10.1186/s12864-021-07746-4

Benchmark of 16S rRNA gene amplicon sequencing using Japanese gut microbiome data from the V1–V2 and V3–V4 primer sets
Cited by: 36
Author(s): Shoichiro Kameoka, Daisuke Motooka, Satoshi Watanabe, Rieko Kubo, Nicolas Jung, Yuki Midorikawa, Natsuko O. Shinozaki, Yu Sawai, Aya Takeda, Shota Nakamura
Software Mentions: 1
Published: almost 5 years ago

10.1186/gb-2007-8-8-r167

Genomic mapping of Suppressor of Hairy-wing binding sites in Drosophila
Cited by: 58
Author(s): Boris Adryan, Gertrud Woerfel, Ian Birch-Machin, Shan Gao, Marie Quick, Lisa Meadows, Steven Russell, Robert A. White
Software Mentions: 1
Published: over 19 years ago

10.1186/1471-2164-15-1133

The genetics of colony form and function in Caribbean Acropora corals
Cited by: 42
Author(s): Elizabeth M. Hemond, Stefan T. Kaluziak, Steven V. Vollmer
Software Mentions: 1
Published: over 12 years ago

10.1186/gb-2009-10-8-r86

Synorth: exploring the evolution of synteny and long-range regulatory interactions in vertebrate genomes
Cited by: 25
Author(s): Xianjun Dong, David Fredman, Boris Lenhard
Software Mentions: 1
Published: over 17 years ago

10.1186/1471-2334-14-526

Bordetella pertussis: an underreported pathogen in pediatric respiratory infections, a prospective cohort study
Cited by: 41
Author(s): G. van den Brink, Jérôme O. Wishaupt, Jacob C. Douma, Nico G. Hartwig, F. G. A. Versteegh
Software Mentions: 1
Published: over 11 years ago

10.1186/gb-2011-12-9-r86

Mutation discovery in mice by whole exome sequencing
Cited by: 102
Author(s): Heather Fairfield, Griffith J Gilbert, Mary Barter, Rebecca R. Corrigan, Michelle Curtain, Yueming Ding, Mark D’Ascenzo, Daniel J. Gerhardt, Chao He, Wenhui Huang, Todd Richmond, Lucy B. Rowe, Frank J. Probst, David E. Bergstrom, Stephen A. Murray, Carol J. Bult, Joel E. Richardson, Benjamin T. Kile, Ivo Gut, Jörg Hager, Snaevar Sigurðsson, Evan Mauceli, Federica Di Palma, Kerstin Lindblad‐Toh, Michael L. Cunningham, Timothy C. Cox, Monica J. Justice, Mona S. Spector, Scott W. Lowe, Thomas Albert, Leah Rae Donahue, Jeffrey A. Jeddeloh, Jay Shendure
Software Mentions: 1
Published: over 15 years ago

10.1186/gb-2011-12-s1-p24

Identification of functional genetic variants associated with prostate cancer through analysis of genome-wide genetic and epigenetic datasets
Cited by: 0
Author(s): McAnthony Tarway, Wei Tang, Ludmila Prokunina–Olsson
Software Mentions: 1
Published: over 15 years ago

10.1186/gb-2012-13-10-r84

Tissue of origin determines cancer-associated CpG island promoter hypermethylation patterns
Cited by: 141
Author(s): Duncan Sproul, Robert Kitchen, Colm E. Nestor, JM Dixon, Andrew H. Sims, David J. Harrison, Bernard Ramsahoye, Richard R. Meehan
Software Mentions: 1
Published: over 14 years ago

10.1186/s12866-021-02286-z

Disturbed microbial ecology in Alzheimer’s disease: evidence from the gut microbiota and fecal metabolome
Cited by: 29
Author(s): Jianxiong Xi, Ding Ding, Huiwei Zhu, Ruru Wang, Feng Su, Wanqing Wu, Zhenxu Xiao, Xiaoniu Liang, Qianhua Zhao, Zhen Hong, Hua Fu, Qianyi Xiao
Software Mentions: 1
Published: almost 5 years ago

10.1186/s12866-020-02037-6

Lower methane emissions were associated with higher abundance of ruminal Prevotella in a cohort of Colombian buffalos
Cited by: 17
Author(s): Sandra Bibiana Aguilar Marín, Claudia Lorena Betancur-Murillo, Gustavo Isaza, Henry Mesa, Juan Jovel
Software Mentions: 1
Published: over 5 years ago

10.1186/s12866-018-1290-9

Different laboratory populations similar bacterial profile? The case of Glossina palpalis gambiensis
Cited by: 4
Author(s): Vangelis Doudoumis, Antonios A. Augustinos, Aggeliki Saridaki, Andrew G. Parker, Adly M. M. Abd-Alla, Kostas Bourtzis, George Tsiamis
Software Mentions: 1
Published: over 7 years ago

10.1186/s12866-020-01843-2

The microbiome of diabetic foot ulcers: a comparison of swab and tissue biopsy wound sampling techniques using 16S rRNA gene sequencing
Cited by: 16
Author(s): Jason Travis, Matthew Malone, Honghua Hu, Abdul Baten, Khalid Johani, Flavia Huygens, Karen Vickery, Kirsten Benkendorff
Software Mentions: 1
Published: about 6 years ago

10.1186/s12866-019-1426-6

Using formalin fixed paraffin embedded tissue to characterize the preterm gut microbiota in necrotising enterocolitis and spontaneous isolated perforation using marginal and diseased tissue
Cited by: 20
Author(s): Christopher J. Stewart, Roxana Fatemizadeh, Pamela Parsons, Christopher A Lamb, Deborah A. Shady, Joseph F. Petrosino, Amy B. Hair
Software Mentions: 1
Published: over 7 years ago

10.1186/s12866-019-1514-7

Bacterial microbiomes of Ixodes scapularis ticks collected from Massachusetts and Texas, USA
Cited by: 42
Author(s): Santosh Thapa, Yan Zhang, Michael S. Allen
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0253607

Birth weight rather than birth length is associated with childhood behavioural problems in a Czech ELSPAC cohort
Cited by: 1
Author(s): Lucie Ráčková, Daniela Kuruczová, Jiří Jarkovský, Julie Bienertová-Vašků
Software Mentions: 1
Published: almost 5 years ago

10.1523/ENEURO.0040-17.2017

Histone Hypervariants H2A.Z.1 and H2A.Z.2 Play Independent and Context-Specific Roles in Neuronal Activity-Induced Transcription of<i>Arc/Arg3.1</i>and Other Immediate Early Genes
Cited by: 37
Author(s): Carissa J. Dunn, Pushpita Sarkar, Emma R. Bailey, Shannon Farris, Mei Zhao, James M. Ward, Serena M. Dudek, Ramendra N. Saha
Software Mentions: 1
Published: almost 9 years ago

10.1186/gb-2013-14-3-r25

Redistribution of H3K27me3 upon DNA hypomethylation results in de-repression of Polycomb target genes
Cited by: 199
Author(s): James P. Reddington, Sara Maria Perricone, Colm E. Nestor, Judith Reichmann, Neil A. Youngson, Masako Suzuki, Diana Reinhardt, Donncha S. Dunican, James Prendergast, Heidi K. Mjoseng, Bernard Ramsahoye, Emma Whitelaw, John M. Greally, Ian R. Adams, Wendy A. Bickmore, Richard R. Meehan
Software Mentions: 1
Published: over 13 years ago

10.1186/gb-2014-15-1-r5

Mammalian conserved ADAR targets comprise only a small fragment of the human editosome
Cited by: 146
Author(s): Yishay Pinto, Haim Y. Cohen, Erez Y. Levanon
Software Mentions: 1
Published: over 12 years ago

10.1186/gb-2013-14-7-r79

PARma: identification of microRNA target sites in AGO-PAR-CLIP data
Cited by: 52
Author(s): Florian Erhard, Lars Dölken, Łukasz Jaśkiewicz, Ralf Zimmer
Software Mentions: 1
Published: over 13 years ago

10.1186/s13059-016-0876-5

The contribution of Alu exons to the human proteome
Cited by: 36
Author(s): Lan Lin, Peng Jiang, Juw Won Park, Jinkai Wang, Zhi-xiang Lu, Maggie P. Y. Lam, Peipei Ping, Yi Xing
Software Mentions: 1
Published: over 10 years ago

10.1186/s13059-017-1225-z

Regulatory landscape fusion in rhabdomyosarcoma through interactions between the PAX3 promoter and FOXO1 regulatory elements
Cited by: 21
Author(s): Cristina Vicente-García, Bárbara Villarejo-Balcells, Ibai Irastorza-Azcárate, Silvia Naranjo, Rafael D. Acemel, Juan J. Tena, Peter Rigby, Damien P. Devos, José Luis Gómez-Skármeta, Jaime J. Carvajal
Software Mentions: 1
Published: about 9 years ago

10.1186/s13059-018-1434-0

Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome
Cited by: 73
Author(s): Luís Zapata, Oriol Pich, Luís Serrano, Fyodor A. Kondrashov, Stephan Ossowski, Martin H. Schaefer
Software Mentions: 1
Published: about 8 years ago

10.1186/s13059-018-1544-8

Reconstruction of avian ancestral karyotypes reveals differences in the evolutionary history of macro- and microchromosomes
Cited by: 40
Author(s): Joana Damas, Jaebum Kim, Marta Farré, Darren K. Griffin, Denis M. Larkin
Software Mentions: 1
Published: over 7 years ago

10.1186/s12866-015-0622-2

Colonization potential to reconstitute a microbe community in patients detected early after fecal microbe transplant for recurrent C. difficile
Cited by: 18
Author(s): Ranjit Kumar, Craig L. Maynard, Peter Eipers, Kelly T. Goldsmith, Travis Ptacek, James Grubbs, Paula Dixon, Donna Howard, David K. Crossman, Michael R. Crowley, William H. Benjamin, Elliot J. Lefkowitz, Casey T. Weaver, Jorge Martín Rodríguez, Casey D. Morrow
Software Mentions: 1
Published: over 10 years ago

10.1186/s12866-020-01860-1

Unveiling protist diversity associated with the Pacific oyster Crassostrea gigas using blocking and excluding primers
Cited by: 4
Author(s): Camille Clérissi, Laure Guillou, Jean-Michel Escoubas, Ève Toulza
Software Mentions: 1
Published: almost 6 years ago

10.1093/gbe/evv012

The Role of DNA Insertions in Phenotypic Differentiation between Humans and Other Primates
Cited by: 4
Author(s): Elizabeth Hellen, Andrew D. Kern
Software Mentions: 1
Published: over 11 years ago

10.1093/gbe/evz254

Genome Assembly of the Dogface Butterfly Zerene cesonia
Cited by: 7
Author(s): Luis Rodriguez-Caro, Jennifer Fenner, Caleb Benson, Steven M. Van Belleghem, Brian A. Counterman
Software Mentions: 1
Published: over 6 years ago

10.1186/gm137

Collaboratively charting the gene-to-phenotype network of human congenital heart defects
Cited by: 28
Author(s): Roland Barriot, Jeroen Breckpot, Bernard Thienpont, Sylvain Brohée, Steven Van Vooren, Bert Coessens, Léon-Charles Tranchevent, Peter Van Loo, Marc Gewillig, Koenraad Devriendt, Yves Moreau
Software Mentions: 1
Published: over 16 years ago

10.1186/s13073-017-0453-x

Identification and characterization of a FOXA2-regulated transcriptional enhancer at a type 2 diabetes intronic locus that controls GCKR expression in liver cells
Cited by: 20
Author(s): Maykel López Rodríguez, Dorota Kaminska, Kati Lappalainen, Jussi Pihlajamäki, Minna U. Kaikkonen, Markku Laakso
Software Mentions: 1
Published: almost 9 years ago

10.1016/j.gpb.2019.03.006

Tung Tree (Vernicia fordii) Genome Provides A Resource for Understanding Genome Evolution and Improved Oil Production
Cited by: 34
Author(s): Lin Zhang, Meilan Liu, Hongxu Long, Wei Dong, Asher Pasha, Eddi Esteban, Wenying Li, Xiaoming Yang, Ze Li, Aixia Song, Duo Ran, Guang Zhao, Yanwei Zeng, Hao Chen, Ming Zou, Jingjing Li, Fan Liang, Meili Xie, Jiang Hu, Depeng Wang, Heping Cao, Nicholas J. Provart, Liangsheng Zhang
Software Mentions: 1
Published: over 6 years ago

10.1186/s41065-016-0022-0

Psychomotor retardation with a 1q42.11–q42.12 deletion
Cited by: 4
Author(s): Jialing He, Yuan Xie, Shu Kong, Wenjun Qiu, Xiaoman Wang, Ding Wang, Xiaofang Sun, Deming Sun
Software Mentions: 1
Published: over 9 years ago

10.1038/s41439-020-00127-5

A reference catalog of DNA palindromes in the human genome and their variations in 1000 Genomes
Cited by: 10
Author(s): Madhavi K. Ganapathiraju, Sandeep Subramanian, Srilakshmi Chaparala, Kalyani B. Karunakaran
Software Mentions: 1
Published: over 5 years ago

10.1001/jamanetworkopen.2021.16839

Genetic Variants Associated With Intraparenchymal Hemorrhage Progression After Traumatic Brain Injury
Cited by: 11
Author(s): Ruchira M. Jha, Benjamin Zusman, Ava M. Puccio, David O. Okonkwo, Matthew Pease, Shashvat M Desai, Matthew R Leach, Yvette P. Conley, Patrick M. Kochanek
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.pbio.2006348

De novo assembly of a young Drosophila Y chromosome using single-molecule sequencing and chromatin conformation capture
Cited by: 84
Author(s): Shivani Mahajan, Kevin H.-C. Wei, Matthew J. Nalley, Lauren Gibilisco, Doris Bachtrog
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0113683

Comparative Salivary Proteome of Hepatitis B- and C-Infected Patients
Cited by: 6
Author(s): Lorena Da Rós Gonçalves, Isabele Batista Campanhon, Romênia R. Domingues, Adriana Franco Paes Leme, Márcia Regina Soares
Software Mentions: 1
Published: over 11 years ago

10.1038/srep34955

Genomic evidence for plant-parasitic nematodes as the earliest Wolbachia hosts
Cited by: 48
Author(s): Amanda M. V. Brown, Sulochana K. Wasala, Dana K. Howe, Amy B. Peetz, Inga A. Zasada, Dee R. Denver
Software Mentions: 1
Published: over 9 years ago

10.1038/srep42222

Genotoxic Effects of Culture Media on Human Pluripotent Stem Cells
Cited by: 13
Author(s): Megha Prakash Bangalore, Syama Adhikarla, Odity Mukherjee, Mitradas M. Panicker
Software Mentions: 1
Published: over 9 years ago

10.1038/s41598-017-15076-3

Detection of subclonal L1 transductions in colorectal cancer by long-distance inverse-PCR and Nanopore sequencing
Cited by: 23
Author(s): Barun Pradhan, Tatiana Cajuso, Riku Katainen, Päivi Sulo, Tomas Tanskanen, Outi Kilpivaara, Esa Pitkänen, Lauri A. Aaltonen, Liisa Kauppi, Kimmo Palin
Software Mentions: 1
Published: over 8 years ago

10.1038/s41598-018-30918-4

A miR172 target-deficient AP2-like gene correlates with the double flower phenotype in roses
Cited by: 45
Author(s): Léa François, Marion Verdenaud, Xiaopeng Fu, Darcy Ruleman, Annick Dubois, Michiel Vandenbussche, Abdelhafid Bendahmane, Olivier Raymond, Jérémy Just, Mohammed Bendahmane
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41598-019-40660-0

DMSO induces drastic changes in human cellular processes and epigenetic landscape in vitro
Cited by: 171
Author(s): Marcha Verheijen, Matthias Lienhard, Yannick Schrooders, Olivia Clayton, Ramona Nudischer, Stefan Boerno, Bernd Timmermann, Nathalie Selevsek, Ralph Schlapbach, Hans Gmuender, Stefano Gotta, J. P. M. Geraedts, Ralf Herwig, Jos Kleinjans, Florian Caiment
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-019-50589-z

Distinct patterns of natural selection determine sub-population structure in the fire blight pathogen, Erwinia amylovora
Cited by: 16
Author(s): Jugpreet Singh, Awais Khan
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-019-53937-1

Highly divergent lineage of narrow-headed vole from the Late Pleistocene Europe
Cited by: 23
Author(s): Mateusz Baca, Danijela Popović, Anna Lemanik, Katarzyna Baca, Ivan Horáček, Adam Nadachowski
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-020-67370-2

Declining genetic diversity of European honeybees along the twentieth century
Cited by: 37
Author(s): Gonçalo Espregueira Themudo, Alba Rey‐Iglesia, Lucía Robles Tascón, Annette Bruun Jensen, Rute R. da Fonseca, Paula F. Campos
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41598-020-72239-5

Genome analysis of American minks reveals link of mutations in Ras-related protein-38 gene to Moyle brown coat phenotype
Cited by: 5
Author(s): Andrey D. Manakhov, Maria Yu. Mintseva, И. А. Андреев, L. I. Uralsky, Tatiana Andreeva, О. В. Трапезов, Evgeny I. Rogaev
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0074077

Are Hotspots Always Hotspots? The Relationship between Diversity, Resource and Ecosystem Functions in the Arctic
Cited by: 39
Author(s): Heike Link, Dieter Piepenburg, Philippe Archambault
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0064133

Home Life: Factors Structuring the Bacterial Diversity Found within and between Homes
Cited by: 266
Author(s): Robert R. Dunn, Noah Fierer, Jessica B. Henley, Jonathan W. Leff, Holly L. Menninger
Software Mentions: 1
Published: about 13 years ago

10.1371/journal.pone.0144204

Context-Dependent Diversity-Effects of Seaweed Consumption on Coral Reefs in Kenya
Cited by: 14
Author(s): Austin T. Humphries, Christopher D. McQuaid, Tim R. McClanahan
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0170622

Longitudinal assessment of sputum microbiome by sequencing of the 16S rRNA gene in non-cystic fibrosis bronchiectasis patients
Cited by: 92
Author(s): Michael J. Cox, Elena Turek, Catherine Hennessy, Ghazala Mirza, Phillip James, Meg Coleman, Andrew Jones, Robert Wilson, Diana Bilton, William Cookson, Miriam F. Moffatt, Michael R. Loebinger
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0082229

Predation Limits Spread of Didemnum vexillum into Natural Habitats from Refuges on Anthropogenic Structures
Cited by: 38
Author(s): Barrie M. Forrest, Lauren Fletcher, Javier Atalah, Richard F. Piola, Grant A. Hopkins
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0239051

The red flour beetle Tribolium castaneum: A model for host-microbiome interactions
Cited by: 5
Author(s): Aparna Agarwal, Deepa Agashe
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0092384

Isotopes and Trace Elements as Natal Origin Markers of Helicoverpa armigera – An Experimental Model for Biosecurity Pests
Cited by: 33
Author(s): Peter Holder, Karen Armstrong, Robert Van Hale, Marc-Alban Millet, Russell Frew, Tim J. Clough, Joel A. Baker
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0200960

Drivers of reef shark abundance and biomass in the Solomon Islands
Cited by: 17
Author(s): Jordan Goetze, Tim Langlois, Joe McCarter, Colin A. Simpfendorfer, Alec Hughes, Jacob Tingo Leve, Stacy D. Jupiter
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0101388

Eutrophication and Dreissena Invasion as Drivers of Biodiversity: A Century of Change in the Mollusc Community of Oneida Lake
Cited by: 14
Author(s): Vadim A. Karatayev, Alexander Y. Karatayev, Lyubov E. Burlakova, Lars G. Rudstam
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0237390

Retention of volunteers and factors influencing program performance of the Senior Care Volunteers Training Program in Jiangsu, China
Cited by: 4
Author(s): Hong Li Chen, Pei Chen, Yu Zhang, Ying Xing, Yuan Yuan Guan, Dao Xiang Cheng, Xian Wen Li
Software Mentions: 1
Published: almost 6 years ago

10.1016/j.dib.2019.104933

Data on environmental analysis of natural antioxidant production from walnut husk by a solar photovoltaic-driven system as a replacement for potentially carcinogenic synthetic antioxidants
Cited by: 5
Author(s): Zahra Khounani, Homa Hosseinzadeh-Bandbafha, Abdul-Sattar Nizami, Alawi Sulaiman, Sayed Amir Hossein Goli, Elham Tavassoli-Kafrani, Akram Ghaffari, Mohammad Ali Rajaeifar, Ki‐Hyun Kim, Ahmad Farhad Talebi, Mortaza Aghbashlo, Meisam Tabatabaei
Software Mentions: 1
Published: over 6 years ago

10.1016/j.stemcr.2017.02.019

Genetic Correction of SOD1 Mutant iPSCs Reveals ERK and JNK Activated AP1 as a Driver of Neurodegeneration in Amyotrophic Lateral Sclerosis
Cited by: 101
Author(s): Akshay Bhinge, Seema C. Namboori, Xiaoyu Zhang, Antonius M.J. VanDongen, Lawrence W. Stanton
Software Mentions: 1
Published: about 9 years ago

10.1128/mBio.00128-17

RNA Sequencing Identifies New RNase III Cleavage Sites in <i>Escherichia coli</i> and Reveals Increased Regulation of mRNA
Cited by: 50
Author(s): Gina C. Gordon, Jeffrey C. Cameron, Brian F. Pfleger
Software Mentions: 1
Published: about 9 years ago

10.1128/mBio.01715-19

Aggregation of Nontuberculous Mycobacteria Is Regulated by Carbon-Nitrogen Balance
Cited by: 15
Author(s): William H. DePas, Megan Bergkessel, Dianne K. Newman
Software Mentions: 1
Published: almost 7 years ago

10.1128/mSphere.00486-18

Discovery of <i>mcr-1</i> -Mediated Colistin Resistance in a Highly Virulent Escherichia coli Lineage
Cited by: 42
Author(s): Brian M. Forde, Hosam M. Zowawi, Patrick N A Harris, Leah W. Roberts, Emad Ibrahim, Nissar Shaikh, Anand Deshmukh, Mazen A. Sid Ahmed, Muna Al Maslamani, Kyra Cottrell, Ella Trembizki, Lana Sundac, Heidi H. Yu, Jian Li, Mark A. Schembri, David M. Whiley, David L. Paterson, Scott A. Beatson
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0195167

First quantification of subtidal community structure at Tristan da Cunha Islands in the remote South Atlantic: from kelp forests to the deep sea
Cited by: 13
Author(s): Jennifer E. Caselle, Scott L. Hamilton, Kathryn Davis, Chris Thompson, Alan Turchik, Ryan S. Jenkinson, Doug Simpson, Enric Sala
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0098975

Multiple Ant Species Tending Lac Insect Kerria yunnanensis (Hemiptera: Kerriidae) Provide Asymmetric Protection against Parasitoids
Cited by: 2
Author(s): Youqing Chen, Lu Zhixing, Lingling Qiao, Benjamin D. Hoffmann, Wei Zhang
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0028054

Do Cues Matter? Highly Inductive Settlement Cues Don't Ensure High Post-Settlement Survival in Sea Urchin Aquaculture
Cited by: 52
Author(s): Benjamin Mos, Kenneth Lawrence Cowden, Shaun Nielsen, Symon A. Dworjanyn
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0237335

Combining physicochemical properties and microbiome data to evaluate the water quality of South African drinking water production plants
Cited by: 10
Author(s): Tawanda Elias Maguvu, Cornelius Carlos Bezuidenhout, Rinaldo K Kritzinger, Karabo Tsholo, Moitshepi Plaatjie, Lesego Molale-Tom, Charlotte Mienie, Roelof Dirk Coertze
Software Mentions: 1
Published: almost 6 years ago

10.3390/jof7010054

Paracoccidioides brasiliensis Isolated from Nine-Banded Armadillos (Dasypus novemcinctus) Reveal Population Structure and Admixture in the Amazon Basin
Cited by: 3
Author(s): Eduardo Bagagli, Daniel R. Matute, Hans Garcia Garces, Bernardo Guerra Tenório, Adalberto Garcia Garces, Lucas Gomes de Brito Alves, Danielle Hamae Yamauchi, Marluce Francisca Hrycyk, Bridget M. Barker, Marcus de Melo Teixeira
Software Mentions: 1
Published: over 5 years ago

10.1093/jhered/esab003

A Reference Genome Assembly of American Bison,<i>Bison bison bison</i>
Cited by: 13
Author(s): Jonas Oppenheimer, Benjamin D. Rosen, Michael P. Heaton, B. L. Vander Ley, Wade R Shafer, Fred T Schuetze, Brad Stroud, L. A. Kuehn, Jennifer C. McClure, Jennifer P. Barfield, Harvey D. Blackburn, Theodore S. Kalbfleisch, Derek M. Bickhart, Kimberly M Davenport, Kristen L. Kuhn, Edward Green, Beth Shapiro, Timothy P. L. Smith
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0091841

Large-Scale Assessment of Mediterranean Marine Protected Areas Effects on Fish Assemblages
Cited by: 139
Author(s): Paolo Guidetti, Pasquale Baiata, Enric Ballesteros, Antonio Franco, Bernat Hereu, Enrique Macpherson, Fiorenza Micheli, António Pais, Pieraugusto Panzalis, Andrew A. Rosenberg, Michel Zabala, Enric Sala
Software Mentions: 1
Published: about 12 years ago

10.7554/eLife.43606

Long-term balancing selection drives evolution of immunity genes in Capsella
Cited by: 60
Author(s): Daniel Koenig, Jörg Hagmann, Rachel Li, Felix Bemm, Tanja Slotte, Barbara Neuffer, Stephen I. Wright, Detlef Weigel
Software Mentions: 1
Published: over 7 years ago

10.7554/eLife.59683

A simple and effective F0 knockout method for rapid screening of behaviour and other complex phenotypes
Cited by: 109
Author(s): François Kroll, Gareth T. Powell, Marcus Ghosh, Gaia Gestri, Paride Antinucci, Timothy J. Hearn, Hande Tunbak, Sumi Lim, Harvey W Dennis, Joseph Fernandez, David Whitmore, Elena Dreosti, Stephen W. Wilson, Ellen J. Hoffman, Jason Rihel
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0096358

An Invasive Vector of Zoonotic Disease Sustained by Anthropogenic Resources: The Raccoon Dog in Northern Europe
Cited by: 38
Author(s): Karmen Süld, Harri Valdmann, Leidi Laurimaa, Egle Soe, John Davison, Urmas Saarma
Software Mentions: 1
Published: about 12 years ago

10.1371/journal.pone.0191232

Evaluation of bloodstream infections, Clostridium difficile infections, and gut microbiota in pediatric oncology patients
Cited by: 23
Author(s): Bryan T. Nycz, Samuel R. Dominguez, Deborah Friedman, Joanne M. Hilden, Diana Ir, Charles E. Robertson, Daniel N. Frank
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0080510

Feeding Preferences of Abyssal Macrofauna Inferred from In Situ Pulse Chase Experiments
Cited by: 24
Author(s): Rachel M. Jeffreys, Ciara Burke, Alan J. Jamieson, Bhavani Narayanaswamy, Henry A. Ruhl, Kenneth L. Smith, Ursula Witte
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0203748

Impact of violacein from Chromobacterium violaceum on the mammalian gut microbiome
Cited by: 14
Author(s): Heidi Pauer, Cristiane Cassiolato Pires Hardoim, Felipe Lopes Teixeira, Karla Rodrigues Miranda, Davi da Silva Barbirato, Denise P. Carvalho, L. Caetano M. Antunes, Álvaro C. Leitão, Leandro Araújo Lobo, Regina Maria Cavalcanti Pilotto Domingues
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0113068

Fast Growing, Healthy and Resident Green Turtles (Chelonia mydas) at Two Neritic Sites in the Central and Northern Coast of Peru: Implications for Conservation
Cited by: 26
Author(s): Ximena Vélez‐Zuazo, Javier Quiñónes, Aldo S. Pacheco, Luciana Klinge, Evelyn Paredes, Sixto Quispe, Shaleyla Kelez
Software Mentions: 1
Published: over 11 years ago

10.7554/eLife.51481

Evolutionary stability of collateral sensitivity to antibiotics in the model pathogen Pseudomonas aeruginosa
Cited by: 48
Author(s): Camilo Barbosa, Roderich Römhild, Philip Rosenstiel, Hinrich Schulenburg
Software Mentions: 1
Published: over 6 years ago

10.18632/oncotarget.10827

Single-strand DNA library preparation improves sequencing of formalin-fixed and paraffin-embedded (FFPE) cancer DNA
Cited by: 25
Author(s): Mathias Stiller, Antje Sucker, Klaus G. Griewank, Daniela E. Aust, Gustavo Baretton, Dirk Schadendorf, Susanne Horn
Software Mentions: 1
Published: almost 10 years ago

10.1371/journal.pone.0139444

Using Fish Population Metrics to Compare the Effects of Artificial Reef Density
Cited by: 16
Author(s): Catheline Y.M. Froehlich, Richard J. Kline
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0081910

Determining the Metabolic Footprints of Hydrocarbon Degradation Using Multivariate Analysis
Cited by: 16
Author(s): Renee J. Smith, Thomas C. Jeffries, Eric M. Adetutu, Peter G. Fairweather, James G. Mitchell
Software Mentions: 1
Published: over 12 years ago

10.18632/oncotarget.24567

Analysis of the 9p21.3 sequence associated with coronary artery disease reveals a tendency for duplication in a CAD patient
Cited by: 5
Author(s): Natalay Kouprina, Mikhail Liskovykh, Nathan Lee, Vladimir N. Noskov, Joshua J. Waterfall, Robert L. Walker, Paul S. Meltzer, Eric J. Topol, Vladimir Larionov
Software Mentions: 1
Published: over 8 years ago

10.18632/oncotarget.27954

Transcriptome analyses of urine RNA reveal tumor markers for human bladder cancer: validated amplicons for RT-qPCR-based detection
Cited by: 6
Author(s): Josephine Dubois, Jacqueline Rueger, Bernhard Haubold, Rosel Kretschmer‐Kazemi Far, Georg Sczakiel
Software Mentions: 1
Published: about 5 years ago

10.1186/1750-1172-9-12

The supposed tumor suppressor gene WWOX is mutated in an early lethal microcephaly syndrome with epilepsy, growth retardation and retinal degeneration
Cited by: 68
Author(s): Ghada M.H. Abdel-Salam, Michaela Thoenes, Hanan H. Afifi, Friederike Körber, Daniel Swan, Hanno J. Bolz
Software Mentions: 1
Published: over 12 years ago

10.1186/s13023-020-01361-4

Mutations in COL1A1/A2 and CREB3L1 are associated with oligodontia in osteogenesis imperfecta
Cited by: 9
Author(s): Kristofer Andersson, B. Malmgren, Eva Albrecht, Ann Nordgren, Fulya Taylan, Göran Dahllöf
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0218274

Exploring the impact of Helicobacter pylori on gut microbiome composition
Cited by: 66
Author(s): Nihar Ranjan Dash, Ghalia Khoder, Aml Mohamed Nada, Mohammad Tahseen Al Bataineh
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0038552

Bacterial and Phytoplankton Responses to Nutrient Amendments in a Boreal Lake Differ According to Season and to Taxonomic Resolution
Cited by: 24
Author(s): Sari Peura, Alexander Eiler, Minna Hiltunen, Hannu Nykänen, Marja Tiirola, Roger Jones
Software Mentions: 1
Published: about 14 years ago

10.3389/fcimb.2012.00133

Comparative Genomics and stx Phage Characterization of LEE-Negative Shiga Toxin-Producing Escherichia coli
Cited by: 81
Author(s): Susan R. Steyert, Jason W. Sahl, Claire M. Fraser, Louise D. Teel, Flemming Scheutz, David A. Rasko
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0094647

Mechanisms Influencing the Spread of a Native Marine Alga
Cited by: 11
Author(s): Dilys Zhang, Tim M. Glasby, Peter J. Ralph, Paul E. Gribben
Software Mentions: 1
Published: about 12 years ago

10.1186/1471-2164-13-S5-S3

A UML profile for the OBO relation ontology
Cited by: 10
Author(s): Gabriela D. A. Guardia, Ricardo Z. N. Vêncio, Cléver Ricardo Guareis de Farias
Software Mentions: 1
Published: over 13 years ago

10.1371/journal.pone.0155055

Bacterial Diversity and Community Structure in Korean Ginseng Field Soil Are Shifted by Cultivation Time
Cited by: 25
Author(s): Ngọc-Lan Nguyen, Yeon-Ju Kim, Van-An Hoang, Sathiyamoorthy Subramaniyam, Jong-Pyo Kang, Chang Ho Kang, Deok‐Chun Yang
Software Mentions: 1
Published: about 10 years ago

10.1371/journal.pone.0100788

Evidence of Season-Dependency in Vegetation Effects on Macrofauna in Temperate Seagrass Meadows (Baltic Sea)
Cited by: 33
Author(s): Maria Włodarska‐Kowalczuk, Emilia Jankowska, Lech Kotwicki, Piotr Bałazy
Software Mentions: 1
Published: almost 12 years ago

10.1371/journal.pone.0238591

Cancer cell line-specific protein profiles in extracellular vesicles identified by proteomics
Cited by: 20
Author(s): Eduarda Guerreiro, Reidun Øvstebø, Bernd Thiede, Daniela Elena Costea, Tine M. Søland, Hilde Kanli Galtung
Software Mentions: 1
Published: almost 6 years ago

10.1186/1748-7188-6-23

ReCoil - an algorithm for compression of extremely large datasets of dna data
Cited by: 35
Author(s): Vladimir Yanovsky
Software Mentions: 1
Published: over 14 years ago

10.1186/s12859-018-2162-x

Live neighbor-joining
Cited by: 10
Author(s): Guilherme P. Telles, Graziela S. Araújo, Maria Emília M. T. Walter, Marcelo M. Brigido, Nalvo F. Almeida
Software Mentions: 1
Published: about 8 years ago

10.1186/s12859-017-1588-x

LW-FQZip 2: a parallelized reference-based compression of FASTQ files
Cited by: 21
Author(s): Zhi Huang, Zhenkun Wen, Qingjin Deng, Yingli Chu, Yiwen Sun, Zexuan Zhu
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0027936

Positive Edge Effects on Forest-Interior Cryptogams in Clear-Cuts
Cited by: 22
Author(s): Alexandro Caruso, Jörgen Rudolphi, Håkan Rydin
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0058998

Small-Scale Habitat Structure Modulates the Effects of No-Take Marine Reserves for Coral Reef Macroinvertebrates
Cited by: 23
Author(s): Pascal Dumas, H. Jimenez, Christophe Peignon, Laurent Wantiez, Mehdi Adjeroud
Software Mentions: 1
Published: over 13 years ago

10.1186/s13104-016-1900-2

AdapterRemoval v2: rapid adapter trimming, identification, and read merging
Cited by: 1,078
Author(s): Mikkel Schubert, Stinus Lindgreen, Ludovic Orlando
Software Mentions: 1
Published: over 10 years ago

10.7717/peerj.2584

VSEARCH: a versatile open source tool for metagenomics
Cited by: 5,816
Author(s): Torbjørn Rognes, Tomáš Flouri, Ben Nichols, Christopher Quince, Frédéric Mahé
Software Mentions: 1
Published: over 9 years ago

10.7717/peerj-cs.404

Accelerated implementation for testing IID assumption of NIST SP 800-90B using GPU
Cited by: 1
Author(s): Kim Yewon, Yongjin Yeom
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0173038

IOPA: I/O-aware parallelism adaption for parallel programs
Cited by: 0
Author(s): Tao Liu, Yi Liu, Qian Chen, Depei Qian
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0204883

Why twenty amino acid residue types suffice(d) to support all living systems
Cited by: 6
Author(s): Robert P. Bywater
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0225871

Comparative effectiveness of probiotic-based formulations on cecal microbiota modulation in broilers
Cited by: 12
Author(s): Denise Russi Rodrigues, W.N. Briggs, Audrey F. Duff, K.M. Chasser, G. R. Murugesan, Chasity Pender, Shelby Ramirez, Luis Valenzuela, Lisa R. Bielke
Software Mentions: 1
Published: about 6 years ago