cran: ggplot2 | Projects | Ecosyste.ms: Papers

10.1128/mBio.02318-20

Adaptation of Arginine Synthesis among Uropathogenic Branches of the Escherichia coli Phylogeny Reveals Adjustment to the Urinary Tract Habitat
Cited by: 11
Author(s): Michael E. Hibbing, Karen W. Dodson, Vasilios Kalas, Swaine L. Chen, Scott J. Hultgren
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12865-020-00344-1

Identification of differentially expressed circulating exosomal lncRNAs in IgA nephropathy patients
Cited by: 17
Author(s): Na Guo, Qin Zhou, Xiang Huang, Jia-Kuo Yu, Qianqian Han, Baoting Nong, Yuanyan Xiong, Peifeng Liang, Jiajia Li, Min Feng, Jun Lv, Qiongqiong Yang
Software Mentions: 4
Published: over 6 years ago

10.1186/s12865-014-0040-5

Quantitative assessment of the robustness of next-generation sequencing of antibody variable gene repertoires from immunized mice
Cited by: 53
Author(s): Victor Greiff, Ulrike Menzel, Ulrike Haessler, Skylar C. Cook, Simon Friedensohn, Tarik A. Khan, Mark Pogson, Ina Hellmann, Sai T. Reddy
Software Mentions: 4
Published: almost 12 years ago

10.1128/mBio.02254-20

CPSF6-Dependent Targeting of Speckle-Associated Domains Distinguishes Primate from Nonprimate Lentiviral Integration
Cited by: 27
Author(s): Wen Li, Parmit K. Singh, Gregory A. Sowd, Gregory J. Bedwell, Sungwoo Jang, Vasudevan Achuthan, Amarachi V. Oleru, Doris Wong, Hind J. Fadel, Kyeongeun Lee, Vineet N. KewalRamani, Eric M. Poeschla, Alon Herschhorn, Alan Engelman
Software Mentions: 4
Published: almost 6 years ago

10.18632/aging.203323

An immune-related lncRNA signature for the prognosis of pancreatic adenocarcinoma
Cited by: 10
Author(s): Bing Qi, Han Liu, Qi Zhou, Ji Li, Xueying Shi, Yu‐Shan Wei, Yinmin Gu, Akio Mizushima, Shilin Xia
Software Mentions: 4
Published: about 5 years ago

10.1128/mBio.00766-20

Codon Usage Optimization in the Prokaryotic Tree of Life: How Synonymous Codons Are Differentially Selected in Sequence Domains with Different Expression Levels and Degrees of Conservation
Cited by: 9
Author(s): José Luis López, Mauricio Javier Lozano, María Laura Fabre, Antonio Lagares
Software Mentions: 4
Published: about 6 years ago

10.1186/s12879-020-05600-8

Describing nearly two decades of Chagas disease in Germany and the lessons learned: a retrospective study on screening, detection, diagnosis, and treatment of Trypanosoma cruzi infection from 2000 – 2018
Cited by: 10
Author(s): Jessica Michelle Guggenbühl Noller, Günter Fröschl, Philip Eisermann, Johannes Jochum, Stefanie Theuring, Ingrid Reiter‐Owona, Alfred Lennart Bissinger, Michael Höelscher, Abhishek Bakuli, Franz-Josef Falkner von Sonnenburg, Camilla Rothe, Gisela Bretzel, Pedro Albajar-Viñas, Lise Grout, Michael Pritsch
Software Mentions: 4
Published: over 5 years ago

10.1186/s13287-019-1218-9

Mesenchymal stem cells transplanted into spinal cord injury adopt immune cell-like characteristics
Cited by: 25
Author(s): Ramil Hakim, Ruxandra Covacu, Vasilios Zachariadis, Arvid Frostell, Sreenivasa Raghavan Sankavaram, Lou Brundin, Mikael Svensson
Software Mentions: 4
Published: over 7 years ago

10.1186/s13395-020-00227-4

Transgenic mice expressing tunable levels of DUX4 develop characteristic facioscapulohumeral muscular dystrophy-like pathophysiology ranging in severity
Cited by: 31
Author(s): Takako I. Jones, Guo-Liang Chew, Pamela Barraza‐Flores, Spencer Schreier, Monique Ramirez, Ryan D. Wuebbles, Dean J. Burkin, Robert K. Bradley
Software Mentions: 4
Published: over 6 years ago

10.3390/s20113031

Performance of a Low-Cost Sensor Community Air Monitoring Network in Imperial County, CA
Cited by: 8
Author(s): Paul English, Heather K. Amato, Esther Bejarano, Graeme Carvlin, Humberto Lugo, Michael Jerrett, Galatea King, Daniel Madrigal, Dan Meltzer, Amanda Northcross, Luis José Imedio Olmedo, Edmund Seto, Christian Torres, A. S. Wilkie, Michelle Wong
Software Mentions: 4
Published: about 6 years ago

10.3390/s20061778

Estimation of Land Surface Temperature in an Agricultural Region of Bangladesh from Landsat 8: Intercomparison of Four Algorithms
Cited by: 11
Author(s): Qutub Uddin Sajib, Tao Wang
Software Mentions: 4
Published: over 6 years ago

10.1126/science.abe3261

Phylogenetic analysis of SARS-CoV-2 in Boston highlights the impact of superspreading events
Cited by: 215
Author(s): Jacob E. Lemieux, Katherine J. Siddle, Bennett Shaw, Christine Loreth, Stephen F. Schaffner, Adrianne Gladden-Young, Gordon Adams, Timelia Fink, Christopher H. Tomkins-Tinch, Lydia A. Krasilnikova, Katherine C. DeRuff, Melissa Rudy, Matthew R. Bauer, Kim A. Lagerborg, Erica Normandin, Sinéad B. Chapman, Steven K. Reilly, Melis N. Anahtar, Aaron E. Lin, Amber Carter, Cameron Myhrvold, Molly Kemball, Sushma Chaluvadi, Caroline Cusick, Katelyn Flowers, Anna Neumann, Felecia Cerrato, Maha Farhat, Damien Slater, Jason B. Harris, John A. Branda, David C. Hooper, Jessie M. Gaeta, Travis P. Baggett, James J. O’Connell, Andreas Gnirke, Tami D. Lieberman, Anthony Philippakis, Meagan Burns, Catherine Brown, Jeremy Luban, Edward T. Ryan, Sarah E Turbett, Regina C. LaRocque, William P. Hanage, Glen R. Gallagher, Lawrence C. Madoff, Sandra Smole, Virginia Pierce, Eric S. Rosenberg, Pardis C. Sabeti, Daniel J. Park, Bronwyn MacInnis
Software Mentions: 4
Published: over 5 years ago

10.1126/scitranslmed.aau6242

Estimating cholera incidence with cross-sectional serology
Cited by: 43
Author(s): Andrew S. Azman, Justin Lessler, Francisco J. Luquero, Taufiqur Rahman Bhuiyan, Ashraful Islam Khan, Fahima Chowdhury, Alamgir Kabir, Marc Gurwith, Ana A. Weil, Jason B. Harris, Stephen B. Calderwood, Edward T. Ryan, Firdausi Qadri, Daniel T. Leung
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-021-99205-z

The effect of non-surgical and surgical mechanical root debridement on infrabony defects: a retrospective study
Cited by: 0
Author(s): Jad Majzoub, Ali Salami, Shayan Barootchi, Lorenzo Tavelli, Hsun‐Liang Chan, Hom‐Lay Wang
Software Mentions: 4
Published: almost 5 years ago

10.1038/s41598-021-99104-3

Microbiome signature and diversity regulates the level of energy production under anaerobic condition
Cited by: 16
Author(s): M. Shaminur Rahman, M. Nazmul Hoque, J. Akter Puspo, M. Rafiul Islam, Niloy Das, Mohammad Anwar Siddique, Md. Anwar Hossain, Munawar Sultana
Software Mentions: 4
Published: almost 5 years ago

10.1038/s41598-021-99127-w

Lung microbiome of stable and exacerbated COPD patients in Tshwane, South Africa
Cited by: 10
Author(s): Tanweer Goolam Mahomed, Rph Peters, Mushal Allam, Arshad Ismail, Senzo Mtshali, Akhter Goolam Mahomed, Veronica Ueckermann, Marleen M. Kock, M.M. Ehlers
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12920-020-0682-5

A pan-cancer study of class-3 semaphorins as therapeutic targets in cancer
Cited by: 37
Author(s): Xiaoli Zhang, Brett Klamer, Jin Li, Soledad Fernández, Lang Li
Software Mentions: 4
Published: over 6 years ago

10.1186/s12920-021-00954-7

Identification of genes and pathways involved in malignant pleural mesothelioma using bioinformatics methods
Cited by: 3
Author(s): Xingsheng Liu, Kun Qian, Gaojun Lu, Peng Chen, Yi Zhang
Software Mentions: 4
Published: over 5 years ago

10.1186/s12920-020-00757-2

Integration analysis of long non-coding RNA (lncRNA) role in tumorigenesis of colon adenocarcinoma
Cited by: 40
Author(s): Arash Poursheikhani, Mohammad Reza Abbaszadegan, Negin Nokhandani, Mohammad Amin Kerachian
Software Mentions: 4
Published: about 6 years ago

10.1038/s41598-021-99261-5

Severe vegetation degradation associated with different disturbance types in a poorly managed urban recreation destination in Iran
Cited by: 5
Author(s): Mohammad Bagher Erfanian, Juha M. Alatalo, Hamid Ejtehadi
Software Mentions: 4
Published: almost 5 years ago

10.1186/1472-6947-11-31

PKreport: report generation for checking population pharmacokinetic model assumptions
Cited by: 6
Author(s): Xiaoyong Sun, Jun Li
Software Mentions: 4
Published: over 15 years ago

10.1038/s41598-021-98979-6

Biodiversity and biocatalyst activity of culturable hydrocarbonoclastic fungi isolated from Marac–Moruga mud volcano in South Trinidad
Cited by: 1
Author(s): Amanda C. Ramdass, Sephra N. Rampersad
Software Mentions: 4
Published: almost 5 years ago

10.1038/s41598-021-98907-8

Transcriptomic profiling of the high-vigour maize (Zea mays L.) hybrid variety response to cold and drought stresses during seed germination
Cited by: 12
Author(s): Heqin Li, Haiwang Yue, Jiping Xie, Junzhou Bu, Li Li, Xueying Xin, Yanming Zhao, Haiyan Zhang, Li Yang, Jianhua Wang, Xuwen Jiang
Software Mentions: 4
Published: almost 5 years ago

10.1038/s41598-021-97337-w

DNA metabarcoding reveals the dietary composition in the endangered black-faced spoonbill
Cited by: 3
Author(s): Pei‐Yu Huang, Emily Shui Kei Poon, Anson Tsz Chun Wong, Ivy Wai Yan So, Yik-Hei Sung, Simon Yung Wa Sin
Software Mentions: 4
Published: almost 5 years ago

10.1038/s41598-021-98423-9

Non-invasive diagnostic tool for Parkinson’s disease by sebum RNA profile with machine learning
Cited by: 11
Author(s): Yuya Uehara, Shinichi Ueno, Haruka Amano-Takeshige, Shuji Suzuki, Yoko Imamichi, Mitsuhisa Fujimaki, Noriyasu Ota, Takatoshi Murase, Tsukasa Inoue, Sachio Saiki, Nobutaka Hattori
Software Mentions: 4
Published: almost 5 years ago

10.1038/s41598-021-97654-0

Assessment of the effectiveness of the EUROFORGEN NAME and Precision ID Ancestry panel markers for ancestry investigations
Cited by: 8
Author(s): Ditte Truelsen, Torben Tvedebrink, Helle Smidt Mogensen, Maryam Sharafi Farzad, Muhammad Adnan Shan, Niels Morling, Vânia Pereira, Claus Børsting
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12866-020-01771-1

Identification and characterization of differentially expressed genes in Caenorhabditis elegans in response to pathogenic and nonpathogenic Stenotrophomonas maltophilia
Cited by: 6
Author(s): Leah J Radeke, Michael A. Herman
Software Mentions: 4
Published: about 6 years ago

10.1186/s12866-017-1132-1

First gene-ontology enrichment analysis based on bacterial coregenome variants: insights into adaptations of Salmonella serovars to mammalian- and avian-hosts
Cited by: 24
Author(s): Arnaud Felten, Meryl Vila Nova, Kévin Durimel, Laurent Guillier, Michel‐Yves Mistou, Nicolas Radomski
Software Mentions: 4
Published: over 8 years ago

10.1186/s12866-018-1333-2

Low recovery of bacterial community after an extreme salinization-desalinization cycle
Cited by: 4
Author(s): Yang Hu, Chengrong Bai, Jian Cai, Kwang‐Tsao Shao, Xiangming Tang, Guang Gao
Software Mentions: 4
Published: almost 8 years ago

10.1186/s12866-018-1154-3

A microbiome case-control study of recurrent acute otitis media identified potentially protective bacterial genera
Cited by: 108
Author(s): Rachael Lappan, Kara Imbrogno, Chisha Sikazwe, Denise Anderson, D. Mok, Harvey Coates, Shyan Vijayasekaran, Paul Bumbak, Christopher C Blyth, Sarra E. Jamieson, Christopher Peacock
Software Mentions: 4
Published: over 8 years ago

10.1186/s12866-018-1283-8

Combining paratransgenesis with SIT: impact of ionizing radiation on the DNA copy number of Sodalis glossinidius in tsetse flies
Cited by: 20
Author(s): Güler Demirbaş-Uzel, Linda De Vooght, Andrew G. Parker, Marc J. B. Vreysen, Robert L. Mach, Jan Van Den Abbeele, Adly M. M. Abd-Alla
Software Mentions: 4
Published: almost 8 years ago

10.1038/s41598-021-97516-9

Phytoplankton communities in temporary ponds under different climate scenarios
Cited by: 6
Author(s): Sofia Celewicz-Gołdyn, Bartłomiej Gołdyn
Software Mentions: 4
Published: almost 5 years ago

10.1038/s41598-021-96886-4

Multiple strain analysis of Streptomyces species from Philippine marine sediments reveals intraspecies heterogeneity in antibiotic activities
Cited by: 11
Author(s): Chuckcris P. Tenebro, Dana Joanne Von L. Trono, Carmela Vannette B. Vicera, Edna M. Sabido, Jovito A. Ysulat, Aaron Joseph M. Macaspac, Kimberly A. Tampus, Trisha Alexis P. Fabrigar, Jonel P. Saludes, Doralyn S. Dalisay
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12866-015-0351-6

The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies
Cited by: 365
Author(s): J. Paul Brooks, D.J. Edwards, Michael Harwich, Maria C. Rivera, Jennifer M. Fettweis, Myrna G. Serrano, Robert Reris, Nihar U. Sheth, Bernice Huang, Philippe H. Girerd, Jerome F. Strauss, Kimberly K. Jefferson, Gregory A. Buck
Software Mentions: 4
Published: over 11 years ago

10.1186/s12866-018-1276-7

Impact of Glossina pallidipes salivary gland hypertrophy virus (GpSGHV) on a heterologous tsetse fly host, Glossina fuscipes fuscipes
Cited by: 4
Author(s): Güler Demirbaş-Uzel, Andrew G. Parker, Marc J. B. Vreysen, Robert L. Mach, Jérémy Bouyer, Peter Takáč, Adly M. M. Abd-Alla
Software Mentions: 4
Published: almost 8 years ago

10.1186/s12866-018-1298-1

RNA interference-based antiviral immune response against the salivary gland hypertrophy virus in Glossina pallidipes
Cited by: 9
Author(s): Irene K. Meki, Henry M. Kariithi, Andrew G. Parker, Marc J. B. Vreysen, V.I.D. Ros, Just M. Vlak, Monique M. van Oers, Adly M. M. Abd-Alla
Software Mentions: 4
Published: almost 8 years ago

10.1186/s12866-019-1500-0

Long-read based de novo assembly of low-complexity metagenome samples results in finished genomes and reveals insights into strain diversity and an active phage system
Cited by: 101
Author(s): Vincent Somerville, Stefanie Lutz, Michael Schmid, Daniel Frei, Aline Moser, Stefan Irmler, Jürg E. Frey, Christian H. Ahrens
Software Mentions: 4
Published: about 7 years ago

10.3390/nu12123599

Se Status Prediction by Food Intake as Compared to Circulating Biomarkers in a West Algerian Population
Cited by: 9
Author(s): Moussa Belhadj, Latifa Sarra Kazi Tani, Nouria Dennouni-Medjati, Yahia Harek, Majda Dali Sahi, Qian Sun, Raban Arved Heller, Ammaria Behar, Laurent Charlet, Lutz Schomburg
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12866-020-01990-6

The effects of exopolysaccharides and exopolysaccharide-producing Lactobacillus on the intestinal microbiome of zebrafish (Danio rerio)
Cited by: 17
Author(s): Chenchen Ma, Hongyang Guo, Haibo Chang, Shi Huang, Shuaiming Jiang, Dongxue Huo, Jiachao Zhang, Xiaopeng Zhu
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12866-016-0801-9

PCR detection of Burkholderia multivorans in water and soil samples
Cited by: 6
Author(s): Charlotte Peeters, Stijn Daenekindt, Peter Vandamme
Software Mentions: 4
Published: about 10 years ago

10.1186/s12866-020-02002-3

Lifestyle modifications result in alterations in the gut microbiota in obese children
Cited by: 21
Author(s): Ky Young Cho
Software Mentions: 4
Published: over 5 years ago

10.1186/s12866-020-02026-9

A longitudinal study on morpho-genetic diversity of pathogenic Rhizoctonia solani from sugar beet and dry beans of western Nebraska
Cited by: 4
Author(s): Saurav Das, T. Plyler-Harveson, Dipak K. Santra, Bijesh Maharjan, Kathy A. Nielson, Robert M. Harveson
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12891-018-2006-x

No difference in the functional improvements between unilateral and bilateral total knee replacements
Cited by: 16
Author(s): Yao-Ming Huang, Chin Lin, Jung-Mou Yang, Leou-Chyr Lin, Chih-Yuan Mou, Kwo-Tsao Chiang, Man-Gang Lee, Hsin‐An Chang, Hsueh-Lu Chang, Wan‐Fu Su, Shih-Jen Yeh, Hung Chang, Chih‐Chien Wang, Sui-Lung Su
Software Mentions: 4
Published: over 8 years ago

10.1186/s12891-021-04109-8

Major ceRNA regulation and key metabolic signature analysis of intervertebral disc degeneration
Cited by: 7
Author(s): Shuai Cao, Jie Li, Kai Yang, Haopeng Li
Software Mentions: 4
Published: over 5 years ago

10.1186/s12891-020-03705-4

Range of abduction in patients with Legg-Calvé-Perthes disease – a nationwide register-based cohort study
Cited by: 2
Author(s): Ahmad El-Harbiti, Yasmin D. Hailer
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-021-81269-6

Chronic BDNF simultaneously inhibits and unmasks superficial dorsal horn neuronal activity
Cited by: 4
Author(s): Sascha R.A. Alles, Max A. Odem, Van B. Lu, Ryan M. Cassidy, Peter A. Smith
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-021-81788-2

Relevance of ddRADseq method for species and population delimitation of closely related and widely distributed wolf spiders (Araneae, Lycosidae)
Cited by: 5
Author(s): Vladislav Ivanov, Yuri M. Marusik, Julien Pétillon, Marko Mutanen
Software Mentions: 4
Published: over 5 years ago

10.18632/aging.202917

Development of a prognostic index and screening of prognosis related genes based on an immunogenomic landscape analysis of bladder cancer
Cited by: 14
Author(s): Genyi Qu, Zhengsheng Liu, Guang Yang, Yong Xu, Maolin Xiang, Chaowei Tang
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-021-80982-6

Antibiotics and the developing intestinal microbiome, metabolome and inflammatory environment in a randomized trial of preterm infants
Cited by: 34
Author(s): Jordan T. Russell, J. Lauren Ruoss, Diomel de la Cruz, Nan Li, Catalina Bazacliu, Laura Patton, Kelley Lobean McKinley, Timothy J. Garrett, Richard A. Polin, Eric W. Triplett, Josef Neu
Software Mentions: 4
Published: over 5 years ago

10.18632/aging.203168

Cell landscape atlas for patients with chronic thromboembolic pulmonary hypertension after pulmonary endarterectomy constructed using single-cell RNA sequencing
Cited by: 8
Author(s): Ran Miao, Xingbei Dong, Juanni Gong, Yidan Li, Xiaojuan Guo, Jianfeng Wang, Qiang Huang, Ying Wang, Jifeng Li, Suqiao Yang, Tuguang Kuang, Jun Wan, Min Liu, Zhenguo Zhai, Jiuchang Zhong, Yuanhua Yang
Software Mentions: 4
Published: about 5 years ago

10.1186/s12887-020-02272-w

Breastfeeding patterns in cohort infants at a high-risk fetal, neonatal and child referral center in Brazil: a correspondence analysis
Cited by: 4
Author(s): Maíra Domingues Bernardes Silva, Raquel de Vasconcellos Carvalhaes de Oliveira, José Ueleres Braga, João Aprígio Guerra de Almeida, Enirtes Caetano Prates Melo
Software Mentions: 4
Published: about 6 years ago

10.1186/s12870-020-02518-w

Plastome phylogenomic study of Gentianeae (Gentianaceae): widespread gene tree discordance and its association with evolutionary rate heterogeneity of plastid genes
Cited by: 27
Author(s): Xu Zhang, Yanxia Sun, Jacob B. Landis, Zhenyu Lv, Jun Shen, Huajie Zhang, Nan Lin, Lijuan Li, Jiao Sun, Tao Deng, Hang Sun, Hengchang Wang
Software Mentions: 4
Published: about 6 years ago

10.1186/s12870-014-0254-y

Phosphite-induced changes of the transcriptome and secretome in Solanum tuberosum leading to resistance against Phytophthora infestans
Cited by: 77
Author(s): Dharani Dhar Burra, Oliver Berkowitz, Pete E. Hedley, Jenny Morris, Svante Resjö, Fredrik Levander, Erland Liljeroth, Erik Andréasson, Erik Alexandersson
Software Mentions: 4
Published: almost 12 years ago

10.1186/s12870-019-2055-9

Metabolite profiling during graft union formation reveals the reprogramming of primary metabolism and the induction of stilbene synthesis at the graft interface in grapevine
Cited by: 25
Author(s): Duyên Prodhomme, Josep Valls, Cyril Hévin, Céline Franc, Ghislaine Hilbert, Gilles de Revel, Tristan Richard, Nathalie Ollat, Sarah Jane Cookson
Software Mentions: 4
Published: over 6 years ago

10.18632/oncotarget.12818

Association of breast cancer risk with genetic variants showing differential allelic expression: Identification of a novel breast cancer susceptibility locus at 4q21
Cited by: 32
Author(s): Yosr Hamdi, Penny Soucy, Véronique Adoue, Kyriaki Michailidou, Sander Canisius, Audrey Lemaçon, Arnaud Droit, Irene L. Andrulis, Hoda Anton‐Culver, Volker Arndt, Caroline Baynes, Carl Blomqvist, Natalia Bogdanova, Stig E. Bojesen, Manjeet K. Bolla, Bernardo Bonanni, Anne‐Lise Børresen‐Dale, Judith S. Brand, Hiltrud Brauch, Hermann Brenner, Annegien Broeks, Barbara Burwinkel, Jenny Chang–Claude, Fergus J. Couch, Angela Cox, Simon S. Cross, Kamila Czene, Hatef Darabi, Joe Dennis, Peter Devilee, Thilo Dörk, Isabel dos‐Santos‐Silva, Mikael Eriksson, Peter A. Fasching, Jonine D. Figueroa, Henrik Flyger, Montserrat García‐Closas, Graham G. Giles, Mark S. Goldberg, Anna González‐Neira, Grethe Irene Grenaker-Alnæs, Pascal Guénel, Lothar Haeberle, Christopher A. Haiman, Ute Hamann, Emily Hallberg, Maartje J. Hooning, John L. Hopper, Anna Jakubowska, Michael E. Jones, Maria Kabisch, Vesa Kataja, Diether Lambrechts, Loı̈c Le Marchand, Annika Lindblom, Jan Lubiński, Arto Mannermaa, Mel Maranian, Sara Margolin, Frederik Marmé, Roger L. Milne, Susan L. Neuhausen, Heli Nevanlinna, Patrick Neven, Curtis Olswold, Julian Peto, Dijana Plaseska‐Karanfilska, Katri Pylkäs, Paolo Radice, Anja Rudolph, Elinor J. Sawyer, Marjanka K. Schmidt, Xiao‐Ou Shu, Melissa C. Southey, Anthony Swerdlow, Rob A.E.M. Tollenaar, Ian Tomlinson, Diana Torres, Thérèse Truong, Celine M. Vachon, Ans M.W. van den Ouweland, Qin Wang, Robert Winqvist, _ kConFab, Aocs Investigators, Wei Zheng, Javier Benı́tez, Georgia Chenevix-Trench, Alison M. Dunning, Paul D.P. Pharoah, Vessela N. Kristensen, Per Hall, Douglas F. Easton, Tomi Pastinen, Silje Nord, Jacques Simard
Software Mentions: 4
Published: almost 10 years ago

10.1186/s12870-021-03180-6

Identification of genetic loci associated with major agronomic traits of wheat (Triticum aestivum L.) based on genome-wide association analysis
Cited by: 5
Author(s): Woo Joo Jung, Yong Jin Lee, Kang Chen, Yong Weon Seo
Software Mentions: 4
Published: almost 5 years ago

10.1038/s41598-020-79491-9

Effects of climate change and land cover on the distributions of a critical tree family in the Philippines
Cited by: 16
Author(s): Sean E. H. Pang, Jose Don T. De Alban, Edward L. Webb
Software Mentions: 4
Published: over 5 years ago

10.18632/aging.203352

Development and validation of prognostic model based on the analysis of autophagy-related genes in colon cancer
Cited by: 8
Author(s): Yongfeng Wang, Kaili Lin, Tianchun Xu, Liuli Wang, Liangyin Fu, Guangming Zhang, Jing Ai, Yajun Jiao, Rongrong Zhu, Xiaoyong Han, Hui Cai
Software Mentions: 4
Published: about 5 years ago

10.1038/s41598-020-80093-8

An enriched biosignature of gut microbiota-dependent metabolites characterizes maternal plasma in a mouse model of fetal alcohol spectrum disorder
Cited by: 20
Author(s): Manjot S Virdee, Nipun Saini, Colin D. Kay, Andrew P. Neilson, Sze Ting Cecilia Kwan, Kaylee K. Helfrich, Sandra M. Mooney, Susan Smith
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-020-79924-5

Urban street tree biodiversity and antidepressant prescriptions
Cited by: 74
Author(s): Melissa R. Marselle, Diana E. Bowler, Jan Watzema, David Eichenberg, Toralf Kirsten, Aletta Bonn
Software Mentions: 4
Published: over 5 years ago

10.1186/s12870-020-02336-0

Morpho-physiological integrators, transcriptome and coexpression network analyses signify the novel molecular signatures associated with axillary bud in chrysanthemum
Cited by: 10
Author(s): Sagheer Ahmad, Cunquan Yuan, Qingqing Yang, Yujie Yang, Tangren Cheng, Jia Wang, Huitang Pan, Qixiang Zhang
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-020-78983-y

Local injections of β-NGF accelerates endochondral fracture repair by promoting cartilage to bone conversion
Cited by: 13
Author(s): Kevin O. Rivera, Fabrizio Russo, Ryan M. Boileau, Ryan E. Tomlinson, Theodore Miclau, Ralph Marcucio, Tejal A. Desai, Chelsea S. Bahney
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-020-78366-3

Human kidney clonal proliferation disclose lineage-restricted precursor characteristics
Cited by: 7
Author(s): Osnat Cohen-Zontag, Rotem Gershon, Orit Harari‐Steinberg, Itamar Kanter, Dorit Omer, Oren Pleniceanu, Gal Tam, Sarit Oriel, H Ben-Hur, Guy Katz, Zohar Dotan, Tomer Kalisky, Benjamin Dekel, Naomi Pode‐Shakked
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-020-78841-x

Gravettian cranial morphology and human group affinities during the European Upper Palaeolithic
Cited by: 6
Author(s): Aurélien Mounier, Yann Heuzé, Mathilde Samsel, Sergey Vasilyev, Laurent Klaric, Sébastien Villotte
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-020-78773-6

Evaluation of methods for the reduction of contaminating host reads when performing shotgun metagenomic sequencing of the milk microbiome
Cited by: 28
Author(s): Min Yap, Conor Feehily, Calum J. Walsh, Mark A. Fenelon, Eileen F. Murphy, Fionnuala M. McAuliffe, Douwe van Sinderen, Paul W. O’Toole, Órla O’Sullivan, Paul D. Cotter
Software Mentions: 4
Published: over 5 years ago

10.1186/s12870-021-03058-7

Reduced free asparagine in wheat grain resulting from a natural deletion of TaASN-B2: investigating and exploiting diversity in the asparagine synthetase gene family to improve wheat quality
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Author(s): Joseph Oddy, Rocío Alarcón‐Reverte, Mark Wilkinson, Karl Ravet, Sarah Raffan, Andrea Minter, Andrew Mead, J. Stephen Elmore, Isabel Moreira de Almeida, Nicholas C. Cryer, Nigel G. Halford, Stephen Pearce
Software Mentions: 4
Published: about 5 years ago

10.1186/s12870-016-0788-2

Genome-wide analysis of Dongxiang wild rice (Oryza rufipogon Griff.) to investigate lost/acquired genes during rice domestication
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Author(s): Fantao Zhang, Tao Xu, Linyong Mao, Shuangyong Yan, Xiwen Chen, Zhenfeng Wu, Rui Chen, Xiangdong Luo, Jingzhong Xie, Shan Gao
Software Mentions: 4
Published: over 10 years ago

10.1038/s41598-020-78589-4

GRAS-Di system facilitates high-density genetic map construction and QTL identification in recombinant inbred lines of the wheat progenitor Aegilops tauschii
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Author(s): Yuka Miki, Kentaro Yoshida, Hiroyuki Enoki, Saburô Kômura, Kazuko Suzuki, Minoru Inamori, Ryo Nishijima, Shigeo Takumi
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-020-77033-x

Moving targets in drug discovery
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Author(s): Barbara Zdrazil, Lars Richter, Nathan Brown, Rajarshi Guha
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12888-021-03154-w

Attention-deficit/hyperactivity disorder with developmental coordination disorder: 24-year follow-up of a population-based sample
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Author(s): Valdemar Landgren, Elisabeth Fernell, Christopher Gillberg, Magnus Landgren, Mats Johnson
Software Mentions: 4
Published: over 5 years ago

10.1186/s12889-020-09278-0

Spatial analysis of factors associated with HIV infection in Malawi: indicators for effective prevention
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Author(s): Jerry John Nutor, Henry Ofori Duah, Pascal Agbadi, Precious Adade Duodu, Kaboni Whitney Gondwe
Software Mentions: 4
Published: about 6 years ago

10.1186/s12889-019-7861-3

Health as an independent predictor of the 2017 French presidential voting behaviour: a cross-sectional analysis
Cited by: 5
Author(s): Jean–David Zeitoun, Matthieu Faron, Sophie de Vaugrigneuse, Jérémie H. Lefèvre
Software Mentions: 4
Published: almost 7 years ago

10.1186/s12889-020-09975-w

Relationship between the duration of smoking and blood pressure in Han and ethnic minority populations: a cross-sectional study in China
Cited by: 5
Author(s): Yuelun Zhang, Yunying Feng, Shi Chen, Siyu Liang, Shirui Wang, Ke Xu, Dongping Ning, Xianxian Yuan, Huijuan Zhu, Hui Pan, Guangliang Shan
Software Mentions: 4
Published: over 5 years ago

10.1186/s12889-021-10961-z

Real time surveillance of COVID-19 space and time clusters during the summer 2020 in Spain
Cited by: 171
Author(s): Nicolás Rosillo, Javier Del-Águila-Mejía, Ayelén Rojas-Benedicto, María Guerrero-Vadillo, Marina Peñuelas, Clara Mazagatos, Jordi Segú-Tell, Rebeca Ramis, Diana Gómez-Barroso
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-020-76645-7

Trait convergence and trait divergence in lake phytoplankton reflect community assembly rules
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Author(s): Gábor Borics, Viktória B‐Béres, István Bácsi, Balázs András Lukács, Enikő T‐Krasznai, Zoltán Botta‐Dukát, Gábor Várbíró
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-020-76048-8

Characterization of somatic mutation-associated microenvironment signatures in acute myeloid leukemia patients based on TCGA analysis
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Author(s): Jun Wang, Feng‐Ting Dao, Lu Yang, Ya‐Zhen Qin
Software Mentions: 4
Published: almost 6 years ago

10.1186/s13104-015-1665-z

Lipid levels in HIV-positive men receiving anti-retroviral therapy are not associated with copy number variation of reverse cholesterol transport pathway genes
Cited by: 0
Author(s): Rebecca Marino, Lawrence A. Kingsley, Shehnaz K. Hussain, Jay H. Bream, Sudhir Penogonda, Priya Duggal, Jeremy Martinson
Software Mentions: 4
Published: almost 11 years ago

10.1038/s41598-020-74753-y

Alcohol use in severely injured trauma patients
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Author(s): Antti Riuttanen, Saara Jäntti, Ville M. Mattila
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12918-018-0596-4

Single molecules can operate as primitive biological sensors, switches and oscillators
Cited by: 10
Author(s): Rosa D. Hernansaiz-Ballesteros, Luca Cardelli, Attila Csikász‐Nagy
Software Mentions: 4
Published: about 8 years ago

10.1111/acel.12479

Characterization of the direct targets of <scp>FOXO</scp> transcription factors throughout evolution
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Author(s): Ashley E. Webb, Anshul Kundaje, Anne Brunet
Software Mentions: 4
Published: over 10 years ago

10.1038/s41598-020-74751-0

HLA-A alleles including HLA-A29 affect the composition of the gut microbiome: a potential clue to the pathogenesis of birdshot retinochoroidopathy
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Author(s): Peter R. Sternes, Tammy M. Martin, Michael Paley, Sarah Diamond, Mark Asquith, Matthew A. Brown, James T. Rosenbaum
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-019-55632-7

Error associated with estimates of Minimum Infection Rate for Endemic West Nile Virus in areas of low mosquito trap density
Cited by: 9
Author(s): Sulagna Chakraborty, Rebecca L. Smith
Software Mentions: 4
Published: over 6 years ago

10.1186/s12917-018-1505-1

The value of necropsy reports for animal health surveillance
Cited by: 18
Author(s): Susanne Küker, Céline Faverjon, Lenz Furrer, John Berezowski, Horst Posthaus, Fabio Rinaldi, Flavie Vial
Software Mentions: 4
Published: about 8 years ago

10.1038/s41598-019-54983-5

Plasma metabolomics in tuberculosis patients with and without concurrent type 2 diabetes at diagnosis and during antibiotic treatment
Cited by: 36
Author(s): Frank Vrieling, Bachti Alisjahbana, Edhyana Sahiratmadja, Reinout van Crevel, Amy C. Harms, Thomas Hankemeier, Tom H. M. Ottenhoff, Simone A. Joosten
Software Mentions: 4
Published: over 6 years ago

10.1186/s12917-018-1406-3

Dynamic network measures reveal the impact of cattle markets and alpine summering on the risk of epidemic outbreaks in the Swiss cattle population
Cited by: 21
Author(s): Beatriz Vidondo, Bernhard Voelkl
Software Mentions: 4
Published: over 8 years ago

10.1186/s12917-020-02430-3

Gut microbiota profiles of commercial laying hens infected with tumorigenic viruses
Cited by: 1
Author(s): Xianhua Wan, Laipeng Xu, Xiaolun Sun, Hui Li, Fengbin Yan, Ruili Han, Hong Li, Zhuanjian Li, Yadong Tian, Xiaojun Liu, Xin Kang, Zhenya Wang, Yanbin Wang
Software Mentions: 4
Published: about 6 years ago

10.1155/2018/1264697

Identification of 170 New Long Noncoding RNAs in<i> Schistosoma mansoni</i>
Cited by: 17
Author(s): Victor Fernandes de Oliveira, Lauro A. G. Moares, Ester Alves Mota, Liana K. Jannotti-Passos, Paulo Marcos Zech Coelho, Ana Carolina Alves de Mattos, Flávia Fernanda Búbula Couto, Brian E. Caffrey, Annalisa Marsico, Renata Guerra‐Sá
Software Mentions: 4
Published: about 8 years ago

10.1016/j.isci.2021.102889

LiquidCNA: Tracking subclonal evolution from longitudinal liquid biopsies using somatic copy number alterations
Cited by: 5
Author(s): Eszter Lakatos, Helen Hockings, Maximilian Mossner, Weini Huang, Michelle Lockley, Trevor A. Graham
Software Mentions: 4
Published: about 5 years ago

10.1111/all.14633

Single‐cell molecular profiling provides a high‐resolution map of basophil and mast cell development
Cited by: 29
Author(s): Fiona Hamey, Winnie Lau, Iwo Kuciński, Xiaonan Wang, Evangelia Diamanti, Nicola K. Wilson, Berthold Göttgens, Joakim S. Dahlin
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41598-019-51118-8

Extensive vegetation browning and drying in forests of India’s Tiger Reserves
Cited by: 7
Author(s): Pradeep Koulgi, Nicholas Clinton, Krithi K. Karanth
Software Mentions: 4
Published: almost 7 years ago

10.1186/s13223-021-00584-9

Expression profiling of ileal mucosa in asthma reveals upregulation of innate immunity and genes characteristic of Paneth and goblet cells
Cited by: 1
Author(s): Jan Krzysztof Nowak, Marzena Dworacka, Nazgul Gubaj, Arystan Dossimov, Zhumabek Dossimov, Jarosław Walkowiak
Software Mentions: 4
Published: about 5 years ago

10.1042/BSR20210759

Metabolic profiling of maternal serum of women at high-risk of spontaneous preterm birth using NMR and MGWAS approach
Cited by: 1
Author(s): Juhi Gupta, Angharad Care, Laura Goodfellow, Žarko Alfirević, Lu‐Yun Lian, Bertram Müller‐Myhsok, Ana Alfirevic, Marie M. Phelan
Software Mentions: 4
Published: almost 5 years ago

10.1042/BSR20203459

CXCL10 is a potential biomarker and associated with immune infiltration in human papillary thyroid cancer
Cited by: 10
Author(s): Xiaojing Qin, Lin Xu, Guoqiang Xue, Huiying Fan, Haoyu Wang, Jing Wu, Da Pei
Software Mentions: 4
Published: over 5 years ago

10.1016/j.jalz.2019.03.007

Inflammatory biomarkers in Alzheimer's disease plasma
Cited by: 118
Author(s): Angharad R. Morgan, Samuel Touchard, Claire Leckey, Caroline O’Hagan, Alejo J. Nevado‐Holgado, Frederik Barkhof, Lars Bertram, Olivier Blin, Isabelle Bos, Valerija Dobričić, Sebastiaan Engelborghs, Giovanni B. Frisoni, Lutz Frölich, Silvey Gabel, Peter Johannsen, Petronella Kettunen, Iwona Kłoszewska, Cristina Legido‐Quigley, Alberto Lleó, Pablo Martínez-Lage, Patrizia Mecocci, Karen Meersmans, José Luís Molinuevo, Gwendoline Peyratout, Julius Popp, Jill C. Richardson, Isabel Sala, Philip Scheltens, Johannes Streffer, Hikka Soininen, Mikel Tainta, Charlotte E. Teunissen, Magda Tsolaki, Rik Vandenberghe, Pieter Jelle Visser, Stephanie J.B. Vos, Lars‐Olof Wahlund, Anders Wallin, Sarah Westwood, Henrik Zetterberg, Simon Lovestone, B. Paul Morgan, Alzheimer’s Disease
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-019-51211-y

Long-term efficacy of imatinib mesylate in patients with advanced Tenosynovial Giant Cell Tumor
Cited by: 38
Author(s): Floortje G M Verspoor, Monique J L Mastboom, Gerjon Hannink, Robert G. Maki, Andrew J. Wagner, Emmanuelle Bompas, Jayesh Desai, Antoîne Italiano, Beatrice Seddon, Winette T.A. van der Graaf, Jean‐Yves Blay, Mehdi Brahmi, Lauriane Eberst, Silvia Stacchiotti, Olivier Mir, Michiel A.J. van de Sande, Hans Gelderblom, P. A. Cassier
Software Mentions: 4
Published: almost 7 years ago

10.1042/BSR20203020

Network-based approach to identify prognosis-related genes in tamoxifen-treated patients with estrogen receptor-positive breast cancer
Cited by: 4
Author(s): Yanyan Wang, Xiaonan Gong, Yujie Zhang
Software Mentions: 4
Published: almost 5 years ago

10.1038/s41598-019-50885-8

Improved gene co-expression network quality through expression dataset down-sampling and network aggregation
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Author(s): Franziska Liesecke, Johan-Owen De Craene, Sébastien Besseau, Vincent Courdavault, Marc Clastre, Valentin Vergès, Nicolas Papon, Nathalie Giglioli-Guivarc’h, Gaëlle Glévarec, Olivier Pichon, Thomas Dugé de Bernonville
Software Mentions: 4
Published: almost 7 years ago

10.1042/BSR20201427

Mining novel cell glycolysis related gene markers that can predict the survival of colon adenocarcinoma patients
Cited by: 16
Author(s): Sihan Chen, Guodong Cao, Wei Wu, Yida Lu, Xueling He, Lei Yang, Ke Chen, Bo Chen, Maoming Xiong
Software Mentions: 4
Published: about 6 years ago

10.1186/s13068-021-01895-0

Overexpression of vesicle-associated membrane protein PttVAP27-17 as a tool to improve biomass production and the overall saccharification yields in Populus trees
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Author(s): Madhavi Latha Gandla, Niklas Mähler, Sacha Escamez, Tomas Skotare, Ogonna Obudulu, Linus Möller, Ilka Nacif Abreu, Joakim Bygdell, Magnus Hertzberg, Torgeir R. Hvidsten, Thomas Moritz, Gunnar Wingsle, Johan Trygg, Hannele Tuominen, Leif J. Jönsson
Software Mentions: 4
Published: over 5 years ago

10.1186/s13195-021-00871-y

Short leukocyte telomeres predict 25-year Alzheimer's disease incidence in non-APOE ε4-carriers
Cited by: 17
Author(s): Fernanda Schäfer Hackenhaar, Maria Josefsson, Annelie Nordin Adolfsson, Mattias Landfors, Karolina Kauppi, Magnus Hultdin, Rolf Adolfsson, Sofie Degerman, Sara Pudas
Software Mentions: 4
Published: about 5 years ago

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