Ecosyste.ms: Papers

10.1093/gigascience/giab039

A large-scale metagenomic survey dataset of the post-weaning piglet gut lumen
Cited 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 Mechanism
Cited 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 culture
Cited 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 data
Cited 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 discordance
Cited 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: over 3 years ago

10.1371/journal.pgen.1008515

Dynamic and regulated TAF gene expression during mouse embryonic germ cell development
Cited 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 activities
Cited 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: about 4 years ago

10.3389/fnins.2021.689188

Identification of the Potential Gene Regulatory Networks and Therapeutics in Aged Mice With Postoperative Neurocognitive Disorder
Cited 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 Translation
Cited 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 wastewater
Cited 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 projections
Cited by: 11
Author(s): Harleen Saini, Alicia A. Bicknell, Sean R. Eddy, Melissa J. Moore
Software Mentions: 7
Published: about 5 years ago

10.7554/eLife.56523

DAZL mediates a broad translational program regulating expansion and differentiation of spermatogonial progenitors
Cited 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 Catalogue
Cited 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 rice
Cited by: 5
Author(s): Bradley W. Tonnessen, A. M. Bossa-Castro, Ramil Mauleon, Nickolai Alexandrov, Jan E. Leach
Software Mentions: 7
Published: almost 6 years ago

10.1186/s13059-018-1521-2

omniCLIP: probabilistic identification of protein-RNA interactions from CLIP-seq data
Cited 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 costimulation
Cited by: 13
Author(s): Dafni A. Glinos, Blagoje Soskic, Cayman Williams, Alan Kennedy, Luke Jostins, David M. Sansom, Gosia Trynka
Software Mentions: 7
Published: about 4 years ago

10.1098/rstb.2019.0255

Dormancy dynamics and dispersal contribute to soil microbiome resilience
Cited 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: over 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 Data
Cited 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 Carcinoma
Cited 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 Stroke
Cited 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 survival
Cited 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 virulence
Cited 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> sequencing
Cited 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 oxytetracycline
Cited 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 Trial
Cited 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 psoriasis
Cited 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 erythematosus
Cited 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 potential
Cited 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 circRNAs
Cited 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 Species
Cited 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: about 5 years ago

10.1186/1471-2164-15-917

Differential expression of endogenous plant cell wall degrading enzyme genes in the stick insect (Phasmatodea) midgut
Cited 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 development
Cited 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 environment
Cited 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 sarcoma
Cited 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 components
Cited 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 Characterizations
Cited 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 metabarcoding
Cited 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 cancer
Cited 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 Syndrome
Cited 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 Exercise
Cited 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: almost 4 years ago

10.1093/aobpla/ply013

Patterns of alternative splicing vary between species during heat stress
Cited by: 25
Author(s): Sumetha Kannan, Gillian Halter, Tanya Renner, Elizabeth R. Waters
Software Mentions: 4
Published: almost 7 years ago

10.1186/1471-2105-13-S17-S22

Personalized cloud-based bioinformatics services for research and education: use cases and the elasticHPC package
Cited 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: 92
Author(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 pathogenicity
Cited 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 extractions
Cited 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 Arabidopsis
Cited 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 1
Cited by: 16
Author(s): Zen H. Lu, Alex di Domenico, Steven H. Wright, Pamela Knight, Bruce Whitelaw, Alan D. Pemberton
Software Mentions: 4
Published: almost 14 years ago

10.1186/s12864-020-07200-x

iCLIP analysis of RNA substrates of the archaeal exosome
Cited 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: about 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 factor
Cited 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 Analysis
Cited 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 Kazakhstan
Cited 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 Anastomosis
Cited 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 II
Cited 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 Infection
Cited 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 stages
Cited 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 Bioreactor
Cited 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 Processing
Cited 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 Technologies
Cited 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 fungi
Cited 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 microbiome
Cited 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: about 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> Locus
Cited 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 vivo
Cited 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 Dryness
Cited 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 Polarization
Cited 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 Promoters
Cited 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 pathways
Cited 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 hotspots
Cited 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 proteins
Cited 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 disease
Cited 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 mollusks
Cited 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: about 8 years ago

10.1002/ece3.3757

Genotyping strategy matters when analyzing hypervariable major histocompatibility complex‐Experience from a passerine bird
Cited 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 genome
Cited 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 Hydra
Cited 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 domestication
Cited 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 System
Cited 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 mechanism
Cited 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 systems
Cited 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-seq
Cited 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, Pv11
Cited 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 Metamorphosis
Cited 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 hunting
Cited 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 sheep
Cited 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 retinopathy
Cited 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 city
Cited 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 sclerosis
Cited 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 Soybean
Cited 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 Mutualist
Cited 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 Slurry
Cited 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 ST131
Cited 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 Microarray
Cited 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 Caves
Cited 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 Yeast
Cited 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 individual
Cited 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 Soehngenia
Cited 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 Recovery
Cited by: 6
Author(s): José Antonio Magdalena, Elia Tomás‐Pejó, Cristina González‐Fernández
Software Mentions: 2
Published: almost 5 years ago