Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: pypi: fastx
https://packages.ecosyste.ms/registries/pypi.org/packages/fastx
Just a simple kseq.h binding
3 versions
Latest release: over 4 years ago
19 downloads last month
Papers Mentioning fastx 197
10.1093/gigascience/giab039
A large-scale metagenomic survey dataset of the post-weaning piglet gut lumenCited by: 8
Author(s): Daniela Gaio, Matthew Z. DeMaere, Kay Anantanawat, G. J. Eamens, Mengmeng Liu, Tiziana Zingali, Linda Falconer, Toni A. Chapman, Steven P. Djordjevic, Aaron E. Darling
Software Mentions: 14
Published: over 3 years ago
10.3390/ijms21010167
RNA-seq and ChIP-seq as Complementary Approaches for Comprehension of Plant Transcriptional Regulatory MechanismCited by: 22
Author(s): Isiaka Ibrahim Muhammad, Sze Ling Kong, Siti Nor Akmar Abdullah, Umaiyal Munusamy
Software Mentions: 12
Published: almost 5 years ago
10.7554/eLife.51276
A genome-wide view of the de-differentiation of central nervous system endothelial cells in cultureCited by: 39
Author(s): Mark F Sabbagh, Jeremy Nathans
Software Mentions: 11
Published: almost 5 years ago
10.1093/gigascience/giz146
Systematic processing of ribosomal RNA gene amplicon sequencing dataCited by: 45
Author(s): Julien Tremblay, Étienne Yergeau
Software Mentions: 10
Published: almost 5 years ago
10.1002/ece3.8018
Delimitation despite discordance: Evaluating the species limits of a confounding species complex in the face of mitonuclear discordanceCited by: 8
Author(s): Thomas J. Firneno, Justin R. O’Neill, Michael W. Itgen, Timothy A. Kihneman, Josiah H. Townsend, Matthew K. Fujita
Software Mentions: 9
Published: about 3 years ago
10.1371/journal.pgen.1008515
Dynamic and regulated TAF gene expression during mouse embryonic germ cell developmentCited by: 15
Author(s): Megan A. Gura, Maria M. Mikedis, Kimberly A. Seymour, Dirk G. de Rooij, David C. Page, Richard N. Freiman
Software Mentions: 8
Published: almost 5 years ago
10.1186/s13073-020-00799-2
Single cell characterization of B-lymphoid differentiation and leukemic cell states during chemotherapy in ETV6-RUNX1-positive pediatric leukemia identifies drug-targetable transcription factor activitiesCited by: 20
Author(s): Juha Mehtonen, Susanna Teppo, Mari Lahnalampi, Aleksi Kokko, Riina Kaukonen, Laura Oksa, Maria Bouvy-Liivrand, Alena Malyukova, Artturi Mäkinen, Saara Laukkanen, Petri Mäkinen, Samuli Rounioja, Pekka Ruusuvuori, Olle Sangfelt, Riikka Lund, Tapio Lönnberg, Olli Lohi, Merja Heinäniemi
Software Mentions: 8
Published: almost 4 years ago
10.3389/fnins.2021.689188
Identification of the Potential Gene Regulatory Networks and Therapeutics in Aged Mice With Postoperative Neurocognitive DisorderCited by: 9
Author(s): Wensi Wu, Yongbo Peng, Jiaxin Zhou, Xiaojun Zhang, Lin Cao, Wei-Jye Lin, Yanan Lu, Jing Wen, Zhi Wang
Software Mentions: 8
Published: over 3 years ago
10.1016/j.molcel.2020.01.007
Mammalian RNA Decay Pathways Are Highly Specialized and Widely Linked to TranslationCited by: 74
Author(s): Alex Tuck, Aneliya Rankova, Alaaddin Bulak Arpat, Luz Angélica Liechti, Daniel Heß, Vytautas Iešmantavičius, Violeta Castelo-Szekely, David Gatfield, Marc Bühler
Software Mentions: 7
Published: over 4 years ago
10.1111/gcb.15302
Stream microbial communities and ecosystem functioning show complex responses to multiple stressors in wastewaterCited by: 44
Author(s): Francis J. Burdon, Yaohui Bai, Marta Reyes, Manu Tamminen, Philipp Staudacher, Simon Mangold, Heinz Singer, Katja Räsänen, Adriano Joss, Scott D. Tiegs, Jukka Jokela, Rik I.L. Eggen, Christian Stamm
Software Mentions: 7
Published: about 4 years ago
10.7554/eLife.47809
Free circular introns with an unusual branchpoint in neuronal projectionsCited by: 11
Author(s): Harleen Saini, Alicia A. Bicknell, Sean R. Eddy, Melissa J. Moore
Software Mentions: 7
Published: almost 5 years ago
10.7554/eLife.56523
DAZL mediates a broad translational program regulating expansion and differentiation of spermatogonial progenitorsCited by: 25
Author(s): Maria M. Mikedis, Yuting Fan, Peter K. Nicholls, Toshihiko Endo, Emily Jackson, Sarah A. Cobb, Dirk G. de Rooij, David C. Page
Software Mentions: 7
Published: over 4 years ago
10.1371/journal.pcbi.1003706
Metagenomic Data Utilization and Analysis (MEDUSA) and Construction of a Global Gut Microbial Gene CatalogueCited by: 54
Author(s): Fredrik Karlsson, Intawat Nookaew, Jens Nielsen
Software Mentions: 7
Published: over 10 years ago
10.1038/s41598-018-38195-x
Shared cis-regulatory architecture identified across defense response genes is associated with broad-spectrum quantitative resistance in riceCited by: 5
Author(s): Bradley W. Tonnessen, A. M. Bossa-Castro, Ramil Mauleon, Nickolai Alexandrov, Jan E. Leach
Software Mentions: 7
Published: over 5 years ago
10.1186/s13059-018-1521-2
omniCLIP: probabilistic identification of protein-RNA interactions from CLIP-seq dataCited by: 18
Author(s): Philipp Drewe-Boß, Hans-Hermann Wessels, Uwe Ohler
Software Mentions: 7
Published: about 6 years ago
10.1038/s41435-020-00118-0
Genomic profiling of T-cell activation suggests increased sensitivity of memory T cells to CD28 costimulationCited by: 13
Author(s): Dafni A. Glinos, Blagoje Soskic, Cayman Williams, Alan Kennedy, Luke Jostins, David M. Sansom, Gosia Trynka
Software Mentions: 7
Published: almost 4 years ago
10.1098/rstb.2019.0255
Dormancy dynamics and dispersal contribute to soil microbiome resilienceCited by: 34
Author(s): Jackson W Sorensen, Ashley Shade
Software Mentions: 6
Published: over 4 years ago
10.1002/ece3.5568
Host identity and phylogeny shape the foliar endophytic fungal assemblages of <i>Ficus</i>Cited by: 16
Author(s): Junwei Liu, Jin Zhao, Gang Wang, Chen Jin
Software Mentions: 6
Published: about 5 years ago
10.1111/1755-0998.13205
A new method of metabarcoding Microsporidia and their hosts reveals high levels of microsporidian infections in mosquitoes (Culicidae)Cited by: 25
Author(s): Artur Trzebny, Anna Słodkowicz-Kowalska, James J. Becnel, Neil D. Sanscrainte, Mirosława Dabert
Software Mentions: 6
Published: over 4 years ago
10.1534/g3.119.400273
DPAC: A Tool for Differential Poly(A)–Cluster Usage from Poly(A)–Targeted RNAseq DataCited by: 16
Author(s): Andrew Routh
Software Mentions: 6
Published: over 5 years ago
10.1016/j.cell.2020.05.039
Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell CarcinomaCited by: 438
Author(s): Andrew L. Ji, Adam J. Rubin, Kim Thrane, Sizun Jiang, David L. Reynolds, Robin M. Meyers, Margaret Guo, Benson M. George, Annelie Mollbrink, Joseph Bergenstråhle, Ludvig Larsson, Yunhao Bai, Bokai Zhu, Aparna Bhaduri, Jordan M. Meyers, Xavier Rovira-Clavé, S. Tyler Hollmig, Sumaira Z. Aasi, Garry P. Nolan, Joakim Lundeberg, Paul A. Khavari
Software Mentions: 6
Published: over 4 years ago
10.1155/2018/8354350
Systematic Analysis of RNA Regulatory Network in Rat Brain after Ischemic StrokeCited by: 11
Author(s): Liu Juan, Kunshan Zhang, Bin Hu, Siguang Li, Qing Li, Yuan Luo, Yang Wang, Zhifeng Deng
Software Mentions: 6
Published: almost 7 years ago
10.1186/s12967-017-1201-0
Whole blood gene expression in adolescent chronic fatigue syndrome: an exploratory cross-sectional study suggesting altered B cell differentiation and survivalCited by: 46
Author(s): Chinh Bkrong Nguyen, Lene Alsøe, Jessica M. Lindvall, Dag Sulheim, Even Fagermoen, Anette Winger, Mari Kaarbø, Hilde Nilsen, Vegard Bruun Wyller
Software Mentions: 6
Published: over 7 years ago
10.1371/journal.pone.0252365
Fusarium graminearum DICER-like-dependent sRNAs are required for the suppression of host immune genes and full virulenceCited by: 19
Author(s): B. Werner, Aline Koch, Ena Šečić, Jonas Engelhardt, Lukas Jelonek, Jens Steinbrenner, Karl‐Heinz Kogel
Software Mentions: 6
Published: over 3 years ago
10.1002/1878-0261.12138
<scp>APE</scp>1/Ref‐1 knockdown in pancreatic ductal adenocarcinoma – characterizing gene expression changes and identifying novel pathways using single‐cell <scp>RNA</scp> sequencingCited by: 26
Author(s): Fenil Shah, Emery Goossens, Nadia M. Atallah, Michelle Grimard, Mark R. Kelley, Melissa L. Fishel
Software Mentions: 5
Published: about 7 years ago
10.1038/s41598-019-40496-8
The dynamics of the antibiotic resistome in the feces of freshly weaned pigs following therapeutic administration of oxytetracyclineCited by: 41
Author(s): Mahdi Ghanbari, Viviana Klose, Fiona Crispie, Paul D. Cotter
Software Mentions: 5
Published: over 5 years ago
10.3390/microorganisms9040854
Changes in Gut Microbiota Correlates with Response to Treatment with Probiotics in Patients with Atopic Dermatitis. A Post Hoc Analysis of a Clinical TrialCited by: 15
Author(s): Eric Climent, Juan F. Martínez-Blanch, Laura Llobregat, Beatriz Ruzafa-Costas, Miguel A Carrión-Gutiérrez, A. Ramírez-Boscá, David Prieto‐Merino, Salvador Genovés, Francisco M. Codoñer, Daniel Ramón, Empar Chenoll, Vicente Navarro-López
Software Mentions: 5
Published: over 3 years ago
10.1038/s41598-018-22125-y
Gut microbial composition in patients with psoriasisCited by: 130
Author(s): Francisco M. Codoñer, A. Ramírez-Boscá, Eric Climent, Miguel A Carrión-Gutiérrez, Mariano Guerrero, Jose Manuel Pérez-Orquín, José Horga de la Parte, Salvador Genovés, Daniel Ramón, Vicente Navarro-López, Empar Chenoll
Software Mentions: 5
Published: over 6 years ago
10.18632/oncotarget.23206
Coagulation cascade and complement system in systemic lupus erythematosusCited by: 19
Author(s): Yan Liang, Shangbo Xie, Changhao Wu, Yuan Hu, Qin Zhang, Si Li, Yin‐Guang Fan, Rui‐Xue Leng, Hai‐Feng Pan, Huabao Xiong, Dong‐Qing Ye
Software Mentions: 5
Published: almost 7 years ago
10.1371/journal.pone.0231695
Genetic algorithm-based personalized models of human cardiac action potentialCited by: 18
Author(s): Dmitrii Smirnov, Andrey Pikunov, Roman Syunyaev, Ruslan Deviatiiarov, Oleg Gusev, Kedar Aras, Anna Gams, Aaron C. Koppel, Igor R. Efimov
Software Mentions: 5
Published: over 4 years ago
10.1186/s13059-021-02497-7
SRCP: a comprehensive pipeline for accurate annotation and quantification of circRNAsCited by: 7
Author(s): Alon Rabin, Michela Zaffagni, Reut Ashwal-Fluss, Inés Lucía Patop, Aarti Jajoo, Shlomo Shenzis, Liran Carmel, Sebastián Kadener
Software Mentions: 5
Published: about 3 years ago
10.3390/genes10110905
MicroRNAs in Vitis vinifera cv. Chardonnay Are Differentially Expressed in Response to Diaporthe SpeciesCited by: 5
Author(s): Aleš Eichmeier, Tomáš Kiss, Eliška Peňázová, Jakub Pečenka, Akila Berraf-Tebbal, Miroslav Baránek, Robert Pokluda, Jana Čechová, David Gramaje, Dariusz Grzebelus
Software Mentions: 5
Published: almost 5 years ago
10.1186/1471-2164-15-917
Differential expression of endogenous plant cell wall degrading enzyme genes in the stick insect (Phasmatodea) midgutCited by: 37
Author(s): Matan Shelomi, W. Cameron Jasper, Joel Atallah, Lynn S. Kimsey, Brian R. Johnson
Software Mentions: 5
Published: almost 11 years ago
10.12688/f1000research.21779.2
A role for MIR828 in pineapple fruit developmentCited by: 6
Author(s): Christopher D. Rock
Software Mentions: 5
Published: over 4 years ago
10.1002/ece3.2685
Transcriptome predictors of coral survival and growth in a highly variable environmentCited by: 53
Author(s): Rachael A. Bay, Stephen R. Palumbi
Software Mentions: 5
Published: over 7 years ago
10.18632/oncotarget.14091
The role of miR-17-92 in the miRegulatory landscape of Ewing sarcomaCited by: 13
Author(s): Raphaela Schwentner, David Herrero-Martín, Maximilian Kauer, Cornelia Mutz, Anna M. Katschnig, Grzegorz Sienski, Javier Alonso, Dave N.T. Aryee, Heinrich Kovar
Software Mentions: 5
Published: almost 8 years ago
10.1371/journal.pgen.1006639
The highly buffered Arabidopsis immune signaling network conceals the functions of its componentsCited by: 102
Author(s): Rachel Hillmer, Kazuhiko Tsuda, Ghanasyam Rallapalli, Shuji Asai, William Truman, Matthew D Papke, Hitoshi Sakakibara, Jonathan D. G. Jones, Chad L. Myers, Fumiaki Katagiri
Software Mentions: 5
Published: over 7 years ago
10.1371/journal.pone.0057190
The Poultry-Associated Microbiome: Network Analysis and Farm-to-Fork CharacterizationsCited by: 103
Author(s): Brian B. Oakley, Cesar A. Morales, J. Eric Line, M. E. Berrang, Richard J. Meinersmann, Glenn E. Tillman, Mark G. Wise, Gregory R. Siragusa, Kelli L. Hiett, Bruce S. Seal
Software Mentions: 5
Published: over 11 years ago
10.3897/mycokeys.39.28109
Great differences in performance and outcome of high-throughput sequencing data analysis platforms for fungal metabarcodingCited by: 52
Author(s): Sten Anslan, R. Henrik Nilsson, Christian Wurzbacher, Petr Baldrián, Leho Tedersoo, Mohammad Bahram
Software Mentions: 5
Published: about 6 years ago
10.1002/1878-0261.12853
Genome‐scale CRISPR screening identifies cell cycle and protein ubiquitination processes as druggable targets for erlotinib‐resistant lung cancerCited by: 10
Author(s): Jieun Lee, Ahyoung Choi, Sung Yup Cho, Yukyung Jun, Deukchae Na, Ahra Lee, Giyong Jang, Jee Young Kwon, Jaesang Kim, Sanghyuk Lee, Charles Lee
Software Mentions: 5
Published: almost 4 years ago
10.3390/nu12041063
Specific Dietary Components and Gut Microbiota Composition are Associated with Obesity in Children and Adolescents with Prader–Willi SyndromeCited by: 16
Author(s): Sonika Garcia-Ribera, Montse Amat-Bou, Eric Climent, M. Villangómez Llobet, Empar Chenoll, Raquel Corripio, Lourdes Ibáñez, Marta Ramón-Krauel, Carles Lerín
Software Mentions: 4
Published: over 4 years ago
10.3390/antiox10020323
Antioxidant Effect of a Probiotic Product on a Model of Oxidative Stress Induced by High-Intensity and Duration Physical ExerciseCited by: 17
Author(s): Maravillas Sánchez-Macarro, Vicente Ávila-Gandía, Silvia Pérez-Piñero, Fernando Cánovas, Ana María García-Muñoz, María Salud Abellán-Ruiz, Desirée Victoria-Montesinos, Antonio J. Luque-Rubia, Eric Climent, Salvador Genovés, Daniel Ramón, Empar Chenoll, Francisco Javier López-Román
Software Mentions: 4
Published: over 3 years ago
10.1093/aobpla/ply013
Patterns of alternative splicing vary between species during heat stressCited by: 25
Author(s): Sumetha Kannan, Gillian Halter, Tanya Renner, Elizabeth R. Waters
Software Mentions: 4
Published: over 6 years ago
10.1186/1471-2105-13-S17-S22
Personalized cloud-based bioinformatics services for research and education: use cases and the elasticHPC packageCited by: 20
Author(s): Mohamed El‐Kalioby, Mohamed Abouelhoda, Jan Walters Kruger, Robert Giegerich, Alexander Sczyrba, Dennis P. Wall, Peter J. Tonellato
Software Mentions: 4
Published: almost 12 years ago
10.1186/1471-2105-5-130
Cited by: 92Author(s): Sook Jung, Christopher Jesudurai, Margaret Staton, Zhidian Du, Stephen P. Ficklin, Il-Hyung Cho, Albert G. Abbott, Jeffrey Tomkins, Dorrie Main
Software Mentions: 4
Published: almost 21 years ago
10.1186/s12862-020-01689-2
Meiotic recombination in the offspring of Microbotryum hybrids and its impact on pathogenicityCited by: 2
Author(s): Britta Bueker, Marco Alexandre Guerreiro, Michael E. Hood, Andreas Brachmann, Sven Rahmann, Dominik Begerow
Software Mentions: 4
Published: about 4 years ago
10.1186/1471-2164-14-586
The importance of tissue specificity for RNA-seq: highlighting the errors of composite structure extractionsCited by: 46
Author(s): Brian R. Johnson, Joel Atallah, David C. Plachetzki
Software Mentions: 4
Published: almost 12 years ago
10.1186/s12864-017-4391-1
Profiling the onset of somatic embryogenesis in ArabidopsisCited by: 37
Author(s): Enrico Magnani, José M. Jiménez‐Gómez, Ludivine Soubigou‐Taconnat, Loïc Lepiniec, Elisa Fiume
Software Mentions: 4
Published: almost 7 years ago
10.1186/1471-2164-12-110
Strain-specific copy number variation in the intelectin locus on the 129 mouse chromosome 1Cited by: 16
Author(s): Zen H. Lu, Alex di Domenico, Steven H. Wright, Pamela Knight, Bruce Whitelaw, Alan D. Pemberton
Software Mentions: 4
Published: over 13 years ago
10.1186/s12864-020-07200-x
iCLIP analysis of RNA substrates of the archaeal exosomeCited by: 2
Author(s): Jochen Bathke, A. Susann Gauernack, Oliver Rupp, Lennart Weber, Christian Preußer, Marcus Lechner, Oliver Roßbach, Alexander Goesmann, Elena Evguenieva‐Hackenberg, Gabriele Klug
Software Mentions: 4
Published: almost 4 years ago
10.1186/1471-2229-14-29
Genome-wide data (ChIP-seq) enabled identification of cell wall-related and aquaporin genes as targets of tomato ASR1, a drought stress-responsive transcription factorCited by: 76
Author(s): Martiniano María Ricardi, Ricardo Mendoza González, Silin Zhong, Pía Guadalupe Domínguez, Tomás Duffy, Pablo Turjanski, Juan D. Salgado Salter, Karina Alleva, Fernando Carrari, James J. Giovannoni, José M. Estevez, Norberto D. Iusem
Software Mentions: 4
Published: almost 11 years ago
10.1155/2013/791051
Streaming Support for Data Intensive Cloud-Based Sequence AnalysisCited by: 7
Author(s): Shady Issa, Romeo Kienzler, Mohamed El‐Kalioby, Peter J. Tonellato, Dennis P. Wall, Rémy Bruggmann, Mohamed Abouelhoda
Software Mentions: 4
Published: almost 12 years ago
10.3390/microorganisms9091818
Sulfidogenic Microbial Communities of the Uzen High-Temperature Oil Field in KazakhstanCited by: 10
Author(s): Д. Ш. Соколова, Е. М. Семенова, Denis S. Grouzdev, Salimat K. Bidzhieva, Т. Л. Бабич, Н. Г. Лойко, A. P. Ershov, Vitaly V. Kadnikov, Alexey V. Beletsky, Andrey V. Mardanov, Nurlan S. Zhaparov, Т. Н. Назина
Software Mentions: 4
Published: about 3 years ago
10.3390/microorganisms8101611
The Microbiota Profile in Inflamed and Non-Inflamed Ileal Pouch–Anal AnastomosisCited by: 2
Author(s): Sabrina Just Kousgaard, Thomas Yssing Michaelsen, Hans Linde Nielsen, Karina Frahm Kirk, Mads Albertsen, Ole Thorlacius-Ussing
Software Mentions: 4
Published: about 4 years ago
10.15252/msb.20166869
Strand‐specific, high‐resolution mapping of modified RNA polymerase IICited by: 46
Author(s): Laura Milligan, Vân Anh Huynh-Thu, Clémentine Delan-Forino, Alex Tuck, Elisabeth Petfalski, Rodrigo Lombraña, Guido Sanguinetti, Grzegorz Kudla, David Tollervey
Software Mentions: 4
Published: over 8 years ago
10.1371/journal.pone.0114461
Inference of the Oxidative Stress Network in Anopheles stephensi upon Plasmodium InfectionCited by: 10
Author(s): Jatin Shrinet, Umesh K. Nandal, T. Adak, Raj K. Bhatnagar, Sujatha Sunil
Software Mentions: 4
Published: almost 10 years ago
10.1371/journal.pone.0204047
Transcriptomics reveal potential vaccine antigens and a drastic increase of upregulated genes during Theileria parva development from arthropod to bovine infective stagesCited by: 13
Author(s): Triza Tonui, Pilar Corredor‐Moreno, Esther Kanduma, Joyce Njuguna, Moses Njahira, Steven Ger Nyanjom, Joana C. Silva, Appolinaire Djikeng, Roger Pellé
Software Mentions: 4
Published: about 6 years ago
10.1371/journal.pone.0158811
Dynamics of the Fouling Layer Microbial Community in a Membrane BioreactorCited by: 39
Author(s): Anja Ziegler, Simon Jon McIlroy, Poul Larsen, Mads Albertsen, Aviaja Anna Hansen, Nicolas Heinen, Per Halkjær Nielsen
Software Mentions: 4
Published: over 8 years ago
10.1371/journal.pone.0132448
A Quantitative Profiling Tool for Diverse Genomic Data Types Reveals Potential Associations between Chromatin and Pre-mRNA ProcessingCited by: 5
Author(s): Isaac Kremsky, Nicolás Bellora, Eduardo Eyras
Software Mentions: 4
Published: over 9 years ago
10.1371/journal.pone.0157600
De Novo Assembly of Human Herpes Virus Type 1 (HHV-1) Genome, Mining of Non-Canonical Structures and Detection of Novel Drug-Resistance Mutations Using Short- and Long-Read Next Generation Sequencing TechnologiesCited by: 43
Author(s): Timokratis Karamitros, Ian Harrison, Renata Piorkowska, Aris Katzourakis, Gkikas Magiorkinis, Jean L. Mbisa
Software Mentions: 4
Published: over 8 years ago
10.1002/ece3.1107
An Illumina metabarcoding pipeline for fungiCited by: 103
Author(s): Miklós Bálint, Philipp-André Schmidt, Rahul Sharma, Marco Thines, Imke Schmitt
Software Mentions: 4
Published: over 10 years ago
10.1186/s12940-018-0394-x
The Ramazzini Institute 13-week pilot study on glyphosate and Roundup administered at human-equivalent dose to Sprague Dawley rats: effects on the microbiomeCited by: 78
Author(s): Qixing Mao, Fabiana Manservisi, Simona Panzacchi, Daniele Mandrioli, I Menghetti, Andrea Vornoli, Luciano Bua, Laura Falcioni, Corina Lesseur, Jia Chen, Fiorella Belpoggi, Jianzhong Hu
Software Mentions: 4
Published: over 6 years ago
10.3389/fpls.2017.01939
De novo Transcriptome Assembly and Comparison of C3, C3-C4, and C4 Species of Tribe Salsoleae (Chenopodiaceae)Cited by: 19
Author(s): Maximilian Lauterbach, Hanno Schmidt, Kumari Billakurthi, Thomas Hankeln, Peter Westhoff, Udo Gowik, Gudrun Kadereit
Software Mentions: 4
Published: almost 7 years ago
10.1534/g3.117.039396
Comparative Genomics of the Ectomycorrhizal Sister Species <i>Rhizopogon vinicolor</i> and <i>Rhizopogon vesiculosus</i> (Basidiomycota: Boletales) Reveals a Divergence of the Mating Type <i>B</i> LocusCited by: 16
Author(s): Alija B. Mujic, Alan Kuo, Andrew Tritt, Anna Lipzen, Cindy Chen, Jenifer Johnson, Aarti Sharma, Kerrie Barry, Igor V. Grigoriev, Joseph W. Spatafora
Software Mentions: 4
Published: over 7 years ago
10.1038/srep25866
Hot spots of DNA double-strand breaks in human rDNA units are produced in vivoCited by: 16
Author(s): Nickolai A. Tchurikov, Dmitry V. Yudkin, М. А. Горбачева, Anastasia I. Kulemzina, I. V. Grischenko, Д. М. Федосеева, D. V. Sosin, Yuri V. Kravatsky, О. В. Кретова
Software Mentions: 4
Published: over 8 years ago
10.1038/s41598-018-26854-y
Transcriptome analysis in Hevea brasiliensis latex revealed changes in hormone signalling pathways during ethephon stimulation and consequent Tapping Panel DrynessCited by: 23
Author(s): Pascal Montoro, Shizhou Wu, Bénédicte Favreau, Eva Herlinawati, Cécile Labrune, Marie‐Laure Martin‐Magniette, Stéphanie Pointet, Maryannick Rio, Julie Leclercq, Sigit Ismawanto, Kuswanhadi
Software Mentions: 4
Published: over 6 years ago
10.1038/s41598-019-44266-4
Transcriptomics Analysis Reveals New Insights into the Roles of Notch1 Signaling on Macrophage PolarizationCited by: 21
Author(s): Chetan P. Hans, Neekun Sharma, Sidharth Sen, Shuai Zeng, Rishabh Dev, Yuyong Jiang, Advitiya Mahajan, Trupti Joshi
Software Mentions: 4
Published: over 5 years ago
10.1128/mSystems.00250-20
Genome-Scale Transcription-Translation Mapping Reveals Features of Zymomonas mobilis Transcription Units and PromotersCited by: 16
Author(s): Jessica M. Vera, Indro Neil Ghosh, Yaoping Zhang, Alex S. Hebert, Joshua J. Coon, Robert Landick
Software Mentions: 4
Published: about 4 years ago
10.7554/eLife.02626
Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathwaysCited by: 80
Author(s): Benoît Ballester, Alejandra Medina-Rivera, Dominic Schmidt, Mar Gonzàlez-Porta, Matthew Carlucci, Marc E. Rothenberg, Kyle Chessman, Aline Faure, Alister P. W. Funnell, Ângela Gonçalves, Claudia Kutter, Margus Lukk, Suraj Menon, William McLaren, Klara Stefflova, Stephen Watt, Matthew T. Weirauch, Merlin Crossley, John C. Marioni, Duncan T. Odom, Paul Flicek, Michael D. Wilson
Software Mentions: 4
Published: about 10 years ago
10.7554/eLife.13087
Transcription-coupled genetic instability marks acute lymphoblastic leukemia structural variation hotspotsCited by: 33
Author(s): Merja Heinäniemi, Tapio Vuorenmaa, Susanna Teppo, Minna U. Kaikkonen, Maria Bouvy-Liivrand, Juha Mehtonen, Henri Niskanen, Vasilios Zachariadis, Saara Laukkanen, Thomas Liuksiala, Kaisa Teittinen, Olli Lohi
Software Mentions: 4
Published: over 8 years ago
10.7554/eLife.52896
Recruitment of mRNAs to P granules by condensation with intrinsically-disordered proteinsCited by: 88
Author(s): Chih Yung S. Lee, Andrea Putnam, Tu Lu, Shuai Xin He, John Paul T. Ouyang, Géraldine Seydoux
Software Mentions: 4
Published: almost 5 years ago
10.1007/s13205-020-02291-5
ddRAD-seq derived genome-wide SNPs, high density linkage map and QTLs for fruit quality traits in strawberry (Fragaria x ananassa)Cited by: 3
Author(s): Sathishkumar Natarajan, Mohammad Rashed Hossain, Hoy‐Taek Kim, Denison Michael Immanuel Jesse, Mostari Jahan Ferdous, Hee-Jeong Jung, Jong-In Park, Ill Sup Nou
Software Mentions: 4
Published: over 4 years ago
10.18632/oncotarget.23614
The mutational landscape of <i>MYCN</i>, <i>Lin28b</i> and <i>ALK</i><i>F1174L</i> driven murine neuroblastoma mimics human diseaseCited by: 6
Author(s): Bram De Wilde, Anneleen Beckers, Sven Lindner, Kristina Althoff, Katleen De Preter, Pauline Depuydt, Pieter Mestdagh, Tom Sante, Steve Lefever, Falk Hertwig, Zhiyu Peng, Leming Shi, Sangkyun Lee, Elien Vandermarliere, Lennart Martens, Björn Menten, Alexander Schramm, Matthias Fischer, Johannes H. Schulte, Jo Vandesompele, Frank Speleman
Software Mentions: 3
Published: almost 7 years ago
10.1186/s12864-016-3080-9
Comparative transcriptomics enlarges the toolkit of known developmental genes in mollusksCited by: 38
Author(s): André Luiz de Oliveira, Tim Wollesen, Alen Kristof, Maik Scherholz, Emanuel Redl, Christiane Todt, Christoph Bleidorn, Andreas Wanninger
Software Mentions: 3
Published: almost 8 years ago
10.1002/ece3.3757
Genotyping strategy matters when analyzing hypervariable major histocompatibility complex‐Experience from a passerine birdCited by: 15
Author(s): Silje L. Rekdal, Jarl Andreas Anmarkrud, Arild Johnsen, Jan T. Lifjeld
Software Mentions: 3
Published: almost 7 years ago
10.1186/1471-2105-9-299
PseudoGeneQuest – Service for identification of different pseudogene types in the human genomeCited by: 16
Author(s): Csaba Ortutay, Mauno Vihinen
Software Mentions: 3
Published: over 16 years ago
10.1038/s42003-019-0680-3
Molecular signature of an ancient organizer regulated by Wnt/β-catenin signalling during primary body axis patterning in HydraCited by: 18
Author(s): Puli Chandramouli Reddy, Akhila Gungi, Suyog Ubhe, Saurabh J. Pradhan, Amol Kolte, Sanjeev Galande
Software Mentions: 3
Published: almost 5 years ago
10.1186/s13059-019-1631-5
Genomic introgression through interspecific hybridization counteracts genetic bottleneck during soybean domesticationCited by: 37
Author(s): Xutong Wang, Liyang Chen, Jianxin Ma
Software Mentions: 3
Published: almost 6 years ago
10.3389/fgene.2015.00139
Transposon insertion mapping with PIMMS – Pragmatic Insertional Mutation Mapping SystemCited by: 3
Author(s): Adam Blanchard, James A. Leigh, Sharon A. Egan, Richard D. Emes
Software Mentions: 3
Published: over 9 years ago
10.1371/journal.pbio.3000242
Intestinal peroxisomal fatty acid β-oxidation regulates neural serotonin signaling through a feedback mechanismCited by: 15
Author(s): Aude Bouagnon, Lin Lin, Shubhi Srivastava, Chung‐Chih Liu, Oishika Panda, Frank C. Schroeder, Supriya Srinivasan, Kaveh Ashrafi
Software Mentions: 3
Published: almost 5 years ago
10.1111/mec.14426
Maintaining their genetic distance: Little evidence for introgression between widely hybridizing species of <i>Geum</i> with contrasting mating systemsCited by: 16
Author(s): Crispin Y. Jordan, Konrad Lohse, Frances Turner, Marian Thomson, Karim Gharbi, Richard A. Ennos
Software Mentions: 3
Published: almost 7 years ago
10.1186/s12864-015-1390-y
Transcript profiling of Populus tomentosa genes in normal, tension, and opposite wood by RNA-seqCited by: 41
Author(s): Jinhui Chen, Beibei Chen, Deqiang Zhang
Software Mentions: 3
Published: over 9 years ago
10.3390/ijms22115798
Genome-Wide Role of HSF1 in Transcriptional Regulation of Desiccation Tolerance in the Anhydrobiotic Cell Line, Pv11Cited by: 6
Author(s): Shoko Tokumoto, Yugo Miyata, Ruslan Deviatiiarov, Takahiro Yamada, Yusuke Hiki, О. С. Козлова, Yuki Yoshida, Richard Cornette, Akira Funahashi, Elena Shagimardanova, Oleg Gusev, Takahiro Kikawada
Software Mentions: 3
Published: over 3 years ago
10.3390/cells10092375
Transcriptome and Methylome Analysis Reveal Complex Cross-Talks between Thyroid Hormone and Glucocorticoid Signaling at Xenopus MetamorphosisCited by: 10
Author(s): Nicolas Buisine, Alexis Grimaldi, Vincent Jonchère, Muriel Rigolet, Corinne Blugeon, Juliette Hamroune, Laurent M. Sachs
Software Mentions: 3
Published: about 3 years ago
10.1371/journal.pone.0227819
Microbiota in foods from Inuit traditional huntingCited by: 11
Author(s): Aviaja Zenia Edna Lyberth Hauptmann, Petronela Paulová, Lars Hestbjerg Hansen, Thomas Sicheritz-Pontén, Gert Mulvad, Dennis Sandris Nielsen
Software Mentions: 3
Published: almost 5 years ago
10.1038/srep18470
Genome-wide analysis of microRNAs identifies the lipid metabolism pathway to be a defining factor in adipose tissue from different sheepCited by: 37
Author(s): Xiangyang Miao, Qingmiao Luo, Xiaoqiong Qin, Yuntao Guo
Software Mentions: 3
Published: almost 9 years ago
10.1038/s41438-018-0020-7
Divergence in the transcriptional landscape between low temperature and freeze shock in cultivated grapevine (Vitis vinifera)Cited by: 49
Author(s): Jason P. Londo, Alisson P. Kovaleski, Jacquelyn Lillis
Software Mentions: 3
Published: over 6 years ago
10.15252/embj.2020107134
LncRNA <i>VEAL2</i> regulates PRKCB2 to modulate endothelial permeability in diabetic retinopathyCited by: 27
Author(s): Paras Sehgal, Samatha Mathew, Ambily Sivadas, Ray A, Jyoti Tanwar, Sushma Vishwakarma, Gyan Ranjan, K. V. Shamsudheen, Rahul C. Bhoyar, Abhishek Pateria, Elvin Leonard, Mukesh Kumar Lalwani, Archana Vats, Rajeev Reddy Pappuru, Mudit Tyagi, Saumya Jakati, Shantanu Sengupta, B. Binukumar, Subhabrata Chakrabarti, Inderjeet Kaur, Rajender K. Motiani, Vinod Scaria, Sridhar Sivasubbu
Software Mentions: 3
Published: over 3 years ago
10.1038/srep29235
A highly diverse, desert-like microbial biocenosis on solar panels in a Mediterranean cityCited by: 31
Author(s): Pedro Dorado-Morales, Cristina Vilanova, Juli Peretó, Francisco M. Codoñer, Daniel Ramón, Manuel Porcar
Software Mentions: 3
Published: over 8 years ago
10.1186/s40035-018-0135-7
GM604 regulates developmental neurogenesis pathways and the expression of genes associated with amyotrophic lateral sclerosisCited by: 11
Author(s): William R. Swindell, Krzysztof Bojanowski, Mark S. Kindy, R.M.W. Chau, Dorothy Ko
Software Mentions: 3
Published: almost 6 years ago
10.3390/ijms21155191
A Genome-Wide View of Transcriptional Responses during Aphis glycines Infestation in SoybeanCited by: 5
Author(s): Luming Yao, Biyun Yang, Xiao‐Pan Ma, Shuangshuang Wang, Zhe Guan, Biao Wang, Yan‐Yi Jiang
Software Mentions: 3
Published: over 4 years ago
10.1534/g3.118.200308
Whole Genome Sequence of the Parasitoid Wasp <i>Microplitis demolitor</i> That Harbors an Endogenous Virus MutualistCited by: 29
Author(s): Gaelen R. Burke, Kimberly K. O. Walden, James B. Whitfield, Hugh M. Robertson, Michael R. Strand
Software Mentions: 3
Published: about 6 years ago
10.3390/foods9050652
An Infant Milk Formula Supplemented with Heat-Treated Probiotic Bifidobacterium animalis subsp. lactis CECT 8145, Reduces Fat Deposition in C. elegans and Augments Acetate and Lactate in a Fermented Infant SlurryCited by: 13
Author(s): Ángela Silva, Núria González, Ana Terrén, Antonio G. Garcı́a, Juan F. Martínez-Blanch, Vanessa Illescas, Javier Morales, Marcos Maroto, Salvador Genovés, Daniel Ramón, Patricia Martorell, Empar Chenoll
Software Mentions: 3
Published: over 4 years ago
10.1371/journal.pone.0176290
Novel genes associated with enhanced motility of Escherichia coli ST131Cited by: 30
Author(s): Asha Kakkanat, Minh-Duy Phan, Alvin W. Lo, Scott A. Beatson, Mark A. Schembri
Software Mentions: 2
Published: over 7 years ago
10.1371/journal.pone.0106314
Comparison of Hepatocellular Carcinoma miRNA Expression Profiling as Evaluated by Next Generation Sequencing and MicroarrayCited by: 66
Author(s): Yoshiki Murakami, Takao Tanahashi, Ryosuke Okada, Hidenori Toyoda, Takashi Kumada, Masaru Enomoto, Akihiro Tamori, Norifumi Kawada, Y-h. Taguchi, Takeshi Azuma
Software Mentions: 2
Published: about 10 years ago
10.3390/microorganisms9061188
Lampenflora in a Show Cave in the Great Basin Is Distinct from Communities on Naturally Lit Rock Surfaces in Nearby Wild CavesCited by: 7
Author(s): Jake Burgoyne, Robin Crepeau, Jacob Reinholdt Jensen, Hayden Smith, Gretchen M. Baker, Steven D. Leavitt
Software Mentions: 2
Published: over 3 years ago
10.1016/j.molcel.2017.01.005
Nuclear RNA Decay Pathways Aid Rapid Remodeling of Gene Expression in YeastCited by: 53
Author(s): Stefan Bresson, Alex Tuck, Desislava P. Staneva, David Tollervey
Software Mentions: 2
Published: over 7 years ago
10.1111/mec.13434
A metagenetic approach to determine the diversity and distribution of cyst nematodes at the level of the country, the field and the individualCited by: 22
Author(s): Sebastian Eves‐van den Akker, Catherine J. Lilley, A. Reid, J. Pickup, Eric Anderson, Peter J. A. Cock, Mark Blaxter, Peter E. Urwin, John T. Jones, Vivian C. Blok
Software Mentions: 2
Published: almost 9 years ago
10.3390/microorganisms8121967
Soehngenia longivitae sp. nov., a Fermenting Bacterium Isolated from a Petroleum Reservoir in Azerbaijan, and Emended Description of the Genus SoehngeniaCited by: 12
Author(s): Т. Н. Назина, Salimat K. Bidzhieva, Denis S. Grouzdev, Д. Ш. Соколова, T. P. Tourova, Sofiya N. Parshina, Alexander N. Avtukh, А. Б. Полтараус, Azhdar K Talybly
Software Mentions: 2
Published: almost 4 years ago
10.3390/molecules24244544
Volatile Fatty Acids Production from Microalgae Biomass: Anaerobic Digester Performance and Population Dynamics during Stable Conditions, Starvation, and Process RecoveryCited by: 6
Author(s): José Antonio Magdalena, Elia Tomás‐Pejó, Cristina González‐Fernández
Software Mentions: 2
Published: almost 5 years ago