10.1371/journal.pcbi.1008980

VCF2CAPS–A high-throughput CAPS marker design from VCF files and its test-use on a genotyping-by-sequencing (GBS) dataset
Cited by: 1
Author(s): Wojciech Wesołowski, Beata Domnicz, Joanna Augustynowicz, Marek Szklarczyk
Software Mentions: 3
Published: over 5 years ago

10.1186/s12864-015-1223-z

Age dependent changes in the LPS induced transcriptome of bovine dermal fibroblasts occurs without major changes in the methylome
Cited by: 14
Author(s): Benjamin B. Green, Stephanie McKay, David E. Kerr
Software Mentions: 3
Published: over 11 years ago

10.7717/peerj.740

First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking
Cited by: 97
Author(s): Yuji Sekiguchi, Akiko Ohashi, Donovan H. Parks, Toshihiro Yamauchi, Gene W. Tyson, Philip Hugenholtz
Software Mentions: 3
Published: over 11 years ago

10.1186/s13073-015-0127-5

Ploidy-Seq: inferring mutational chronology by sequencing polyploid tumor subpopulations
Cited by: 6
Author(s): Ankit Malhotra, Yong Wang, Jill Waters, Ken Chen, Funda Meric‐Bernstam, Ira M. Hall, Nicholas E. Navin
Software Mentions: 3
Published: almost 12 years ago

10.1038/s41598-017-17484-x

Comparative analysis of the genomes of Stylophora pistillata and Acropora digitifera provides evidence for extensive differences between species of corals
Cited by: 109
Author(s): Christian Cr Voolstra, Yong Li, Yi Jin Liew, Sebastian Baumgarten, Didier Zoccola, Jean‐François Flot, Sylvie Tambutté, Denis Allemand, Manuel Aranda
Software Mentions: 3
Published: almost 9 years ago

10.1186/s13059-015-0837-4

Genomic legacy of the African cheetah, Acinonyx jubatus
Cited by: 159
Author(s): Pavel Dobrynin, Shi Ping Liu, Gaik Tamazian, Zijun Xiong, Andrey A. Yurchenko, Ksenia Krasheninnikova, Sergei Kliver, Anne Schmidt‐Küntzel, Klaus‐Peter Koepfli, Warren E. Johnson, Lukas F. K. Kuderna, Raquel García-Pérez, Marc de Manuel, Ricardo Godinez, Aleksey Komissarov, Alex Makunin, Vladimir Brukhin, Wei‐Lin Qiu, Long Zhang, Fang Li, Jine Yi, Carlos A. Driscoll, Agostinho Antunes, Tarás K. Oleksyk, Eduardo Eizirik, Polina L. Perelman, Melody E. Roelke, David E. Wildt, Mark Diekhans, Tomàs Marquès‐Bonet, Laurie Marker, Jong Bhak, Jun Wang, Guojie Zhang, Stephen J. O’Brien
Software Mentions: 3
Published: almost 11 years ago

10.1186/1471-2164-15-249

Characterization of the pigmented shell-forming proteome of the common grove snail Cepaea nemoralis
Cited by: 73
Author(s): Karlheinz Mann, Daniel J. Jackson
Software Mentions: 3
Published: almost 13 years ago

10.1186/s12864-017-3499-7

Visualization of consensus genome structure without using a reference genome
Cited by: 3
Author(s): Isao Tada, Yasuhiro Tanizawa, Masanori Arita
Software Mentions: 3
Published: over 9 years ago

10.1186/gb-2014-15-2-r39

Genome sequencing of the high oil crop sesame provides insight into oil biosynthesis
Cited by: 226
Author(s): Linhai Wang, Shanlin Yu, Chaobo Tong, Yingzhong Zhao, Yan Liu, Chi Song, Yanxin Zhang, Xudong Zhang, Ying Wang, Wei Hua, Donghua Li, Dan Li, Fang Li, Jingyin Yu, Chunyan Xu, Xuelian Han, Shunmou Huang, Shuaishuai Tai, Junyi Wang, Xun Xu, Yingrui Li, Liu S, Rajeev K. Varshney, Jun Wang, Xiurong Zhang
Software Mentions: 3
Published: almost 13 years ago

10.3390/genes12030417

Molecular Characterization, Gene Evolution and Expression Analysis of the F-Box Gene Family in Tomato (Solanum lycopersicum)
Cited by: 9
Author(s): Fulei Mo, Nian Zhang, Yefeng Qiu, Lingjun Meng, Mozhen Cheng, Jiayin Liu, Lanning Yao, Rui Lv, Yuxin Liu, Yao Zhang, Xiuling Chen, Aoxue Wang
Software Mentions: 3
Published: over 5 years ago

10.3390/genes12050784

Genome-Wide Analysis of Potassium Channel Genes in Rice: Expression of the OsAKT and OsKAT Genes under Salt Stress
Cited by: 48
Author(s): Zahra Musavizadeh, Hamid Najafi-Zarrini, Seyed Kamal Kazemitabar, Seyyed Hamidreza Hashemi, Sahar Faraji, Gianni Barcaccia, Parviz Heidari
Software Mentions: 3
Published: over 5 years ago

10.3892/mmr.2015.3318

PUFA diets alter the microRNA expression profiles in an inflammation rat model
Cited by: 34
Author(s): Zheng Zhang, Yubin Ge, Jinyu Zhang, Meilan Xue, Quan Li, Dongliang Lin, Wenhui Ma
Software Mentions: 3
Published: over 11 years ago

10.1186/s12859-018-2425-6

Tigmint: correcting assembly errors using linked reads from large molecules
Cited by: 86
Author(s): Shaun D. Jackman, Lauren Coombe, Justin Chu, René L. Warren, Ben Vandervalk, Sarah Yeo, Zhen‐Zhen Xue, Hamid Mohamadi, Jöerg Bohlmann, Steven J.M. Jones, İnanç Birol
Software Mentions: 3
Published: almost 8 years ago

10.3390/genes10070544

Seasonal Stability and Dynamics of DNA Methylation in Plants in a Natural Environment
Cited by: 18
Author(s): Tasuku Ito, Hiroaki Nishio, Yoshiaki Tarutani, Naoko Emura, Mie N. Honjo, Atsushi Toyoda, Asao Fujiyama, Tetsuji Kakutani, Hiroshi Kudoh
Software Mentions: 3
Published: over 7 years ago

10.1186/gb-2012-13-8-r74

Gene functionalities and genome structure in Bathycoccus prasinos reflect cellular specializations at the base of the green lineage
Cited by: 139
Author(s): Hervé Moreau, Bram Verhelst, Arnaud Couloux, Évelyne Derelle, Stéphane Rombauts, Nigel Grimsley, Michiel Van Bel, Julie Poulain, Michaël Katinka, Martin F. Hohmann‐Marriott, Gwenaël Piganeau, Pierre Rouzé, Corinne Da Silva, Patrick Wincker, Yves Van de Peer, Klaas Vandepoele
Software Mentions: 3
Published: almost 15 years ago

10.1093/g3journal/jkab002

<i>De novo</i>whole-genome assembly and resequencing resources for the roan (<i>Hippotragus equinus</i>), an iconic African antelope
Cited by: 4
Author(s): Margarida Gonçalves, Hans R. Siegismund, Bettine Jansen van Vuuren, Klaus‐Peter Koepfli, Nathalie Ferrand, Raquel Godinho
Software Mentions: 3
Published: over 5 years ago

10.1534/g3.116.037150

The Long Noncoding RNA Transcriptome of<i>Dictyostelium discoideum</i>Development
Cited by: 8
Author(s): Rafael D. Rosengarten, Balaji Santhanam, Janez Kokošar, Gad Shaulsky
Software Mentions: 3
Published: over 9 years ago

10.1093/molbev/msaa109

Understanding the Early Evolutionary Stages of a Tandem Drosophilamelanogaster-Specific Gene Family: A Structural and Functional Population Study
Cited by: 12
Author(s): Bryan D. Clifton, Jamie Jimenez, Ashlyn Kimura, Zeinab Chahine, Pablo Librado, Alejandro Sánchez‐Gracia, Mashya Abbassi, Francisco Carranza, Carolus Chan, Marcella Marchetti, Wanting Zhang, Minjun Shi, Christine Hein Vu, Shu Dan Yeh, Laura Fanti, Xiao Qin Xia, Julio Rozas, José M. Ranz
Software Mentions: 3
Published: over 6 years ago

10.3389/fpls.2021.633310

Chromosome-Level Genome Assembly of the American Cranberry (Vaccinium macrocarpon Ait.) and Its Wild Relative Vaccinium microcarpum
Cited by: 27
Author(s): Luis Díaz-Garcia, Luis Fernando García-Ortega, María González-Rodriguez, Luis Delaye, Massimo Iorizzo, Juan Zalapa
Software Mentions: 3
Published: over 5 years ago

10.1534/g3.115.026666

The <i>HIST1</i> Locus Escapes Reprogramming in Cloned Bovine Embryos
Cited by: 5
Author(s): Byungkuk Min, Sunwha Cho, Jung Sun Park, Kyuheum Jeon, Yong‐Kook Kang
Software Mentions: 3
Published: over 10 years ago

10.1186/s13059-018-1552-8

Comparative genomics reveals the distinct evolutionary trajectories of the robust and complex coral lineages
Cited by: 56
Author(s): Hua Ying, Ira Cooke, Susanne Sprungala, Weiwen Wang, David C. Hayward, Yurong Tang, Gavin A. Huttley, Eldon E. Ball, Sylvain Forêt, David J. Miller
Software Mentions: 3
Published: almost 8 years ago

10.3390/microorganisms8020182

Complete Genome Sequence Reveals Evolutionary and Comparative Genomic Features of Xanthomonas albilineans Causing Sugarcane Leaf Scald
Cited by: 14
Author(s): Huili Zhang, Mbuya Sylvain Ntambo, Philippe Rott, Gongyou Chen, Lilan Chen, Mei-Ting Huang, San‐Ji Gao
Software Mentions: 3
Published: over 6 years ago

10.3390/microorganisms8070981

Comparison of Rumen Microbiota and Serum Biochemical Indices in White Cashmere Goats Fed Ensiled or Sun-Dried Mulberry Leaves
Cited by: 15
Author(s): Yaoyue Wang, Qingmiao Shen, Shu Zhong, Yulin Chen, Yuxin Yang
Software Mentions: 3
Published: over 6 years ago

10.3389/fpls.2016.01083

De novo Assembly and Characterization of the Transcriptome of Broomcorn Millet (Panicum miliaceum L.) for Gene Discovery and Marker Development
Cited by: 21
Author(s): Hong Yue, Le Wang, Hui Liu, Wenjie Yue, Xianghong Du, Weining Song, Xiaojun Nie
Software Mentions: 3
Published: about 10 years ago

10.1186/1471-2105-14-95

CGAP: a new comprehensive platform for the comparative analysis of chloroplast genomes
Cited by: 34
Author(s): Jinkui Cheng, Zhiai Xu, Guomin Ren, Zhihua Liu
Software Mentions: 3
Published: over 13 years ago

10.3389/fmicb.2021.674952

Genomics-Enabled Novel Insight Into the Pathovar-Specific Population Structure of the Bacterial Leaf Streak Pathogen Xanthomonas translucens in Small Grain Cereals
Cited by: 19
Author(s): Syed Mashab Ali Shah, Moein Khojasteh, Qi Wang, S. Mohsen Taghavi, Zhi-Hong Xu, Pejman Khodaygan, Lifang Zou, Sedighe Mohammadikhah, Gongyou Chen, Ebrahim Osdaghi
Software Mentions: 3
Published: over 5 years ago

10.3389/fpls.2019.00586

Phylogenomic Approaches to DNA Barcoding of Herbal Medicines: Developing Clade-Specific Diagnostic Characters for Berberis
Cited by: 27
Author(s): Marco Kreuzer, Caroline Howard, Bhim Adhikari, Colin A. Pendry, Julie A. Hawkins
Software Mentions: 3
Published: over 7 years ago

10.3389/fmicb.2020.01930

New Plasmodium vivax Genomes From the China-Myanmar Border
Cited by: 5
Author(s): Awtum Brashear, Adam C Huckaby, Qi Fan, Luke J Dillard, Yubing Hu, Yuling Li, Yan Zhao, Zenglei Wang, Yaming Cao, Jun Miao, Jennifer L. Guler, Liwang Cui
Software Mentions: 3
Published: about 6 years ago

10.3389/fmicb.2018.02668

Ancestrality and Mosaicism of Giant Viruses Supporting the Definition of the Fourth TRUC of Microbes
Cited by: 41
Author(s): Philippe Colson, Anthony Levasseur, Bernard La Scola, Vikas Sharma, Arshan Nasir, Pierre Pontarotti, Gustavo Caetano‐Anollés, Didier Raoult
Software Mentions: 3
Published: almost 8 years ago

10.1186/s13099-016-0084-6

Genome sequence of Escherichia coli NCCP15653, a group D strain isolated from a diarrhea patient
Cited by: 2
Author(s): Min Jung Kwak, Myoung Soo Kim, Soon Kyeong Kwon, Seung Hak Cho, Jihyun F. Kim
Software Mentions: 3
Published: over 10 years ago

10.1186/s40168-019-0638-1

Genome-resolved metagenomics of eukaryotic populations during early colonization of premature infants and in hospital rooms
Cited by: 52
Author(s): Matthew R. Olm, Patrick T. West, Brandon Brooks, Brian Firek, Robyn Baker, Michael J. Morowitz, Jillian F. Banfield
Software Mentions: 3
Published: over 7 years ago

10.3389/fmicb.2021.682356

Comparative Transcriptome and Endophytic Bacterial Community Analysis of Morchella conica SH
Cited by: 3
Author(s): Bei Lü, Guo Wu, Yu Sun, Liang S. Zhang, Xiao Wu, Wei Jiang, Peng Li, Yan Huang, Jin B. Wang, Yong Zhao, Hua Liu, Li Song, Qin Mo, Ai H. Pan, Yan Yang, Xuan Long, Wei Cui, Chao Zhang, Xu Wang, Xue Tang
Software Mentions: 3
Published: over 5 years ago

10.3389/fmicb.2016.00941

Diversity and Distribution of Prokaryotes within a Shallow-Water Pockmark Field
Cited by: 23
Author(s): Donato Giovannelli, Giuseppe d’Errico, Federica Fiorentino, Daniele Fattorini, Francesco Regoli, Lorenzo Angeletti, Tatjana Bakran‐Petricioli, Costantino Vetriani, Mustafa Yücel, Marco Taviani, Elena Manini
Software Mentions: 3
Published: over 10 years ago

10.1099/mgen.0.000265

Insertion sequences drive the emergence of a highly adapted human pathogen
Cited by: 18
Author(s): Erwin Sentausa, Pauline Basso, Alice Berry, Annie Adrait, Gwendoline Bellement, Yohann Couté, Stephen Lory, Sylvie Elsen, Ina Attrée
Software Mentions: 3
Published: about 6 years ago

10.3390/v11030267

Gram-Positive Bacteria-Like DNA Binding Machineries Involved in Replication Initiation and Termination Mechanisms of Mimivirus
Cited by: 3
Author(s): Motohiro Akashi, Masaharu Takemura
Software Mentions: 3
Published: over 7 years ago

10.1155/2017/1278932

Empirical Comparison of Visualization Tools for Larger-Scale Network Analysis
Cited by: 39
Author(s): Georgios A. Pavlopoulos, David Páez-Espino, Nikos C. Kyrpides, Ioannis Iliopoulos
Software Mentions: 3
Published: over 9 years ago

10.3389/fmicb.2020.01142

Underlying Mechanism of Wild Radix pseudostellariae in Tolerance to Disease Under the Natural Forest Cover
Cited by: 10
Author(s): Hongmiao Wu, Jinshen Xia, Xianjin Qin, Huiming Wu, Shengkai Zhang, Yanlin Zhao, Christopher Rensing, Wenxiong Lin
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-018-20862-8

Variation in Raw Milk Microbiota Throughout 12 Months and the Impact of Weather Conditions
Cited by: 79
Author(s): Nan Li, Yuezhu Wang, Chunping You, Jianke Ren, Chen Wan-yi, Huajun Zheng, Zhenmin Liu
Software Mentions: 3
Published: over 8 years ago

10.3389/fpls.2021.684619

Identification, Characterization, and Expression Profile Analysis of the mTERF Gene Family and Its Role in the Response to Abiotic Stress in Barley (Hordeum vulgare L.)
Cited by: 4
Author(s): Tingting Li, Wenqiu Pan, Yiyuan Yuan, Ying Liu, Yihan Li, Xiaoyu Wu, Fei Wang, Licao Cui
Software Mentions: 3
Published: over 5 years ago

10.1186/s13059-019-1631-5

Genomic introgression through interspecific hybridization counteracts genetic bottleneck during soybean domestication
Cited by: 37
Author(s): Xutong Wang, Liyang Chen, Jianxin Ma
Software Mentions: 3
Published: over 7 years ago

10.1186/1471-2164-15-255

Genome-wide variations in a natural isolate of the nematode Caenorhabditis elegans
Cited by: 19
Author(s): Ismael A. Vergara, Maja Tarailo‐Graovac, Christian Frech, Jun Wang, Zhaozhao Qin, Ting Zhang, Rong She, Jeffrey Shih-Chieh Chu, Ke Wang, Nansheng Chen
Software Mentions: 3
Published: over 12 years ago

10.1186/s12864-021-07378-8

Genome-wide characterization of the WAK gene family and expression analysis under plant hormone treatment in cotton
Cited by: 19
Author(s): Dou Liu, Zhifang Li, Qian Shen, Huiran Shi, Huaizhu Li, Wenbo Wang, Changsong Zou, Hǎihóng Shāng, Hongbin Li, Gao Xiao
Software Mentions: 3
Published: over 5 years ago

10.1111/tpj.14115

High intraspecific diversity of <i>Restorer‐of‐fertility‐like</i> genes in barley
Cited by: 21
Author(s): Joanna Melonek, Ruonan Zhou, Philipp E. Bayer, David Edwards, Nils Stein, Ian Small
Software Mentions: 3
Published: almost 8 years ago

10.1186/s12864-019-6319-4

Genome-wide identification, phylogeny, and expression analysis of the SBP-box gene family in Euphorbiaceae
Cited by: 14
Author(s): Jing Li, Xiaotong Gao, Shiye Sang, Changning Liu
Software Mentions: 3
Published: almost 7 years ago

10.1111/tpj.14538

Transposons played a major role in the diversification between the closely related almond and peach genomes: results from the almond genome sequence
Cited by: 82
Author(s): Tyler Alioto, Konstantinos G. Alexiou, Amélie Bardil, Fabio Barteri, Raúl Castanera, Fernando Cruz, Amit Dhingra, Henri Duval, Angel V. Fernández i Martí, Leonor Frías, Beatriz Galán, José Luis Garcı́a, Werner Howad, Jèssica Gómez‐Garrido, Marta Gut, Irene Julca, Jordi Morata, Pere Puigdomènech, Paolo Ribeca, María José Rubio Cabetas, Anna Vlasova, M. Wirthensohn, Jordi García-Más, Toni Gabaldón, Josep M. Casacuberta, Pere Arús
Software Mentions: 3
Published: almost 7 years ago

10.1186/1471-2164-14-617

Genome and transcriptome sequencing of the halophilic fungus Wallemia ichthyophaga: haloadaptations present and absent
Cited by: 99
Author(s): Janja Zajc, Yongfeng Liu, Wenkui Dai, Zhenyu Yang, Jingzhi Hu, Cene Gostinčar, Nina Gunde‐Cimerman
Software Mentions: 3
Published: about 13 years ago

10.1111/1751-7915.13655

Geographic pattern of antibiotic resistance genes in the metagenomes of the giant panda
Cited by: 20
Author(s): Ting Hu, Qinlong Dai, Hua Chen, Zheng Zhang, Qiang Dai, Xun Gu, Xiangdong Yang, Yang Zhang, Lifeng Zhu
Software Mentions: 3
Published: about 6 years ago

10.1099/mgen.0.000154

Comparative transcriptomics of Aspergillus fumigatus strains upon exposure to human airway epithelial cells
Cited by: 16
Author(s): Tonya Watkins, Hong Liu, Matthew Chung, Tracy H. Hazen, Julie C. Dunning Hotopp, Scott G. Filler, Vincent M. Bruno
Software Mentions: 3
Published: over 8 years ago

10.1099/mgen.0.000188

A complete high-quality MinION nanopore assembly of an extensively drug-resistant Mycobacterium tuberculosis Beijing lineage strain identifies novel variation in repetitive PE/PPE gene regions
Cited by: 32
Author(s): Arnold Bainomugisa, Tânia Duarte, Evelyn Lavu, Sushil Pandey, Chris Coulter, Ben J. Marais, Lachlan Coin
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-018-37792-0

Diversified secondary metabolite biosynthesis gene repertoire revealed in symbiotic dinoflagellates
Cited by: 20
Author(s): Girish Beedessee, Kanako Hisata, Michael C. Roy, Frances M. Van Dolah, Noriyuki Satoh, Eiichi Shoguchi
Software Mentions: 3
Published: over 7 years ago

10.3389/fmicb.2019.01325

Cultivation and Transcriptional Analysis of a Canonical Nitrospira Under Stable Growth Conditions
Cited by: 29
Author(s): Aniela B. Mundinger, Christopher E. Lawson, Mike S. M. Jetten, Hanna Koch, Sebastian Lücker
Software Mentions: 3
Published: over 7 years ago

10.3389/fmicb.2017.01448

PacBio But Not Illumina Technology Can Achieve Fast, Accurate and Complete Closure of the High GC, Complex Burkholderia pseudomallei Two-Chromosome Genome
Cited by: 33
Author(s): Jade L. L. Teng, Man Lung Yeung, Elaine Chan, Lilong Jia, Chi Ho Lin, Yi Huang, Herman Tse, Samson S. Y. Wong, Pak C. Sham, Susanna K. P. Lau, Patrick C. Y. Woo
Software Mentions: 3
Published: about 9 years ago

10.1186/1471-2164-13-545

Comparative genomics of the classical Bordetella subspecies: the evolution and exchange of virulence-associated diversity amongst closely related pathogens
Cited by: 98
Author(s): Jihye Park, Ying Zhang, Anne M. Buboltz, Xuqing Zhang, Stephan C. Schuster, Umesh Ahuja, Minghsun Liu, Jeff F. Miller, Mohammed Sebaihia, Stephen D. Bentley, Julian Parkhill, Eric T. Harvill
Software Mentions: 3
Published: about 14 years ago

10.3390/plants10091874

Analysis of PRX Gene Family and Its Function on Cell Lignification in Pears (Pyrus bretschneideri)
Cited by: 3
Author(s): Zhihua Xie, Weikang Rui, Yazhou Yuan, Xiaofei Song, Xing Liu, Xin Gong, Jianping Bao, Shaoling Zhang, Khanizadeh Shahrokh, Shutian Tao
Software Mentions: 3
Published: about 5 years ago

10.1038/s41375-018-0103-3

Whole-genome sequencing of multiple myeloma reveals oncogenic pathways are targeted somatically through multiple mechanisms
Cited by: 62
Author(s): Phuc H. Hoang, Sara E. Dobbins, Alex J. Cornish, Daniel Chubb, Philip Law, Martin Kaiser, Richard S. Houlston
Software Mentions: 3
Published: over 8 years ago

10.3389/fmicb.2020.00082

Comparative Genomic Analysis of a Novel Strain of Taiwan Hot-Spring Cyanobacterium Thermosynechococcus sp. CL-1
Cited by: 25
Author(s): Yen I. Cheng, Li-Dek Chou, Yi Fang Chiu, Hsin Ta Hsueh, Chih Horng Kuo, Hsiu-An Chu
Software Mentions: 3
Published: over 6 years ago

10.1111/acel.13357

Age‐related telomere attrition causes aberrant gene expression in sub‐telomeric regions
Cited by: 8
Author(s): Xiao Dong, Shixiang Sun, Lei Zhang, Seung-Soo Kim, Zhidong Tu, Cristina Montagna, Alexander Y. Maslov, Yousin Suh, Tao Wang, Judith Campisi, Jan Vijg
Software Mentions: 3
Published: over 5 years ago

10.1038/s41375-020-0762-8

Comprehensive diagnostics of acute myeloid leukemia by whole transcriptome RNA sequencing
Cited by: 38
Author(s): Wibowo Arindrarto, Daniel Borràs, Ruben A.L. De Groen, Redmar R van den Berg, Irene J. Locher, Saskia A.M.E. van Diessen, Rosalie van der Holst, Edith D. van der Meijden, M. Willy Honders, Rick H. de Leeuw, Wina Verlaat, Inge Jedema, Wilma G. M. Kroes, Jeroen Knijnenburg, Tom van Wezel, Joost S.P. Vermaat, Peter J.M. Valk, Bart Janssen, Peter de Knijff, Cornelis A.M. van Bergen, Erik B. van den Akker, Peter A C ‘t Hoen, Szymon M. Kiełbasa, Jeroen F. J. Laros, Marieke Griffioen, Hendrik Veelken
Software Mentions: 3
Published: over 6 years ago

10.3389/fmicb.2021.660002

Whole-Genome Analysis of Mycobacterium avium subsp. paratuberculosis IS900Insertions Reveals Strain Type-Specific Modalities
Cited by: 6
Author(s): Cyril Condé, Marian Price-Carter, Thierry Cochard, Maxime Branger, Karen Stevenson, Richard J. Whittington, John P. Bannantine, Franck Biet
Software Mentions: 3
Published: over 5 years ago

10.3389/fmicb.2019.00805

Prevalence of Antibiotic and Heavy Metal Resistance Determinants and Virulence-Related Genetic Elements in Plasmids of Staphylococcus aureus
Cited by: 23
Author(s): Michał Bukowski, Rafał Piwowarczyk, Anna Mądry, Rafal Zagorski-Przybylo, Marcin Hydzik, Benedykt Władyka
Software Mentions: 3
Published: over 7 years ago

10.3389/fmicb.2018.01763

Comprehensive Insights Into Composition, Metabolic Potentials, and Interactions Among Archaeal, Bacterial, and Viral Assemblages in Meromictic Lake Shunet in Siberia
Cited by: 11
Author(s): Yuting Wu, Cheng‐Yu Yang, Pei‐Wen Chiang, Chwan-Lu Tseng, Hsiu‐Hui Chiu, Isaam Saeed, Bayanmunkh Baatar, D. Yu. Rogozin, Saman K. Halgamuge, А. Г. Дегерменджи, Sen‐Lin Tang
Software Mentions: 3
Published: about 8 years ago

10.3389/fmicb.2019.01446

Pan-Genomic and Polymorphic Driven Prediction of Antibiotic Resistance in Elizabethkingia
Cited by: 13
Author(s): Bryan Naidenov, Alexander Lim, Karyn Willyerd, Nathanial Torres, William L. Johnson, Hong Jin Hwang, Peter R. Hoyt, John E. Gustafson, Charles Chen
Software Mentions: 3
Published: over 7 years ago

10.3389/fimmu.2017.01063

Gut REG3γ-Associated Lactobacillus Induces Anti-inflammatory Macrophages to Maintain Adipose Tissue Homeostasis
Cited by: 16
Author(s): Yugang Huang, Houbao Qi, Zhiqian Zhang, Enlin Wang, Huan Yun, Hui Yan, Xiaomin Su, Yingquan Liu, Zenzen Tang, Yuan Gao, Wencong Shang, Zhou Jiang, Tianze Wang, Yongzhe Che, Yuan Zhang, Rongcun Yang
Software Mentions: 3
Published: about 9 years ago

10.1186/s12859-014-0422-y

YersiniaBase: a genomic resource and analysis platform for comparative analysis of Yersinia
Cited by: 9
Author(s): Shi Tan, Avirup Dutta, Nicholas S. Jakubovics, Mia Yang Ang, Cheuk Chuen Siow, Naresh V.R. Mutha, Hamed Heydari, Wei Yee Wee, George T.F. Wong, Siew Woh Choo
Software Mentions: 3
Published: almost 12 years ago

10.3389/fgene.2021.713224

Genome-Wide Identification and Expression Analysis of Metal Tolerance Protein Gene Family in Medicago truncatula Under a Broad Range of Heavy Metal Stress
Cited by: 18
Author(s): Ahmed H. El-Sappah, Rania G. Elbaiomy, Ahmed S. Elrys, Yu Wang, Yumin Zhu, Qiulan Huang, Yan Ke, Xingbo Zhao, Yun Li, Khaled A. El‐Tarabily, Jia Li
Software Mentions: 3
Published: about 5 years ago

10.3389/fgene.2014.00319

Bioremediation in marine ecosystems: a computational study combining ecological modeling and flux balance analysis
Cited by: 11
Author(s): Marianna Taffi, Nicola Paoletti, Claudio Angione, Sandra Pucciarelli, Mauro Marini, Píetro Lió
Software Mentions: 3
Published: about 12 years ago

10.1186/s13068-017-0885-y

Metagenomic mining pectinolytic microbes and enzymes from an apple pomace-adapted compost microbial community
Cited by: 23
Author(s): Man Zhou, Peng Guo, Tao Wang, Limin Gao, Hang Yin, Cheng Cai, Jie Gu, Xin Lü
Software Mentions: 3
Published: about 9 years ago

10.1186/s13068-020-1651-0

Proteomic analysis reflects an environmental alkalinization-coupled pH-dependent mechanism of regulating lignocellulases in Trichoderma guizhouense NJAU4742
Cited by: 6
Author(s): Youzhi Miao, Xing Chen, Tuo Li, Han Zhu, Tang Si-yu, Dongyang Liu, Qirong Shen
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12866-020-02024-x

High-throughput sequencing analysis of the rhizosphere arbuscular mycorrhizal fungi (AMF) community composition associated with Ferula sinkiangensis
Cited by: 15
Author(s): Yunfeng Luo, Zhongke Wang, Ya-Ling He, Guifang Li, Xinhua Lv, Zhuang Li
Software Mentions: 3
Published: almost 6 years ago

10.1042/BSR20191139

Comprehensive analysis of long noncoding RNA and mRNA in five colorectal cancer tissues and five normal tissues
Cited by: 4
Author(s): Zhenxu Zhou, Xiaoming Chen, Yuqi Zhang, Peng Liu, Xiangyang Xue, Guoxin Li
Software Mentions: 3
Published: over 6 years ago

10.1186/1471-2105-13-S8-S8

An eQTL biological data visualization challenge and approaches from the visualization community
Cited by: 10
Author(s): Christopher W. Bartlett, Soo Yeon Cheong, Liping Hou, Jesse Paquette, Pek Yee Lum, Günter Jäger, Florian Battke, Corinna Vehlow, Julian Heinrich, Kay Nieselt, Ryo Sakai, Jan Aerts, William C. Ray
Software Mentions: 3
Published: over 14 years ago

10.1371/journal.pone.0131673

Tissue-Specific Evolution of Protein Coding Genes in Human and Mouse
Cited by: 43
Author(s): Nadezda Kryuchkova-Mostacci, Marc Robinson‐Rechavi
Software Mentions: 3
Published: over 11 years ago

10.3390/cancers12040820

Frequent FOXA1-Activating Mutations in Extramammary Paget’s Disease
Cited by: 12
Author(s): Takuya Takeichi, Yusuke Okuno, Takaaki Matsumoto, Nobuyuki Tsunoda, Kyogo Suzuki, Kana Tanahashi, Michihiro Kono, Toyone Kikumori, Yoshinao Muro, Masashi Akiyama
Software Mentions: 3
Published: over 6 years ago

10.1186/s12864-017-4110-y

Evolution and expression analysis reveal the potential role of the HD-Zip gene family in regulation of embryo abortion in grapes (Vitis vinifera L.)
Cited by: 45
Author(s): Zhiqian Li, Chen Zhang, Yurui Guo, Weili Niu, Yuejin Wang, Yan Xu
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pone.0027121

Whole-Genome Comparison of Two Campylobacter jejuni Isolates of the Same Sequence Type Reveals Multiple Loci of Different Ancestral Lineage
Cited by: 27
Author(s): Patrick J. Biggs, Paul Fearnhead, Grant S. Hotter, Vathsala Mohan, Julie Collins-Emerson, Errol Kwan, Thomas E. Besser, Adrian L. Cookson, Philip E. Carter, Nigel P. French
Software Mentions: 3
Published: almost 15 years ago

10.3390/biom8040182

Identification of the Genetic Variation and Gene Exchange between Citrus Trifoliata and Citrus Clementina
Cited by: 4
Author(s): Tianjia Liu, Jingjing Zhou, Fa-Yi Chen, Zhi-Meng Gan, Yongping Li, Jin‐Zhi Zhang, Chun-Gen Hu
Software Mentions: 3
Published: almost 8 years ago

10.1186/s12870-019-2122-2

Target sequencing reveals genetic diversity, population structure, core-SNP markers, and fruit shape-associated loci in pepper varieties
Cited by: 29
Author(s): Heshan Du, Jingjing Yang, Bin Chen, Xiaofen Zhang, Jian Zhang, Kun Yang, Sansheng Geng, Changlong Wen
Software Mentions: 3
Published: almost 7 years ago

10.1186/1754-6834-7-66

The complete genome of Blastobotrys (Arxula) adeninivorans LS3 - a yeast of biotechnological interest
Cited by: 55
Author(s): Gotthard Kunze, Claude Gaillardin, Małgorzata Czernicka, Pascal Durrens, Tiphaine Martin, Erik Böer, Toni Gabaldón, José Almeida Cruz, Emmanuel Talla, Christian Marck, André Goffeau, Valérie Barbe, Philippe Baret, Keith Baronian, Sebastian Beier, Claudine Bleykasten, R. Bode, Serge Casarégola, Laurence Despons, Cécile Fairhead, Martin Giersberg, Przemysław Piotr Gierski, Urs Hähnel, Anja Hartmann, Dagmara Jankowska, Claire Jubin, Paul P. Jung, Ingrid Lafontaine, Véronique Leh-Louis, Marc Lemaire, Marina Marcet‐Houben, Martin Mascher, Guillaume Morel, Guy‐Franck Richard, Jan Riechen, Christine Sacerdot, Anasua Sarkar, Guilhem Savel, Joseph Schacherer, David James Sherman, Nils Stein, Marie Laure Straub, Agnès Thierry, Anke Trautwein-Schult, Benoît Vacherie, Éric Westhof, Sebastian Worch, Bernard Dujon, Jean Luc Souciet, Patrick Wincker, Uwe Scholz, Cécile Neuvéglise
Software Mentions: 3
Published: almost 13 years ago

10.1371/journal.pone.0231867

Characterizing rhizome bud dormancy in Polygonatum kingianum: Development of novel chill models and determination of dormancy release mechanisms by weighted correlation network analysis
Cited by: 4
Author(s): Yue Wang, Donovan Bailey, Shikai Yin, Xin Dong
Software Mentions: 3
Published: over 6 years ago

10.3390/s20123362

The Role of Dactylis Glomerata and Diesel Oil in the Formation of Microbiome and Soil Enzyme Activity
Cited by: 13
Author(s): Agata Borowik, Jadwiga Wyszkowska, M. Kucharski, J. Kucharski
Software Mentions: 3
Published: over 6 years ago

10.1186/s12870-018-1386-2

High-resolution genetic linkage map of European pear (Pyrus communis) and QTL fine-mapping of vegetative budbreak time
Cited by: 23
Author(s): Gilad Gabay, Yardena Dahan, Yacov Izhaki, Adi Faigenboim, Giora Ben-Ari, Yonatan Elkind, Moshe A. Flaishman
Software Mentions: 3
Published: about 8 years ago

10.1186/s12864-020-06877-4

Pervasive duplication, biased molecular evolution and comprehensive functional analysis of the PP2C family in Glycine max
Cited by: 4
Author(s): Kai Fan, Yunrui Chen, Zhijun Mao, Fang Yao, Zhaowei Li, Weiwei Lin, Yongqiang Zhang, Jianping Liu, Jinwen Huang
Software Mentions: 3
Published: over 6 years ago

10.1038/s42003-020-1060-8

The genome of pest Rhynchophorus ferrugineus reveals gene families important at the plant-beetle interface
Cited by: 36
Author(s): Khaled M. Hazzouri, Naganeeswaran Sudalaimuthuasari, Biduth Kundu, David R. Nelson, Mohammad Ali Al-Deeb, Alain Le Mansour, J. Spencer Johnston, Claude Desplan, Khaled M. A. Amiri
Software Mentions: 3
Published: over 6 years ago

10.3389/fninf.2018.00052

BRANT: A Versatile and Extendable Resting-State fMRI Toolkit
Cited by: 49
Author(s): Kaibin Xu, Yong Liu, Yafeng Zhan, Jiaji Ren, Tianzi Jiang
Software Mentions: 3
Published: about 8 years ago

10.3389/fneur.2020.00184

Identification of Co-expressed Genes Between Atrial Fibrillation and Stroke
Cited by: 13
Author(s): Yanfei Zhang, Ling‐Bing Meng, Meng-lei Hao, Jiao Yang, Tong Zou
Software Mentions: 3
Published: over 6 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

10.1016/j.celrep.2019.05.014

Breakage-Fusion-Bridge Events Trigger Complex Genome Rearrangements and Amplifications in Developmentally Arrested T Cell Lymphomas
Cited by: 13
Author(s): Joy J. Bianchi, Valentine Murigneux, Marie Bedora-Faure, Chloé Lescale, Ludovic Deriano
Software Mentions: 3
Published: over 7 years ago

10.3389/fnins.2017.00358

Altered Functional Connectivity Following an Inflammatory White Matter Injury in the Newborn Rat: A High Spatial and Temporal Resolution Intrinsic Optical Imaging Study
Cited by: 7
Author(s): Edgar Guevara, Wyston C. Pierre, Camille Tessier, Luis Akakpo, Irène Londono, Frédéric Lesage, Gregory A. Lodygensky
Software Mentions: 3
Published: over 9 years ago

10.1073/pnas.2005536117

Molecular causes of an evolutionary shift along the parasitism–mutualism continuum in a bacterial symbiont
Cited by: 12
Author(s): Paul Herrera, Lisa N Schuster, Cécilia Wentrup, Lena König, Thomas Kempinger, Hyunsoo Na, Jasmin Schwarz, Stephan Köstlbacher, Florian Wascher, Markus Zojer, Thomas Rattei, Matthias Horn
Software Mentions: 3
Published: about 6 years ago

10.1093/pcmedi/pbab012

Spaceflight decelerates the epigenetic clock orchestrated with a global alteration in DNA methylome and transcriptome in the mouse retina
Cited by: 7
Author(s): Zhong Chen, Seta Stanbouly, Nina C. Nishiyama, Xin Chen, Michael D. Delp, Hongyu Qiu, Xiao Wen Mao, Charles Wang
Software Mentions: 3
Published: over 5 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

10.3389/fonc.2021.591893

Screening and Identification of Key Biomarkers of Gastric Cancer: Three Genes Jointly Predict Gastric Cancer
Cited by: 3
Author(s): Mengjie Shan, Ling‐Bing Meng, Peng Guo, Yuanmeng Zhang, Dexian Kong, Ya-Bin Liu
Software Mentions: 3
Published: about 5 years ago

10.3390/ijerph17031009

Geographical Patterns of Algal Communities Associated with Different Urban Lakes in China
Cited by: 15
Author(s): Shengnan Chen, Hao He, Rongrong Zong, Kaiwen Liu, Miaomiao Yan, Lei Xu, Yutian Miao
Software Mentions: 3
Published: over 6 years ago

10.3389/fonc.2018.00183

Genome-Wide Analysis of Interchromosomal Interaction Probabilities Reveals Chained Translocations and Overrepresentation of Translocation Breakpoints in Genes in a Cutaneous T-Cell Lymphoma Cell Line
Cited by: 8
Author(s): Anne Steininger, Grit Ebert, B Becker, Chalid Assaf, Markus Möbs, Christian A. Schmidt, Piotr Grabarczyk, Lars Riff Jensen, Grzegorz K. Przybylski, Matthias Port, Andreas W. Kuß, Reinhard Ullmann
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.ppat.1008778

Profiling of immune related genes silenced in EBV-positive gastric carcinoma identified novel restriction factors of human gammaherpesviruses
Cited by: 11
Author(s): Guillaume Fiches, Dawei Zhou, Weili Kong, Ayan Biswas, Elshafa H. Ahmed, Robert A. Baiocchi, Jian Zhu, Netty Santoso
Software Mentions: 3
Published: about 6 years ago

10.3390/ijms19092525

Opposite Polarity Monospore Genome De Novo Sequencing and Comparative Analysis Reveal the Possible Heterothallic Life Cycle of Morchella importuna
Cited by: 28
Author(s): Wei Liu, LianFu Chen, Yingli Cai, Qianqian Zhang, Yinbing Bian
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.ppat.1008337

Comprehensive analysis of iron utilization by Mycobacterium tuberculosis
Cited by: 52
Author(s): Lei Zhang, R. Curtis Hendrickson, Virginia Meikle, Elliot J. Lefkowitz, Thomas R. Ioerger, Michael Niederweis
Software Mentions: 3
Published: over 6 years ago

10.1093/jxb/erz256

Dissecting the genome-wide genetic variants of milling and appearance quality traits in rice
Cited by: 24
Author(s): Gopal Misra, Roslen Anacleto, Saurabh Badoni, Vito M. Butardo, Lilia Molina, Andreas Graner, Matty Demont, Matthew K. Morell, Nese Sreenivasulu
Software Mentions: 3
Published: over 7 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

10.3389/fpls.2020.00176

Performance of Mapping Approaches for Whole-Genome Bisulfite Sequencing Data in Crop Plants
Cited by: 14
Author(s): Claudius Grehl, M. Wagner, Ioana Lemnian, Bruno Glaser, Ivo Große
Software Mentions: 3
Published: over 6 years ago