10.1186/s12864-020-06871-w

Genome compartmentalization predates species divergence in the plant pathogen genus Zymoseptoria
Cited by: 29
Author(s): Alice Feurtey, Cécile Lorrain, Daniel Croll, Christoph Eschenbrenner, Michael Freitag, Michael Habig, Janine Haueisen, Mareike Möller, Klaas Schotanus, Eva H. Stukenbrock
Software Mentions: 4
Published: about 6 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
Cited by: 33
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

10.1371/journal.pone.0255822

Evaluation of the severity of nonalcoholic fatty liver disease through analysis of serum exosomal miRNA expression
Cited by: 5
Author(s): Jeong‐An Gim, Soo Min Bang, Young‐Sun Lee, Sun Young Yim, Young Kul Jung, Hayeon Kim, Baek-hui Kim, Ji Hoon Kim, Yeon Seok Seo, Hyung Joon Yim, Jong Eun Yeon, Soon Ho Um, Kwan Soo Byun
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0146916

Parallel Mapping of Antibiotic Resistance Alleles in Escherichia coli
Cited by: 15
Author(s): Sophie Weiss, Thomas J. Mansell, Pooneh Mortazavi, Rob Knight, Ryan T. Gill
Software Mentions: 4
Published: over 10 years ago

10.1186/s12870-021-03057-8

Comparative analysis of de novo genomes reveals dynamic intra-species divergence of NLRs in pepper
Cited by: 4
Author(s): Myung-Shin Kim, Geun Young Chae, Soohyun Oh, Jihyun Kim, Hyunggon Mang, Seungill Kim, Doil Choi
Software Mentions: 4
Published: over 5 years ago

10.3390/ijerph16203966

Spatial-Temporal Variation of Bacterial Communities in Sediments in Lake Chaohu, a Large, Shallow Eutrophic Lake in China
Cited by: 16
Author(s): Lei Zhang, Yu Cheng, Guang Gao, Jiahu Jiang
Software Mentions: 4
Published: almost 7 years ago

10.1186/s12870-019-1708-z

The wild sweetpotato (Ipomoea trifida) genome provides insights into storage root development
Cited by: 30
Author(s): Ming Li, Songtao Yang, Wei Xü, Zhien Pu, Jiayi Feng, Zhangying Wang, Cong Zhang, Peng Ma, Chunguang Du, Feng Lin, Changhe Wei, Shuai Qiao, Hongda Zou, Lei Zhang, Yán Li, Huan Yang, Anzhong Liao, Wei Song, Zhongren Zhang, Ji Li, Kai Wang, Yizheng Zhang, Hao Lin, Jinbo Zhang, Wen-Fang Tan
Software Mentions: 4
Published: over 7 years ago

10.1128/mSystems.00024-17

Transcriptional Variation of Diverse Enteropathogenic <i>Escherichia coli</i> Isolates under Virulence-Inducing Conditions
Cited by: 11
Author(s): Tracy H. Hazen, Sean C. Daugherty, Amol C. Shetty, James P. Nataro, David A. Rasko
Software Mentions: 4
Published: about 9 years ago

10.1128/mSystems.00692-19

The Gut Microbiota in Camellia Weevils Are Influenced by Plant Secondary Metabolites and Contribute to Saponin Degradation
Cited by: 39
Author(s): Shouke Zhang, Jinping Shu, Huai‐Jun Xue, Wei Zhang, Yabo Zhang, Yaning Liu, Linxin Fang, Yangdong Wang, Haojie Wang
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0213535

Possible cross-feeding pathway of facultative methylotroph Methyloceanibacter caenitepidi Gela4 on methanotroph Methylocaldum marinum S8
Cited by: 22
Author(s): Mio Takeuchi, Haruka Ozaki, Satoshi Hiraoka, Yoichi Kamagata, Susumu Sakata, Hideyoshi Yoshioka, Wataru Iwasaki
Software Mentions: 4
Published: over 7 years ago

10.1186/s40246-018-0170-6

Forward and reverse mutations in stages of cancer development
Cited by: 11
Author(s): Taobo Hu, Yogesh Kumar, Shazia Iram, Si Duan, Yang Li, Lei Chen, Jinfei Chen, Rong Yin, Ava Kwong, Gilberto Ka Kit Leung, Wai Kin Mat, Zhenggang Wu, Xi Long, Colin Chan, Si Chen, Peggy Lee, Siu Kin Ng, Timothy Y. C. Ho, Jianfeng Yang, Xueliang Ding, Suk Ying Tsang, Xinrui Zhou, Danhua Zhang, Enbo Zhou, Lin Xu, Wai-sang Poon, Hongyang Wang, Hong Xue
Software Mentions: 4
Published: about 8 years ago

10.1093/infdis/jiz318

High-Throughput Sequencing-Based Investigation of Viruses in Human Cancers by Multienrichment Approach
Cited by: 13
Author(s): Sarah Mollerup, Maria E. Asplund, Jens Friis-Nielsen, Kristín Rós Kjartansdóttir, Helena Fridholm, Thomas Arn Hansen, José Alejandro Romero Herrera, Christopher J. Barnes, Randi Holm Jensen, Stine Raith Richter, Ida Broman Nielsen, Carlotta Pietroni, David E. Alquezar‐Planas, Alba Rey‐Iglesia, Pernille V. S. Olsen, Ewa Rajpert De Meyts, Line Groth‐Pedersen, Christian von Buchwald, David Hebbelstrup Jensen, Robert Gniadecki, Estrid Høgdall, Jill Levin Langhoff, Imre Pete, Ildikó Vereczkey, Zsolt Baranyai, Karen Dybkær, Hans Erik Johnsen, Torben Steiniche, Peter Hokland, Jacob Rosenberg, Ulrik Baandrup, Thomas Sicheritz-Pontén, Eske Willerslev, Søren Brunak, Ole Lund, Tobias Mourier, Lasse Vinner, Jose M. G. Izarzugaza, Lars Peter Nielsen, Anders J. Hansen
Software Mentions: 4
Published: over 7 years ago

10.1128/mBio.01650-17

<i>De Novo</i> Assembly and Phasing of Dikaryotic Genomes from Two Isolates of <i>Puccinia coronata</i> f. sp. <i>avenae</i> , the Causal Agent of Oat Crown Rust
Cited by: 45
Author(s): Marisa E. Miller, Ying Zhang, Vahid Omidvar, Jana Sperschneider, Benjamin Schwessinger, Castle Raley, Jonathan M. Palmer, Diana Garnica, Narayana M. Upadhyaya, John P. Rathjen, Jennifer Taylor, Robert Park, Peter N. Dodds, Cory D. Hirsch, Shahryar F. Kianian, Melania Figueroa
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pone.0165059

Drug Repositioning through Systematic Mining of Gene Coexpression Networks in Cancer
Cited by: 19
Author(s): Alexander E. Ivliev, Peter A.C. ’t Hoen, Dmitrii Borisevich, Yuri Nikolsky, Marina G. Sergeeva
Software Mentions: 4
Published: almost 10 years ago

10.1371/journal.pone.0067511

Evolutionary Dynamics of the Accessory Genome of Listeria monocytogenes
Cited by: 55
Author(s): Henk C. den Bakker, Christopher A. Desjardins, Allison Griggs, Joseph E. Peters, Qiandong Zeng, Sarah Young, Chinnappa D. Kodira, Chandri Yandava, Theresa A. Hepburn, Brian J. Haas, Bruce W. Birren, Martin Wiedmann
Software Mentions: 4
Published: over 13 years ago

10.1038/s41598-020-76347-0

Integrative genomic meta-analysis reveals novel molecular insights into cystic fibrosis and ΔF508-CFTR rescue
Cited by: 7
Author(s): Rachel Hodos, Matthew D. Strub, Shyam Ramachandran, Li Li, Paul B. McCray, Joel T. Dudley
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0089445

RNA CoMPASS: A Dual Approach for Pathogen and Host Transcriptome Analysis of RNA-Seq Datasets
Cited by: 38
Author(s): Guiyin Xu, Michael J. Strong, Michelle Lacey, Carl Baribault, Erik K. Flemington, Christopher M. Taylor
Software Mentions: 4
Published: over 12 years ago

10.1038/s41598-020-57546-1

Genomic Survey of Salt Acclimation-Related Genes in the Halophilic Cyanobacterium Euhalothece sp. Z-M001
Cited by: 14
Author(s): Hee Wook Yang, Ji-Young Song, Sung Mi Cho, Hak Cheol Kwon, Cheol‐Ho Pan, Youn‐Il Park
Software Mentions: 4
Published: over 6 years ago

10.1186/s12859-015-0818-3

misFinder: identify mis-assemblies in an unbiased manner using reference and paired-end reads
Cited by: 11
Author(s): Xiao Zhu, Ho-fung Leung, Rongjie Wang, Francis Y. L. Chin, Siu Ming Yiu, Guangri Quan, Yajie Li, Rui Zhang, Qinghua Jiang, Bo Liu, Yucui Dong, Guohui Zhou, Yadong Wang
Software Mentions: 4
Published: almost 11 years ago

10.1038/s41598-020-61633-8

MicroRNA hsa-mir-3923 serves as a diagnostic and prognostic biomarker for gastric carcinoma
Cited by: 11
Author(s): Xiaohui Yang, Ze Zhang, Lichao Zhang, Li Zhou
Software Mentions: 4
Published: over 6 years ago

10.1093/bioinformatics/btt294

SVGenes: a library for rendering genomic features in scalable vector graphic format
Cited by: 2
Author(s): Graham J. Etherington, Dan MacLean
Software Mentions: 4
Published: over 13 years ago

10.7554/eLife.46149

Identification of potential biomarkers of vaccine inflammation in mice
Cited by: 23
Author(s): Paul F. McKay, Deniz Cizmeci, Yoann Aldon, Jeroen Maertzdorf, January Weiner, Stefan H. E. Kaufmann, David Lewis, Robert A. van den Berg, Giuseppe Del Giudice, Robin J. Shattock
Software Mentions: 4
Published: over 7 years ago

10.1186/s12870-020-02744-2

Application of genome-wide insertion/deletion markers on genetic structure analysis and identity signature of Malus accessions
Cited by: 6
Author(s): Xuan Wang, Fei Shen, Yuan Gao, Kun Wang, Ruiting Chen, Jun Luo, Lili Yang, Xi Zhang, Changwei Qiu, Wei Li, Ting Wu, Xuefeng Xu, Yi Wang, Cong Peng, Zhenhai Han, Xinzhong Zhang
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12864-018-4708-8

Small RNA-based prediction of hybrid performance in maize
Cited by: 20
Author(s): Felix Seifert, Alexander Thiemann, Tobias A. Schrag, Dominika Rybka, Albrecht E. Melchinger, Matthias Frisch, Stefan Scholten
Software Mentions: 4
Published: over 8 years ago

10.1186/s12870-016-0933-y

Identification by the DArTseq method of the genetic origin of the Coffea canephora cultivated in Vietnam and Mexico
Cited by: 39
Author(s): Andréa Garavito, Christophe Montagnon, Romain Guyot, Benoît Bertrand
Software Mentions: 4
Published: almost 10 years ago

10.3390/ijms22010347

Global Genome Conformational Programming during Neuronal Development Is Associated with CTCF and Nuclear FGFR1—The Genome Archipelago Model
Cited by: 8
Author(s): Brandon Decker, Michał Liput, Hussam Abdellatif, Donald Yergeau, Yongho Bae, Josep Miquel Jornet, Ewa K. Stachowiak, Michal K. Stachowiak
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pone.0199902

Annotation, classification, genomic organization and expression of the Vitis vinifera CYPome
Cited by: 8
Author(s): Tina Ilc, Gautier Arista, Raquel Tavares, Nicolas Navrot, Éric Duchêne, Amandine Velt, Frédéric Choulet, Etienne Paux, Marc Fischer, David R. Nelson, Philippe Hugueney, Danièle Werck‐Reichhart, Camille Rustenholz
Software Mentions: 4
Published: over 8 years ago

10.7554/eLife.20983

A molecular portrait of maternal sepsis from Byzantine Troy
Cited by: 32
Author(s): Alison Devault, Tatum D Mortimer, Andrew Kitchen, Henrike Kiesewetter, Jacob Enk, G. Brian Golding, John Southon, Melanie Kuch, Ana T. Duggan, William Aylward, Shea N. Gardner, Jonathan Allen, Andrew King, Gerard D. Wright, Makoto Kuroda, Kengo Kato, Derek E. G. Briggs, Gino Fornaciari, Edward C. Holmes, Hendrik N. Poinar, Caitlin S. Pepperell
Software Mentions: 4
Published: almost 10 years ago

10.1371/journal.pone.0041374

Comprehensive Identification and Annotation of Cell Type-Specific and Ubiquitous CTCF-Binding Sites in the Human Genome
Cited by: 121
Author(s): Hebing Chen, Yao Tian, Wenjie Shu, Xiaochen Bo, Shengqi Wang
Software Mentions: 4
Published: about 14 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: over 7 years ago

10.1038/s41438-021-00471-9

The genome of Magnolia biondii Pamp. provides insights into the evolution of Magnoliales and biosynthesis of terpenoids
Cited by: 27
Author(s): Shanshan Dong, Min Liu, Yang Liu, Fei Chen, Ting Yang, Lu Chen, Xingtan Zhang, Xing Guo, Dongming Fang, Linzhou Li, Tian Deng, Zhen Yao, Xiaoan Lang, Yiqing Gong, Ernest Wu, Yaling Wang, Yamei Shen, Xun Gong, Huan Liu, Shouzhou Zhang
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pntd.0007680

Comparative and functional genomics of the protozoan parasite Babesia divergens highlighting the invasion and egress processes
Cited by: 24
Author(s): Luís Miguel González, Karel Estrada, Ricardo Grande, Verónica Jiménez-Jacinto, Leticia Vega‐Alvarado, Elena Sevilla, Jorge de la Barrera, Isabel Cuesta, Ángel Zaballos, José M. Bautista, Cheryl A. Lobo, Alejandro Sánchez-Flores, Estrella Montero
Software Mentions: 4
Published: about 7 years ago

10.1093/gigascience/gix015

Enhancing knowledge discovery from cancer genomics data with Galaxy
Cited by: 7
Author(s): Marco A. Albuquerque, Bruno M. Grande, Elie Ritch, Prasath Pararajalingam, Selin Jessa, Martin Krzywinski, Jasleen K. Grewal, Sohrab P. Shah, Paul C. Boutros, Ryan D. Morin
Software Mentions: 4
Published: over 9 years ago

10.1093/gigascience/giz012

Haplotype-phased genome and evolution of phytonutrient pathways of tetraploid blueberry
Cited by: 138
Author(s): Marivi Colle, Courtney P. Leisner, Ching Man Wai, Shujun Ou, Kevin A. Bird, Jie Wang, Jennifer H. Wisecaver, Alan E. Yocca, Elizabeth I. Alger, Haibao Tang, Zhiyong Xiong, Pete Callow, Gil Ben-Zvi, Avital Brodt, Kobi Baruch, Thomas Swale, Lily Shiue, Guo Qing Song, Kevin L. Childs, Anthony L. Schilmiller, Nicholi Vorsa, C. Robin Buell, Robert VanBuren, Ning Jiang, Patrick P. Edger
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-018-35086-z

RETRACTED ARTICLE: Non-coding RNAome of RPE cells under oxidative stress suggests unknown regulative aspects of Retinitis pigmentosa etiopathogenesis
Cited by: 16
Author(s): Luigi Donato, Concetta Scimone, Carmela Rinaldi, Rosalia D’Angelo, Antonina Sidoti
Software Mentions: 4
Published: almost 8 years ago

10.1371/journal.pntd.0008237

Comprehensive analysis of the secreted proteome of adult Necator americanus hookworms
Cited by: 20
Author(s): Jayden Logan, Mark S. Pearson, Srikanth S. Manda, Young Jun Choi, Matthew A. Field, Ramon M. Eichenberger, Jason Mulvenna, Shivashankar H. Nagaraj, Ricardo Toshio Fujiwara, Pedro Henrique Gazzinelli-Guimarães, Lilian Lacerda Bueno, Vitor Luís Tenório Mati, Jeffrey M. Bethony, Makedonka Mitreva, Javier Sotillo, Alex Loukas
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pgen.1005954

Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding
Cited by: 102
Author(s): Shubha Vij, Heiner Kuhl, Irina M. Kuznetsova, Aleksey Komissarov, Andrey A. Yurchenko, Peter van Heusden, Siddharth Singh, Natascha May Thevasagayam, Sai Rama Sridatta Prakki, K. Purushothaman, Jolly M. Saju, Junhui Jiang, Stanley Kimbung Mbandi, Mario Jonas, Amy Tong, Sarah Mwangi, Doreen Lau, Si Yan Ngoh, Woei Chang Liew, Xueyan Shen, Lawrence S. Hon, James Drake, Matthew Boitano, Richard J. Hall, Chen-Shan Chin, Ramkumar Lachumanan, Jonas Korlach, Vladimir A. Trifonov, Мarsel R. Kabilov, Alexey E. Tupikin, Darrell Green, Simon Moxon, Tyler Garvin, Fritz J. Sedlazeck, Gregory W. Vurture, G. Gopikrishna, Vinaya Kumar Katneni, Tansyn H. Noble, Vinod Scaria, Sridhar Sivasubbu, Dean R. Jerry, Stephen J. O’Brien, Michael C. Schatz, Tamás Dalmay, Stephen W. Turner, Si Lok, Alan Christoffels, László Orbán
Software Mentions: 4
Published: over 10 years ago

10.1186/s13073-021-00889-9

Single-cell sequencing of the small and AT-skewed genome of malaria parasites
Cited by: 4
Author(s): Shiwei Liu, Adam C Huckaby, Audrey C. Brown, Christopher C. Moore, Ian Burbulis, Michael J. McConnell, Jennifer L. Guler
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-020-07141-5

Genomic differences between the new Fusarium oxysporum f. sp. apii (Foa) race 4 on celery, the less virulent Foa races 2 and 3, and the avirulent on celery f. sp. coriandrii
Cited by: 9
Author(s): Peter M. Henry, Sukhwinder Kaur, Quyen Anh Tran Pham, Radwan Barakat, Samuel Brinker, Hannah Haensel, Oleg Daugovish, Lynn Epstein
Software Mentions: 4
Published: almost 6 years ago

10.1371/journal.pgen.1008452

Transcriptional and genomic parallels between the monoxenous parasite Herpetomonas muscarum and Leishmania
Cited by: 12
Author(s): Megan A. Sloan, Karen Brooks, Thomas D. Otto, Mandy Sanders, James A. Cotton, Petros Ligoxygakis
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pntd.0009719

Maxicircle architecture and evolutionary insights into Trypanosoma cruzi complex
Cited by: 6
Author(s): Luisa Berná, Gonzalo Greif, Sebastián Pita, Paula Faral-Tello, Florencia Díaz-Viraqué, Rita de Cássia Moreira de Souza, Gustavo Adolfo Vallejo, Fernando Álvarez-Valín, Carlos Robello
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pgen.1000832

U87MG Decoded: The Genomic Sequence of a Cytogenetically Aberrant Human Cancer Cell Line
Cited by: 238
Author(s): Michael J. Clark, Nils Homer, Brian D. O’Connor, Zugen Chen, Ascia Eskin, Hane Lee, Barry Merriman, Stanley F. Nelson
Software Mentions: 4
Published: over 16 years ago

10.1186/s12864-020-06820-7

Mining ancient microbiomes using selective enrichment of damaged DNA molecules
Cited by: 6
Author(s): Clemens L. Weiß, Marie-Theres Gansauge, Ayinuer Aximu‐Petri, Matthias Meyer, Hernán A. Burbano
Software Mentions: 4
Published: over 6 years ago

10.1093/gbe/evy188

Genome Wide Identification of Mutational Hotspots in the Apicomplexan Parasite Neospora caninum and the Implications for Virulence
Cited by: 17
Author(s): Larissa Calarco, Joel Barratt, John Ellis
Software Mentions: 4
Published: about 8 years ago

10.1038/s41598-019-49915-2

RNAseq analysis reveals drought-responsive molecular pathways with candidate genes and putative molecular markers in root tissue of wheat
Cited by: 52
Author(s): Mir Asif Iquebal, Pradeep Sharma, Rahul Singh Jasrotia, Sarika Jaiswal, Amandeep Kaur, Monika Saroha, U. B. Angadi, Sonia Sheoran, Rajender Singh, Gyanendra Singh, Anil Rai, Ruchi Tiwari, Dinesh Kumar
Software Mentions: 4
Published: about 7 years ago

10.1186/s12864-016-2502-z

Comparative genomic analyses reveal broad diversity in botulinum-toxin-producing Clostridia
Cited by: 71
Author(s): Charles H. D. Williamson, Jason W. Sahl, Theresa J. Smith, Gary Xie, Brian Foley, Leonard A. Smith, Rafael Fernández, Miia Lindström, Hannu Korkeala, Paul Keim, Jeffrey T. Foster, Karen K. Hill
Software Mentions: 4
Published: over 10 years ago

10.1186/s13059-018-1392-6

Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions
Cited by: 99
Author(s): Paul Bailey, Christian Schudoma, William J. Jackson, Erin Baggs, Gulay Dagdas, Wilfried Haerty, Matthew J. Moscou, Ksenia V. Krasileva
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pcbi.1008390

Ten simple rules for writing a paper about scientific software
Cited by: 1
Author(s): Joseph D. Romano, Jason H. Moore
Software Mentions: 4
Published: almost 6 years ago

10.3390/plants10061154

Genome-Wide Identification and Genetic Variations of the Starch Synthase Gene Family in Rice
Cited by: 9
Author(s): Hongjia Zhang, Seong-Ho Jang, San Mar Lar, Ah-Rim Lee, Fangyuan Cao, Jeonghwan Seo, Soon-Wook Kwon
Software Mentions: 4
Published: over 5 years ago

10.1186/s12864-015-1954-x

Genome-wide analysis reveals the extent of EAV-HP integration in domestic chicken
Cited by: 8
Author(s): David Wragg, Andrew S. Mason, Lejun Yu, Richard Kuo, Raman Akinyanju Lawal, Takele Taye Desta, Joram M. Mwacharo, Chang-Yeon Cho, Stephen J. Kemp, David W. Burt, Olivier Hanotte
Software Mentions: 4
Published: about 11 years ago

10.1186/s13059-020-02138-5

Ultrasensitive deletion detection links mitochondrial DNA replication, disease, and aging
Cited by: 40
Author(s): Scott A. Lujan, Matthew J. Longley, Margaret H. Humble, Christopher A. Lavender, Adam Burkholder, Emma L. Blakely, Charlotte L. Alston, Gráinne Gorman, D.M. Turnbull, Robert McFarland, Robert W. Taylor, Thomas A. Kunkel, William C. Copeland
Software Mentions: 4
Published: about 6 years ago

10.1186/s12864-015-1825-5

Whole transcriptomic analysis of the plant-beneficial rhizobacterium Bacillus amyloliquefaciens SQR9 during enhanced biofilm formation regulated by maize root exudates
Cited by: 124
Author(s): Nan Zhang, Dongqing Yang, Dandan Wang, Youzhi Miao, Jiahui Shao, Xuan Zhou, Zhihui Xu, Qing Li, Haichao Feng, Shuqing Liu, Qirong Shen, Ruifu Zhang
Software Mentions: 4
Published: about 11 years ago

10.1186/s12864-015-1233-x

Sequence and analysis of a whole genome from Kuwaiti population subgroup of Persian ancestry
Cited by: 27
Author(s): Gaurav Thareja, Sumi Elsa John, Prashantha Hebbar, Kazem Behbehani, Thangavel Alphonse Thanaraj, Osama Alsmadi
Software Mentions: 4
Published: over 11 years ago

10.3390/genes9080379

Genomic and Biotechnological Characterization of the Heavy-Metal Resistant, Arsenic-Oxidizing Bacterium Ensifer sp. M14
Cited by: 22
Author(s): George C. diCenzo, Klaudia Dębiec, Jan Krzysztoforski, Witold Uhrynowski, Alessio Mengoni, Camilla Fagorzi, Adrian Górecki, Łukasz Dziewit, Tomasz Bajda, Grzegorz Rzepa, Łukasz Drewniak
Software Mentions: 4
Published: about 8 years ago

10.1534/g3.120.401550

Solyntus, the New Highly Contiguous Reference Genome for Potato (<i>Solanum tuberosum</i>)
Cited by: 34
Author(s): Natascha van Lieshout, Ate van der Burgt, Michiel E. de Vries, Menno ter Maat, David Eickholt, Danny Esselink, Martijn van Kaauwen, Linda Kodde, Richard G. F. Visser, P. Lindhout, Richard Finkers
Software Mentions: 4
Published: about 6 years ago

10.1111/pbi.12520

Genome‐wide dissection of AP2/ERF and HSP90 gene families in five legumes and expression profiles in chickpea and pigeonpea
Cited by: 89
Author(s): Gaurav Agarwal, Vanika Garg, Himabindu Kudapa, Dadakhalandar Doddamani, Lekha T. Pazhamala, Aamir W. Khan, Mahendar Thudi, Suk-Ha Lee, Rajeev K. Varshney
Software Mentions: 4
Published: over 10 years ago

10.1186/s12915-020-00802-7

A chromosome-level assembly of the cat flea genome uncovers rampant gene duplication and genome size plasticity
Cited by: 25
Author(s): Timothy Driscoll, Victoria I. Verhoeve, Joseph J. Gillespie, J. Spencer Johnston, Mark L. Guillotte, Kristen E. Rennoll-Bankert, M. Sayeedur Rahman, Darren E. Hagen, Christine G. Elsik, Kevin R. Macaluso, Abdu F. Azad
Software Mentions: 4
Published: over 6 years ago

10.3390/genes7040013

Bioinformatics Analysis of MAPKKK Family Genes in Medicago truncatula
Cited by: 10
Author(s): Wei Li, Hanyun Xu, Ying Liu, Lili Song, Changhong Guo, Yongjun Shu
Software Mentions: 4
Published: over 10 years ago

10.1186/s13059-016-1053-6

Age-related accrual of methylomic variability is linked to fundamental ageing mechanisms
Cited by: 114
Author(s): Roderick C. Slieker, Maarten van Iterson, René Luijk, Marian Beekman, Daria V. Zhernakova, Matthijs Moed, Hailiang Mei, M.A. van Galen, Patrick Deelen, Marc Jan Bonder, Alexandra Zhernakova, André G. Uitterlinden, Ettje F. Tigchelaar, Coen D. A. Stehouwer, Casper G. Schalkwijk, Carla Kallen, Albert Hofman, Diana van Heemst, Eco J. C. de Geus, Jenny van Dongen, Joris Deelen, Leonard H van den Berg, Joyce B. J. van Meurs, Ritsert C. Jansen, Peter A.C. ’t Hoen, Lude Franke, Cisca Wijmenga, Jan H. Veldink, Morris A. Swertz, Marleen M.J. van Greevenbroek, Cornelia M. van Duijn, Dorret I. Boomsma, P. Eline Slagboom, Bastiaan T. Heijmans
Software Mentions: 4
Published: about 10 years ago

10.1111/pbi.12835

Genotyping-by-sequencing through transcriptomics: implementation in a range of crop species with varying reproductive habits and ploidy levels
Cited by: 27
Author(s): M. Michelle Malmberg, Luke W. Pembleton, Rebecca C. Baillie, Michelle C. Drayton, Shimna Sudheesh, Sukhjiwan Kaur, Hiroshi Shinozuka, Preeti Verma, Germán Spangenberg, Hans D. Daetwyler, John W. Forster, Noel O. I. Cogan
Software Mentions: 4
Published: about 9 years ago

10.1111/pbi.13516

Genome‐wide association coupled gene to gene interaction studies unveil novel epistatic targets among major effect loci impacting rice grain chalkiness
Cited by: 23
Author(s): Gopal Misra, Saurabh Badoni, Sabiha Parween, Rakesh Kumar Singh, Hei Leung, Olufunmilayo Ladejobi, Richard Mott, Nese Sreenivasulu
Software Mentions: 4
Published: almost 6 years ago

10.1534/g3.115.020016

Transcriptomic Features of Bovine Blastocysts Derived by Somatic Cell Nuclear Transfer
Cited by: 20
Author(s): Byungkuk Min, Sunwha Cho, Jung Sun Park, Yun-Gyeong Lee, Namshin Kim, Yong‐Kook Kang
Software Mentions: 4
Published: almost 11 years ago

10.3389/fpls.2015.00918

Genome-wide survey and comprehensive expression profiling of Aux/IAA gene family in chickpea and soybean
Cited by: 61
Author(s): Vikash Singh, Mukesh Jain
Software Mentions: 4
Published: almost 11 years ago

10.1186/1471-2164-13-202

Comparing thousands of circular genomes using the CGView Comparison Tool
Cited by: 234
Author(s): Jason R. Grant, Adriano S. Arantes, Paul Stothard
Software Mentions: 4
Published: over 14 years ago

10.3389/fpls.2017.00819

Structural and Functional Insights into WRKY3 and WRKY4 Transcription Factors to Unravel the WRKY–DNA (W-Box) Complex Interaction in Tomato (Solanum lycopersicum L.). A Computational Approach
Cited by: 37
Author(s): Mohd Aamir, Vinay Kumar Singh, Mukesh Meena, Ram Sanmukh Upadhyay, Vijai Kumar Gupta, Surendra Singh
Software Mentions: 4
Published: over 9 years ago

10.1534/g3.116.037556

Construction of a High-Density American Cranberry (<i>Vaccinium macrocarpon</i>Ait.) Composite Map Using Genotyping-by-Sequencing for Multi-pedigree Linkage Mapping
Cited by: 27
Author(s): Brandon Schlautman, Giovanny Covarrubias‐Pazaran, Luis Diaz‐Garcia, Massimo Iorizzo, James J. Polashock, Edward Grygleski, Nicholi Vorsa, Juan Zalapa
Software Mentions: 4
Published: over 9 years ago

10.7717/peerj.3216

Analysis of genomic variation in lung adenocarcinoma patients revealed the critical role of PI3K complex
Cited by: 9
Author(s): Zhao min Deng, Lizhu Lin, Wen Qiu, Yong qun Zhang, Hong Zhong, Ping Liao, Wu Yun
Software Mentions: 4
Published: over 9 years ago

10.1186/1471-2164-14-918

POMO - Plotting Omics analysis results for Multiple Organisms
Cited by: 3
Author(s): Jake Lin, Richard Kreisberg, Aleksi Kallio, Andrew T. Dudley, Matti Nykter, Ilya Shmulevich, Patrick May, Reija Autio
Software Mentions: 4
Published: almost 14 years ago

10.3389/fmicb.2018.00280

Physiological and Metagenomic Characterizations of the Synergistic Relationships between Ammonia- and Nitrite-Oxidizing Bacteria in Freshwater Nitrification
Cited by: 14
Author(s): Mingwei Cai, Siu-Kin Ng, Chee Kent Lim, Hsu Feng Lu, Yangyang Jia, Patrick K. H. Lee
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pcbi.1003107

Bacteria-Human Somatic Cell Lateral Gene Transfer Is Enriched in Cancer Samples
Cited by: 125
Author(s): David R. Riley, Karsten B. Sieber, Kelly Robinson, James R. White, Ashwinkumar Ganesan, Syrus Nourbakhsh, Julie C. Dunning Hotopp
Software Mentions: 4
Published: over 13 years ago

10.1093/bioinformatics/btw116

Goldilocks: a tool for identifying genomic regions that are ‘just right’
Cited by: 2
Author(s): Samuel M. Nicholls, Amanda Clare, Joshua C. Randall
Software Mentions: 4
Published: over 10 years ago

10.3389/fmicb.2020.01092

Detecting Introgression Between Members of the Fusarium fujikuroi and F. oxysporum Species Complexes by Comparative Mitogenomics
Cited by: 8
Author(s): Balázs Brankovics, A.D. van Diepeningen, G. Sybren de Hoog, Theo A. J. van der Lee, C. Waalwijk
Software Mentions: 4
Published: over 6 years ago

10.7717/peerj.3162

The genomic sequence of<i>Exiguobacterium chiriqhucha</i>str. N139 reveals a species that thrives in cold waters and extreme environmental conditions
Cited by: 14
Author(s): Ana Gutiérrez-Preciado, Carlos Vargas-Chávez, Mariana Reyes-Prieto, Omar Federico Ordoñez, Diego Santos-García, Tania Rosas-Pérez, Jorge Valdivia-Anistro, Eria A. Rebollar, Andrés Saralegui, Andrés Moya, Enrique Merino, Marı́a Eugenia Farı́as, Amparo Latorre, Valeria Souza
Software Mentions: 4
Published: over 9 years ago

10.3389/fmicb.2019.01400

Complete Assembly of the Genome of an Acidovorax citrulli Strain Reveals a Naturally Occurring Plasmid in This Species
Cited by: 11
Author(s): Rongzhi Yang, Diego Santos-García, Francisco Pérez‐Montaño, Gustavo Mateus da Silva, Mei Zhao, Irene Jiménez‐Guerrero, Tally Rosenberg, Gong Chen, Inbar Plaschkes, Shai Morin, R. R. Walcott, Saul Burdman
Software Mentions: 4
Published: over 7 years ago

10.3389/fpls.2016.01245

Mining for Candidate Genes in an Introgression Line by Using RNA Sequencing: The Anthocyanin Overaccumulation Phenotype in Brassica
Cited by: 20
Author(s): Lulu Xie, Fēi Li, Shifan Zhang, Hui Zhang, Wei Qian, Pei-Rong Li, Shujiang Zhang, Rifei Sun
Software Mentions: 4
Published: about 10 years ago

10.1038/s41598-017-02110-7

Revealing genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles under osmotic stress in Escherichia coli K-12 MG1655
Cited by: 31
Author(s): Sang Woo Seo, Ye Gao, Donghyuk Kim, Richard Szubin, Joseph Yang, Byung-Kwan Cho, Bernhard Ø. Palsson
Software Mentions: 4
Published: over 9 years ago

10.3389/fpls.2017.01279

Sequence Polymorphisms and Structural Variations among Four Grapevine (Vitis vinifera L.) Cultivars Representing Sardinian Agriculture
Cited by: 23
Author(s): Luca Mercenaro, G. Nieddu, Andrea Porceddu, Mario Pezzotti, Salvatore Camiolo
Software Mentions: 4
Published: about 9 years ago

10.1371/journal.ppat.1008334

Two waves of pro-inflammatory factors are released during the influenza A virus (IAV)-driven pulmonary immunopathogenesis
Cited by: 32
Author(s): Junsong Zhang, Jun Li, Yuhong Yuan, Feng Huang, Rong Ma, Baohong Luo, Zhihui Xi, Ting Pan, Bingfeng Liu, Yiwen Zhang, Xu Zhang, Yong Luo, Jin Wang, Meng Zhao, Gen Liu, Kai Deng, Hui Zhang
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.ppat.1009812

Mouse papillomavirus type 1 (MmuPV1) DNA is frequently integrated in benign tumors by microhomology-mediated end-joining
Cited by: 12
Author(s): Lulu Yu, Vladimır Majerčiak, Xiangyang Xue, Aayushi Uberoi, Alexei V. Lobanov, Xiongfong Chen, Maggie Cam, Stephen H. Hughes, Paul F. Lambert, Zhi-Ming Zheng
Software Mentions: 4
Published: about 5 years ago

10.1186/s12977-015-0148-6

An integrated map of HIV genome-wide variation from a population perspective
Cited by: 83
Author(s): Guangdi Li, Supinya Piampongsant, Nuno Rodrigues Faria, Arnout Voet, Andrea-Clemencia Pineda-Peña, Ricardo Khouri, Philippe Lemey, Anne‐Mieke Vandamme, Kristof Theys
Software Mentions: 4
Published: over 11 years ago

10.3389/fpls.2016.01416

Comparative Analysis of miRNAs and Their Target Transcripts between a Spontaneous Late-Ripening Sweet Orange Mutant and Its Wild-Type Using Small RNA and Degradome Sequencing
Cited by: 19
Author(s): Juxun Wu, Saisai Zheng, Guizhi Feng, Hualin Yi
Software Mentions: 4
Published: about 10 years ago

10.1038/srep18616

Developmental genes significantly afflicted by aberrant promoter methylation and somatic mutation predict overall survival of late-stage colorectal cancer
Cited by: 15
Author(s): Ning An, Xue Yang, Shujun Cheng, Guiqi Wang, Kaitai Zhang
Software Mentions: 4
Published: almost 11 years ago

10.1038/srep22398

Gene dysregulation is restored in the Parkinson’s disease MPTP neurotoxic mice model upon treatment of the therapeutic drug CuII(atsm)
Cited by: 12
Author(s): Lesley Cheng, Camelia Quek, Lin W. Hung, Robyn A. Sharples, Nicki A. Sherratt, Kevin J. Barnham, Andrew F. Hill
Software Mentions: 4
Published: over 10 years ago

10.3389/fnut.2020.00150

High-Resolution Mass Spectrometer–Based Ultra-Deep Profile of Milk Whey Proteome in Indian Zebu (Sahiwal) Cattle
Cited by: 17
Author(s): Alka Chopra, Syed Azmal Ali, Shveta Bathla, Preeti Rawat, Vikas Vohra, Sudarshan Kumar, Ashok Kumar Mohanty
Software Mentions: 4
Published: about 6 years ago

10.3389/fpls.2021.666310

Aux/IAA and ARF Gene Families in Salix suchowensis: Identification, Evolution, and Dynamic Transcriptome Profiling During the Plant Growth Process
Cited by: 9
Author(s): Suyun Wei, Yingnan Chen, Jing Hou, Yonghua Yang, Tongming Yin
Software Mentions: 4
Published: over 5 years ago

10.3389/fonc.2020.01778

Seven-Gene Signature Based on Glycolysis Is Closely Related to the Prognosis and Tumor Immune Infiltration of Patients With Gastric Cancer
Cited by: 36
Author(s): Shanshan Yu, Chuan Hu, Luya Cai, Xuedan Du, Fan Lin, Qiongjie Yu, Lixiao Liu, Cheng Zhang, Xuan Li, Wenfeng Li, Yu Zhan
Software Mentions: 4
Published: about 6 years ago

10.1038/s41598-017-11327-5

Genome-wide identification and co-expression network analysis provide insights into the roles of auxin response factor gene family in chickpea
Cited by: 26
Author(s): Vikash Singh, Mohan Singh Rajkumar, Rohini Garg, Mukesh Jain
Software Mentions: 4
Published: about 9 years ago

10.3389/fpls.2018.01332

Genome-Wide Identification, Characterization, and Expression Profiling of the Legume BZR Transcription Factor Gene Family
Cited by: 28
Author(s): Yueying Li, Liangliang He, Jing Li, Jianghua Chen, Changning Liu
Software Mentions: 3
Published: about 8 years ago

10.3389/fpls.2019.01514

Genome-Wide Comparisons of Mutations Induced by Carbon-Ion Beam and Gamma-Rays Irradiation in Rice via Resequencing Multiple Mutants
Cited by: 23
Author(s): Gangyi Yang, Wenlong Luo, Jian Zhang, Xian-cheng Yan, Yuguo Du, Libin Zhou, Wenjian Li, Hui Wang, Zhiqiang Chen, Tao Guo
Software Mentions: 3
Published: almost 7 years ago

10.3389/fpls.2021.668623

The Wild Sugarcane and Sorghum Kinomes: Insights Into Expansion, Diversification, and Expression Patterns
Cited by: 16
Author(s): Alexandre Hild Aono, Ricardo José Gonzaga Pimenta, Ana Letycia Basso Garcia, Fernando Henrique Correr, Guilherme Kenichi Hosaka, Marishani Marin Carrasco, Cláudio Benício Cardoso-Silva, Melina Cristina Mancini, Danilo Augusto Sforça, Lucas Borges dos Santos, James Shiniti Nagai, Luciana Rossini Pinto, Marcos Guimarães de Andrade Landell, Monalisa Sampaio Carneiro, Thiago Willian Almeida Balsalobre, Marcos G. Quiles, Welison Andrade Pereira, Gabriel Rodrigues Alves Margarido, Anete Pereira de Souza
Software Mentions: 3
Published: over 5 years ago

10.3389/fmicb.2015.00569

RNA-Seq analysis of isolate- and growth phase-specific differences in the global transcriptomes of enteropathogenic Escherichia coli prototype isolates
Cited by: 27
Author(s): Tracy H. Hazen, Sean C. Daugherty, Amol C. Shetty, Anup Mahurkar, Owen White, James B. Kaper, David A. Rasko
Software Mentions: 3
Published: over 11 years ago

10.3389/fpls.2014.00789

Genome-wide analysis and expression profiling suggest diverse roles of GH3 genes during development and abiotic stress responses in legumes
Cited by: 38
Author(s): Vikash Singh, Mukesh Jain, Rohini Garg
Software Mentions: 3
Published: over 11 years ago

10.3389/fpls.2020.545042

Molecular Evolution and Expansion of the KUP Family in the Allopolyploid Cotton Species Gossypium hirsutum and Gossypium barbadense
Cited by: 3
Author(s): Kai Fan, Zhijun Mao, Jiaxin Zheng, Yunrui Chen, Zhaowei Li, Weiwei Lin, Yongqiang Zhang, Jinwen Huang, Wenxiong Lin
Software Mentions: 3
Published: about 6 years ago

10.1038/s41598-017-15363-z

LPPtiger software for lipidome-specific prediction and identification of oxidized phospholipids from LC-MS datasets
Cited by: 45
Author(s): Zhixu Ni, Georgia Angelidou, Ralf Hoffmann, Maria Fedorova
Software Mentions: 3
Published: almost 9 years ago

10.1038/s41598-017-03528-9

Genetic Determinants of Crop Timing and Quality Traits in Two Interspecific Petunia Recombinant Inbred Line Populations
Cited by: 8
Author(s): Yufang Guo, Wei Kuang Lin, Qiuxia Chen, Verónica Vallejo, Ryan M. Warner
Software Mentions: 3
Published: over 9 years ago

10.1038/srep20957

A genome-wide search for epigenetically regulated genes in zebra finch using MethylCap-seq and RNA-seq
Cited by: 9
Author(s): Sandra Steyaert, Jolien Diddens, Jeroen Galle, Ellen De Meester, Sarah De Keulenaer, Antje Bakker, Nina Sohnius-Wilhelmi, Carolina Frankl-Vilches, Annemie Van der Linden, Wim Van Criekinge, Wim Vanden Berghe, Tim De Meyer
Software Mentions: 3
Published: over 10 years ago

10.3389/fpls.2016.01186

Origination, Expansion, Evolutionary Trajectory, and Expression Bias of AP2/ERF Superfamily in Brassica napus
Cited by: 31
Author(s): Xiaoming Song, Jinpeng Wang, Xiao Ma, Yuxian Li, Tianyu Lei, Li Wang, Weina Ge, Di Guo, Zhenyi Wang, Chunjin Li, Zhao Jian-jun, Xiyin Wang
Software Mentions: 3
Published: about 10 years ago

10.1038/s41597-019-0014-9

Genome-wide identification and characterization of long noncoding and circular RNAs in germline stem cells
Cited by: 14
Author(s): Xiaoyong Li, Geng Tian, Yue Zhao, Ji Wu
Software Mentions: 3
Published: over 7 years ago

10.1038/s41597-019-0291-3

A de novo genome assembly of the dwarfing pear rootstock Zhongai 1
Cited by: 23
Author(s): C. Ou, Fei Wang, Jiahong Wang, Li Song, Yanjie Zhang, Ming Fang, Li Ma, Yanan Zhao, Shuling Jiang
Software Mentions: 3
Published: almost 7 years ago

10.3389/fonc.2021.669270

A Comprehensive RNA Study to Identify circRNA and miRNA Biomarkers for Docetaxel Resistance in Breast Cancer
Cited by: 11
Author(s): Peide Huang, Fengyu Li, Zongchao Mo, Chunyu Geng, Wen Fang, Chunyan Zhang, Jia Guo, Song Wu, Lin Li, Nils Brünner, Jan Stenvang
Software Mentions: 3
Published: over 5 years ago