Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: pypi: bowtie
https://packages.ecosyste.ms/registries/pypi.org/packages/bowtie
Interactive Dashboard Toolkit.
43 versions
Latest release: about 6 years ago
1 dependent package
221 downloads last month
Papers Mentioning bowtie 1,566
10.1371/journal.pgen.1009538
Transcriptome-wide investigation of stop codon readthrough in Saccharomyces cerevisiaeCited by: 16
Author(s): Kotchaphorn Mangkalaphiban, Feng He, Robin Ganesan, Chan Wu, Richard E. Baker, Allan Jacobson
Software Mentions: 15
Published: over 3 years ago
10.1186/s12864-015-2140-x
GenomicInteractions: An R/Bioconductor package for manipulating and investigating chromatin interaction dataCited by: 54
Author(s): Nathan Harmston, Elizabeth Ing-Simmons, Malcolm Perry, Anja Barešić, Boris Lenhard
Software Mentions: 15
Published: almost 9 years ago
10.1371/journal.pone.0256196
Finding differentially expressed sRNA-Seq regions with srnadiffCited by: 2
Author(s): Matthias Zytnicki, Ignacio González
Software Mentions: 15
Published: about 3 years ago
10.1371/journal.pone.0248202
Host-specific gene expression as a tool for introduction success in Naupactus parthenogenetic weevilsCited by: 1
Author(s): Ava Mackay-Smith, Mary Kate Dornon, R.E. Lucier, Annalisa Okimoto, Flavia Mendonca de Sousa, Marcela Silvina Rodriguero, Viviana A. Confalonieri, Analía Alicia Lanteri, Andrea S. Sequeira
Software Mentions: 14
Published: over 3 years ago
10.1371/journal.pcbi.1003000
Transcriptome Profiling of Giardia intestinalis Using Strand-specific RNA-SeqCited by: 55
Author(s): Oscar Franzén, Jon Jerlström-Hultqvist, Elin Einarsson, Johan Ankarklev, Marcela Ferella, Björn Andersson, Staffan G. Svärd
Software Mentions: 13
Published: over 11 years ago
10.3390/ijms21010167
RNA-seq and ChIP-seq as Complementary Approaches for Comprehension of Plant Transcriptional Regulatory MechanismCited by: 22
Author(s): Isiaka Ibrahim Muhammad, Sze Ling Kong, Siti Nor Akmar Abdullah, Umaiyal Munusamy
Software Mentions: 12
Published: almost 5 years ago
10.7554/eLife.34409
General decapping activators target different subsets of inefficiently translated mRNAsCited by: 40
Author(s): Feng He, Alper Çelik, Chan Wu, Allan Jacobson
Software Mentions: 12
Published: almost 6 years ago
10.1016/j.devcel.2018.11.009
From Pioneer to Repressor: Bimodal foxd3 Activity Dynamically Remodels Neural Crest Regulatory Landscape In VivoCited by: 90
Author(s): Martyna Lukoseviciute, Daria Gavriouchkina, Ruth M. Williams, Tatiana Hochgreb-Hägele, Upeka Senanayake, Vanessa Chong, Supat Thongjuea, Emmanouela Repapi, Adam J. Mead, Tatjana Sauka‐Spengler
Software Mentions: 11
Published: almost 6 years ago
10.3389/fgene.2020.580580
Global Analysis of Transcription Start Sites in the New Ovine Reference Genome (Oar rambouillet v1.0)Cited by: 20
Author(s): Mazdak Salavati, Alex Caulton, Richard Clark, Iveta Gažová, Timothy P. L. Smith, Kim C. Worley, Noelle E. Cockett, Alan Archibald, Shannon Clarke, Brenda M. Murdoch, Emily L. Clark
Software Mentions: 11
Published: about 4 years ago
10.3389/fgene.2020.00548
Rcirc: An R Package for circRNA Analyses and VisualizationCited by: 8
Author(s): Peisen Sun, Haoming Wang, Guanglin Li
Software Mentions: 11
Published: over 4 years ago
10.3389/fgene.2018.00461
TEsmall Identifies Small RNAs Associated With Targeted Inhibitor Resistance in MelanomaCited by: 4
Author(s): Kathryn O’Neill, Wen‐Wei Liao, Asmita Patel, Molly Gale Hammell
Software Mentions: 10
Published: about 6 years ago
10.1002/ece3.5064
North‐facing slopes and elevation shape asymmetric genetic structure in the range‐restricted salamander <i>Plethodon shenandoah</i>Cited by: 10
Author(s): Kevin P. Mulder, Nandadevi Cortés-Rodríguez, Evan H. Campbell Grant, Adrianne B. Brand, Robert C. Fleischer
Software Mentions: 10
Published: over 5 years ago
10.1242/dev.193060
Extensive nuclear gyration and pervasive non-genic transcription during primordial germ cell development in zebrafishCited by: 4
Author(s): Stefan Redl, António Miguel de Jesus Domingues, Edoardo Caspani, Stefanie Möckel, Willi Salvenmoser, María Méndez-Lago, René F. Ketting
Software Mentions: 10
Published: almost 5 years ago
10.15252/msb.20188339
Linking aberrant chromatin features in chronic lymphocytic leukemia to transcription factor networksCited by: 31
Author(s): Jan‐Philipp Mallm, Murat Iskar, Naveed Ishaque, Lara Klett, Sabrina J. Kugler, Jose M. Muiño, Vladimir B. Teif, Alexandra M Poos, Sebastian Großmann, Fabian Erdel, Daniele Tavernari, Sandra D. Koser, Sabrina Schumacher, Benedikt Brors, Rainer König, Daniel Remondini, Martin Vingron, Stephan Stilgenbauer, Peter Lichter, Marc Zapatka, Daniel Mertens, Karsten Rippe
Software Mentions: 10
Published: over 5 years ago
10.1371/journal.pgen.1007102
Binding of high mobility group A proteins to the mammalian genome occurs as a function of AT-contentCited by: 16
Author(s): Daniele Colombo, Lukas Burger, Tuncay Baubec, Dirk Schübeler
Software Mentions: 10
Published: almost 7 years ago
10.1186/s12859-016-1125-3
Reusable, extensible, and modifiable R scripts and Kepler workflows for comprehensive single set ChIP-seq analysisCited by: 3
Author(s): Nathan James Allen Cormier, Tyler Kolisnik, Mark Bieda
Software Mentions: 10
Published: over 8 years ago
10.1002/advs.201901850
<i>Mesostigma viride</i> Genome and Transcriptome Provide Insights into the Origin and Evolution of StreptophytaCited by: 29
Author(s): Zhe Liang, Yuke Geng, Changmian Ji, Hongwu Du, Chui Eng Wong, Qian Zhang, Ye Zhang, Pingxian Zhang, Adeel Riaz, Sadaruddin Chachar, Yike Ding, Jing Wen, Yun-Wen Wu, Mingcheng Wang, Hongkun Zheng, Yanmin Wu, Viktor Demko, Lisha Shen, Han Xiao, Pengpeng Zhang, Xiaofeng Gu, Hao Yu
Software Mentions: 10
Published: about 5 years ago
10.1186/s12864-019-5870-3
Comprehensive assessment of multiple biases in small RNA sequencing reveals significant differences in the performance of widely used methodsCited by: 56
Author(s): Carrie Wright, Anandita Rajpurohit, Emily E. Burke, Courtney Williams, Leonardo Collado‐Torres, Martha Kimos, Nicholas J. Brandon, A.J. Cross, Daniel R. Weinberger, Joo Heon Shin
Software Mentions: 9
Published: over 5 years ago
10.3390/ijms151221788
Interactome Mapping Reveals Important Pathways in Skeletal Muscle Development of PigsCited by: 3
Author(s): Jianhua Cao, Tinghua Huang, Xinyun Li, Zhao Song
Software Mentions: 9
Published: almost 10 years ago
10.1186/s12859-018-2287-y
miRge 2.0 for comprehensive analysis of microRNA sequencing dataCited by: 54
Author(s): Yin Lu, Alexander S. Baras, Marc K. Halushka
Software Mentions: 9
Published: over 6 years ago
10.1038/s41598-017-14576-6
Sequencing genomes from mixed DNA samples - evaluating the metagenome skimming approach in lichenized fungiCited by: 37
Author(s): Meiser Anjuli, Jürgen Otte, Imke Schmitt, Francesco Dal Grande
Software Mentions: 9
Published: about 7 years ago
10.1038/s41598-017-07880-8
Global mapping of miRNA-target interactions in cattle (Bos taurus)Cited by: 19
Author(s): Troels K. H. Scheel, Michael J. Moore, Joseph M. Luna, Eiko Nishiuchi, John Fak, Robert B. Darnell, Charles M. Rice
Software Mentions: 9
Published: about 7 years ago
10.1186/s12915-021-01123-z
The stem rust fungus Puccinia graminis f. sp. tritici induces centromeric small RNAs during late infection that are associated with genome-wide DNA methylationCited by: 12
Author(s): Jana Sperschneider, Ashley Jones, Jamila Nasim, Bo Xu, Silke Jacques, Chengcheng Zhong, Narayana M. Upadhyaya, Rohit Mago, Yiheng Hu, Melania Figueroa, Karam B. Singh, Eric A. Stone, Ming-Bo Wang, Jennifer Taylor, Peter N. Dodds
Software Mentions: 9
Published: about 3 years ago
10.1038/s42003-021-01948-y
High biodiversity in a benzene-degrading nitrate-reducing culture is sustained by a few primary consumersCited 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
10.1186/s12859-020-03667-3
Evaluating metagenomics tools for genome binning with real metagenomic datasets and CAMI datasetsCited by: 49
Author(s): Yi Yue, Hao Huang, Qi Zhao, Huimin Dou, Xinyi Liu, Tian-Fei Han, Yue Chen, Xiangjun Song, Youhua Zhang, Jing Tu
Software Mentions: 9
Published: over 4 years ago
10.1186/s13059-020-02141-w
Improved reference genome of the arboviral vector Aedes albopictusCited by: 61
Author(s): Umberto Palatini, Reem A. Masri, Luciano V. Cosme, Sergey Koren, Françoise Thibaud‐Nissen, James K. Biedler, Flávia Krsticevic, J. Spencer Johnston, Rebecca Halbach, Jacob E. Crawford, Igor Antoshechkin, Anna‐Bella Failloux, Elisa Pischedda, Michele Marconcini, Jay Ghurye, Arang Rhie, Atashi Sharma, Д. А. Карагодин, James Jenrette, Stephanie Gamez, Pascal Miesen, Patrick Masterson, Adalgisa Caccone, Maria V. Sharakhova, Zhijian Tu, Philippos Aris Papathanos, Ronald P. van Rij, Omar S. Akbari, Jeffrey R. Powell, Adam M. Phillippy, Mariangela Bonizzoni
Software Mentions: 9
Published: about 4 years ago
10.7554/eLife.42675
The Hox transcription factor Ubx stabilizes lineage commitment by suppressing cellular plasticity in DrosophilaCited by: 20
Author(s): Katrin Domsch, Julie Carnesecchi, Vanessa Disela, Jana Friedrich, Nils Trost, Olga Ermakova, Maria Polychronidou, Ingrid Lohmann
Software Mentions: 9
Published: over 5 years ago
10.7554/eLife.39380
Intergenerational epigenetic inheritance of cancer susceptibility in mammalsCited by: 38
Author(s): Bluma J. Lesch, Zuzana Tóthová, Elizabeth A. Morgan, Zhicong Liao, Roderick T. Bronson, Benjamin L. Ebert, David C. Page
Software Mentions: 9
Published: over 5 years ago
10.3389/fgene.2019.00981
CircCode: A Powerful Tool for Identifying circRNA Coding AbilityCited by: 49
Author(s): Peisen Sun, Guanglin Li
Software Mentions: 9
Published: about 5 years ago
10.7554/eLife.58081
IER5, a DNA damage response gene, is required for Notch-mediated induction of squamous cell differentiationCited by: 11
Author(s): Pan Li, Madeleine E. Lemieux, Tom Thomas, Julia M. Rogers, Colin H. Lipper, Winston Lee, C. Anderson Johnson, Lynette M. Sholl, Andrew P. South, Jarrod A. Marto, Guillaume Adelmant, Stephen C. Blacklow, Jon C. Aster
Software Mentions: 9
Published: about 4 years ago
10.7554/eLife.44036
Neuroblast-specific open chromatin allows the temporal transcription factor, Hunchback, to bind neuroblast-specific lociCited by: 38
Author(s): Sonia Sen, Sachin Chanchani, Tony D. Southall, Chris Q. Doe
Software Mentions: 8
Published: almost 6 years ago
10.7554/eLife.38519
Insulin mutations impair beta-cell development in a patient-derived iPSC model of neonatal diabetesCited by: 106
Author(s): Diego Balboa, Jonna Saarimäki-Vire, Daniel Borshagovski, Mantas Survila, Päivi Lindholm, Emilia Galli, Solja Eurola, Jarkko Ustinov, Heli Grym, Hanna Huopio, Juha Partanen, Kirmo Wartiovaara, Timo Otonkoski
Software Mentions: 8
Published: almost 6 years ago
10.1186/s13072-020-00353-9
Distinct and overlapping roles of STAG1 and STAG2 in cohesin localization and gene expression in embryonic stem cellsCited by: 20
Author(s): Nicole L. Arruda, Zachary Carico, Megan Justice, Ying Frances Liu, Junjie Zhou, Holden C. Stefan, Jill M. Dowen
Software Mentions: 8
Published: about 4 years ago
10.1128/mSystems.00122-17
Market Integration Predicts Human Gut Microbiome Attributes across a Gradient of Economic DevelopmentCited by: 27
Author(s): Keaton Stagaman, Tara J Cepon-Robins, Melissa A. Liebert, Theresa E. Gildner, Samuel S. Urlacher, Felicia C. Madimenos, Karen Guillemin, J. Josh Snodgrass, Lawrence S. Sugiyama, Brendan J. M. Bohannan
Software Mentions: 8
Published: over 6 years ago
10.1038/srep44736
Vector Integration Sites Identification for Gene-Trap Screening in Mammalian Haploid CellsCited by: 5
Author(s): Jian Yu, Constance Ciaudo
Software Mentions: 8
Published: over 7 years ago
10.1007/s12551-018-0489-1
Hi-C analysis: from data generation to integrationCited by: 62
Author(s): Koustav Pal, Mattia Forcato, Francesco Ferrari
Software Mentions: 8
Published: almost 6 years ago
10.1371/journal.pone.0153782
Using Synthetic Mouse Spike-In Transcripts to Evaluate RNA-Seq Analysis ToolsCited by: 11
Author(s): Dena Leshkowitz, Ester Feldmesser, Gilgi Friedlander, Ghil Jona, Elena Ainbinder, Yisrael Parmet, Shirley Horn‐Saban
Software Mentions: 8
Published: over 8 years ago
10.1186/s13059-019-1747-7
Cell type-specific epigenetic links to schizophrenia risk in the brainCited by: 65
Author(s): Isabel Mendizabal, Stefano Berto, Noriyoshi Usui, Kazuya Toriumi, Paramita Chatterjee, Connor Douglas, Iksoo Huh, Hyeonsoo Jeong, Thomas S. Layman, Carol A. Tamminga, Todd M. Preuss, Genevieve Konopka, Soojin V. Yi
Software Mentions: 8
Published: over 5 years ago
10.1371/journal.ppat.1009602
Single cell analysis of host response to helminth infection reveals the clonal breadth, heterogeneity, and tissue-specific programming of the responding CD4+ T cell repertoireCited by: 5
Author(s): Ivy K. Brown, Nathan Dyjack, Mindy M. Miller, S. Harsha Krovi, Cydney Rios, Rachel A. Woolaver, Laura Harmacek, Ting-Hui Tu, Brian P. O’Connor, Thomas Danhorn, Brian Vestal, Laurent Gapin, Clemencia Pinilla, Max A. Seibold, James Scott‐Browne, Radleigh Santos, R. Lee Reinhardt
Software Mentions: 8
Published: over 3 years ago
10.1038/s41598-019-45193-0
Description of strongly heat-inducible heat shock protein 70 transcripts from Baikal endemic amphipodsCited by: 7
Author(s): Polina Drozdova, Daria Bedulina, Ekaterina Madyarova, Lorena Rivarola-Duarte, S Schreiber, Peter F. Stadler, Till Luckenbach, Maxim A. Timofeyev
Software Mentions: 8
Published: over 5 years ago
10.1186/s13059-020-02075-3
Single-cell ATAC-seq signal extraction and enhancement with SCATECited by: 29
Author(s): Zhicheng Ji, Weiqiang Zhou, Wenpin Hou, Hongkai Ji
Software Mentions: 8
Published: over 4 years ago
10.1186/s12915-019-0726-5
Multi-species annotation of transcriptome and chromatin structure in domesticated animalsCited by: 80
Author(s): Sylvain Foissac, Sarah Djebali, Kylie Munyard, Nathalie Vialaneix, Andrea Rau, Kévin Muret, Diane Esquerré, Matthias Zytnicki, Thomas Derrien, Philippe Bardou, Fany Blanc, Cédric Cabau, Elisa Crisci, Sophie Dhorne–Pollet, Françoise Drouet, Thomas Faraut, Ignacio González, Adeline Goubil, Sonia Lacroix‐Lamandé, Fabrice Laurent, Sylvain Marthey, Maria Marti-Marimon, Raphaëlle Momal-Leisenring, Florence Mompart, Pascale Quéré, David Robelin, Magali San Cristobal, Gwenola Tosser‐Klopp, Silvia Vincent‐Naulleau, Stéphane Fabre, Marie-Hélène Pinard van der Laan, Christophe Klopp, Michèle Tixier‐Boichard, Hervé Acloque, Sandrine Lagarrigue, Elisabetta Giuffra
Software Mentions: 8
Published: almost 5 years ago
10.3389/fpls.2021.647375
Molecular Evolution and Organization of Ribosomal DNA in the Hawkweed Tribe Hieraciinae (Cichorieae, Asteraceae)Cited by: 11
Author(s): Judith Fehrer, Renata Slavíková, Ladislava Paštová, Jiřina Josefiová, Patrik Mráz, Jindřich Chrtek, Yann Bertrand
Software Mentions: 8
Published: over 3 years ago
10.1186/s13073-020-00812-8
Transcriptome-wide profiles of circular RNA and RNA-binding protein interactions reveal effects on circular RNA biogenesis and cancer pathway expressionCited by: 89
Author(s): Trine Line Hauge Okholm, Shashank Sathe, Samuel S. Park, Andreas Bjerregaard Kamstrup, Asta Mannstaedt Rasmussen, Archana Shankar, Zong Ming Chua, Niels Fristrup, Morten Muhlig Nielsen, Søren Vang, Lars Dyrskjøt, Stefan Aigner, Christian Kroun Damgaard, G Yeo, Jakob Skou Pedersen
Software Mentions: 8
Published: almost 4 years ago
10.1016/j.cell.2017.04.013
The Cohesin Release Factor WAPL Restricts Chromatin Loop ExtensionCited by: 607
Author(s): Judith H.I. Haarhuis, Robin H. van der Weide, Vincent A. Blomen, J. Omar Yáñez-Cuna, Mario Amendola, Marjon S. van Ruiten, Peter H.L. Krijger, Hans Teunissen, René H. Medema, Bas van Steensel, Thijn R. Brummelkamp, Elzo de Wit, Benjamin D. Rowland
Software Mentions: 8
Published: over 7 years ago
10.3390/ijms21114014
Ionising Radiation Induces Promoter DNA Hypomethylation and Perturbs Transcriptional Activity of Genes Involved in Morphogenesis during Gastrulation in ZebrafishCited by: 6
Author(s): Sophia Murat El Houdigui, Christelle Adam-Guillermin, Olivier Armant
Software Mentions: 8
Published: over 4 years ago
10.3390/biomedicines9091253
Alterations in Circulating Monocytes Predict COVID-19 Severity and Include Chromatin Modifications Still Detectable Six Months after RecoveryCited by: 24
Author(s): Alberto Utrero‐Rico, Cecilia González-Cuadrado, Marta Chivite-Lacaba, Óscar Cabrera-Marante, Rocío Laguna‐Goya, Patricia Almendro-Vázquez, Carmen Díaz-Pedroche, María Ruiz-Ruigómez, Antonio Lalueza, María Dolores Folgueira, Enrique Vázquez, Ana Quintas, Marcos J. Berges-Buxeda, Moisés Martín-Rodriguez, Ana Dopazo, Antonio Serrano-Hernández, Estela Paz‐Artal, Estela Paz‐Artal
Software Mentions: 8
Published: about 3 years ago
10.3390/biom10060878
High-Throughput Identification of Adapters in Single-Read Sequencing DataCited by: 3
Author(s): Asan M. S. H. Mohideen, Steinar Johansen, Igor Babiak
Software Mentions: 8
Published: over 4 years ago
10.1371/journal.pgen.1009435
A cohesin cancer mutation reveals a role for the hinge domain in genome organization and gene expressionCited by: 14
Author(s): Zachary Carico, Holden C. Stefan, Megan Justice, Askar Yimit, Jill M. Dowen
Software Mentions: 8
Published: over 3 years ago
10.1016/j.stem.2020.03.005
GATA3 Mediates a Fast, Irreversible Commitment to BMP4-Driven Differentiation in Human Embryonic Stem CellsCited by: 42
Author(s): Alexandra Gunne-Braden, Adrienne E. Sullivan, Borzo Gharibi, Rahuman S. Malik Sheriff, Alok Kumar Maity, Yi Fang Wang, A. Edwards, Ming Jiang, Michael Howell, Robert Goldstone, Roy Wollman, Philip East, Silvia Santos
Software Mentions: 8
Published: over 4 years ago
10.1111/pbi.12958
The developmental dynamics of the <i>Populus</i> stem transcriptomeCited by: 92
Author(s): Qing Chao, Zili Gao, Dong Zhang, Biligen-Gaowa Zhao, Fengqin Dong, Chunxiang Fu, Lijun Liu, Bai-Chen Wang
Software Mentions: 8
Published: over 6 years ago
10.3390/ijms22158285
Maize DNA Methylation in Response to Drought Stress Is Involved in Target Gene Expression and Alternative SplicingCited by: 14
Author(s): Qi Wang, Jie Xu, Xuemei Pu, Haozhe Lv, Yanjun Liu, Huihui Ma, Fengkai Wu, Qingjun Wang, Xin Feng, Tianhong Liu, Qinghua Tang, Yanli Lu
Software Mentions: 8
Published: over 3 years ago
10.1186/s12870-019-1693-2
A k-mer grammar analysis to uncover maize regulatory architectureCited by: 32
Author(s): Maria Katherine Mejía‐Guerra, Edward S. Buckler
Software Mentions: 8
Published: over 5 years ago
10.1371/journal.pone.0200925
PNPase knockout results in mtDNA loss and an altered metabolic gene expression programCited by: 12
Author(s): Eriko Shimada, Fasih M. Ahsan, Mahta Nili, Dian Huang, Sean Atamdede, Tara TeSlaa, Dana Case, Xiang Yu, Brian D. Gregory, Benjamin J. Perrin, Carla M. Koehler, Michael A. Teitell
Software Mentions: 8
Published: over 6 years ago
10.7717/peerj.8522
Detection and characterization of microRNA expression profiling and its target genes in response to canine parvovirus in Crandell Reese Feline Kidney cellsCited by: 8
Author(s): Phongsakorn Chuammitri, Soulasack Vannamahaxay, Benjaporn Sornpet, Kidsadagon Pringproa, Prapas Patchanee
Software Mentions: 8
Published: over 4 years ago
10.1038/s42003-020-01637-2
Horseshoe crab genomes reveal the evolution of genes and microRNAs after three rounds of whole genome duplicationCited by: 23
Author(s): Wenyan Nong, Zhe Qu, Yiqian Li, Tom Barton-Owen, Hon Kit Wong, Ho Yin Yip, Hoi Ting Lee, Satya Narayana, Tobias Baril, Thomas Swale, Jianquan Cao, Ting‐Fung Chan, Hoi Shan Kwan, Sai Ming Ngai, Gianni Panagiotou, Pei‐Yuan Qian, Jian Qiu, Kevin Yuk‐Lap Yip, Normaz Wana Ismail, Siddhartha Pati, Akbar John, Stephen S. Tobe, William G. Bendena, Siu Gin Cheung, Alexander Hayward, Jerome H.L. Hui
Software Mentions: 8
Published: almost 4 years ago
10.1002/1878-0261.12569
Single‐cell RNA‐seq reveals the invasive trajectory and molecular cascades underlying glioblastoma progressionCited by: 34
Author(s): Bo Pang, Jiu Hua Xu, Jing Hu, Fenghua Guo, Linyun Wan, Mingjiang Cheng, Lin Pang
Software Mentions: 7
Published: about 5 years ago
10.1016/j.molcel.2020.01.007
Mammalian RNA Decay Pathways Are Highly Specialized and Widely Linked to TranslationCited by: 74
Author(s): Alex Tuck, Aneliya Rankova, Alaaddin Bulak Arpat, Luz Angélica Liechti, Daniel Heß, Vytautas Iešmantavičius, Violeta Castelo-Szekely, David Gatfield, Marc Bühler
Software Mentions: 7
Published: over 4 years ago
10.1186/s13059-021-02265-7
ReSeq simulates realistic Illumina high-throughput sequencing dataCited by: 7
Author(s): Stephan Schmeing, Mark D. Robinson
Software Mentions: 7
Published: over 3 years ago
10.1186/s12915-020-0752-3
Bivalent promoter hypermethylation in cancer is linked to the H327me3/H3K4me3 ratio in embryonic stem cellsCited by: 33
Author(s): Donnchadh S. Dunican, Heidi K. Mjoseng, Leanne Duthie, Ilya M. Flyamer, Wendy A. Bickmore, Richard R. Meehan
Software Mentions: 7
Published: over 4 years ago
10.1186/s13059-020-02098-w
Population variation in miRNAs and isomiRs and their impact on human immunity to infectionCited by: 11
Author(s): Maxime Rotival, Katherine J. Siddle, Martin Silvert, Julien Pothlichet, Hélène Quach, Lluı́s Quintana-Murci
Software Mentions: 7
Published: over 4 years ago
10.1371/journal.pgen.1007784
Maternal and zygotic gene regulatory effects of endogenous RNAi pathwaysCited by: 17
Author(s): Miguel Vasconcelos Almeida, António Miguel de Jesus Domingues, René F. Ketting
Software Mentions: 7
Published: over 5 years ago
10.1371/journal.pgen.1002704
Extent, Causes, and Consequences of Small RNA Expression Variation in Human Adipose TissueCited 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.ccell.2020.06.004
Single-Cell RNA-Seq Reveals Cellular Hierarchies and Impaired Developmental Trajectories in Pediatric EpendymomaCited by: 86
Author(s): Johannes Gojo, Bernhard Englinger, Li Jiang, Jens Martin Hübner, McKenzie Shaw, Olivia A. Hack, Sibylle Madlener, Dominik Kirchhofer, Ilon Liu, Jason W. Pyrdol, Volker Hovestadt, Emanuele Mazzola, Nathan D. Mathewson, Maria Trissal, Daniela Lötsch, Christian Dorfer, Christine Haberler, Angela Halfmann, Lisa Mayr, Andreas Peyrl, René Geyeregger, Benjamin Schwalm, Monica Mauermann, Kristian W. Pajtler, Till Milde, Marni E. Shore, Jack Geduldig, Kristine Pelton, Thomas Czech, Orr Ashenberg, Kai W. Wucherpfennig, Orit Rozenblatt-Rosen, Sanda Alexandrescu, Keith L. Ligon, Stefan M. Pfister, Aviv Regev, Irene Slavc, Walter Berger, Mario L. Suvà, Marcel Kool, Mariella G. Filbin
Software Mentions: 7
Published: over 4 years ago
10.1186/s12864-019-6349-y
Molecular evolution and expression of opsin genes in Hydra vulgarisCited by: 16
Author(s): Aide Macias-Muñoz, Rabi Murad, A Mortazavi
Software Mentions: 7
Published: almost 5 years ago
10.1371/journal.pcbi.1009382
Biomedical Data Commons (BMDC) prioritizes B-lymphocyte non-coding genetic variants in Type 1 DiabetesCited by: 3
Author(s): Samantha N. Piekos, Sadhana Gaddam, Pranav Bhardwaj, Prashanth Radhakrishnan, Ramanathan V. Guha, Anthony E. Oro
Software Mentions: 7
Published: about 3 years ago
10.18632/aging.203208
miRNAs generated from Meg3-Mirg locus are downregulated during agingCited by: 1
Author(s): Ana-Mihaela Lupan, Evelyn Gabriela Rusu, Mihai Bogdan Preda, Catalina Iolanda Marinescu, Cristina Ivan, Alexandrina Burlacu
Software Mentions: 7
Published: over 3 years ago
10.3389/fnins.2021.600462
Dysregulation of MicroRNAs and PIWI-Interacting RNAs in a Caenorhabditis elegans Parkinson’s Disease Model Overexpressing Human α-Synuclein and Influence of tdp-1Cited by: 10
Author(s): Linjing Shen, Changliang Wang, Liang Chen, Garry Wong
Software Mentions: 7
Published: over 3 years ago
10.1371/journal.pgen.1008593
Parallel and nonparallel genomic responses contribute to herbicide resistance in Ipomoea purpurea, a common agricultural weedCited by: 35
Author(s): Megan Van Etten, Kristin M. Lee, Shu‐Mei Chang, Regina S. Baucom
Software Mentions: 7
Published: over 4 years ago
10.1534/g3.114.012526
Polymorphism Identification and Improved Genome Annotation of <i>Brassica rapa</i> Through Deep RNA SequencingCited by: 30
Author(s): Upendra Kumar Devisetty, Michaeal F. Covington, An V. Tat, Saradadevi Lekkala, Julin N. Maloof
Software Mentions: 7
Published: about 10 years ago
10.1186/1471-2105-12-452
eXframe: reusable framework for storage, analysis and visualization of genomics experimentsCited by: 5
Author(s): Amit Sinha, Emily Merrill, Scott A. Armstrong, Tim W. Clark, Sudeshna Das
Software Mentions: 7
Published: almost 13 years ago
10.1186/s13007-021-00791-w
Small-scale sequencing enables quality assessment of Ribo-Seq data: an example from Arabidopsis cell cultureCited by: 3
Author(s): Amir Mahboubi, Nicolas Delhomme, Sara Lea Häggström, Johannes Hanson
Software Mentions: 7
Published: about 3 years ago
10.1038/s41598-019-52584-w
Identifying inaccuracies in gene expression estimates from unstranded RNA-seq dataCited by: 8
Author(s): Mikhail Pomaznoy, Ashu Sethi, Jason A. Greenbaum, Bjoern Peters
Software Mentions: 7
Published: almost 5 years ago
10.1038/s41598-017-16353-x
The microbiomes of blowflies and houseflies as bacterial transmission reservoirsCited by: 85
Author(s): Ana Carolina M. Junqueira, Aakrosh Ratan, Enzo Acerbi, Daniela I. Drautz–Moses, Balakrishnan N. V. Premkrishnan, Paul Igor Costea, Bodo Linz, Rikky W. Purbojati, Daniel F. Paulo, Nicolas E. Gaultier, Poorani Subramanian, Nur A. Hasan, Rita R. Colwell, Peer Bork, Ana Maria Lima de Azeredo-Espin, Donald A. Bryant, Stephan C. Schuster
Software Mentions: 7
Published: almost 7 years ago
10.1038/s41598-018-24863-5
Long non-coding RNAs involved in the regulatory network during porcine pre-implantation embryonic development and iPSC inductionCited by: 15
Author(s): Zhong Liu, Haiyuan Mu, Bingqiang Wen, Wei Zhang, Qingqing Wei, Ge Gao, Jianyong Han, Suying Cao
Software Mentions: 7
Published: over 6 years ago
10.1038/s41418-021-00751-w
Bromodomain protein BRDT directs ΔNp63 function and super-enhancer activity in a subset of esophageal squamous cell carcinomasCited by: 17
Author(s): Xin Wang, Ana P. Kutschat, Mitsuko Yamada, Evangelos Prokakis, Patricia Böttcher, Koji Tanaka, Yuichiro Doki, Feda H. Hamdan, Steven A. Johnsen
Software Mentions: 7
Published: over 3 years ago
10.1186/s12864-015-1270-5
Expression and regulation of long noncoding RNAs in TLR4 signaling in mouse macrophagesCited by: 43
Author(s): Aiping Mao, Jun Shen, Zhixiang Zuo
Software Mentions: 7
Published: over 9 years ago
10.1038/s41419-021-04067-y
Single cell transcriptomics reveal trans-differentiation of pancreatic beta cells following inactivation of the TFIID subunit Taf4Cited by: 6
Author(s): Thomas Kleiber, Guillaume Davidson, Gabrielle Mengus, Igor Martianov, Irwin Davidson
Software Mentions: 7
Published: about 3 years ago
10.1016/j.omtn.2017.08.010
Profiling the Mismatch Tolerance of Argonaute 2 through Deep Sequencing of Sliced Polymorphic Viral RNAsCited 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
10.1186/s13059-017-1197-z
H2A monoubiquitination in Arabidopsis thaliana is generally independent of LHP1 and PRC2 activityCited by: 66
Author(s): Yue Zhou, Francisco J. Romero–Campero, Ángeles Gómez-Zambrano, Franziska Turck, Myriam Calonje
Software Mentions: 7
Published: over 7 years ago
10.1002/ece3.4756
Symbiont type and environmental factors affect transcriptome‐wide gene expression in the coral <i>Montipora capitata</i>Cited by: 9
Author(s): Martin Helmkampf, M. Renee Bellinger, Monika Frazier, Misaki Takabayashi
Software Mentions: 7
Published: almost 6 years ago
10.7554/eLife.31977
Integration of human pancreatic islet genomic data refines regulatory mechanisms at Type 2 Diabetes susceptibility lociCited by: 101
Author(s): Matthias Thurner, Martijn van de Bunt, Jason Torres, Anubha Mahajan, Vibe Nylander, Amanda J. Bennett, Kyle J. Gaulton, Amy Barrett, Carla Burrows, Christopher G. Bell, Robert Lowe, Stephan Beck, Vardhman K. Rakyan, Anna L. Gloyn, Mark I. McCarthy
Software Mentions: 7
Published: over 6 years ago
10.7554/eLife.66668
GAF is essential for zygotic genome activation and chromatin accessibility in the early Drosophila embryoCited by: 66
Author(s): Marissa M Gaskill, Tyler J. Gibson, Elizabeth D Larson, Melissa M. Harrison
Software Mentions: 7
Published: over 3 years ago
10.7554/eLife.62161
Human ORC/MCM density is low in active genes and correlates with replication time but does not delimit initiation zonesCited by: 18
Author(s): Nina Kirstein, Alexander Buschle, Xia Wu, Stefan Krebs, Helmut Blum, Elisabeth Kremmer, Ina Vorberg, Wolfgang Hammerschmidt, Laurent Lacroix, Olivier Hyrien, Benjamin Audit, Aloys Schepers
Software Mentions: 7
Published: over 3 years ago
10.7554/eLife.12845
Two FGFRL-Wnt circuits organize the planarian anteroposterior axisCited by: 90
Author(s): M. Lucila Scimone, Lauren E. Cote, Travis Rogers, Peter W. Reddien
Software Mentions: 7
Published: over 8 years ago
10.7554/eLife.59889
Cohesin residency determines chromatin loop patternsCited by: 45
Author(s): Lorenzo Costantino, Hsieh Ts, Rebecca Lamothe, Xavier Darzacq, Douglas Koshland
Software Mentions: 7
Published: almost 4 years ago
10.15252/embj.2020104569
Translation is required for miRNA‐dependent decay of endogenous transcriptsCited by: 15
Author(s): Adriano Biasini, Baroj Abdulkarim, Stefano de Pretis, Jennifer Y. Tan, Rajika Arora, Harry Wischnewski, René Dreos, Mattia Pelizzola, Constance Ciaudo, Ana C. Marques
Software Mentions: 6
Published: almost 4 years ago
10.3389/fimmu.2021.626255
Dissecting the Role of BET Bromodomain Proteins BRD2 and BRD4 in Human NK Cell FunctionCited by: 13
Author(s): Adam P. Cribbs, P. Filippakopoulos, Martin Philpott, Graham Wells, Henry Penn, Henrik Oerum, Viia Valge-Archer, Marc Feldmann, U. Oppermann
Software Mentions: 6
Published: over 3 years ago
10.1080/20013078.2020.1785746
Influence of species and processing parameters on recovery and content of brain tissue‐derived extracellular vesiclesCited by: 62
Author(s): Yiyao Huang, Lesley Cheng, Andrey Turchinovich, Vasiliki Mahairaki, Juan C. Troncoso, Olga Pletniková, Norman J. Haughey, Laura J. Vella, Andrew F. Hill, Lei Zheng, Kenneth W. Witwer
Software Mentions: 6
Published: over 4 years ago
10.3389/fimmu.2021.688493
Cohesin Core Complex Gene Dosage Contributes to Germinal Center Derived Lymphoma Phenotypes and OutcomesCited by: 4
Author(s): Martín A. Rivas, Ceyda Durmaz, Andreas Kloetgen, Cristopher R Chin, Zhengming Chen, Bhavneet Bhinder, Amnon Koren, Aaron D. Viny, Christopher D. Scharer, Jeremy M. Boss, Olivier Elemento, Christopher E. Mason, Ari Melnick
Software Mentions: 6
Published: about 3 years ago
10.1002/stem.2521
Zeb2 Regulates Cell Fate at the Exit from Epiblast State in Mouse Embryonic Stem CellsCited by: 37
Author(s): Agata Stryjewska, Ruben Dries, Tim Pieters, Griet Verstappen, Andrea Conidi, Kathleen Coddens, Annick Francis, Lieve Umans, Wilfred F. J. van IJcken, Geert Berx, Leo A. van Grunsven, Frank Grosveld, Steven Goossens, Jody J. Haigh, Danny Huylebroeck
Software Mentions: 6
Published: almost 8 years ago
10.3389/fcell.2021.561086
Comprehensive miRNome-Wide Profiling in a Neuronal Cell Model of Synucleinopathy Implies Involvement of Cell Cycle GenesCited by: 6
Author(s): Elisabeth Findeiss, Sigrid C. Schwarz, Valentin Evsyukov, Thomas W. Rösler, Matthias Höllerhage, Tasnim Chakroun, Niko-Petteri Nykänen, Yimin Shen, Wolfgang Wurst, Michael Köhl, Jörg Tost, Günter U. Höglinger
Software Mentions: 6
Published: over 3 years ago
10.15252/emmm.201708587
Reinstating plasticity and memory in a tauopathy mouse model with an acetyltransferase activatorCited by: 54
Author(s): Snehajyoti Chatterjee, Raphaelle Cassel, Anne Schneider‐Anthony, Karine Mérienne, Brigitte Cosquer, Laura Tzeplaeff, Sarmistha Sinha, Manoj Kumar, Piyush Chaturbedy, M. Eswaramoorthy, Stéphanie Le Gras, Céline Keime, Olivier Bousiges, P. Dutar, Petnoï Petsophonsakul, Claire Rampon, Jean‐Christophe Cassel, Luc Buée, David Blum, Tapas K. Kundu, Anne‐Laurence Boutillier
Software Mentions: 6
Published: about 6 years ago
10.7554/eLife.20235
Successful transmission and transcriptional deployment of a human chromosome via mouse male meiosisCited by: 4
Author(s): Christina Ernst, Jeremy Pike, Sarah J. Aitken, Hannah K. Long, Nils Eling, Lovorka Stojic, Michelle C. Ward, Frances Connor, Timothy F. Rayner, Margus Lukk, Robert J. Klose, Claudia Kutter, Duncan T. Odom
Software Mentions: 6
Published: almost 8 years ago
10.1242/dev.167833
Single cell transcriptome analysis of human, marmoset and mouse embryos reveals common and divergent features of preimplantation developmentCited by: 145
Author(s): Thorsten Boroviak, Giuliano Giuseppe Stirparo, Sabine Dietmann, Irene Hernando-Herraez, Hisham Mohammed, Wolf Reik, Austin Smith, Erika Sasaki, Jennifer Nichols, Paul Bertone
Software Mentions: 6
Published: about 6 years ago
10.1002/1878-0261.12968
Phosphorylation of the androgen receptor at Ser81 is co‐sustained by CDK1 and CDK9 and leads to AR‐mediated transactivation in prostate cancerCited by: 14
Author(s): Xintao Gao, Jintai Liang, LiYang Wang, Zhaoyang Zhang, Peipei Yuan, Jiaxin Wang, Youhe Gao, Fen Ma, Carla Calagua, Huihui Ye, Olga Voznesensky, Shaogang Wang, Tao Wang, Jihong Liu, Shaoyong Chen, Xiaohui Liu
Software Mentions: 6
Published: over 3 years ago
10.1186/1471-2105-13-154
TAPDANCE: An automated tool to identify and annotate transposon insertion CISs and associations between CISs from next generation sequence dataCited by: 50
Author(s): Aaron L. Sarver, Jesse Erdman, Timothy K. Starr, David A. Largaespada, Kevin A.T. Silverstein
Software Mentions: 6
Published: over 12 years ago
10.1186/s13742-015-0060-y
VirAmp: a galaxy-based viral genome assembly pipelineCited by: 31
Author(s): Yinan Wan, Daniel W. Renner, István Albert, Moriah L. Szpara
Software Mentions: 6
Published: over 9 years ago
10.1093/gbe/evu133
Settling Down: The Genome of Serratia symbiotica from the Aphid Cinara tujafilina Zooms in on the Process of Accommodation to a Cooperative Intracellular LifeCited by: 77
Author(s): Alejandro Manzano-Marı́n, Amparo Latorre
Software Mentions: 6
Published: over 10 years ago
10.1111/mec.14711
Genome‐wide evidence for divergent selection between populations of a major agricultural pathogenCited by: 64
Author(s): Fanny E. Hartmann, Bruce A. McDonald, Daniel Croll
Software Mentions: 6
Published: over 6 years ago