pypi: blast | Projects | Ecosyste.ms: Papers

10.1371/journal.pgen.1004531

Positive Selection and Multiple Losses of the LINE-1-Derived L1TD1 Gene in Mammals Suggest a Dual Role in Genome Defense and Pluripotency
Cited by: 21
Author(s): Richard N. McLaughlin, Janet M. Young, Lei Yang, Rafik Neme, Holly A. Wichman, Harmit S. Malik
Software Mentions: 3
Published: about 12 years ago

10.1155/2015/292950

Challenges of the Unknown: Clinical Application of Microbial Metagenomics
Cited by: 14
Author(s): Graham Rose, David Wooldridge, Catherine Anscombe, Edward T. Mee, Raju Misra, Saheer E. Gharbia
Software Mentions: 3
Published: over 11 years ago

10.1186/1471-2148-7-135

Extensive variation in synonymous substitution rates in mitochondrial genes of seed plants
Cited by: 220
Author(s): Jeffrey P. Mower, Pascal Touzet, Julie S Gummow, Lynda F. Delph, Jeffrey D. Palmer
Software Mentions: 3
Published: about 19 years ago

10.3389/fmicb.2018.01635

New Biological Insights Into How Deforestation in Amazonia Affects Soil Microbial Communities Using Metagenomics and Metagenome-Assembled Genomes
Cited by: 49
Author(s): Marie E. Kroeger, Tom O. Delmont, A. Murat Eren, Kyle Meyer, Jiarong Guo, Kiran Yasmin Khan, Jorge L. Mazza Rodrigues, Brendan J. M. Bohannan, Susannah G. Tringe, Clóvis Daniel Borges, James M. Tiedje, Siu Mui Tsai, Klaus Nüsslein
Software Mentions: 3
Published: about 8 years ago

10.3389/fcimb.2020.00374

TickSialoFam (TSFam): A Database That Helps to Classify Tick Salivary Proteins, a Review on Tick Salivary Protein Function and Evolution, With Considerations on the Tick Sialome Switching Phenomenon
Cited by: 36
Author(s): José M. C. Ribeiro, Ben J. Mans
Software Mentions: 3
Published: about 6 years ago

10.1099/ijsem.0.004837

Belnapia mucosa sp. nov. and Belnapia arida sp. nov., isolated from desert biocrust
Cited by: 7
Author(s): Esther Molina‐Menor, Àngela Vidal‐Verdú, Leila Satari, Alba Calonge-García, Javier Pascual, Juli Peretó, Manuel Porcar
Software Mentions: 3
Published: about 5 years ago

10.1111/febs.14976

Burkholderia pseudomallei <scp>d</scp> ‐alanine‐ <scp>d</scp> ‐alanine ligase; detailed characterisation and assessment of a potential antibiotic drug target
Cited by: 3
Author(s): L. Diaz-Saez, Leah S. Torrie, Stuart P. McElroy, David W. Gray, William N. Hunter
Software Mentions: 3
Published: about 7 years ago

10.1002/2211-5463.12084

Age‐dependent transcriptional and epigenomic responses to light exposure in the honey bee brain
Cited by: 15
Author(s): Nils B. Becker, Robert Kucharski, Wolfgang Rößler, Ryszard Maleszka
Software Mentions: 3
Published: over 10 years ago

10.3389/fcimb.2020.00041

Tick-Borne Encephalitis Virus Infection Alters the Sialome of Ixodes ricinus Ticks During the Earliest Stages of Feeding
Cited by: 9
Author(s): Charles E. Hart, José M. C. Ribeiro, Mária Kazimírová, Saravanan Thangamani
Software Mentions: 3
Published: over 6 years ago

10.1186/1471-2164-8-428

Genome-wide transcriptional analysis of grapevine berry ripening reveals a set of genes similarly modulated during three seasons and the occurrence of an oxidative burst at vèraison
Cited by: 226
Author(s): S. Pilati, Michele Perazzolli, A. Malossini, Alessandro Cestaro, L. Dematté, Paolo Fontana, A. Dal Rì, Roberto Viola, Riccardo Velasco, C. Moser
Software Mentions: 3
Published: almost 19 years ago

10.1111/j.1742-4658.2009.06893.x

Talin 2 is a large and complex gene encoding multiple transcripts and protein isoforms
Cited by: 58
Author(s): Emmanuel Debrand, Yasmine El Jai, Lorraine Spence, Neil Bate, Uta Praekelt, Catrin Pritchard, Susan J. Monkley, David R. Critchley
Software Mentions: 3
Published: over 17 years ago

10.1186/1471-2105-15-61

CDSbank: taxonomy-aware extraction, selection, renaming and formatting of protein-coding DNA or amino acid sequences
Cited by: 2
Author(s): Bart Hazes
Software Mentions: 3
Published: over 12 years ago

10.1186/1471-2164-15-853

Cyclic nucleotide-gated ion channel gene family in rice, identification, characterization and experimental analysis of expression response to plant hormones, biotic and abiotic stresses
Cited by: 109
Author(s): Zarqa Nawaz, Kaleem Ullah Kakar, Mumtaz Ali Saand, Qingyao Shu
Software Mentions: 3
Published: almost 12 years ago

10.1186/1471-2164-12-104

Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae)
Cited by: 176
Author(s): José Blanca, Joaquı́n Cañizares, Cristina Roig, Peio Ziarsolo, F. Nuez, Belén Picó
Software Mentions: 3
Published: over 15 years ago

10.1128/AEM.02885-19

Nutrient Level Determines Biofilm Characteristics and Subsequent Impact on Microbial Corrosion and Biocide Effectiveness
Cited by: 48
Author(s): Silvia J. Salgar-Chaparro, Kateřina Lepková, Thunyaluk Pojtanabuntoeng, Adam Darwin, Laura L. Machuca
Software Mentions: 3
Published: over 6 years ago

10.1186/s12859-015-0833-4

GigaTON: an extensive publicly searchable database providing a new reference transcriptome in the pacific oyster Crassostrea gigas
Cited by: 33
Author(s): Guillaume Rivière, Christophe Klopp, Ibouniyamine Nabihoudine, Arnaud Huvet, Pierre Boudry, Pascal Favrel
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pgen.1000732

Exceptional Diversity, Non-Random Distribution, and Rapid Evolution of Retroelements in the B73 Maize Genome
Cited by: 332
Author(s): Regina S. Baucom, James C. Estill, Cristian Chaparro, Naadira C. Upshaw, Ansuya Jogi, Jean-Marc Deragon, Richard P. Westerman, Phillip SanMiguel, Jeffrey L. Bennetzen
Software Mentions: 3
Published: almost 17 years ago

10.3390/biology10080732

Sequencing and Chromosome-Scale Assembly of Plant Genomes, Brassica rapa as a Use Case
Cited by: 10
Author(s): Benjamin Istace, Caroline Belser, Cyril Falentin, Karine Labadie, Franz Boideau, Gwenaëlle Deniot, Loeiz Maillet, Corinne Cruaud, Laurie Bertrand, Anne‐Marie Chèvre, Patrick Wincker, Mathieu Rousseau‐Gueutin, Jean‐Marc Aury
Software Mentions: 3
Published: about 5 years ago

10.3389/fmicb.2014.00531

Phylogeny and phylogeography of functional genes shared among seven terrestrial subsurface metagenomes reveal N-cycling and microbial evolutionary relationships
Cited by: 58
Author(s): Maggie C. Y. Lau, Connor Cameron, Cara Magnabosco, C. Titus Brown, Faye Schilkey, Sharon L. Grim, Sarah Hendrickson, Michael J. Pullin, Barbara Sherwood Lollar, Esta van Heerden, Thomas L. Kieft, Tullis C. Onstott
Software Mentions: 3
Published: almost 12 years ago

10.1534/g3.111.001834

Integration of the Draft Sequence and Physical Map as a Framework for Genomic Research in Soybean (Glycine max (L.) Merr.) and Wild Soybean (Glycine soja Sieb. and Zucc.)
Cited by: 8
Author(s): Jung Min Ha, Brian Abernathy, William M. Nelson, David Grant, Xiaolei Wu, Henry T. Nguyen, Gary Stacey, Yeisoo Yu, Rod A. Wing, Randy C. Shoemaker, Scott A. Jackson
Software Mentions: 3
Published: over 14 years ago

10.7554/eLife.23435

Co-expression of xenopsin and rhabdomeric opsin in photoreceptors bearing microvilli and cilia
Cited by: 49
Author(s): Oliver Vöcking, Ioannis Kourtesis, Sharat Chandra Tumu, Harald Hausen
Software Mentions: 3
Published: about 9 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

10.1186/1758-2946-6-33

In Silicotarget fishing: addressing a “Big Data” problem by ligand-based similarity rankings with data fusion
Cited by: 46
Author(s): Xian Liu, Xu Yue, Shanshan Li, Yulan Wang, Jiantang Peng, Cheng Luo, Xiaomin Luo, Mingyue Zheng, Kaixian Chen, Hualiang Jiang
Software Mentions: 3
Published: over 12 years ago

10.1038/s41437-021-00438-5

Whole genome sequencing reveals high differentiation, low levels of genetic diversity and short runs of homozygosity among Swedish wels catfish
Cited by: 7
Author(s): Axel Jensen, Mette Lillie, Kristofer Bergström, Per Larsson, Jacob Höglund
Software Mentions: 3
Published: over 5 years ago

10.1093/gigascience/giaa148

Chromosome-level reference genome of the European wasp spiderArgiope bruennichi: a resource for studies on range expansion and evolutionary adaptation
Cited by: 29
Author(s): Monica M. Sheffer, Anica Hoppe, Henrik Krehenwinkel, Gabriele Uhl, Andreas W. Kuß, Lars Riff Jensen, C. J. Jensen, Rosemary G. Gillespie, Katharina J. Hoff, Stefan Prost
Software Mentions: 3
Published: over 5 years ago

10.1111/jcmm.14154

Absence of PARP‐1 affects Cxcl12 expression by increasing DNA demethylation
Cited by: 7
Author(s): Anja Tolić, Nevena Grdović, Svetlana Dinić, Jovana Rajić, Miloš Đorđević, Marija Sinadinović, Jelena Arambašić Jovanović, Mirjana Mihailović, Goran Poznanović, Aleksandra Uskoković, Melita Vidaković
Software Mentions: 3
Published: over 7 years ago

10.1038/s41597-020-0480-0

An improved high-quality genome assembly and annotation of Tibetan hulless barley
Cited by: 23
Author(s): Xingquan Zeng, Tong Xu, Zhihao Ling, Yulin Wang, Xiangfeng Li, Shuqing Xu, Qijun Xu, Zha Sang, Wangmu Qimei, Yuzhen Basang, Jiabu Dunzhu, Mingzhai Yu, Hongjun Yuan, Nyima Tashi
Software Mentions: 3
Published: over 6 years ago

10.1186/gb-2007-8-11-r242

Quantification of ortholog losses in insects and vertebrates
Cited by: 60
Author(s): Stefan Wyder, Evgenia V. Kriventseva, Reinhard Schröder, Tatsuhiko Kadowaki, Evgeny M. Zdobnov
Software Mentions: 3
Published: over 19 years ago

10.1111/jcmm.16550

Effect of lncRNA‐ATB/miR‐651‐3p/Yin Yang 1 pathway on trophoblast‐endothelial cell interaction networks
Cited by: 10
Author(s): Yangxue Yin, Jiashuo Zhang, Hongbiao Yu, Min Liu, Xuelian Zheng, Rong Zhou
Software Mentions: 3
Published: over 5 years ago

10.1038/s41438-020-00424-8

Genome sequencing and phylogenetic analysis of allotetraploid Salix matsudana Koidz
Cited by: 24
Author(s): Jian Zhang, Huwei Yuan, Yujuan Li, Yanhong Chen, Guoyuan Liu, Meixia Ye, Chunmei Yu, Bolin Lian, Fei Zhong, Yuna Jiang, Junfeng Xu
Software Mentions: 3
Published: almost 6 years ago

10.1111/jam.12516

Bacterial community dynamics during the early stages of biofilm formation in a chlorinated experimental drinking water distribution system: implications for drinking water discolouration
Cited by: 78
Author(s): Isabel Douterelo, Rebecca Sharpe, Joby Boxall
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.ppat.1000181

Evidence for Restriction of Ancient Primate Gammaretroviruses by APOBEC3 but Not TRIM5α Proteins
Cited by: 35
Author(s): David Pérez-Caballero, Steven J. Soll, Paul D. Bieniasz
Software Mentions: 3
Published: almost 18 years ago

10.18632/oncotarget.27406

Characterization of unique PMEPA1 gene splice variants (isoforms d and e) from RNA Seq profiling provides novel insights into prognostic evaluation of prostate cancer
Cited by: 7
Author(s): Shashwat Sharad, Allissa Dillman, Zsófia Sztupinszki, Zoltán Szállási, Inger L. Rosner, Jennifer Cullen, Shiv Srivastava, Alagarsamy Srinivasan, Hua Li
Software Mentions: 3
Published: over 6 years ago

10.1016/j.sjbs.2021.03.036

Structure insights of SARS-CoV-2 open state envelope protein and inhibiting through active phytochemical of ayurvedic medicinal plants from Withania somnifera
Cited by: 7
Author(s): Raed Alharbi
Software Mentions: 3
Published: over 5 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: over 14 years ago

10.1186/gb-2012-13-2-r14

Chromatin structure changes around satellite repeats on the Schistosoma mansoni female sex chromosome suggest a possible mechanism for sex chromosome emergence
Cited by: 30
Author(s): Julie M. J. Lepesant, Céline Cosseau, Jérôme Boissier, Michael Freitag, Julien Portela, Déborah Climent, Cécile Perrin, Adhemar Zerlotini, Christoph Grunau
Software Mentions: 3
Published: over 14 years ago

10.1186/2047-217X-2-10

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
Cited by: 584
Author(s): Keith Bradnam, Joseph Fass, A. A. Alexandrov, Paul Baranay, Michael Bechner, İnanç Birol, Sébastien Boisvert, Jarrod Chapman, Guillaume Chapuis, Rayan Chikhi, Hamidreza Chitsaz, Wen Chi Chou, Jacques Corbeil, Cristian Del Fabbro, T. Roderick Docking, Richard Durbin, Dent Earl, Scott J. Emrich, P.I. Fedotov, Nuno A. Fonseca, Ganeshkumar Ganapathy, Richard A. Gibbs, Sante Gnerre, Élénie Godzaridis, Steve Goldstein, Matthias Haimel, Giles Hall, David Haussler, Joseph Hiatt, Isaac Ho, Jason T. Howard, Martin Hunt, Shaun D. Jackman, David B. Jaffe, Erich D. Jarvis, Huaiyang Jiang, С. В. Казаков, Paul J. Kersey, Jacob O. Kitzman, James Knight, Sergey Koren, Tak Wah Lam, Dominique Lavenier, François Laviolette, Yingrui Li, Zhenyu Li, Binghang Liu, Yue Liu, Ruibang Luo, Iain MacCallum, Matthew D. MacManes, Nicolas Maillet, Sergey Melnikov, Delphine Naquin, Zemin Ning, Thomas D. Otto, Benedict Paten, Octávio S. Paulo, Adam M. Phillippy, Francisco Pina‐Martins, Michael Place, Dariusz Przybylski, Xiang Qin, Carson Qu, Filipe J. Ribeiro, Stephen Richards, Daniel S. Rokhsar, J. Graham Ruby, Simone Scalabrin, Michael C. Schatz, David C. Schwartz, Alexey Sergushichev, Ted Sharpe, Timothy I. Shaw, Jay Shendure, Yujian Shi, Jared T. Simpson, Henry Song, Fedor Tsarev, Francesco Vezzi, Riccardo Vicedomini, Bruno Miguel Vieira, Jun Wang, Kim C. Worley, Shuangye Yin, Siu Ming Yiu, Jianying Yuan, Guojie Zhang, Hao Zhang, Shiguo Zhou, Ian F Korf
Software Mentions: 3
Published: about 13 years ago

10.1093/gigascience/gix040

A combined meta-barcoding and shotgun metagenomic analysis of spontaneous wine fermentation
Cited by: 52
Author(s): Peter R. Sternes, Danna Lee, Dariusz R. Kutyna, Anthony R. Borneman
Software Mentions: 3
Published: over 9 years ago

10.1093/jxb/erv553

Comparative cell-specific transcriptomics reveals differentiation of C4photosynthesis pathways in switchgrass and other C4lineages
Cited by: 45
Author(s): Xiaolan Rao, Nan Lu, Guifen Li, Jin Nakashima, Yuhong Tang, Richard A. Dixon
Software Mentions: 3
Published: over 10 years ago

10.1186/s13059-016-0883-6

Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes
Cited by: 156
Author(s): Anna Vlasova, Salvador Capella-Gutiérrez, Martha Rendón-Anaya, Miguel Ángel Hernández‐Oñate, André E. Minoche, Ionas Erb, Francisco Câmara, Pablo Prieto Barja, André Corvelo, Walter Sanseverino, Gastón Westergaard, Juliane C. Dohm, George J. Pappas, Soledad Saburido-Álvarez, Darek Kedra, Irene González González, Luca Cozzuto, Jèssica Gómez-Garrido, María A. Aguilar-Morón, Núria Andreu, O. Mario Aguilar, Jordi García-Más, Maik Zehnsdorf, Martı́n Vázquez, Alfonso Delgado‐Salinas, Luis Delaye, Ernesto Lowy, Alejandro Mentaberry, Rosana Pereira Vianello-Brondani, José Luis Garcı́a, Tyler Alioto, Federico Sánchez, Heinz Himmelbauer, Marta Santalla, Cédric Notredame, Toni Gabaldón, Alfredo Herrera-Estrella, Roderic Guigó
Software Mentions: 3
Published: over 10 years ago

10.1038/srep39749

An expressed, endogenous Nodavirus-like element captured by a retrotransposon in the genome of the plant parasitic nematode Bursaphelenchus xylophilus
Cited by: 13
Author(s): James A. Cotton, Sascha Steinbiss, Toshiro Yokoi, Isheng Jason Tsai, Taisei Kikuchi
Software Mentions: 3
Published: almost 10 years ago

10.1093/gigascience/giy075

Binning enables efficient host genome reconstruction in cnidarian holobionts
Cited by: 15
Author(s): Juan Sebastián Celis, Daniel Wibberg, Catalina Ramírez‐Portilla, Oliver Rupp, Alexander Sczyrba, Anderson M. Winkler, Jörn Kalinowski, Thomas Wilke
Software Mentions: 3
Published: about 8 years ago

10.1186/s13059-016-1090-1

Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx
Cited by: 119
Author(s): Federico Abascal, André Corvelo, Fernando Cruz, José Luis Villanueva‐Cañas, Anna Vlasova, Marina Marcet‐Houben, Begoña Martínez‐Cruz, Jade Yu Cheng, Pablo Prieto, Vı́ctor Quesada, Javier Quilez, Gang Li, Francisca García, Miriam Rubio-Camarillo, Leonor Frías, Paolo Ribeca, Salvador Capella-Gutiérrez, José Manuel Vázquez Rodríguez, Francisco Câmara, Ernesto Lowy, Luca Cozzuto, Ionas Erb, Michael L. Tress, José Manuel Rodriguez, Jorge Ruiz-Orera, Ferrán Reverter, Mireia Casas-Marcé, Laura García-España Soriano, Javier R. Arango, Sophia Derdak, Beatriz Galán, Julie Blanc, Marta Gut, Belén Lorente-Galdós, Marta Andrés-Nieto, Carlos López‐Otín, Alfonso Valencia, Ivo Gut, José Luis Garcı́a, Roderic Guigó, William J. Murphy, Aurora Ruiz‐Herrera, Tomàs Marquès-Bonet, Guglielmo Roma, Cédric Notredame, Thomas Mailund, Mar Albà, Toni Gabaldón, Tyler Alioto, José A. Godoy
Software Mentions: 3
Published: almost 10 years ago

10.1111/jcmm.16358

Analysis of T‐cell receptor repertoire in peripheral blood of patients with pancreatic cancer and other pancreatic diseases
Cited by: 2
Author(s): Hui Wang, Yue Yuan, Chunfeng Lu, Siqi Zhou, Yixuan Zhang, Jing Zhao, Chenghu Xu, Jie Yang, Haochen Su, Borui Li, Xi-Han Li, Pin Wang, Guifang Xu, Lei Wang, Xiaoping Zou, Shanshan Bao, Shu Zhang, Ying Lv
Software Mentions: 2
Published: over 5 years ago

10.1186/s12711-018-0442-6

Copy number variation in the MSRB3 gene enlarges porcine ear size through a mechanism involving miR-584-5p
Cited by: 26
Author(s): Congying Chen, Chenlong Liu, Xinwei Xiong, Shouguo Fang, Hui Yang, Zhiyan Zhang, Jun Ren, Yuanmei Guo, Lusheng Huang
Software Mentions: 2
Published: almost 8 years ago

10.1186/gb-2007-8-1-r9

Cited by: 52
Author(s): John Wang, Stephanie Jemielity, Paolo Uva, Yannick Wurm, Johannes Gräff, Laurent Keller
Software Mentions: 2
Published: over 19 years ago

10.1186/s13059-016-0915-2

CRISPR library designer (CLD): software for multispecies design of single guide RNA libraries
Cited by: 64
Author(s): Florian Heigwer, Tianzuo Zhan, Marco Breinig, J. Winter, Dirk Brügemann, Svenja Leible, Michael Boutros
Software Mentions: 2
Published: over 10 years ago

10.1186/s13059-020-01980-x

Diverse genetic mechanisms underlie worldwide convergent rice feralization
Cited by: 47
Author(s): Jie Qiu, Jia Lu, Dongya Wu, Xifang Weng, Lijuan Chen, Jian Sun, Meihong Chen, Limin Mao, Bowen Jiang, Chu-Yu Ye, Guilherme Menegol Turra, Longbiao Guo, Guoyou Ye, Qian Zhu, Toshiyuki Imaizumi, Beng Kah Song, Laura Scarabel, Aldo Merotto, Kenneth M. Olsen, Longjiang Fan
Software Mentions: 2
Published: over 6 years ago

10.1093/gbe/evz266

Evolutionary History of the Toll-Like Receptor Gene Family across Vertebrates
Cited by: 64
Author(s): Guangshuai Liu, Huanxin Zhang, Chao Zhao, Honghai Zhang
Software Mentions: 2
Published: almost 7 years ago

10.1186/s13073-015-0259-7

Whole-genome sequencing reveals transmission of vancomycin-resistant Enterococcus faecium in a healthcare network
Cited by: 58
Author(s): Hayley J. Brodrick, Kathy E. Raven, Ewan M. Harrison, Beth Blane, Sandra Reuter, M. Estée Török, Julian Parkhill, Sharon J. Peacock
Software Mentions: 2
Published: over 10 years ago

10.1186/s13073-018-0574-x

Genomic exploration of sequential clinical isolates reveals a distinctive molecular signature of persistent Staphylococcus aureus bacteraemia
Cited by: 42
Author(s): Stefano Giulieri, Sarah L. Baines, Romain Guérillot, Torsten Seemann, Anders Gonçalves da Silva, Mark B. Schultz, Ruth C. Massey, Natasha E Holmes, Timothy P. Stinear, Benjamin P Howden
Software Mentions: 2
Published: about 8 years ago

10.1111/gbi.12316

A combined lipidomic and 16S <scp>rRNA</scp> gene amplicon sequencing approach reveals archaeal sources of intact polar lipids in the stratified Black Sea water column
Cited by: 49
Author(s): Martina Sollai, Laura Villanueva, Ellen C. Hopmans, Gert‐Jan Reichart, Jaap S. Sinninghe Damsté
Software Mentions: 2
Published: almost 8 years ago

10.1111/gcbb.12280

Association mapping in Salix viminalis L. (Salicaceae) – identification of candidate genes associated with growth and phenology
Cited by: 29
Author(s): Henrik R. Hallingbäck, Johan Fogelqvist, Stephen J. Powers, Juan Luis Turrion-Gomez, Rachel Rossiter, Joanna S. Amey, Tom Martin, Martin Weih, Niclas Gyllenstrand, A. Karp, Ulf Lagercrantz, Steven J. Hanley, Sofia Berlin, Ann Christin Rönnberg‐Wästljung
Software Mentions: 2
Published: about 11 years ago

10.1186/s13099-019-0297-6

Compositional and functional differences in human gut microbiome with respect to equol production and its association with blood lipid level: a cross-sectional study
Cited by: 23
Author(s): Wei Zheng, Yue Ma, Aihua Zhao, Tao He, Na Lyu, Zhengqiang Pan, Geqi Mao, Yan Liu, Jing Li, Peiyu Wang, Jun Wang, Baoli Zhu, Yumei Zhang
Software Mentions: 2
Published: over 7 years ago

10.1038/s41437-019-0260-9

Conservation genomic analysis reveals ancient introgression and declining levels of genetic diversity in Madagascar’s hibernating dwarf lemurs
Cited by: 14
Author(s): Rachel C. Williams, Marina B. Blanco, Jelmer W. Poelstra, Kelsie E Hunnicutt, Aaron A. Comeault, Anne D. Yoder
Software Mentions: 2
Published: about 7 years ago

10.1038/s41438-020-0265-9

Intra- and interspecific diversity analyses in the genus Eremurus in Iran using genotyping-by-sequencing reveal geographic population structure
Cited by: 8
Author(s): Hanieh Hadizadeh, Bochra Amina Bahri, Peng Qi, H. Dayton Wilde, Katrien M. Devos
Software Mentions: 2
Published: over 6 years ago

10.1038/s41438-020-0333-1

High-density genetic map construction and identification of loci controlling flower-type traits in Chrysanthemum (Chrysanthemum × morifolium Ramat.)
Cited by: 25
Author(s): Xueqin Song, Yuhui Xu, Guolian Kang, Guangxun Fan, Fan Zhang, Chengyan Deng, Silan Dai, Hua He, Huaigen Xin, Yingying Li
Software Mentions: 2
Published: about 6 years ago

10.3390/insects11110736

Gene Sequences of Potential Targets of Insecticidal PF2 Lectin Identified from the Larval De Novo Transcriptome of the Mexican Bean Weevil (Zabrotes Subfasciatus; Boheman 1833)
Cited by: 3
Author(s): Irlanda Lagarda-Díaz, Miguel Ángel Hernández‐Oñate, José Ángel Huerta‐Ocampo, Ana María Guzmán-Partida, Joy J. Winzerling, Dawn L. Geiser, Luz Vázquez–Moreno
Software Mentions: 2
Published: almost 6 years ago

10.3390/insects12060563

The Draft Genome of Yellow Stem Borer, an Agriculturally Important Pest, Provides Molecular Insights into Its Biology, Development and Specificity Towards Rice for Infestation
Cited by: 2
Author(s): Divya Kattupalli, Kalyani M. Barbadikar, B. Vishalakshi, Suneel Ballichatla, R Athulya, A. P. Padmakumari, Swati Saxena, Kishor Gaikwad, Sridhar Yerram, K. Premalatha, Sheshu Madhav Maganti
Software Mentions: 2
Published: over 5 years ago

10.1186/s40104-018-0260-2

Molecular characterization and expression patterns of Nanog gene validating its involvement in the embryonic development and maintenance of spermatogonial stem cells of farmed carp, Labeo rohita
Cited by: 14
Author(s): Swagat Kumar Patra, Vemulawada Chakrapani, Meenati Manjari Soren, Jitendra Kumar Sundaray, Manoj Panda, Hirak Kumar Barman
Software Mentions: 2
Published: over 8 years ago

10.1186/s40104-019-0408-8

Evaluation of heat stress effects on cellular and transcriptional adaptation of bovine granulosa cells
Cited by: 48
Author(s): Adnan Khan, Junling Dou, Yachun Wang, Xiaolong Jiang, Muhammad Zahoor Khan, Hanpeng Luo, Τahir Usman, Huabin Zhu
Software Mentions: 2
Published: over 6 years ago

10.1186/s40709-016-0038-7

NaCl stress-induced transcriptomics analysis of Salix linearistipularis (syn. Salix mongolica)
Cited by: 7
Author(s): Nan Gui-xian, Yan Zhang, Song Li, Imshik Lee, Tetsuo Takano, Shenkui Liu
Software Mentions: 2
Published: over 10 years ago

10.34172/jcvtr.2020.02

Novel single nucleotide mutations in exon-10 of human coagulationFactor V gene in patients with pulmonary thromboembolism
Cited by: 1
Author(s): Latheef Kasala, D. Rajasekhar, V. Vanajakshamma
Software Mentions: 2
Published: over 6 years ago

10.1002/prot.24915

The value of protein structure classification information-Surveying the scientific literature
Cited by: 19
Author(s): Naomi Fox, Steven E. Brenner, John-Marc Chandonia
Software Mentions: 2
Published: about 11 years ago

10.1186/1477-5956-8-56

Proteome changes in platelets activated by arachidonic acid, collagen, and thrombin
Cited by: 45
Author(s): Pavel Májek, Zuzana Reicheltová, Jana Štikarová, Jiřı́ Suttnar, Alžběta Sobotková, Jan E. Dyr
Software Mentions: 2
Published: almost 16 years ago

10.1186/s12284-017-0147-4

Genome-wide Association Analysis Tracks Bacterial Leaf Blight Resistance Loci In Rice Diverse Germplasm
Cited by: 48
Author(s): Christine Jade Dilla-Ermita, Erwin Tandayu, Venice Margarette Juanillas, Jeffrey Detras, Dennis N. Lozada, Maria Stefanie Dwiyanti, Casiana Vera Cruz, Edwige Gaby Nkouaya Mbanjo, E. Y. Ardales, Maria Genaleen Q. Diaz, Merlyn S. Mendioro, Michael J. Thomson, Tobias Kretzschmar
Software Mentions: 2
Published: over 9 years ago

10.1038/sdata.2015.15

De novo transcriptome assembly databases for the central nervous system of the medicinal leech
Cited by: 22
Author(s): Dror Hibsh, Hadas Schori, Sol Efroni, Orit Shefi
Software Mentions: 2
Published: over 11 years ago

10.1038/srep14446

Transcriptome and gene expression analysis of DHA producer Aurantiochytrium under low temperature conditions
Cited by: 52
Author(s): Zhenhua Ma, Yuxiang Tan, Guizhong Cui, Yingang Feng, Qiu Cui, Xiaojin Song
Software Mentions: 2
Published: almost 11 years ago

10.1038/srep17551

Transcriptomes reveal the genetic mechanisms underlying ionic regulatory adaptations to salt in the crab-eating frog
Cited by: 14
Author(s): Yong Shao, Lijun Wang, Li Zhong, Mingsheng Hong, Hong‐Man Chen, Robert W. Murphy, Dong‐Dong Wu, Yaping Zhang, Jing Che
Software Mentions: 2
Published: almost 11 years ago

10.1038/srep21016

Comparative genomics of mitochondria in chlorarachniophyte algae: endosymbiotic gene transfer and organellar genome dynamics
Cited by: 21
Author(s): Goro Tanifuji, John M. Archibald, Takeji Hashimoto
Software Mentions: 2
Published: over 10 years ago

10.1038/srep23234

A MicroRNA-Mediated Insulin Signaling Pathway Regulates the Toxicity of Multi-Walled Carbon Nanotubes in Nematode Caenorhabditis elegans
Cited by: 44
Author(s): Yunli Zhao, Yang Jiao, Dayong Wang
Software Mentions: 2
Published: over 10 years ago

10.1038/srep25708

Transcriptomic responses of the calanoid copepod Calanus finmarchicus to the saxitoxin producing dinoflagellate Alexandrium fundyense
Cited by: 28
Author(s): Vittoria Roncalli, Matthew Cieslak, Petra H. Lenz
Software Mentions: 2
Published: over 10 years ago

10.1038/srep26621

Metagenomic sequencing reveals the relationship between microbiota composition and quality of Chinese Rice Wine
Cited by: 104
Author(s): Xutao Hong, Jing Chen, Lin Liu, Huan Wu, Hai-Qin Tan, Guangfa Xie, Qian Xu, Huijun Zhang, Wenjing Yu, Lan Wang, Nan Qin
Software Mentions: 2
Published: over 10 years ago

10.1038/srep32006

Genome-wide identification of cassava R2R3 MYB family genes related to abscission zone separation after environmental-stress-induced abscission
Cited by: 26
Author(s): Wenbin Liao, Yiling Yang, Yayun Li, Gan Wang, Ming Peng
Software Mentions: 2
Published: about 10 years ago

10.1038/srep39034

Biology of archaea from a novel family Cuniculiplasmataceae (Thermoplasmata) ubiquitous in hyperacidic environments
Cited by: 26
Author(s): Olga V. Golyshina, Ilya V. Kublanov, Hai Tran, Aleksei A. Korzhenkov, Heinrich Lünsdorf, Taras Y. Nechitaylo, С. Н. Гаврилов, Stepan V. Toshchakov, Peter N. Golyshin
Software Mentions: 2
Published: almost 10 years ago

10.1186/1750-1172-8-3

Haploinsufficiency of two histone modifier genes on 6p22.3, ATXN1 and JARID2, is associated with intellectual disability
Cited by: 18
Author(s): Tuva Barøy, Doriana Misceo, Petter Strømme, Asbjørg Stray-Pedersen, Asbjørn Holmgren, Olaug K. Rødningen, Anne Blomhoff, Johan Robert Helle, Alice Stormyr, Bjørn Tvedt, Madeleine Fannemel, Eirik Frengen
Software Mentions: 2
Published: over 13 years ago

10.1186/s12967-021-02882-7

The fecal microbiota of patients with pancreatic ductal adenocarcinoma and autoimmune pancreatitis characterized by metagenomic sequencing
Cited by: 29
Author(s): Wenli Zhou, Zhang De, Zhengpeng Li, Huiqing Jiang, Jingnan Li, Rongrong Ren, Xuefeng Gao, Jianfeng Li, Xin Wang, Weifeng Wang, Yunsheng Yang
Software Mentions: 2
Published: over 5 years ago

10.1186/s12864-019-5545-0

An insight into the sialotranscriptome and virome of Amazonian anophelines
Cited by: 21
Author(s): Vera Margarete Scarpassa, Humberto Julio Debat, Ronildo Baiatone Alencar, José Ferreira Saraiva, Eric Calvo, Bruno Arcà, José M. C. Ribeiro
Software Mentions: 2
Published: over 7 years ago

10.1186/s12859-018-2452-3

PCRdrive: the largest qPCR assay archive to date and endless potential for lab workflow revitalization
Cited by: 0
Author(s): Florian Bürger, Michele Angioni, Gianluca Russo, Martina Schad, Jim Kallarackal
Software Mentions: 2
Published: almost 8 years ago

10.1111/j.1462-2920.2010.02193.x

Ironing out the wrinkles in the rare biosphere through improved OTU clustering
Cited by: 1,150
Author(s): Susan M. Huse, David B. Mark Welch, Hilary G. Morrison, Mitchell L. Sogin
Software Mentions: 2
Published: about 16 years ago

10.1186/1471-2164-11-384

Transcriptome sequencing and comparative analysis of cucumber flowers with different sex types
Cited by: 167
Author(s): Sheng Guo, Yi Zheng, Je‐Gun Joung, Shiqiang Liu, Zhonghua Zhang, Oswald Crasta, Bruno W. S. Sobral, Yong Xu, Sanwen Huang, Zhangjun Fei
Software Mentions: 2
Published: over 16 years ago

10.1080/22221751.2020.1773745

Genetic cluster analysis of SARS-CoV-2 and the identification of those responsible for the major outbreaks in various countries
Cited by: 45
Author(s): Xuemei Yang, Ning Dong, Edward Wai Chi Chan, Sheng Chen
Software Mentions: 2
Published: over 6 years ago

10.1099/mgen.0.000497

Intraspecies plasmid and genomic variation of Mycobacterium kubicae revealed by the complete genome sequences of two clinical isolates
Cited by: 7
Author(s): Jo Hendrix, L. Elaine Epperson, David Durbin, Jennifer R. Honda, Michael Strong
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2164-15-1080

Next-generation sequencing of flow-sorted wheat chromosome 5D reveals lineage-specific translocations and widespread gene duplications
Cited by: 31
Author(s): Stuart J. Lucas, Bala Anı Akpınar, Hana Šimková, Marie Kubaláková, Jaroslav Doležel, Hikmet Budak
Software Mentions: 2
Published: almost 12 years ago

10.1080/22221751.2018.1563455

Detection of human parvovirus 4 DNA in the patients with acute encephalitis syndrome during seasonal outbreaks of the disease in Gorakhpur, India
Cited by: 6
Author(s): Vidya A. Arankalle, Navin Srivastava, K. P. Kushwaha, Agnibha Sen, Ashwini Y. Ramdasi, Priyanka Patel, Sumeet Kuthe, Bangari Haldipur, Gajanan N. Sakpal, Kavita S. Lole, Nilesh Ingle
Software Mentions: 2
Published: over 7 years ago

10.1111/j.1462-2920.2008.01667.x

The Cry48Aa-Cry49Aa binary toxin fromBacillus sphaericusexhibits highly restricted target specificity
Cited by: 37
Author(s): Gareth Wyn Jones, Margaret C. Wirth, R. G. Monnerat, Colin Berry
Software Mentions: 2
Published: about 18 years ago

10.1186/1471-2105-13-334

Protein interface classification by evolutionary analysis
Cited by: 126
Author(s): José M. Duarte, Adam Srebniak, Martin A. Schärer, Guido Capitani
Software Mentions: 2
Published: almost 14 years ago

10.1186/s12864-014-1205-6

Transcriptomic characterisation and genomic glimps into the toxigenic dinoflagellate Azadinium spinosum, with emphasis on polykeitde synthase genes
Cited by: 39
Author(s): Jan M. Meyer, Christian Rödelsperger, Karsten Eichholz, Urban Tillmann, Allan Cembella, Angela McGaughran, Uwe John
Software Mentions: 2
Published: over 11 years ago

10.1007/s00284-014-0629-1

The Diversity of Bacteria Isolated from Antarctic Freshwater Reservoirs Possessing the Ability to Produce Polyhydroxyalkanoates
Cited by: 27
Author(s): Sławomir Ciesielski, Dorota Górniak, Justyna Możejko, Aleksander Świątecki, Jakub Grzesiak, Marek K. Zdanowski
Software Mentions: 2
Published: over 12 years ago

10.1002/ece3.2028

Population genomics of local adaptation versus speciation in coral reef fishes ( Hypoplectrus spp, Serranidae)
Cited by: 31
Author(s): Sophie Picq, W. Owen McMillan, Oscar Puebla
Software Mentions: 2
Published: over 10 years ago

10.1099/mgen.0.000598

A global transcriptomic analysis of Staphylococcus aureus biofilm formation across diverse clonal lineages
Cited by: 16
Author(s): Brooke R Tomlinson, Morgan E Malof, Lindsey N. Shaw
Software Mentions: 2
Published: about 5 years ago

10.1155/2019/3780245

Iterative Variable Gene Discovery from Whole Genome Sequencing with a Bootstrapped Multiresolution Algorithm
Cited by: 1
Author(s): David N. Olivieri, Francisco Gambón-Deza
Software Mentions: 2
Published: over 7 years ago

10.1099/mgen.0.000166

chewBBACA: A complete suite for gene-by-gene schema creation and strain identification
Cited by: 162
Author(s): Mickael Silva, Miguel P. Machado, Diogo N. Silva, Mirko Rossi, Jacob Moran-Gilad, Susana Santos, Mário Ramirez, João André Carriço
Software Mentions: 2
Published: over 8 years ago

10.1186/1471-2164-15-685

Discovery of common sequences absent in the human reference genome using pooled samples from next generation sequencing
Cited by: 18
Author(s): Yu Liu, Mehmet Koyutürk, Sean Maxwell, Min Xiang, Marty L Veigl, Richard S. Cooper, Bamidele O. Tayo, Li Li, Thomas LaFramboise, Benlian Wang, Xiaofeng Zhu, Mark R. Chance
Software Mentions: 2
Published: over 12 years ago

10.1016/j.csbj.2017.01.002

Deep Assessment of Genomic Diversity in Cassava for Herbicide Tolerance and Starch Biosynthesis
Cited by: 14
Author(s): Jorge Duitama, Lina Kafuri, Daniel Tello, Ana Marı́a Leiva, Bernhard J. Hofinger, Sneha Datta, Zaida Lentini, Ericson Aranzales, Bradley J. Till, Hernán Ceballos
Software Mentions: 2
Published: over 9 years ago

10.1002/ece3.5708

Multiple freshwater invasions of the tapertail anchovy (Clupeiformes: Engraulidae) of the Yangtze River
Cited by: 9
Author(s): Fangyuan Cheng, Qian Wang, Pierpaolo Maisano Delser, Chenhong Li
Software Mentions: 2
Published: almost 7 years ago

10.1111/1462-2920.13036

Closing the gaps on the viral photosystem‐ <scp>I</scp> psa <scp>DCAB</scp> gene organization
Cited by: 7
Author(s): Sheila Roitman, José Flores‐Uribe, Alon Philosof, Ben Knowles, Forest Rohwer, J. Cesar Ignacio‐Espinoza, Matthew B. Sullivan, Francisco M. Cornejo‐Castillo, Pablo Sánchez, Silvia G. Acinas, Chris L. Dupont, Oded Béjà
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0103160

Characterization of Hepatitis C Virus Genotypes by Direct Sequencing of HCV 5′UTR Region of Isolates from Saudi Arabia
Cited by: 13
Author(s): Medhat K. Shier, Mohammad S. El-Wetidy, Hebatallah H. Ali, Mohammad M. Al‐Qattan
Software Mentions: 2
Published: about 12 years ago

10.1186/1471-2164-12-164

Taxonomically restricted genes are associated with the evolution of sociality in the honey bee
Cited by: 130
Author(s): Brian R. Johnson, Neil D. Tsutsui
Software Mentions: 2
Published: over 15 years ago

10.1371/journal.pone.0208735

Genome wide characterization of enterotoxigenic Escherichia coli serogroup O6 isolates from multiple outbreaks and sporadic infections from 1975-2016
Cited by: 8
Author(s): Vaishnavi Pattabiraman, Lee S. Katz, Jessica C. Chen, Andre McCullough, Eija Trees
Software Mentions: 2
Published: over 7 years ago

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