bioconductor: ShortRead | Projects

10.1186/s12859-016-1241-0

systemPipeR: NGS workflow and report generation environment
Cited by: 148
Author(s): Tyler W. H. Backman, Thomas Girke
Software Mentions: 19
Published: about 8 years ago

Enhancer Evolution across 20 Mammalian Species
Cited by: 626
Author(s): Diego Villar, Camille Berthelot, Sarah Aldridge, Tim Rayner, Margus Lukk, Miguel Pignatelli, Thomas J. Park, Robert Deaville, Jonathan Thor Erichsen, Anna J. Jasinska, James M. A. Turner, Mads F. Bertelsen, Elizabeth P. Murchison, Paul Flicek, Duncan T. Odom
Software Mentions: 17
Published: almost 10 years ago

10.1186/1471-2105-11-237

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data
Cited by: 868
Author(s): Lihua Julie Zhu, Claude Gazin, Nathan D. Lawson, Hervé Pagès, Simon Lin, David S. Lapointe, Michael R. Green
Software Mentions: 16
Published: over 14 years ago

10.1371/journal.pone.0225615

An indigenous Saccharomyces uvarum population with high genetic diversity dominates uninoculated Chardonnay fermentations at a Canadian winery
Cited by: 9
Author(s): Garrett C. McCarthy, Sydney Morgan, Jonathan T. Martiniuk, Brianne L. Newman, Stephanie McCann, Vivien Measday, Daniel M. Durall
Software Mentions: 14
Published: almost 4 years ago

10.1371/journal.pcbi.1003118

Software for Computing and Annotating Genomic Ranges
Cited by: 2,902
Author(s): Michael Lawrence, Wolfgang Huber, Hervé Pagès, Patrick Aboyoun, Marc Carlson, Robert Gentleman, Martin Morgan, Vincent J. Carey
Software Mentions: 14
Published: over 11 years ago

10.3389/fnmol.2017.00045

Screening the Molecular Framework Underlying Local Dendritic mRNA Translation
Cited by: 4
Author(s): Sanjeev V. Namjoshi, Kimberly F. Raab‐Graham
Software Mentions: 10
Published: over 7 years ago

10.1371/journal.pone.0041762

Large-scale identification of microRNA targets in murine Dgcr8-deficient embryonic stem cell lines.
Cited by: 7
Author(s): Matthew P Davis, Cei Abreu‐Goodger, Stijn van Dongen, Dong Lu, P. Täte, Nenad Bartoniček, Claudia Kutter, Pentao Liu, William C. Skarnes, Anton J. Enright, Ian Dunham
Software Mentions: 10
Published: almost 13 years ago

10.7554/eLife.50004

Casposase structure and the mechanistic link between DNA transposition and spacer acquisition by CRISPR-Cas
Cited by: 15
Author(s): A.B. Hickman, Shweta Kailasan, Pavol Genzor, Astrid D. Haase, Fred Dyda
Software Mentions: 9
Published: almost 5 years ago

10.1093/bioinformatics/bts477

easyRNASeq: a bioconductor package for processing RNA-Seq data
Cited by: 96
Author(s): Nicolas Delhomme, Ismaël Padioleau, Eileen E. M. Furlong, Lars M. Steinmetz
Software Mentions: 9
Published: over 12 years ago

10.1371/journal.pone.0056024

Novel Pancreatic Endocrine Maturation Pathways Identified by Genomic Profiling and Causal Reasoning
Cited by: 14
Author(s): Alex Gutteridge, J. Michael Rukstalis, Daniel Ziemek, Mark Tié, Lin Ji, Rebeca Ramos-Zayas, Nancy A. Nardone, Lisa D. Norquay, Martin Brenner, Kim San Tang, John D. McNeish, Rebecca K. Rowntree
Software Mentions: 9
Published: almost 12 years ago

10.1371/journal.pone.0204877

Rare haplotype load as marker for lethal mutagenesis
Cited by: 7
Author(s): Josep Gregori, María Eugenia Soria, Isabel Gallego, Mercedes Guerrero-Murillo, Juan Ignacio Esteban, Josep Quer, Celia Perales, Esteban Domingo
Software Mentions: 9
Published: about 6 years ago

10.1038/s42003-021-01948-y

High biodiversity in a benzene-degrading nitrate-reducing culture is sustained by a few primary consumers
Cited by: 9
Author(s): Chrats Melkonian, Lucas Fillinger, Siavash Atashgahi, Ulisses Nunes da Rocha, Eric Kuiper, Brett G. Olivier, Martin Braster, Willi Gottstein, Rick Helmus, John R. Parsons, Hauke Smidt, Marcelle van der Waals, Jan Gerritse, Bernd W. Brandt, Wilfred F. M. Röling, Douwe Molenaar, Rob J.M. van Spanning
Software Mentions: 9
Published: over 3 years ago

10.1371/journal.pone.0031630

Optimizing a Massive Parallel Sequencing Workflow for Quantitative miRNA Expression Analysis
Cited by: 33
Author(s): Francesca Cordero, Marco Beccuti, Maddalena Arigoni, Susanna Donatelli, Raffaele Calogero
Software Mentions: 8
Published: almost 13 years ago

10.1186/1471-2164-15-284

ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases
Cited by: 743
Author(s): Li Shen, Ning‐Yi Shao, Xiaochuan Liu, Eric J. Nestler
Software Mentions: 8
Published: almost 11 years ago

10.1371/journal.pgen.1002704

Extent, Causes, and Consequences of Small RNA Expression Variation in Human Adipose Tissue
Cited by: 45
Author(s): Leopold Parts, Åsa K. Hedman, Sarah Keildson, Andrew Knights, Cei Abreu‐Goodger, Martijn van de Bunt, José Afonso Guerra-Assunção, Nenad Bartoniček, Stijn van Dongen, Reedik Mägi, James Nisbet, Amy Barrett, Mattias Rantalainen, Alexandra C. Nica, Michael A. Quail, Kerrin S. Small, Daniel Glass, Anton J. Enright, John Winn, Panos Deloukas, Emmanouil T. Dermitzakis, Mark I. McCarthy, Timothy D. Spector, Richard Durbin, Cecilia M. Lindgren
Software Mentions: 7
Published: over 12 years ago

10.1016/j.omtn.2017.08.010

Profiling the Mismatch Tolerance of Argonaute 2 through Deep Sequencing of Sliced Polymorphic Viral RNAs
Cited by: 2
Author(s): Pantazis Theotokis, Louise Usher, Christopher K. Kortschak, Ed C. Schwalbe, Sterghios A. Moschos
Software Mentions: 7
Published: almost 7 years ago

10.3390/pathogens10010066

Contamination Sources and Transmission Routes for Campylobacter on (Mixed) Broiler Farms in Belgium, and Comparison of the Gut Microbiota of Flocks Colonized and Uncolonized with Campylobacter
Cited by: 8
Author(s): Karolien Hertogs, Annelies Haegeman, Dries Schaumont, Philippe Gelaude, Lieven De Zutter, Jeroen Dewulf, Marc Heyndrickx, Geertrui Rasschaert
Software Mentions: 7
Published: almost 4 years ago

10.3389/fgene.2012.00287

Bioinformatics of Cancer ncRNA in High Throughput Sequencing: Present State and Challenges
Cited by: 9
Author(s): Natasha Andressa Nogueira Jorge, Carlos Gil Ferreira, Fábio Passetti
Software Mentions: 7
Published: almost 13 years ago

10.1186/s12864-017-3683-9

Reduced changes in protein compared to mRNA levels across non-proliferating tissues
Cited by: 72
Author(s): Kobi Perl, Kathy Ushakov, Yair Pozniak, Ofer Yizhar-Barnea, Yoni Bhonker, Shaked Shivatzki, Tamar Geiger, Karen B. Avraham, Ron Shamir
Software Mentions: 6
Published: over 7 years ago

10.1371/journal.pone.0086536

Dual Targeting of MEK and PI3K Pathways Attenuates Established and Progressive Pulmonary Fibrosis
Cited by: 22
Author(s): Satish K. Madala, Ramakrishna Edukulla, Mukta Phatak, Stephanie Schmidt, Cynthia Davidson, Thomas H. Acciani, Thomas R. Korfhagen, Mario Medvedovic, Timothy D. Le Cras, Kimberly Wagner, William D. Hardie
Software Mentions: 6
Published: almost 11 years ago

10.1016/j.cell.2011.11.058

Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages
Cited by: 504
Author(s): Dominic Schmidt, Petra Schwalie, Michael D. Wilson, Benoît Ballester, Ângela Gonçalves, Claudia Kutter, Gordon D. Brown, Aileen Marshall, Paul Flicek, Duncan T. Odom
Software Mentions: 6
Published: almost 13 years ago

10.1371/journal.pone.0235294

Comparative RNA-Seq analyses of Drosophila plasmatocytes reveal gene specific signatures in response to clean injury and septic injury
Cited by: 22
Author(s): Elodie Ramond, Jan Paul Dudzic, Bruno Lemaître
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pone.0097379

Direct Sequencing from the Minimal Number of DNA Molecules Needed to Fill a 454 Picotiterplate
Cited by: 12
Author(s): Mária Džunková, Marc García-Garcerá, Llúcia Martínez-Priego, Giussepe D’Auria, Francesc Calafell, Andrés Moya
Software Mentions: 6
Published: over 10 years ago

10.1186/s12943-017-0691-y

Multi-omics of 34 colorectal cancer cell lines - a resource for biomedical studies
Cited by: 212
Author(s): Kaja Christine Graue Berg, Peter W. Eide, Ina A. Eilertsen, Bjarne Johannessen, Jarle Bruun, Stine A. Danielsen, Merete Bjørnslett, Leonardo A. Meza‐Zepeda, Mette Eknæs, Guro Elisabeth Lind, Ola Myklebost, Rolf Inge Skotheim, Anita Sveen, Ragnhild Lothe
Software Mentions: 6
Published: over 7 years ago

10.7554/eLife.22057

T cell receptor repertoires of mice and humans are clustered in similarity networks around conserved public CDR3 sequences
Cited by: 121
Author(s): Asaf Madi, Asaf Poran, Eric Shifrut, Shlomit Reich-Zeliger, Erez Greenstein, Irena Zaretsky, Tomer Arnon, François Van Laethem, Alfred Singer, Jinghua Lu, Peter D. Sun, Irun R. Cohen, Nir Friedman
Software Mentions: 6
Published: over 7 years ago

10.1186/s12859-019-2961-8

FastqCleaner: an interactive Bioconductor application for quality-control, filtering and trimming of FASTQ files
Cited by: 11
Author(s): Leandro Gabriel Roser, Fernán Agüero, Daniel O. Sánchez
Software Mentions: 6
Published: over 5 years ago

10.1289/ehp.1307297

Disruption of Aryl Hydrocarbon Receptor Homeostatic Levels during Embryonic Stem Cell Differentiation Alters Expression of Homeobox Transcription Factors that Control Cardiomyogenesis
Cited by: 46
Author(s): Qin Wang, Jing Chen, Chih‐Wei Ko, Yunxia Fan, Vinicius Carreira, Yinglei Chen, Ying Xia, Mario Medvedovic, Alvaro Puga
Software Mentions: 6
Published: about 11 years ago

10.1186/gb-2012-13-10-r95

Genome-wide promoter methylation analysis in neuroblastoma identifies prognostic methylation biomarkers
Cited by: 60
Author(s): Anneleen Decock, Maté Ongenaert, Jasmien Hoebeeck, Katleen De Preter, Gert Van Peer, Wim Van Criekinge, Ruth Ladenstein, Johannes H. Schulte, Rosa Noguera, Raymond Stallings, An Van Damme, Geneviève Laureys, Joëlle Vermeulen, Tom Van Maerken, Frank Speleman, Jo Vandesompele
Software Mentions: 5
Published: almost 13 years ago

10.1038/srep25948

Integrated metabolomic and transcriptome analyses reveal finishing forage affects metabolic pathways related to beef quality and animal welfare
Cited by: 58
Author(s): José A. Carrillo, Yanghua He, Yaokun Li, Jianan Liu, R.A. Erdman, Tad S. Sonstegard, Jiuzhou Song
Software Mentions: 5
Published: over 8 years ago

10.1038/s41598-020-75128-z

Novel genomic targets of valosin-containing protein in protecting pathological cardiac hypertrophy
Cited by: 5
Author(s): Ning Zhou, Xin Chen, Jing Xi, Ben Ma, Christiana Leimena, Shaunrick Stoll, Gangjian Qin, Charles Wang, Hongyu Qiu
Software Mentions: 5
Published: about 4 years ago

10.1111/1462-2920.15484

Effect of salinity on cable bacteria species composition and diversity
Cited by: 19
Author(s): Ann‐Sofie Dam, Ian P. G. Marshall, Nils Risgaard‐Petersen, Laurine D. W. Burdorf, Ugo Marzocchi
Software Mentions: 5
Published: over 3 years ago

10.1002/ece3.5924

Wild Dictyostelium discoideum social amoebae show plastic responses to the presence of nonrelatives during multicellular development
Cited by: 10
Author(s): Suegene Noh, Lauren Christopher, Joan E. Strassmann, David C. Queller
Software Mentions: 5
Published: almost 5 years ago

10.1186/s12864-019-5511-x

RNA-seq based transcriptional analysis of Saccharomyces cerevisiae and Lachancea thermotolerans in mixed-culture fermentations under anaerobic conditions
Cited by: 35
Author(s): Kirti Shekhawat, Hugh-G. Patterton, Florian F. Bauer, Mathabatha Evodia Setati
Software Mentions: 5
Published: almost 6 years ago

10.3389/fpls.2020.597589

Chloroplast Electron Chain, ROS Production, and Redox Homeostasis Are Modulated by COS-OGA Elicitation in Tomato (Solanum lycopersicum) Leaves
Cited by: 3
Author(s): Sophie Moreau, Géraldine van Aubel, Rekin’s Janky, Pierre Van Cutsem
Software Mentions: 5
Published: almost 4 years ago

10.1186/s12865-014-0040-5

Quantitative assessment of the robustness of next-generation sequencing of antibody variable gene repertoires from immunized mice
Cited by: 53
Author(s): Victor Greiff, Ulrike Menzel, Ulrike Haessler, Skylar C. Cook, Simon Friedensohn, Tarik A. Khan, Mark Pogson, Ina Hellmann, Sai T. Reddy
Software Mentions: 4
Published: about 10 years ago

10.1002/ece3.4122

A nuclear DNA barcode for eastern North American oaks and application to a study of hybridization in an Arboretum setting
Cited by: 13
Author(s): Elisabeth Fitzek, Adline Delcamp, Erwan Guichoux, Marlene Hahn, Matthew S. Lobdell, Andrew L. Hipp
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0258207

A new phenothiazine derivate is active against Clostridioides difficile and shows low cytotoxicity
Cited by: 3
Author(s): Troels Ronco, Francisca Maria Aragao, Lasse Saaby, Jørn B. Christensen, A. Permin, Andrew R. Williams, Stig Milan Thamsborg, Rikke Heidemann Olsen
Software Mentions: 4
Published: about 3 years ago

10.3897/BDJ.5.e10792

Arthropod and oligochaete assemblages from grasslands of the southern Kenai Peninsula, Alaska
Cited by: 10
Author(s): Matthew L. Bowser, John M. Morton, John D. Hanson, Dawn R. Magness, Mallory Okuly
Software Mentions: 4
Published: almost 8 years ago

10.1128/mSystems.00029-19

Ultrahigh-Throughput Multiplexing and Sequencing of >500-Base-Pair Amplicon Regions on the Illumina HiSeq 2500 Platform
Cited by: 82
Author(s): Johanna B. Holm, Michael S. Humphrys, Courtney K. Robinson, Matthew L. Settles, Sandra Ott, Li Fu, Hongqiu Yang, Pawel Gajer, Xin He, Elias McComb, Patti E. Gravitt, Khalil G. Ghanem, Rebecca M. Brotman, Jacques Ravel
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0107259

Optimization of Extraction of Circulating RNAs from Plasma – Enabling Small RNA Sequencing
Cited by: 48
Author(s): Melanie Spornraft, Benedikt Kirchner, Bettina Haase, Vladimı́r Beneš, Michael W. Pfaffl, Irmgard Riedmaier
Software Mentions: 4
Published: about 10 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 8 years ago

10.1186/gb-2013-14-3-r28

The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage
Cited by: 272
Author(s): H. Bradley Shaffer, Patrick Minx, Daniel E. Warren, Andrew M. Shedlock, Robert C. Thomson, Nicole Valenzuela, John Abramyan, Chris T. Amemiya, Daleen Badenhorst, Kyle K. Biggar, Glen M. Borchert, Christopher W. Botka, Rachel M. Bowden, Edward L. Braun, Anne M. Bronikowski, Benoit G. Bruneau, Leslie T. Buck, Blanche Capel, Todd A. Castoe, Michael Czerwinski, Kim D. Delehaunty, Scott V. Edwards, Catrina C. Fronick, Matthew K. Fujita, Lucinda A. Fulton, Tina Graves, Edward Green, Wilfried Haerty, Ramkumar Hariharan, Omar Hernández, LaDeana W. Hillier, Alisha K. Holloway, Daniel E. Janes, Fredric J. Janzen, Cyriac Kandoth, Lesheng Kong, A. P. Jason de Koning, Yang Li, Robert Literman, Suzanne E. McGaugh, Lindsey Mork, Michelle O’Laughlin, Ryan T. Paitz, David D. Pollock, Chris P. Ponting, S. Radhakrishnan, Brian J. Raney, Joy M. Richman, John St. John, Tonia S. Schwartz, Arun Sethuraman, Phillip Q. Spinks, Kenneth B. Storey, Nay Thane, Tomáš Vinař, Laura M. Zimmerman, Wesley C. Warren, Elaine R. Mardis, Richard K. Wilson
Software Mentions: 4
Published: almost 12 years ago

10.3389/fphys.2016.00606

Host-Microbiome Interaction and Cancer: Potential Application in Precision Medicine
Cited by: 30
Author(s): Alejandra Contreras, Benjamin Cocom-Chan, Georgina Hernández-Montes, Tobías Portillo-Bobadilla, Osbaldo Resendis‐Antonio
Software Mentions: 4
Published: almost 8 years ago

10.1371/journal.pone.0093975

A Framework Phylogeny of the American Oak Clade Based on Sequenced RAD Data
Cited by: 190
Author(s): Andrew L. Hipp, Deren A. R. Eaton, Jeannine Cavender‐Bares, Elisabeth Fitzek, Rick Nipper, Paul S. Manos
Software Mentions: 4
Published: over 10 years ago

10.1038/srep20064

Digital detection of endonuclease mediated gene disruption in the HIV provirus
Cited by: 21
Author(s): Ruth Hall Sedlak, Shu Liang, Nixon Niyonzima, Harshana S. De Silva Feelixge, Pavitra Roychoudhury, Alexander L. Greninger, Nicholas Weber, Sandrine Boissel, Andrew M. Scharenberg, Anqi Cheng, Amalia Magaret, Roger E. Bumgarner, Daniel Stone, Keith R. Jerome
Software Mentions: 4
Published: almost 9 years ago

10.1186/s12862-017-1087-8

Rethinking the evolution of eukaryotic metabolism: novel cellular partitioning of enzymes in stramenopiles links serine biosynthesis to glycolysis in mitochondria
Cited by: 21
Author(s): Melania Abrahamian, Meenakshi S. Kagda, Audrey M. V. Ah‐Fong, Howard S. Judelson
Software Mentions: 4
Published: almost 7 years ago

10.1093/ve/veaa073

Population structure of Cydia pomonella granulovirus isolates revealed by quantitative analysis of genetic variation
Cited by: 9
Author(s): Jiangbin Fan, Johannes A. Jehle, Jörg T. Wennmann
Software Mentions: 4
Published: about 4 years ago

10.3389/fimmu.2013.00379

CD4+ T Cell-Receptor Repertoire Diversity is Compromised in the Spleen but Not in the Bone Marrow of Aged Mice Due to Private and Sporadic Clonal Expansions
Cited by: 29
Author(s): Eric Shifrut, Kuti Baruch, Hilah Gal, Wilfred Ndifon, Aleksandra Deczkowska, Michal Schwartz, Nir Friedman
Software Mentions: 4
Published: almost 12 years ago

10.1038/micronano.2017.18

Measurement of copy number variation in single cancer cells using rapid-emulsification digital droplet MDA
Cited by: 13
Author(s): Samuel Kim, Gayatri Premasekharan, Iain C. Clark, Hawi B. Gemeda, Pamela L. Paris, Adam R. Abate
Software Mentions: 3
Published: over 7 years ago

10.1128/AEM.02200-17

Promising Prebiotic Candidate Established by Evaluation of Lactitol, Lactulose, Raffinose, and Oligofructose for Maintenance of a Lactobacillus-Dominated Vaginal Microbiota
Cited by: 48
Author(s): Stephanie L. Collins, Amy McMillan, Shannon Seney, Charlotte van der Veer, Remco Kort, Mark W. Sumarah, Gregor Reid
Software Mentions: 3
Published: over 6 years ago

10.1186/1471-2148-12-94

Uninformative polymorphisms bias genome scans for signatures of selection
Cited by: 131
Author(s): Marius Roesti, Walter Salzburger, Daniel Berner
Software Mentions: 3
Published: over 12 years ago

10.1186/1471-2164-13-383

The regulatory effect of miRNAs is a heritable genetic trait in humans
Cited by: 23
Author(s): Paul Geeleher, R. Stephanie Huang, Eric R. Gamazon, Aaron Golden, Cathal Seoighe
Software Mentions: 3
Published: over 12 years ago

10.1186/1471-2164-13-385

Genetic changes during a laboratory adaptive evolution process that allowed fast growth in glucose to an Escherichia coli strain lacking the major glucose transport system
Cited by: 38
Author(s): César Aguilar, Adelfo Escalante, Noemí Flores, R. Anda, Fernando Riveros-Mckay, Guillermo Gosset, Enrique Morett, Francisco Bolívar
Software Mentions: 3
Published: over 12 years ago

10.1186/s12864-015-1700-4

Read count-based method for high-throughput allelic genotyping of transposable elements and structural variants
Cited by: 0
Author(s): Aléxandre Kuhn, Yao Min Ong, Stephen R. Quake, William F. Burkholder
Software Mentions: 3
Published: over 9 years ago

10.1186/1471-2164-13-83

Identification and characterization of microRNAs in Phaseolus vulgaris by high-throughput sequencing
Cited by: 83
Author(s): Pablo Peláez, Sebastián A. Trejo, Luis P. Íñiguez, Georgina Estrada-Navarrete, Alejandra A. Covarrubias, José Luis Reyes, Federico Sánchez
Software Mentions: 3
Published: over 12 years ago

10.1002/mbo3.565

Transcriptome analysis and anaerobic C4‐dicarboxylate transport in Actinobacillus succinogenes
Cited by: 8
Author(s): Mi Na Rhie, Byeonghyeok Park, Hyeok Jin Ko, In Geol Choi, Ok Bin Kim
Software Mentions: 3
Published: almost 7 years ago

10.1111/pbi.13136

Genome of ‘Charleston Gray’, the principal American watermelon cultivar, and genetic characterization of 1,365 accessions in the U.S. National Plant Germplasm System watermelon collection
Cited by: 83
Author(s): Shan Wu, Xin Wang, Umesh K. Reddy, Honghe Sun, Kan Bao, Lei Gao, Linyong Mao, Takshay Patel, Carlos E. Ortíz, Venkata Lakshmi Abburi, Padma Nimmakayala, Sandra Branham, Patrick Wechter, Laura Massey, Kai-Shu Ling, Chandrasekar S. Kousik, Sue A. Hammar, Yaakov Tadmor, Vitaly Portnoy, Amit Gur, Nurit Katzir, Nihat Guner, Angela R. Davis, Alvaro G. Hernandez, Chris Wright, Cecilia McGregor, Robert L. Jarret, Xingping Zhang, Yong Xu, Todd C. Wehner, Rebecca Grumet, Amnon Levi, Zhangjun Fei
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pgen.1002565

Tcf7 Is an Important Regulator of the Switch of Self-Renewal and Differentiation in a Multipotential Hematopoietic Cell Line
Cited by: 92
Author(s): Jia Qian Wu, Montrell Seay, Vincent P. Schulz, Manoj Hariharan, David Tuck, Lian Jin, Jie Du, Minyi Shi, Zhijia Ye, Mark Gerstein, M Snyder, Sherman M. Weissman
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pgen.1004851

A Cbx8-Containing Polycomb Complex Facilitates the Transition to Gene Activation during ES Cell Differentiation
Cited by: 62
Author(s): Catherine Creppe, Anna M. Palau, Roberto Malinverni, Vanesa Valero, Marcus Buschbeck
Software Mentions: 3
Published: almost 10 years ago

10.1371/journal.pgen.1007238

EAT1 transcription factor, a non-cell-autonomous regulator of pollen production, activates meiotic small RNA biogenesis in rice anther tapetum
Cited by: 68
Author(s): Seijiro Ono, Hua Liu, Katsutoshi Tsuda, Eigo Fukai, Keisuke Tanaka, Takuji Sasaki, Ken–Ichi Nonomura
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pone.0146706

Genetic Diversity Affects the Daily Transcriptional Oscillations of Marine Microbial Populations
Cited by: 6
Author(s): Irina N. Shilova, Julie Robidart, Edward F. DeLong, Jonathan P. Zehr
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pone.0096727

Comprehensive Evaluation and Optimization of Amplicon Library Preparation Methods for High-Throughput Antibody Sequencing
Cited by: 53
Author(s): Ulrike Menzel, Victor Greiff, Tarik A. Khan, Ulrike Haessler, Ina Hellmann, Simon Friedensohn, Skylar C. Cook, Mark Pogson, Sai T. Reddy
Software Mentions: 3
Published: over 10 years ago

10.1038/s41418-021-00771-6

MECOM permits pancreatic acinar cell dedifferentiation avoiding cell death under stress conditions
Cited by: 19
Author(s): Elyne Backx, Elke Wauters, Jonathan Baldan, Mathias Van Bulck, Ellis Michiels, Yves Heremans, Diedert Luc De Paep, Mineo Kurokawa, Susumu Goyama, Luc Bouwens, Patrick Jacquemin, Isabelle Houbracken, Ilse Rooman
Software Mentions: 3
Published: over 3 years ago

10.1080/22221751.2021.1969868

Host-dependent editing of SARS-CoV-2 in COVID-19 patients
Cited by: 12
Author(s): Josep Gregori, María Francesca Cortese, María Piñana, Carolina Campos, Damir García-Cehic, Cristina Andrés, Josep F. Abril, María Gema Codina, Ariadna Rando, Juliana Esperalba, Elena Sulleiro, Joan Joseph, Narcís Saubi, Sergi Colomer-Castell, Mari Carmen Martin, Carla Castillo, Juan Ignacio Esteban, Tomàs Pumarola, Francisco Rodríguez‐Frías, Andrés Antón, Josep Quer
Software Mentions: 3
Published: almost 4 years ago

10.3389/fcell.2021.697832

A Novel Mechanism of Cannabidiol in Suppressing Hepatocellular Carcinoma by Inducing GSDME Dependent Pyroptosis
Cited by: 36
Author(s): Fugen Shangguan, Hongfei Zhou, Nengfang Ma, Shanshan Wu, Huimin Huang, Guihua Jin, Shijia Wu, Weilong Hong, Weiwei Zhuang, Hongping Xia, Linhua Lan
Software Mentions: 3
Published: over 3 years ago

10.3389/fgene.2015.00340

Transfection of microRNA Mimics Should Be Used with Caution
Cited by: 124
Author(s): Hyun Yong Jin, Alicia González-Martín, Ana V. Miletic, Maoyi Lai, Sarah Knight, Mohsen Sabouri-Ghomi, Steven R. Head, Matthew S. Macauley, Robert C. Rickert, Changchun Xiao
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: almost 13 years ago

10.3389/fpls.2018.01147

Making a Better Home: Modulation of Plant Defensive Response by Brevipalpus Mites
Cited by: 19
Author(s): Gabriella Dias Arena, Pedro Luis Ramos-González, Luana Aparecida Rogerio, Marcelo Ribeiro-Alves, Clare L. Casteel, Juliana Freitas-Astúa, Marcos Antônio Machado
Software Mentions: 3
Published: over 6 years ago

10.1093/jxb/eraa132

Mild drought in the vegetative stage induces phenotypic, gene expression, and DNA methylation plasticity in Arabidopsis but no transgenerational effects
Cited by: 43
Author(s): Tom J. M. Van Dooren, Amanda Bortolini Silveira, Elodie Gilbault, José M. Jiménez‐Gómez, Antoine Martin, Liên Bach, Sébastien Tisné, Leandro Quadrana, Olivier Loudet, Vincent Colot
Software Mentions: 3
Published: over 4 years ago

10.1093/pcmedi/pbab012

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

10.1038/s41597-019-0253-9

Prenatal hypoxia-induced epigenomic and transcriptomic reprogramming in rat fetal and adult offspring hearts
Cited by: 16
Author(s): Xin Chen, Li Zhang, Charles Wang
Software Mentions: 3
Published: about 5 years ago

10.1128/mBio.02136-21

Protospacer-Adjacent Motif Specificity during Clostridioides difficile Type I-B CRISPR-Cas Interference and Adaptation
Cited by: 3
Author(s): Anna Maikova, Pierre Boudry, Anna Shiriaeva, Aleksandra Vasileva, Anaïs Boutserin, Sofia Medvedeva, Ekaterina Semenova, Konstantin Severinov, Olga Soutourina
Software Mentions: 3
Published: about 3 years ago

10.1101/2020.08.04.20167874

Swab-Seq: A high-throughput platform for massively scaled up SARS-CoV-2 testing
Cited by: 39
Author(s): Joshua S. Bloom, Laila Sathe, Chetan Munugala, Eric M. Jones, Molly Gasperini, Nathan B. Lubock, Fauna Yarza, Erin Thompson, Kyle M. Kovary, Jimin Park, Dawn Marquette, Stephania Kay, Mark Lucas, TreQuan Love, A. Sina Booeshaghi, Oliver F. Brandenberg, Longhua Guo, James Boocock, Myles Hochman, Scott W. Simpkins, Isabella Lin, Nathan LaPierre, Duke Hong, Yi Zhang, Gabriel Oland, Bianca Judy Choe, Sukantha Chandrasekaran, Evann E. Hilt, Manish J. Butte, Robert Damoiseaux, Clifford Kravit, Aaron Cooper, Yi Yin, Lior Pachter, Omai B. Garner, Jonathan Flint, Eleazar Eskin, Chongyuan Luo, Sriram Kosuri, Leonid Kruglyak, Valerie A. Arboleda
Software Mentions: 3
Published: over 4 years ago

10.3389/fcimb.2020.625576

Phylogeography of Human and Animal Coxiella burnetii Strains: Genetic Fingerprinting of Q Fever in Belgium
Cited by: 12
Author(s): Sara Tomaiuolo, Samira Boarbi, Tiziano Fancello, Patrick P. Michel, Damien Desqueper, Fabien Grégoire, Jozefien Callens, David Frétin, Bert Devriendt, Eric Cox, Marcella Mori
Software Mentions: 2
Published: over 3 years ago

10.3390/microorganisms9061223

The Microbiota of Modified-Atmosphere-Packaged Cooked Charcuterie Products throughout Their Shelf-Life Period, as Revealed by a Complementary Combination of Culture-Dependent and Culture-Independent Analysis
Cited by: 12
Author(s): Evelyne Duthoo, Geertrui Rasschaert, Frédéric Leroy, Stefan Weckx, Marc Heyndrickx, Koen De Reu
Software Mentions: 2
Published: over 3 years ago

10.1038/srep44447

Abseq: Ultrahigh-throughput single cell protein profiling with droplet microfluidic barcoding
Cited by: 208
Author(s): Payam Shahi, Samuel Kim, John Haliburton, Zev J. Gartner, Adam R. Abate
Software Mentions: 2
Published: over 7 years ago

10.3390/molecules25194466

Polyunsaturated Fatty Acids of Both the Omega-3 and the Omega-6 Family Abrogate the Cytokine-Induced Upregulation of miR-29a-3p by Endothelial Cells
Cited by: 5
Author(s): Daniel Maucher, Birte Schmidt, Kevin Kuhlmann, Julia Schümann
Software Mentions: 2
Published: about 4 years ago

10.1038/s41598-020-71181-w

Multidrug transporter MRP4/ABCC4 as a key determinant of pancreatic cancer aggressiveness
Cited by: 8
Author(s): Ana Sahores, Alejandro Enrique Carozzo, María May, Natalia Gómez, Nicolás Di Siervi, M. De Sousa Serro, Agustín Yaneff, A. Rodríguez-González, Martı́n C. Abba, Carina Shayo, Carlos Davio
Software Mentions: 2
Published: about 4 years ago

10.3389/fgene.2013.00301

The anti-miR21 antagomir, a therapeutic tool for colorectal cancer, has a potential synergistic effect by perturbing an angiogenesis-associated miR30
Cited by: 26
Author(s): Minsun Song, John J. Rossi
Software Mentions: 2
Published: almost 11 years ago

10.1038/s41598-021-95166-5

Feeding sites promoting wildlife-related tourism might highly expose the endangered Yunnan snub-nosed monkey (Rhinopithecus bieti) to parasite transmission
Cited by: 4
Author(s): Eve Afonso, Rong Fu, Amaël Dupaix, A.-C. Goydadin, ZhongHua Yu, Cécile Callou, Petra Villette, Patrick Giraudoux, Li Li
Software Mentions: 2
Published: over 3 years ago

10.1186/s13075-016-0931-3

Anti-RANKL treatment inhibits erosive joint destruction and lowers inflammation but has no effect on bone formation in the delayed-type hypersensitivity arthritis (DTHA) model
Cited by: 5
Author(s): Sara Marie Atkinson, J. Bleil, R. Maier, Anja A. Kühl, Mette Thorn, Kyle Serikawa, Brian Fox, Kim Kruse, Claus Haase, Søren Skov, Anneline Nansen, Uta Syrbe
Software Mentions: 2
Published: almost 9 years ago

10.18632/oncotarget.25744

RNA sequencing reveals upregulation of a transcriptomic program associated with stemness in metastatic prostate cancer cells selected for taxane resistance
Cited by: 14
Author(s): Christina K. Cajigas-Du Ross, Shannalee R. Martinez, Leanne Woods-Burnham, Alfonso M. Durán, Sourav Roy, Anamika Basu, Joshua Ramirez, Greisha L. Ortiz-Hernández, Leslimar Ríos-Colón, Evgeny Chirshev, Evelyn S. Sanchez-Hernández, Ubaldo Soto, Céline Greco, Claude Boucheix, Xin Chen, Juli Unternaehrer, Charles Wang, Carlos A. Casiano
Software Mentions: 2
Published: over 6 years ago

10.17912/micropub.biology.000397

Transcriptional Response to a Dauer-Inducing Ascaroside Cocktail in Late L1 in C. elegans.
Cited by: 3
Author(s): Sarah M Cohen, Jessica J. Sun, Frank C. Schroeder, Paul W. Sternberg
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0086175

Using Environmental DNA to Census Marine Fishes in a Large Mesocosm
Cited by: 355
Author(s): Ryan P. Kelly, Jesse A. Port, Kevan M. Yamahara, Larry B. Crowder
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0147873

Transcriptome Analysis of the SL221 Cells at the Early Stage during Spodoptera litura Nucleopolyhedrovirus Infection
Cited by: 8
Author(s): Yu Qian, Yongqiang Xiong, Jianliang Liu, Dongling Wen, Xiaohui Wu, Hang Yin
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0176197

New gSSR and EST-SSR markers reveal high genetic diversity in the invasive plant Ambrosia artemisiifolia L. and can be transferred to other invasive Ambrosia species
Cited by: 23
Author(s): Lucie Meyer, Romain Causse, Fanny Pernin, Romain Scalone, Géraldine Bailly, Bruno Chauvel, Christophe Délye, Valérie Le Corre
Software Mentions: 2
Published: over 7 years ago

10.3390/ijms160922046

Identification of Conserved and Novel MicroRNAs during Tail Regeneration in the Mexican Axolotl
Cited by: 15
Author(s): Micah D. Gearhart, Jami R. Erickson, Andrew Walsh, Karen Echeverri
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0084461

Putative Sugar Transporters of the Mustard Leaf Beetle Phaedon cochleariae: Their Phylogeny and Role for Nutrient Supply in Larval Defensive Glands
Cited by: 16
Author(s): Magdalena Stock, René R. Gretscher, Marco Groth, Simone Eiserloh, Wilhelm Boland, Antje Burse
Software Mentions: 2
Published: almost 11 years ago

10.1113/JP279810

Regulation of microRNA‐221, ‐222, ‐21 and ‐27 in articular cartilage subjected to abnormal compressive forces
Cited by: 10
Author(s): Paulina Stadnik, Sophie Gilbert, Jessica Tarn, Sarah Charlton, Andrew Skelton, M.J. Barter, Victor Colin Duance, David A. Young, Emma Jane Blain
Software Mentions: 2
Published: about 4 years ago

10.3390/ijms18020284

Impact of Polyunsaturated Fatty Acids on miRNA Profiles of Monocytes/Macrophages and Endothelial Cells—A Pilot Study
Cited by: 28
Author(s): Claudia Roessler, Kevin Kuhlmann, Christine Hellwing, Anja Leimert, Julia Schümann
Software Mentions: 2
Published: almost 8 years ago

10.3390/diagnostics10090701

Sepsis Diagnostics: Intensive Care Scoring Systems Superior to MicroRNA Biomarker Testing
Cited by: 1
Author(s): Fabian Link, Knut Krohn, Anna-Maria Burgdorff, Annett Christel, Julia Schümann
Software Mentions: 2
Published: about 4 years ago

10.1242/dmm.022905

Depletion of regulatory T cells leads to an exacerbation of delayed-type hypersensitivity arthritis in C57BL/6 mice that can be counteracted by IL-17 blockade
Cited by: 9
Author(s): Sara Marie Atkinson, Ute Hoffmann, Alf Hamann, Emil Bach, Niels Banhos Danneskiold‐Samsøe, Karsten Kristiansen, Kyle Serikawa, Brian Fox, Kim Kruse, Claus Haase, Søren Skov, Anneline Nansen
Software Mentions: 2
Published: almost 9 years ago

10.15252/emmm.201606188

Plasmodium falciparum var genes expressed in children with severe malaria encode <scp>CIDR</scp> α1 domains
Cited by: 74
Author(s): Jakob S. Jespersen, Christian W. Wang, Sixbert I. Mkumbaye, Daniel T. R. Minja, Bent Petersen, Louise Turner, Jens E. V. Petersen, John Lusingu, Thor G. Theander, Thomas Lavstsen
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pbio.1001950

A Trihelix DNA Binding Protein Counterbalances Hypoxia-Responsive Transcriptional Activation in Arabidopsis
Cited by: 77
Author(s): Beatrice Giuntoli, Seung Cho Lee, Francesco Licausi, Monika Kosmacz, Teruko Oosumi, Joost T. van Dongen, Julia Bailey‐Serres, Pierdomenico Perata
Software Mentions: 2
Published: about 10 years ago

10.1186/1471-2164-15-1002

A high-throughput screening strategy for detecting CRISPR-Cas9 induced mutations using next-generation sequencing
Cited by: 80
Author(s): Charles C. Bell, Graham Magor, Kevin R. Gillinder, Andrew C. Perkins
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0038040

Phylogenetic Analysis of a Spontaneous Cocoa Bean Fermentation Metagenome Reveals New Insights into Its Bacterial and Fungal Community Diversity
Cited by: 102
Author(s): Koen Illeghems, Luc De Vuyst, Zoi Papalexandratou, Stefan Weckx
Software Mentions: 1
Published: over 12 years ago

10.1371/journal.pone.0030619

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data
Cited by: 2,314
Author(s): Ravi K. Patel, Mukesh Jain
Software Mentions: 1
Published: almost 13 years ago

10.1371/journal.pone.0085148

Overexpression of Dimethylarginine Dimethylaminohydrolase 1 Attenuates Airway Inflammation in a Mouse Model of Asthma
Cited by: 20
Author(s): Kayla G. Kinker, Aaron M. Gibson, Stacey A. Bass, Brandy P. Day, Jingyuan Deng, Mario Medvedovic, Julio A. Landero Figueroa, Gurjit K. Khurana Hershey, Weiguo Chen
Software Mentions: 1
Published: almost 11 years ago

10.1038/s41598-019-49241-7

Identification of stably expressed housekeeping miRNAs in endothelial cells and macrophages in an inflammatory setting
Cited by: 10
Author(s): Fabian Link, Knut Krohn, Julia Schümann
Software Mentions: 1
Published: about 5 years ago

10.1186/s13046-021-01986-8

Integrated multi-omics analyses on patient-derived CRC organoids highlight altered molecular pathways in colorectal cancer progression involving PTEN
Cited by: 20
Author(s): Marta Codrich, Emiliano Dalla, Catia Mio, Giulia Antoniali, Matilde Clarissa Malfatti, Stefania Marzinotto, Mariaelena Pierobon, Elisa Baldelli, Carla Di Loreto, Giuseppe Damante, Giovanni Terrosu, Carlo Pucillo, Gianluca Tell
Software Mentions: 1
Published: over 3 years ago

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