pypi: cutadapt | Projects | Ecosyste.ms: Papers

10.1093/gbe/evw262

Salmonid chromosome evolution as revealed by a novel method for comparing RADseq linkage maps
Cited by: 38
Author(s): Ben J. G. Sutherland, Thierry Gosselin, Éric Normandeau, Manuel Lamothe, Nathalie Isabel, Céline Audet, Louis Bernatchez
Software Mentions: 4
Published: almost 10 years ago

10.1093/gbe/evy155

Pattern of DNA Methylation in Daphnia: Evolutionary Perspective
Cited by: 43
Author(s): Jouni Kvist, Camila Gonçalves Athanásio, Omid Shams Solari, James Brown, John K. Colbourne, Michael E. Pfrender, Leda Mirbahai
Software Mentions: 4
Published: about 8 years ago

10.1186/s13073-021-00826-w

Comprehensive molecular characterization of gastric cancer patients from phase II second-line ramucirumab plus paclitaxel therapy trial
Cited by: 16
Author(s): Seung Tae Kim, K. Jason, Sung Yong Oh, Kyung Kim, Jung Yong Hong, Won Ki Kang, Jeeyun Lee
Software Mentions: 4
Published: over 5 years ago

10.1093/gigascience/giaa158

ChiRA: an integrated framework for chimeric read analysis from RNA-RNA interactome and RNA structurome data
Cited by: 4
Author(s): Pavankumar Videm, Anup Kumar, Oleg Zharkov, Björn Grüning, Rolf Backofen
Software Mentions: 4
Published: over 5 years ago

10.1172/JCI130809

A stress-responsive enhancer induces dynamic drug resistance in acute myeloid leukemia
Cited by: 25
Author(s): Mark S. Williams, Fabio Amaral, Fabrizio Simeoni, Tim C. P. Somervaille
Software Mentions: 4
Published: over 6 years ago

10.3390/jcm8060849

MicroRNA Profile of HCV Spontaneous Clarified Individuals, Denotes Previous HCV Infection
Cited by: 10
Author(s): Óscar Brochado-Kith, Alicia Gómez Sanz, Luis Miguel Real, Javier Crespo, Pablo Ryan, Juan Macı́as, Joaquín Cabezas, Jesús Troya, Juan A Pineda, María Teresa Arias-Loste, Victorino Díez Viñas, María Ángeles Jiménez-Sousa, Luz María Medrano, Isabel Cuesta de la Plaza, Sara Monzón, Salvador Resino, Amanda Fernández‐Rodríguez
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.ppat.1006084

Microbial Community Composition Impacts Pathogen Iron Availability during Polymicrobial Infection
Cited by: 24
Author(s): Apollo Stacy, Nader Abraham, Peter Jorth, Marvin Whiteley
Software Mentions: 4
Published: almost 10 years ago

10.1371/journal.ppat.1009812

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

10.1098/rsos.180903

Bracketing phenogenotypic limits of mammalian hybridization
Cited by: 26
Author(s): Yoland Savriama, Mia Valtonen, Juhana Kammonen, Pasi Rastas, Olli‐Pekka Smolander, Ari Löytynoja, Teemu J. Häkkinen, Ian J. Corfe, Sylvain Gerber, Isaac Salazar‐Ciudad, Lars Paulín, Liisa Holm, Ari Löytynoja, Petri Auvinen, Jukka Jernvall
Software Mentions: 4
Published: almost 8 years ago

10.1186/s12977-020-00544-y

Comparative analysis of human microglial models for studies of HIV replication and pathogenesis
Cited by: 34
Author(s): Ammara Mohammad, J. Hammonds, Mario Pujato, Christopher N. Mayhew, Krishna M. Roskin, Paul Spearman
Software Mentions: 4
Published: almost 6 years ago

10.1038/s41597-019-0141-3

Microbiomes of Velloziaceae from phosphorus-impoverished soils of the campos rupestres, a biodiversity hotspot
Cited by: 8
Author(s): Antônio Pedro Camargo, Rafael Soares Correa de Souza, Patrícia de Britto Costa, Isabel Rodrigues Gerhardt, Ricardo A. Dante, Grazielle Sales Teodoro, Anna Abrahão, Hans Lambers, Marcelo Falsarella Carazzolle, Marcel Huntemann, Alicia Clum, Brian Foster, Bryce Foster, Simon Roux, Krishna Palaniappan, Neha Varghese, Supratim Mukherjee, T. B. K. Reddy, Chris Daum, Alex Copeland, I. Min A. Chen, Natalia Ivanova, Nikos C. Kyrpides, Christa Pennacchio, Emiley A. Eloe‐Fadrosh, Paulo Arruda, Rafael S. Oliveira
Software Mentions: 4
Published: about 7 years ago

10.1038/s41598-017-01943-6

Transcriptome analysis of dominant-negative Brd4 mutants identifies Brd4-specific target genes of small molecule inhibitor JQ1
Cited by: 16
Author(s): Tim-Michael Decker, Michael Kluge, Stefan Krebs, Nilay Shah, Helmut Blum, Caroline C. Friedel, Dirk Eick
Software Mentions: 4
Published: over 9 years ago

10.1038/s41598-017-15955-9

Previous crop and rotation history effects on maize seedling health and associated rhizosphere microbiome
Cited by: 64
Author(s): María‐Soledad Benítez, Shannon L. Osborne, R. Michael Lehman
Software Mentions: 4
Published: almost 9 years ago

10.1038/s41598-018-19684-5

Homeolog expression analysis in an allotriploid non-model crop via integration of transcriptomics and proteomics
Cited by: 23
Author(s): Jelle van Wesemael, Yann Hueber, Ewaut Kissel, Nádia Alves Campos, Rony Swennen, Sébastien Carpentier
Software Mentions: 4
Published: over 8 years ago

10.1038/s41598-019-42560-9

De Novo Transcriptome Assembly and Functional Annotation in Five Species of Bats
Cited by: 22
Author(s): Diana D. Moreno-Santillán, Carlos Machaín-Williams, Georgina Hernández-Montes, Jorge Ortega
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-019-42911-6

Habitat-dependent composition of bacterial and fungal communities in biological soil crusts from Oman
Cited by: 30
Author(s): Raeid M. M. Abed, Alexandra Tamm, Christiane Hassenrück, Ahmed Al‐Rawahi, Emilio Rodríguez‐Caballero, Sabine Fiedler, Stefanie Maier, Bettina Weber
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-019-42865-9

Differences in resource use lead to coexistence of seed-transmitted microbial populations
Cited by: 15
Author(s): Gloria Torres-Cortés, Benjamin J. Garcia, Stéphane Compant, Samir Rezki, Piet Jones, Anne Préveaux, Martial Briand, Alain Roulet, Olivier Bouchez, Daniel Jacobson, Matthieu Barret
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-019-51056-5

Down-regulation of CK2α correlates with decreased expression levels of DNA replication minichromosome maintenance protein complex (MCM) genes
Cited by: 4
Author(s): Susanne Schaefer, Thomas Koed Doktor, Sabrina B Frederiksen, Kathleen Chea, Mirka Hlavacova, Georg M. Bruun, Maj Rabjerg, Brage S. Andresen, Isabel Domı́nguez, Bárbara Guerra
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41598-019-53892-x

Performance assessment of total RNA sequencing of human biofluids and extracellular vesicles
Cited by: 46
Author(s): Celine Everaert, Hetty Helsmoortel, Anneleen Decock, Eva Hulstaert, Ruben Van Paemel, Kimberly Verniers, Justine Nuytens, Jasper Anckaert, Nele Nijs, Joeri Tulkens, Bert Dhondt, An Hendrix, Pieter Mestdagh, Jo Vandesompele
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41598-020-65638-1

Genomic analyses of early responses to radiation in glioblastoma reveal new alterations at transcription, splicing, and translation levels
Cited by: 11
Author(s): Saket Choudhary, Suzanne Perea Burns, Hoda Mirsafian, Wenzheng Li, Dat T. Vo, Mu Qiao, Xiufen Lei, Andrew D. Smith, Luiz O. F. Penalva
Software Mentions: 4
Published: over 6 years ago

10.1186/s40303-016-0017-9

αT-catenin in restricted brain cell types and its potential connection to autism
Cited by: 20
Author(s): Stephen Sai Folmsbee, Douglas R. Wilcox, Koen Tyberghein, Pieter De Bleser, Warren G. Tourtellotte, Jolanda van Hengel, Frans van Roy, Cara J. Gottardi
Software Mentions: 4
Published: over 10 years ago

10.7554/eLife.47891

Epimutations are associated with CHROMOMETHYLASE 3-induced de novo DNA methylation
Cited by: 54
Author(s): Jered M. Wendte, Yinwen Zhang, Lexiang Ji, Xiulin Shi, Rashmi R. Hazarika, Yadollah Shahryary, Frank Johannes, Robert J. Schmitz
Software Mentions: 4
Published: about 7 years ago

10.7554/eLife.67577

Broad geographic sampling reveals the shared basis and environmental correlates of seasonal adaptation in Drosophila
Cited by: 57
Author(s): Heather E. Machado, Alan O. Bergland, Ryan W. Taylor, Susanne Tilk, Emily L. Behrman, Kelly A. Dyer, Daniel K. Fabian, Thomas Flatt, Josefa González, Talia L. Karasov, Bernard Kim, Iryna Kozeretska, Brian P. Lazzaro, Thomas J. S. Merritt, John E. Pool, Katherine R. O’Brien, Subhash Rajpurohit, Paula R. Roy, Stephen W. Schaeffer, Svitlana Serga, Paul S. Schmidt, Dmitri A. Petrov
Software Mentions: 4
Published: about 5 years ago

10.7554/eLife.20983

A molecular portrait of maternal sepsis from Byzantine Troy
Cited by: 32
Author(s): Alison Devault, Tatum D Mortimer, Andrew Kitchen, Henrike Kiesewetter, Jacob Enk, G. Brian Golding, John Southon, Melanie Kuch, Ana T. Duggan, William Aylward, Shea N. Gardner, Jonathan Allen, Andrew King, Gerard D. Wright, Makoto Kuroda, Kengo Kato, Derek E. G. Briggs, Gino Fornaciari, Edward C. Holmes, Hendrik N. Poinar, Caitlin S. Pepperell
Software Mentions: 4
Published: over 9 years ago

10.7554/eLife.58041

Mitochondrial fatty acid synthesis coordinates oxidative metabolism in mammalian mitochondria
Cited by: 52
Author(s): Sara M. Nowinski, Ashley Solmonson, Scott F. Rusin, J. Alan Maschek, Claire Bensard, Sarah Fogarty, Mi Young Jeong, Sandra Lettlová, Jordan A. Berg, Jeffrey T. Morgan, Yeyun Ouyang, Bradley C. Naylor, João A. Paulo, Katsuhiko Funai, James E. Cox, Steven P. Gygi, Dennis R. Winge, Ralph J. DeBerardinis, Jared Rutter
Software Mentions: 4
Published: about 6 years ago

10.7554/eLife.65760

Morphological and genomic shifts in mole-rat ‘queens’ increase fecundity but reduce skeletal integrity
Cited by: 8
Author(s): Rachel A Johnston, Philippe Vullioud, Jack Thorley, Henry Kirveslahti, Leyao Shen, Sayan Mukherjee, Courtney M. Karner, Tim Clutton‐Brock, Jenny Tung
Software Mentions: 4
Published: over 5 years ago

10.7554/eLife.38014

Decoupling the impact of microRNAs on translational repression versus RNA degradation in embryonic stem cells
Cited by: 52
Author(s): Jacob W. Freimer, TJ Hu, Robert Blelloch
Software Mentions: 4
Published: about 8 years ago

10.7554/eLife.41337

Programmed genome editing of the omega-1 ribonuclease of the blood fluke, Schistosoma mansoni
Cited by: 83
Author(s): Wannaporn Ittiprasert, Victoria H. Mann, Shannon E. Karinshak, Avril Coghlan, Gabriel Rinaldi, Geetha Sankaranarayanan, Apisit Chaidee, Toshihiko Tanno, Chutima Kumkhaek, Pannathee Prangtaworn, Margaret M. Mentink–Kane, Christina J Cochran, Patrick Driguez, Nancy Holroyd, Alan S. Tracey, Rutchannee Rodpai, Bart Everts, Cornelis H. Hokke, Karl F. Hoffmann, Matthew Berriman, Paul J. Brindley
Software Mentions: 4
Published: over 7 years ago

10.7554/eLife.50530

Viral miRNA adaptor differentially recruits miRNAs to target mRNAs through alternative base-pairing
Cited by: 5
Author(s): Carlos Gorbea, Tim Mosbruger, David A. Nix, Demián Cazalla
Software Mentions: 4
Published: about 7 years ago

10.7554/eLife.28625

The C. elegans neural editome reveals an ADAR target mRNA required for proper chemotaxis
Cited by: 30
Author(s): Sarah N. Deffit, Brian A. Yee, Aidan C. Manning, Suba Rajendren, Pranathi Vadlamani, Emily C. Wheeler, Alain Domissy, Michael C. Washburn, G Yeo, Heather A. Hundley
Software Mentions: 4
Published: about 9 years ago

10.7554/eLife.63545

Mutations in SKI in Shprintzen–Goldberg syndrome lead to attenuated TGF-β responses through SKI stabilization
Cited by: 20
Author(s): Ilaria Gori, Roger George, A. Purkiss, Stephanie Strohbuecker, Rebecca A. Randall, R.W. Ogrodowicz, Virginie Carmignac, Laurence Faivre, Dhira Joshi, Svend Kjær, Caroline S. Hill
Software Mentions: 4
Published: over 5 years ago

10.3390/ijms19092500

Co-Expression Network Analysis Identifies miRNA–mRNA Networks Potentially Regulating Milk Traits and Blood Metabolites
Cited by: 12
Author(s): Adolf A. Ammah, Duy Ngoc, Nathalie Bissonnette, Nicolas Gévry, Eveline M. Ibeagha‐Awemu
Software Mentions: 4
Published: about 8 years ago

10.3390/ijms20143583

Ureaplasma Species Modulate Cytokine and Chemokine Responses in Human Brain Microvascular Endothelial Cells
Cited by: 6
Author(s): Christine Silwedel, Christian P. Speer, Axel Haarmann, Markus Fehrholz, Heike Claus, Nicolas Schlegel, Kirsten Glaser
Software Mentions: 4
Published: about 7 years ago

10.3390/ijms20236040

Whole Genome Expression Analyses of miRNAs and mRNAs Suggest the Involvement of miR-320a and miR-155-3p and their Targeted Genes in Lithium Response in Bipolar Disorder
Cited by: 27
Author(s): Claudia Pisanu, Eleni Merkouri Papadima, Carla Melis, Donatella Congiu, Annalisa Loizedda, Nicola Orrù, Stefano Calza, Sandro Orrù, Carlo Carcassi, Giovanni Severino, Raffaella Ardau, Caterina Chillotti, Maria Del Zompo, Alessio Squassina
Software Mentions: 4
Published: almost 7 years ago

10.3390/ijms21062079

Whole-Genome Uterine Artery Transcriptome Profiling and Alternative Splicing Analysis in Rat Pregnancy
Cited by: 4
Author(s): Kathirvel Gopalakrishnan, Sathish Kumar
Software Mentions: 4
Published: over 6 years ago

10.3390/ijms21093262

Whole-Genome Deep Sequencing Reveals Host-Driven in-planta Evolution of Columnea Latent Viroid (CLVd) Quasi-Species Populations
Cited by: 5
Author(s): Parichate Tangkanchanapas, Annelies Haegeman, Tom Ruttink, Monica Höfte, Kris De Jonghe
Software Mentions: 4
Published: over 6 years ago

10.3390/ijms21124453

YBX1 Indirectly Targets Heterochromatin-Repressed Inflammatory Response-Related Apoptosis Genes through Regulating CBX5 mRNA
Cited by: 7
Author(s): Andreas Kloetgen, Sujitha Duggimpudi, Konstantin Schuschel, Kebria Hezaveh, Daniel Picard, Heiner Schaal, Marc Remke, Jan‐Henning Klusmann, Arndt Borkhardt, Alice C. McHardy, Jessica I. Hoell
Software Mentions: 4
Published: about 6 years ago

10.3390/ijms21186946

Proteomic and Transcriptomic Patterns during Lipid Remodeling in Nannochloropsis gaditana
Cited by: 13
Author(s): Chris J. Hulatt, Irina Smolina, Adam Dowle, Martina Kopp, Ghana Kalerammana Vasanth, Galice Hoarau, René H. Wijffels, Viswanath Kiron
Software Mentions: 4
Published: almost 6 years ago

10.3390/ijms21238898

MicroRNA Profiling in Oesophageal Adenocarcinoma Cell Lines and Patient Serum Samples Reveals a Role for miR-451a in Radiation Resistance
Cited by: 8
Author(s): Frederike Butz, Ann-Kathrin Eichelmann, George C. Mayne, Tingting Wang, Isabell Bastian, Karen Chiam, Shashikanth Marri, Pamela J. Sykes, Bas P. L. Wijnhoven, Eelke Toxopeus, Michael Michael, Christos S. Karapetis, Richard Hummel, David I. Watson, Damian J. Hussey
Software Mentions: 4
Published: almost 6 years ago

10.1186/s12974-019-1413-8

More than just inflammation: Ureaplasma species induce apoptosis in human brain microvascular endothelial cells
Cited by: 18
Author(s): Christine Silwedel, Axel Haarmann, Markus Fehrholz, Heike Claus, Christian P. Speer, Kirsten Glaser
Software Mentions: 4
Published: over 7 years ago

10.1186/s12974-018-1170-0

Novel insights into neuroinflammation: bacterial lipopolysaccharide, tumor necrosis factor α, and Ureaplasma species differentially modulate atypical chemokine receptor 3 responses in human brain microvascular endothelial cells
Cited by: 15
Author(s): Christine Silwedel, Christian P. Speer, Axel Haarmann, Markus Fehrholz, Heike Claus, Mathias Buttmann, Kirsten Glaser
Software Mentions: 4
Published: over 8 years ago

10.1080/20002297.2021.1946316

Microbial characteristics across different tongue coating types in a healthy population
Cited by: 5
Author(s): Hairong Chen, Qingwei Li, Min Li, Sheng Liu, Chensi Yao, Zixiong Wang, Zhixin Zhao, Ping Liu, Fan Yang, Xinjian Li, Jun Wang, Yi-Xin Zeng, Xiaolin Tong
Software Mentions: 4
Published: over 5 years ago

10.1016/j.isci.2021.102783

AMPK activation reverts mouse epiblast stem cells to naive state
Cited by: 4
Author(s): Yajing Liu, Junko Yamane, Akito Tanaka, Wataru Fujibuchi, Jun Yamashita
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0194023

ER-positive breast cancer cells are poised for RET-mediated endocrine resistance
Cited by: 18
Author(s): Sachi Horibata, Edward J. Rice, Chinatsu Mukai, Brooke A. Marks, Kelly L. Sams, Hui Zheng, Lynne J. Anguish, Scott A. Coonrod, Charles G. Danko
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-017-14301-3

Exosomal microRNA signatures in multiple sclerosis reflect disease status
Cited by: 178
Author(s): Saeideh Ebrahimkhani, Fatemeh Vafaee, Paul E. Young, Suzy S J Hur, Simon Hawke, Emma Devenney, Heidi Beadnall, Michael Barnett, Catherine M. Suter, Michael E. Buckland
Software Mentions: 3
Published: almost 9 years ago

10.7554/eLife.23623

The dynamic three-dimensional organization of the diploid yeast genome
Cited by: 55
Author(s): Seungsoo Kim, Ivan Liachko, Donna Garvey Brickner, Kate B. Cook, William Stafford Noble, Jason H. Brickner, Jay Shendure, Maitreya J. Dunham
Software Mentions: 3
Published: over 9 years ago

10.3389/fimmu.2020.00661

Neutrophil Extracellular Trap Induced Dendritic Cell Activation Leads to Th1 Polarization in Type 1 Diabetes
Cited by: 40
Author(s): Zuzana Paračková, Irena Zentsová, Petra Vrabcová, Adam Klocperk, Zdenĕk Šumnı́k, Štěpánka Průhová, Lenka Petruželková, Robert Häsler, Anna Šedivá
Software Mentions: 3
Published: over 6 years ago

10.1186/s12864-016-3168-2

Novel equine tissue miRNAs and breed-related miRNA expressed in serum
Cited by: 27
Author(s): Alicja Pacholewska, Núria Mach, Xavier Mata, Anne Vaiman, Laurent Schibler, Éric Barrey, V. Gerber
Software Mentions: 3
Published: almost 10 years ago

10.1371/journal.pone.0201851

Small RNAs detected in exosomes derived from the MH7A synovial fibroblast cell line with TNF-α stimulation
Cited by: 19
Author(s): Yosuke Takamura, Wataru Aoki, Atsushi Satomura, Seiji Shibasaki
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.pone.0114598

Impact of the Genetic Background on the Composition of the Chicken Plasma MiRNome in Response to a Stress
Cited by: 14
Author(s): Marie-Laure Endale Ahanda, Tatiana Zerjal, Sophie Dhorne–Pollet, Andrea Rau, Amanda M. Cooksey, Elisabetta Giuffra
Software Mentions: 3
Published: almost 12 years ago

10.7554/eLife.52981

Losing Dnmt3a dependent methylation in inhibitory neurons impairs neural function by a mechanism impacting Rett syndrome
Cited by: 37
Author(s): Laura A. Lavery, Kerstin Ure, Ying-Wooi Wan, Chongyuan Luo, Alexander J Trostle, Wei Wang, Haijing Jin, José López López, Jacinta Lucero, Mark A. Durham, Rosa Castanon, Joseph R. Nery, Zhandong Liu, Margaret A. Goodell, Joseph R. Ecker, M. Margarita Behrens, Huda Y Zoghbi
Software Mentions: 3
Published: over 6 years ago

10.3390/ani11041150

Whole Blood Transcriptome Profiling Reveals Positive Effects of Olive Leaves-Supplemented Diet on Cholesterol in Goats
Cited by: 1
Author(s): Andrea Ianni, Francesca Bennato, Camillo Martino, Martina Colapietro, Giuseppe Martino
Software Mentions: 3
Published: over 5 years ago

10.3389/fbioe.2020.603145

No Tangible Effects of Field-Grown Cisgenic Potatoes on Soil Microbial Communities
Cited by: 9
Author(s): Sascha Krause, Astrid Näther, Vilma Ortiz Cortes, Ewen Mullins, G.J.T. Kessel, L.A.P. Lotz, Christoph C. Tebbe
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12859-014-0357-3

NeatFreq: reference-free data reduction and coverage normalization for De Novosequence assembly
Cited by: 16
Author(s): Jamison McCorrison, Pratap Venepally, Indresh Singh, Derrick E. Fouts, Roger S. Lasken, Barbara A. Methé
Software Mentions: 3
Published: almost 12 years ago

10.1186/s12881-018-0744-0

Evidence for long noncoding RNA GAS5 up-regulationin patients with Klinefelter syndrome
Cited by: 19
Author(s): Michele Salemi, Rossella Cannarella, Rosita A. Condorelli, Laura Cimino, Federico Ridolfo, Giorgio Giurato, Corrado Romano, Sandro La Vignera, Aldo E. Calogero
Software Mentions: 3
Published: over 7 years ago

10.26508/lsa.202000659

Dynamic changes in RNA–protein interactions and RNA secondary structure in mammalian erythropoiesis
Cited by: 2
Author(s): Mengge Shan, Xinjun Ji, Kevin A. Janssen, Ian M. Silverman, Jesse Humenik, Ben Garcia, Stephen A. Liebhaber, Brian D. Gregory
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-017-16193-9

PinAPL-Py: A comprehensive web-application for the analysis of CRISPR/Cas9 screens
Cited by: 66
Author(s): Philipp N. Spahn, Tyler Bath, Ryan J. Weiss, Jihoon Kim, Jeffrey D. Esko, Nathan E. Lewis, Olivier Harismendy
Software Mentions: 3
Published: almost 9 years ago

10.3389/fimmu.2012.00386

Automated cleaning and pre-processing of immunoglobulin gene sequences from high-throughput sequencing
Cited by: 13
Author(s): Miri Michaeli, Hila Noga, Hilla Tabibian‐Keissar, Iris Barshack, Ramit Mehr
Software Mentions: 3
Published: over 14 years ago

10.3389/fimmu.2021.707217

Haplotype-Specific Expression Analysis of MHC Class II Genes in Healthy Individuals and Rheumatoid Arthritis Patients
Cited by: 9
Author(s): Miranda Houtman, Espen Hesselberg, Lars Rönnblom, Lars Klareskog, Vivianne Malmström, Leonid Padyukov
Software Mentions: 3
Published: about 5 years ago

10.7554/eLife.58836

Gene autoregulation by 3’ UTR-derived bacterial small RNAs
Cited by: 32
Author(s): Mona Hoyos, Michaela Huber, Konrad U. Förstner, Kai Papenfort
Software Mentions: 3
Published: about 6 years ago

10.1038/sdata.2017.67

Single-cell transcriptome of early embryos and cultured embryonic stem cells of cynomolgus monkeys
Cited by: 40
Author(s): Tomonori Nakamura, Yukihiro Yabuta, Ikuhiro Okamoto, Kotaro Sasaki, Chizuru Iwatani, Hideaki Tsuchiya, Mitinori Saitou
Software Mentions: 3
Published: over 9 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: about 10 years ago

10.3389/fimmu.2021.695148

CD32+CD4+ T Cells Sharing B Cell Properties Increase With Simian Immunodeficiency Virus Replication in Lymphoid Tissues
Cited by: 8
Author(s): Nicolas Huot, Philippe Rascle, Cyril Planchais, Vanessa Contreras, Caroline Passaes, Roger Le Grand, Anne-Sophie Beignon, Étienne Kornobis, Rachel Legendre, Hugo Varet, Asier Sáez‐Cirión, Hugo Mouquet, Béatrice Jacquelin, Michaela Müller‐Trutwin
Software Mentions: 3
Published: over 5 years ago

10.1186/s13075-018-1688-7

T-cell transcriptomics from peripheral blood highlights differences between polymyositis and dermatomyositis patients
Cited by: 19
Author(s): Miranda Houtman, Louise Ekholm, Espen Hesselberg, Karine Chemin, Vivianne Malmström, Ann M. Reed, Ingrid E. Lundberg, Leonid Padyukov
Software Mentions: 3
Published: about 8 years ago

10.3389/fimmu.2020.01033

Adjuvanting Allergen Extracts for Sublingual Immunotherapy: Calcitriol Downregulates CXCL8 Production in Primary Sublingual Epithelial Cells
Cited by: 3
Author(s): Michael Pelst, Clara Hôbart, Charlotte Wallaeys, H. de Rooster, Yannick Gansemans, Filip Van Nieuwerburgh, Bert Devriendt, Eric Cox
Software Mentions: 3
Published: over 6 years ago

10.1038/srep28984

An emerging zoonotic clone in the Netherlands provides clues to virulence and zoonotic potential of Streptococcus suis
Cited by: 37
Author(s): Niels Willemse, Kate J. Howell, Lucy A. Weinert, Annet Heuvelink, Yvonne Pannekoek, Jaap A. Wagenaar, Hilde E. Smith, Arie van der Ende, Constance Schultsz
Software Mentions: 3
Published: about 10 years ago

10.1002/prp2.632

Ascorbate sensitizes human osteosarcoma cells to the cytostatic effects of cisplatin
Cited by: 8
Author(s): Naohiro Oka, Akiyoshi Komuro, Hideharu Amano, Suman Dash, Masahiko Honda, Kyoko Ota, Shunji Nishimura, Takeshi Ueda, Masao Akagi, Hitoshi Okada
Software Mentions: 3
Published: about 6 years ago

10.3390/microorganisms9091843

Influence of Tall Fescue Epichloë Endophytes on Rhizosphere Soil Microbiome
Cited by: 9
Author(s): Kishan Mahmud, Kendall Lee, Nicholas S. Hill, Anaas Mergoum, Ali Missaoui
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0194036

Allele-specific DNA methylation of disease susceptibility genes in Japanese patients with inflammatory bowel disease
Cited by: 11
Author(s): Hirofumi Chiba, Yoichi Kakuta, Yoshitaka Kinouchi, Yosuke Kawai, Kazuhiro Watanabe, Munenori Nagao, Takeo Naito, Motoyuki Onodera, Rintaro Moroi, Masatake Kuroha, Yoshitake Kanazawa, Tsutomu Kimura, Hisashi Shiga, Katsuya Endo, Kenichi Negoro, Masao Nagasaki, Michiaki Unno, Tooru Shimosegawa
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0242880

A shotgun metagenomic investigation of the microbiota of udder cleft dermatitis in comparison to healthy skin in dairy cows
Cited by: 7
Author(s): Lisa Ekman, Elisabeth Bagge, Ann-Kristin Nyman, Karin Persson Waller, Märit Pringle, Bo Segerman
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0209846

Bioinformatic analysis of long-lasting transcriptional and translational changes in the basolateral amygdala following acute stress
Cited by: 19
Author(s): Stephanie E. Sillivan, Meghan E. Jones, Sarah E. Jamieson, Gavin Rumbaugh, Courtney A. Miller
Software Mentions: 3
Published: over 7 years ago

10.1038/s41597-019-0140-4

Transcriptome profiling of interaction effects of soybean cyst nematodes and soybean aphids on soybean
Cited by: 11
Author(s): Surendra Neupane, Febina M. Mathew, Adam J. Varenhorst, Madhav P. Nepal
Software Mentions: 3
Published: about 7 years ago

10.3389/fmicb.2020.596156

Substrate Pre-loading Influences Initial Colonization of GAC Biofilter Biofilms
Cited by: 1
Author(s): Wen Qin, Frederik Hammes
Software Mentions: 3
Published: over 5 years ago

10.3390/microorganisms8060915

Importance of Defluviitalea raffinosedens for Hydrolytic Biomass Degradation in Co-Culture with Hungateiclostridium thermocellum
Cited by: 12
Author(s): Regina Rettenmaier, Martina Schneider, Bernhard Munk, Michael Lebuhn, Sebastian Jünemann, Alexander Sczyrba, Irena Maus, Vladimir V. Zverlov, Wolfgang Liebl
Software Mentions: 3
Published: over 6 years ago

10.3389/fendo.2018.00158

Integrated Characterization of MicroRNA and mRNA Transcriptome in Papillary Thyroid Carcinoma
Cited by: 13
Author(s): Azliana Mohamad Yusof, A. Rahman A. Jamal, Rohaizak Muhammad, Shahrun Niza Abdullah Suhaimi, Isa Mohamed Rose, Sazuita Saidin, Nurul Syakima Ab Mutalib
Software Mentions: 3
Published: over 8 years ago

10.18632/oncotarget.19483

Identification of hub genes involved in the development of hepatocellular carcinoma by transcriptome sequencing
Cited by: 8
Author(s): Yongchang Zheng, Junyu Long, Liangcai Wu, Haohai Zhang, Lin Li, Ying Zheng, Anqiang Wang, Jianzhen Lin, Xiaobo Yang, Xinting Sang, Ke Hu, Jie Pan, Haitao Zhao
Software Mentions: 3
Published: about 9 years ago

10.1186/s13229-019-0285-1

RNA sequencing of identical twins discordant for autism reveals blood-based signatures implicating immune and transcriptional dysregulation
Cited by: 13
Author(s): Ayden Saffari, Matt Arno, Eric Nasser, Angelica Ronald, Chloe Wong, Leonard C Schalkwyk, Jonathan Mill, Frank Dudbridge, Emma L. Meaburn
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pone.0182638

Epigenetic differences between monozygotic twins discordant for amyotrophic lateral sclerosis (ALS) provide clues to disease pathogenesis
Cited by: 35
Author(s): Paul E. Young, Stephen Kum Jew, Michael E. Buckland, Roger Pamphlett, Catherine M. Suter
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pone.0095633

Hybridization Capture Reveals Evolution and Conservation across the Entire Koala Retrovirus Genome
Cited by: 39
Author(s): Kyriakos Tsangaras, Matthew C. Siracusa, Nikolas Nikolaidis, Yasuko Ishida, Pin Cui, Hanna Vielgrader, Kristofer M. Helgen, Alfred L. Roca, Alex D. Greenwood
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pgen.1009761

The CovR regulatory network drives the evolution of Group B Streptococcus virulence
Cited by: 11
Author(s): Maria-Vittoria Mazzuoli, Maëlle Daunesse, Hugo Varet, Isabelle Rosinski‐Chupin, Rachel Legendre, Odile Sismeiro, Myriam Gominet, P.A. Kaminski, Philippe Glaser, Claudia Chica, Patrick Trieu-Cuot, Arnaud Firon
Software Mentions: 3
Published: about 5 years ago

10.3390/ijms22136843

Comparison of Gut Bacterial Communities of Grapholita molesta (Lepidoptera: Tortricidae) Reared on Different Host Plants
Cited by: 23
Author(s): Xiangqun Yuan, Xuan Zhang, Xueying Liu, Yanlu Dong, Zizheng Yan, Dongbiao Lv, Ping Wang, Yiping Li
Software Mentions: 3
Published: about 5 years ago

10.1186/s12974-017-0924-4

Differential effects of FTY720 on the B cell compartment in a mouse model of multiple sclerosis
Cited by: 19
Author(s): Kathrin Bail, Quirin Notz, Damiano M. Rovituso, Andrea Schampel, Marie Wunsch, Tobias Koeniger, Verena Schropp, Richa Bharti, Claus‐Jürgen Scholz, Konrad Foerstner, Christoph Kleinschnitz, Stefanie Küerten
Software Mentions: 3
Published: about 9 years ago

10.1186/s42523-021-00110-7

The link between broiler flock heterogeneity and cecal microbiome composition
Cited by: 13
Author(s): Randi Lundberg, Christian Scharch, Dorthe Sandvang
Software Mentions: 3
Published: about 5 years ago

10.1186/s13068-020-01715-x

Improvement of sabinene tolerance of Escherichia coli using adaptive laboratory evolution and omics technologies
Cited by: 18
Author(s): Tong Wu, Jinfeng Liu, Meijie Li, Ge Zhang, Lijuan Liu, Li Xing, Xiao Men, Ming Xian, Haibo Zhang
Software Mentions: 3
Published: over 6 years ago

10.3389/fmicb.2021.643945

Evaluation of Three Prokaryote Primers for Identification of Prokaryote Community Structure and Their Abode Preference in Three Distinct Wetland Ecosystems
Cited by: 2
Author(s): Kavita Kumari, Malay Naskar, Md. Aftabuddin, Soma Das Sarkar, Bandana Das Ghosh, Uttam Kumar Sarkar, Subir Nag, Chayna Jana, Basanta Kumar Das
Software Mentions: 3
Published: about 5 years ago

10.1093/molbev/msab061

The Genomic Architecture of Adaptation to Larval Malnutrition Points to a Trade-off with Adult Starvation Resistance in <i>Drosophila</i>
Cited by: 11
Author(s): Tadeusz J. Kawecki, Berra Erkoşar, Cindy Dupuis, Brian Hollis, R. Craig Stillwell, Martin Kapun
Software Mentions: 3
Published: over 5 years ago

10.1038/srep35436

Integrating Candida albicans metabolism with biofilm heterogeneity by transcriptome mapping
Cited by: 34
Author(s): Ranjith Rajendran, Ali May, Leighann Sherry, Ryan Kean, Craig Williams, Brian Jones, Karl Burgess, Jaap Heringa, Sanne Abeln, Bernd W. Brandt, Carol A. Munro, Gordon Ramage
Software Mentions: 3
Published: almost 10 years ago

10.1371/journal.pone.0222531

Pathogen surveillance in the informal settlement, Kibera, Kenya, using a metagenomics approach
Cited by: 22
Author(s): René S. Hendriksen, Oksana Lukjancenko, Patrick Munk, Mathis Hjort Hjelmsø, Jennifer R. Verani, Eric Ng’eno, Godfrey Bigogo, Samuel Kiplangat, Traoré Soumana Oumar, Lasse Bergmark, Timo Röder, John Neatherlin, Clayton Onyango, Tine Hald, Susanne Karlsmose, Sünje Johanna Pamp, Barry S. Fields, Joel M. Montgomery, Frank Møller Aarestrup
Software Mentions: 3
Published: almost 7 years ago

10.1186/s12885-020-07571-0

Targeted nanopore sequencing for the identification of ABCB1 promoter translocations in cancer
Cited by: 6
Author(s): Mark S. Williams, Naseer J. Basma, Fabio Amaral, Gillian Williams, John Weightman, Wolfgang Breitwieser, Louisa Nelson, Stephen S. Taylor, Daniel H. Wiseman, Tim C. P. Somervaille
Software Mentions: 3
Published: almost 6 years ago

10.3390/life11060558

The Effect of a Total Fishmeal Replacement by Arthrospira platensis on the Microbiome of African Catfish (Clarias gariepinus)
Cited by: 6
Author(s): Simon Rosenau, Elisa Oertel, Alexander C. Mott, Jens Tetens
Software Mentions: 3
Published: over 5 years ago

10.3390/ijms19051399

High-Throughput Sequencing of microRNAs in Glucocorticoid Sensitive Paediatric Inflammatory Bowel Disease Patients
Cited by: 14
Author(s): Sara De Iudicibus, Marianna Lucafò, Nicola Vitulo, Stefano Martelossi, Rosanna Zimbello, Fabio De Pascale, Claudio Forcato, Samuele Naviglio, Alessia Di Silvestre, Marco Gerdol, Gabriele Stocco, Giorgio Valle, Alessandro Ventura, Matteo Bramuzzo, Giuliana Decorti
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-019-52444-7

A specific fungal transcription factor controls effector gene expression and orchestrates the establishment of the necrotrophic pathogen lifestyle on wheat
Cited by: 27
Author(s): Darcy A. B. Jones, Evan John, Kasia Rybak, H. Phan, Karam B. Singh, Shao-Yu Lin, Peter S. Solomon, Richard P. Oliver, Kar‐Chun Tan
Software Mentions: 3
Published: almost 7 years ago

10.3390/ijms20194742

Causes and Consequences of A Glutamine Induced Normoxic HIF1 Activity for the Tumor Metabolism
Cited by: 17
Author(s): Matthias Kappler, Ulrike Pabst, Claus Weinholdt, Helge Täubert, Swetlana Rot, Tom Kaune, Johanna Kotrba, Martin Porsch, Antje Güttler, Matthias Bache, Knut Krohn, Fabian Bull, Anne Riemann, Claudia Wickenhauser, Barbara Seliger, Johannes Schubert, Bilal Al‐Nawas, Oliver Thews, Ivo Große, Dirk Vordermark, Alexander W. Eckert
Software Mentions: 3
Published: almost 7 years ago

10.3389/fmicb.2021.629169

Targeting the Active Rhizosphere Microbiome of Trifolium pratense in Grassland Evidences a Stronger-Than-Expected Belowground Biodiversity-Ecosystem Functioning Link
Cited by: 15
Author(s): Sara Fareed Mohamed Wahdan, Anna Heintz‐Buschart, Chakriya Sansupa, Benjawan Tanunchai, Yuting Wu, Martin Schädler, Matthias Noll, Witoon Purahong, François Buscot
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-019-52712-6

Whole blood transcriptome analysis in ewes fed with hemp seed supplemented diet
Cited by: 18
Author(s): Marco Iannaccone, Andrea Ianni, Felice Contaldi, Salvatore Esposito, Camillo Martino, Francesca Bennato, Elisabetta De Angelis, Lisa Grotta, Francesco Pomilio, Daniele Giansante, Giuseppe Martino
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pone.0145575

Effects of Fertilization and Sampling Time on Composition and Diversity of Entire and Active Bacterial Communities in German Grassland Soils
Cited by: 35
Author(s): Sarah Herzog, Franziska Wemheuer, Bernd Wemheuer, Rolf Daniel
Software Mentions: 3
Published: over 10 years ago

10.18632/oncotarget.8209

C-terminal truncated hepatitis B virus X protein promotes hepatocellular carcinogenesis through induction of cancer and stem cell-like properties
Cited by: 41
Author(s): Kai-Yu Ng, Stella Chai, Man Tong, Xin‐Yuan Guan, Chi-Ho Lin, Yick–Pang Ching, Dan Xie, Alfred S.L. Cheng, Stephanie Ma
Software Mentions: 3
Published: over 10 years ago

10.1186/s12885-018-4567-3

Deep sequencing of human papillomavirus positive loco-regionally advanced oropharyngeal squamous cell carcinomas reveals novel mutational signature
Cited by: 13
Author(s): Christian Grónhøj Larsen, David Hebbelstrup Jensen, Tina Klitmøller Agander, Katalin Kiss, Estrid Høgdall, Lena Specht, Frederik Otzen Bagger, Finn Cilius Nielsen
Software Mentions: 3
Published: over 8 years ago

10.18632/oncotarget.6922

Histone H3 lysine 4 acetylation and methylation dynamics define breast cancer subtypes
Cited by: 88
Author(s): Terri L. Messier, Jonathan A. R. Gordon, Joseph R. Boyd, Coralee E. Tye, Gillian Browne, Janet L. Stein, Jane B. Lian
Software Mentions: 3
Published: over 10 years ago

10.1186/s12974-019-1545-x

Differential transcriptional profiles identify microglial- and macrophage-specific gene markers expressed during virus-induced neuroinflammation
Cited by: 81
Author(s): Ana Beatriz DePaula-Silva, Carlos Gorbea, Daniel J. Doty, Jane E. Libbey, John Michael S. Sanchez, Tyler J. Hanak, Demián Cazalla, Robert S. Fujinami
Software Mentions: 3
Published: about 7 years ago

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Papers Mentioning cutadapt 1,562