions: 1
Published: over 3 years ago

10.1186/gb-2014-15-3-r44

Inferring gene function from evolutionary change in signatures of translation efficiency
Cited by: 44
Author(s): Anita Kriško, Tea Copic, Toni Gabaldón, Ben Lehner, Fran Supek
Software Mentions: 1
Published: almost 11 years ago

10.1038/s41598-021-86913-9

Interleukin-6 as an enhancer of anti-angiogenic therapy for ovarian clear cell carcinoma
Cited by: 15
Author(s): Toshiyuki Seki, Nozomu Yanaihara, Jason S. Shapiro, Misato Saito, Junya Tabata, Ryo Yokomizo, Daito Noguchi, Takafumi Kuroda, Ayako Kawabata, Jun Suzuki, Kazuaki Takahashi, Haruka Matsuzawa, Misayo Miyake, Masataka Takenaka, Yasushi Iida, Satoshi Yanagida, Aikou Okamoto
Software Mentions: 1
Published: over 3 years ago

10.7759/cureus.13564

Scientometric Data and Open Access Publication Policies of Clinical Allergy and Immunology Journals
Cited by: 1
Author(s): Gökhan Tazegül, Emre Emre
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pone.0022914

Inability of Prevotella bryantii to Form a Functional Shine-Dalgarno Interaction Reflects Unique Evolution of Ribosome Binding Sites in Bacteroidetes
Cited by: 33
Author(s): Tomaž Accetto, Gorazd Avguštin
Software Mentions: 1
Published: over 13 years ago

10.3390/ijms20040802

Exploration of miRNA and mRNA Profiles in Fresh and Frozen-Thawed Boar Sperm by Transcriptome and Small RNA Sequencing
Cited by: 35
Author(s): Dinghui Dai, Izhar Hyder Qazi, Mingxia Ran, Keke Liang, Yan Zhang, Ming Zhang, Guangbin Zhou, Christiana Angel, Changjun Zeng
Software Mentions: 1
Published: almost 6 years ago

10.3389/fpls.2016.00817

MicroRNAs As Potential Targets for Abiotic Stress Tolerance in Plants
Cited by: 277
Author(s): Varsha Shriram, Vinay Kumar, R. M. Devarumath, Tushar Khare, Shabir Hussain Wani
Software Mentions: 1
Published: over 8 years ago