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: over 5 years ago
1 dependent package
221 downloads last month

Papers Mentioning bowtie 1,566

10.1161/CIRCULATIONAHA.119.039596
Widespread Translational Control of Fibrosis in the Human Heart by RNA-Binding Proteins
Cited by: 74
Author(s): Sonia Chothani, Sebastian Schäfer, Eleonora Adami, V. Sivakumar, Anissa A. Widjaja, Sarah R. Langley, Jessie Tan, Mao Wang, Nicholas M Quaife, Chee Jian Pua, G. D’Agostino, Shamini Guna Shekeran, Benjamin L. George, Si Ching Lim, Elaine Yiqun Cao, Sebastiaan van Heesch, Franziska Witte, Leanne E. Felkin, Eleni G. Christodoulou, Jinqiao Dong, Susanne Blachut, Giannino Patone, Paul J.R. Barton, Norbert Hübner, Stuart A. Cook, Owen J. L. Rackham
Software Mentions: 6
Published: over 4 years ago
10.3390/ijms20061321
Cellular Gene Expression during Hepatitis C Virus Replication as Revealed by Ribosome Profiling
Cited by: 14
Author(s): Gesche K. Gerresheim, Jochen Bathke, Audrey M. Michel, Dmitry E. Andreev, Lyudmila Shalamova, Oliver Roßbach, Pan Hu, Dieter Glebe, Markus Fricke, Manja Marz, Alexander Goesmann, Stephen J Kiniry, Pavel V. Baranov, Ivan N. Shatsky, Michael Niepmann
Software Mentions: 6
Published: about 5 years ago
10.1111/acel.13153
Epigenome signatures landscaped by histone H3K9me3 are associated with the synaptic dysfunction in Alzheimer's disease
Cited by: 44
Author(s): Min Young Lee, Jung‐Hee Lee, Seung Jae Hyeon, Hyesun Cho, Yu Jin Hwang, Jong Yeon Shin, Ann C. McKee, Neil W. Kowall, Jong‐Il Kim, Thor D. Stein, Daehee Hwang, Hoon Ryu
Software Mentions: 6
Published: about 4 years ago
10.1016/j.cell.2016.09.027
Molecular Diversity of Midbrain Development in Mouse, Human, and Stem Cells
Cited by: 620
Author(s): Gioele La Manno, Daniel Gyllborg, Simone Codeluppi, Kaneyasu Nishimura, Carmen Saltó, Amit Zeisel, Lars E. Borm, Simon Stott, Enrique M. Toledo, J. Carlos Villaescusa, Peter Lönnerberg, Jesper Ryge, Roger A. Barker, Ernest Arenas, Sten Linnarsson
Software Mentions: 6
Published: over 7 years ago
10.1038/s41598-021-86032-5
A hierarchical regulatory network analysis of the vitamin D induced transcriptome reveals novel regulators and complete VDR dependency in monocytes
Cited by: 18
Author(s): Timothy Warwick, Marcel H. Schulz, Stefan Günther, Ralf Gilsbach, Antonio Neme, Carsten Carlberg, Ralf P. Brandes, Sabine Seuter
Software Mentions: 6
Published: about 3 years ago
10.1038/s41598-020-73376-7
RNA oxidation in chromatin modification and DNA-damage response following exposure to formaldehyde
Cited by: 17
Author(s): Juan C. Gonzalez-Rivera, Mark W. Sherman, Dongyu Wang, Jamie C. L. Chuvalo-Abraham, Lea Hildebrandt Ruiz, Lydia M. Contreras
Software Mentions: 6
Published: over 3 years ago
10.1038/s41598-018-37397-7
Temporal dynamics in meta longitudinal RNA-Seq data
Cited by: 4
Author(s): Sangwon Oh, Congjun Li, R.L. Baldwin, Seongho Song, Fang Liu, Robert W. Li
Software Mentions: 6
Published: over 5 years ago
10.1038/s41598-019-38979-9
Integrative modeling reveals key chromatin and sequence signatures predicting super-enhancers
Cited by: 10
Author(s): Aziz Khan, Xuegong Zhang
Software Mentions: 6
Published: about 5 years ago
10.1371/journal.pgen.1009645
An enhancer screen identifies new suppressors of small-RNA-mediated epigenetic gene silencing
Cited by: 1
Author(s): Yukiko Shimada, Sarah H. Carl, Merle Skribbe, Valentin Flury, Tahsin Kuzdere, Georg Kempf, Marc Bühler
Software Mentions: 6
Published: almost 3 years ago
10.1371/journal.pone.0053822
Efficient and Comprehensive Representation of Uniqueness for Next-Generation Sequencing by Minimum Unique Length Analyses
Cited by: 31
Author(s): Helena Storvall, Daniel Ramsköld, Rickard Sandberg
Software Mentions: 6
Published: over 11 years ago
10.1371/journal.pgen.1008516
Ligand dependent gene regulation by transient ERα clustered enhancers
Cited by: 17
Author(s): Bharath Saravanan, Deepanshu Soota, Zubairul Islam, Sudeshna Majumdar, Rajat Mann, Sweety Meel, Umer Farooq, Kaivalya Walavalkar, Srimonta Gayen, Anurag Kumar Singh, Sridhar Hannenhalli, Dimple Notani
Software Mentions: 6
Published: over 4 years ago
10.1186/s12864-017-3860-x
Genome analysis of Diploscapter coronatus: insights into molecular peculiarities of a nematode with parthenogenetic reproduction
Cited by: 29
Author(s): Hideaki Hiraki, Hiroshi Kagoshima, Christopher Kraus, Philipp H. Schiffer, Yumiko Ueta, Michael Kroiher, Einhard Schierenberg, Yuji Kohara
Software Mentions: 6
Published: almost 7 years ago
10.1371/journal.pone.0123380
Global Developmental Gene Programing Involves a Nuclear Form of Fibroblast Growth Factor Receptor-1 (FGFR1)
Cited by: 41
Author(s): Christopher Terranova, Sridhar T. Narla, Yu Wei Lee, Jonathan Bard, Abhirath Parikh, Ewa K. Stachowiak, Emmanuel S. Tzanakakis, Michael Buck, Barbara Birkaya, Michal K. Stachowiak
Software Mentions: 6
Published: about 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 Life
Cited by: 77
Author(s): Alejandro Manzano-Marı́n, Amparo Latorre
Software Mentions: 6
Published: almost 10 years ago
10.1186/s12870-017-1070-y
Plant-RRBS, a bisulfite and next-generation sequencing-based methylome profiling method enriching for coverage of cytosine positions
Cited by: 12
Author(s): Martin Schmidt, Michiel Van Bel, Magdalena Wołoszyńska, Bram Slabbinck, Cindy Martens, Marc De Block, Frederik Coppens, Mieke Van Lijsebettens
Software Mentions: 6
Published: almost 7 years ago
10.1186/s13100-019-0180-5
Transcriptome analyses of tumor-adjacent somatic tissues reveal genes co-expressed with transposable elements
Cited by: 20
Author(s): Nicky Chung, G. M. Jonaid, Sophia Quinton, Austin Ross, Corinne E. Sexton, Adrian Alberto, Cody Clymer, Daphnie Churchill, Omar Navarro Leija, Mira V. Han
Software Mentions: 6
Published: over 4 years ago
10.1371/journal.pone.0072614
DistMap: A Toolkit for Distributed Short Read Mapping on a Hadoop Cluster
Cited by: 46
Author(s): Ram Vinay Pandey, Christian Schlötterer
Software Mentions: 6
Published: over 10 years ago
10.1186/s12864-019-6034-1
De novo profiling of RNA viruses in Anopheles malaria vector mosquitoes from forest ecological zones in Senegal and Cambodia
Cited by: 19
Author(s): Eugeni Belda, Ferdinand Nanfack-Minkeu, Karin Eiglmeier, Guillaume Carissimo, Inge Holm, Mawlouth Diallo, Diawo Diallo, Amélie Vantaux, Saorin Kim, Igor V. Sharakhov, Kenneth D. Vernick
Software Mentions: 6
Published: over 4 years ago
10.1111/mec.14711
Genome‐wide evidence for divergent selection between populations of a major agricultural pathogen
Cited by: 64
Author(s): Fanny E. Hartmann, Bruce A. McDonald, Daniel Croll
Software Mentions: 6
Published: almost 6 years ago
10.1371/journal.pgen.1009432
Region-specific H3K9me3 gain in aged somatic tissues in Caenorhabditis elegans
Cited by: 12
Author(s): Chenglin Li, Mintie Pu, Wenke Wang, Amaresh Chaturbedi, Felicity J Emerson, Siu Sylvia Lee
Software Mentions: 6
Published: over 2 years ago
10.1186/s12859-019-2955-6
Polymorphic edge detection (PED): two efficient methods of polymorphism detection from next-generation sequencing data
Cited by: 3
Author(s): Akio Miyao, Jianyu Song Kiyomiya, Kei Iida, Koji Doi, Hiroshi Yasue
Software Mentions: 6
Published: almost 5 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 cancer
Cited 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: about 3 years ago
10.1038/sdata.2017.51
Transcriptomic analysis of gene signatures associated with sickle pain
Cited by: 8
Author(s): Jinny Paul, Anupam Aich, Juan E. Abrahante, Ying Wang, Rebecca S. LaRue, Susan K. Rathe, Krystina R. Kalland, Aditya Mittal, Ritu Jha, Fei Peng, David A. Largaespada, Anindya Bagchi, Kalpna Gupta
Software Mentions: 6
Published: about 7 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: almost 7 years ago
10.1186/1471-2105-15-167
PVT: An Efficient Computational Procedure to Speed up Next-generation Sequence Analysis
Cited by: 4
Author(s): Ranjan Kumar Maji, Arijita Sarkar, Sunirmal Khatua, Subhasis Dasgupta, Zhumur Ghosh
Software Mentions: 6
Published: almost 10 years ago
10.1371/journal.pgen.1009591
RDC complex executes a dynamic piRNA program during Drosophila spermatogenesis to safeguard male fertility
Cited by: 17
Author(s): Peiwei Chen, Yicheng Luo, Alexei A. Aravin
Software Mentions: 6
Published: over 2 years ago
10.1186/s40104-019-0412-z
Co-expression network analysis predicts a key role of microRNAs in the adaptation of the porcine skeletal muscle to nutrient supply
Cited by: 13
Author(s): Emilio Mármol-Sánchez, Yuliaxis Ramayo-Caldas, Raquel Quintanilla, Tainã Figueiredo Cardoso, Rayner González-Prendes, J. Tibau, Marcel Amills
Software Mentions: 6
Published: over 4 years ago
10.1186/s13059-017-1321-0
The nuclear receptor ERβ engages AGO2 in regulation of gene transcription, RNA splicing and RISC loading
Cited by: 55
Author(s): Roberta Tarallo, Giorgio Giurato, Giuseppina Bruno, Maria Ravo, Francesca Rizzo, Annamaria Salvati, Luca Ricciardi, Giovanna Marchese, Angela Cordella, Teresa Rocco, Valerio Gigantino, Biancamaria Pierri, Giovanni Cimmino, Luciano Milanesi, Concetta Ambrosino, Tuula A. Nyman, Giovanni Nassa, Alessandro Weisz
Software Mentions: 6
Published: over 6 years ago
10.1186/s12864-019-5946-0
Prediction of regulatory long intergenic non-coding RNAs acting in trans through base-pairing interactions
Cited by: 19
Author(s): Jules Deforges, Rodrigo S. Reis, Philippe Jacquet, Dominique Jacques Vuarambon, Yves Poirier
Software Mentions: 6
Published: almost 5 years ago
10.1186/s12864-017-3568-y
Conserved expression of transposon-derived non-coding transcripts in primate stem cells
Cited by: 41
Author(s): LeeAnn Ramsay, Maria C. Marchetto, Maxime Caron, Shu-Huang Chen, Stephan Busche, Tony Kwan, Tomi Pastinen, Fred H. Gage, Guillaume Bourque
Software Mentions: 6
Published: about 7 years ago
10.1186/1471-2105-15-337
Bison: bisulfite alignment on nodes of a cluster
Cited by: 12
Author(s): Devon P. Ryan, Dan Ehninger
Software Mentions: 6
Published: over 9 years ago
10.1371/journal.ppat.1007518
Comprehensive profiling of translation initiation in influenza virus infected cells
Cited by: 22
Author(s): Heather M. Machkovech, Jesse D. Bloom, Arvind R. Subramaniam
Software Mentions: 6
Published: over 5 years ago
10.1186/s12864-016-2963-0
iTAR: a web server for identifying target genes of transcription factors using ChIP-seq or ChIP-chip data
Cited by: 2
Author(s): Chi Yang, Erik H. Andrews, Min-Hsuan Chen, Wanyu Wang, Jeremy J.W. Chen, Mark Gerstein, Chun-Chi Liu, Chao Cheng
Software Mentions: 6
Published: almost 8 years ago
10.1186/s13742-015-0060-y
VirAmp: a galaxy-based viral genome assembly pipeline
Cited by: 31
Author(s): Yinan Wan, Daniel W. Renner, István Albert, Moriah L. Szpara
Software Mentions: 6
Published: about 9 years ago
10.1186/s12864-019-5453-3
Genome-wide signatures of local adaptation among seven stoneflies species along a nationwide latitudinal gradient in Japan
Cited by: 15
Author(s): Maribet Gamboa, Kozo Watanabe
Software Mentions: 6
Published: over 5 years ago
10.1371/journal.pgen.1005465
YAP1 Exerts Its Transcriptional Control via TEAD-Mediated Activation of Enhancers
Cited by: 272
Author(s): Christoph Stein, Anaïs F. Bardet, Guglielmo Roma, Sebastian Bergling, Ieuan Clay, Alexandra Ruchti, Claudia Agarinis, Tobias Schmelzle, Tewis Bouwmeester, Dirk Schübeler, Andreas Bauer
Software Mentions: 6
Published: over 8 years ago
10.1534/g3.116.027045
Differential Expression of Genes Involved in Host Recognition, Attachment, and Degradation in the Mycoparasite <i>Tolypocladium ophioglossoides</i>
Cited by: 20
Author(s): C. Alisha Quandt, Yanming Di, Justin Elser, Pankaj Jaiswal, Joseph W. Spatafora
Software Mentions: 6
Published: about 8 years ago
10.26508/lsa.201800175
A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs
Cited by: 16
Author(s): Charlotte Soneson, Michael I. Love, Rob Patro, Shobbir Hussain, Dheeraj Malhotra, Mark D. Robinson
Software Mentions: 6
Published: over 5 years ago
10.1534/g3.119.400180
Hybrid Assembly of the Genome of the Entomopathogenic Nematode <i>Steinernema carpocapsae</i> Identifies the X-Chromosome
Cited by: 12
Author(s): Lorrayne Serra, Marissa Macchietto, Aide Macias-Muñoz, Cassandra McGill, Isaryhia Rodriguez, Bryan Rodriguez, Rabi Murad, A Mortazavi
Software Mentions: 6
Published: almost 5 years ago
10.1371/journal.pcbi.1003731
iRegulon: From a Gene List to a Gene Regulatory Network Using Large Motif and Track Collections
Cited by: 654
Author(s): Rekin’s Janky, Annelien Verfaillie, Hana Imrichová, Bram Van de Sande, Laura Standaert, Valerie Christiaens, Gert Hulselmans, Koen Herten, Marina Naval-Sánchez, Delphine Potier, Dmitry Svetlichnyy, Zeynep Kalender Atak, Mark Fiers, Jean‐Christophe Marine, Stein Aerts
Software Mentions: 6
Published: almost 10 years ago
10.1534/g3.112.002527
Alignment-Free Population Genomics: An Efficient Estimator of Sequence Diversity
Cited by: 9
Author(s): Bernhard Haubold, Peter Pfaffelhuber
Software Mentions: 6
Published: almost 12 years ago
10.1534/g3.113.006742
The Developmental Transcriptome of the Mosquito <i>Aedes aegypti</i>, an Invasive Species and Major Arbovirus Vector
Cited by: 184
Author(s): Omar S. Akbari, Igor Antoshechkin, Henry Amrhein, Brian A. Williams, Rose DiLoreto, Jeremy E. Sandler, Bruce A. Hay
Software Mentions: 6
Published: over 10 years ago
10.3389/fphys.2019.01370
A Dynamic Transcriptional Analysis Reveals IL-6 Axis as a Prominent Mediator of Surgical Acute Response in Non-ischemic Mouse Heart
Cited by: 1
Author(s): Sally Badawi, Alexandre Paccalet, Zeina Harhous, Bruno Pillot, Lionel Augeul, Fabien Van Coppenolle, Joël Lachuer, Mazen Kurdi, Claire Crola Da Silva, Michel Ovize, Gabriel Bidaux
Software Mentions: 6
Published: over 4 years ago
10.3389/fpls.2018.01212
A Bioinformatics Pipeline for the Analysis and Target Prediction of RNA Effectors in Bidirectional Communication During Plant–Microbe Interactions
Cited by: 12
Author(s): Silvia Zanini, Ena Šečić, Lukas Jelonek, Karl-Heinz Kögel
Software Mentions: 6
Published: over 5 years ago
10.1371/journal.pone.0029685
A Powerful Method for Transcriptional Profiling of Specific Cell Types in Eukaryotes: Laser-Assisted Microdissection and RNA Sequencing
Cited by: 104
Author(s): Marc W. Schmid, Anja Schmidt, Ulrich C. Klostermeier, Matthias Barann, Philip Rosenstiel, Ueli Grossniklaus
Software Mentions: 6
Published: over 12 years ago
10.1038/s41598-017-17407-w
Activity-Dependent Regulation of Alternative Cleavage and Polyadenylation During Hippocampal Long-Term Potentiation
Cited by: 37
Author(s): Mariana Fontes, Ayşegül Güvenek, Riki Kawaguchi, Dinghai Zheng, Alden Huang, Victoria M. Ho, Patrick B. Chen, Xiaochuan Liu, Thomas J. O’Dell, Giovanni Coppola, Bin Tian, Kelsey C. Martin
Software Mentions: 6
Published: over 6 years ago
10.1111/acel.12890
Cell‐free DNA as a biomarker of aging
Cited by: 68
Author(s): Yee Voan Teo, Miriam Capri, Cristina Morsiani, G Pizza, Ana Maria Caetano Faria, Claudio Franceschi, Nicola Neretti
Software Mentions: 6
Published: over 5 years ago
10.1016/j.stem.2019.03.017
Complementary Activity of ETV5, RBPJ, and TCF3 Drives Formative Transition from Naive Pluripotency
Cited by: 78
Author(s): Tüzer Kalkan, Susanne Bornelöv, Carla Mulas, Evangelia Diamanti, Tim Lohoff, Markus Ralser, Sjors Middelkamp, Patrick Lombard, Jennifer Nichols, Austin Smith
Software Mentions: 5
Published: about 5 years ago
10.1111/tpj.14769
The Arabidopsis transcription factor AINTEGUMENTA orchestrates patterning genes and auxin signaling in the establishment of floral growth and form
Cited by: 33
Author(s): Beth A. Krizek, Ivory C. Blakley, Yen‐Yi Ho, Nowlan H. Freese, Ann E. Loraine
Software Mentions: 5
Published: about 4 years ago
10.1016/j.celrep.2021.109101
Chromatin accessibility governs the differential response of cancer and T cells to arginine starvation
Cited by: 18
Author(s): Nicholas T. Crump, Andreas V. Hadjinicolaou, Meng Xia, John Walsby-Tickle, Uzi Gileadi, Ji‐Li Chen, Mashiko Setshedi, Lars Rønn Olsen, I-Jun Lau, Laura Godfrey, Lynn Quek, Zhanru Yu, Erica Ballabio, Mike Bogetofte Barnkob, Giorgio Napolitani, Mariolina Salio, Hashem Koohy, Benedikt M. Kessler, Stephen Taylor, Paresh Vyas, James McCullagh, Thomas A. Milne, Vincenzo Cerundolo
Software Mentions: 5
Published: about 3 years ago
10.1186/s12885-019-5537-0
Identification of ADGRE5 as discriminating MYC target between Burkitt lymphoma and diffuse large B-cell lymphoma
Cited by: 8
Author(s): Karsten Kleo, Lora Dimitrova, Elisabeth Oker, Nancy Tomaszewski, Erika Gebel Berg, Franziska Taruttis, Julia C. Engelmann, Philipp Schwarzfischer, Jörg Reinders, Rainer Spang, Wolfram Gronwald, Peter J. Oefner, Michael Hummel
Software Mentions: 5
Published: about 5 years ago
10.1186/s12864-019-5801-3
Identification of key genes and molecular mechanisms associated with low egg production of broiler breeder hens in ad libitum
Cited by: 15
Author(s): Zehui Wei, Pengcheng Li, Sijia Huang, Purevsuren Lkhagvagarav, Mengqi Zhu, C. Liang, Caixia Jia
Software Mentions: 5
Published: almost 5 years ago
10.3390/ijms21031067
Full-Length Transcriptome Assembly of Italian Ryegrass Root Integrated with RNA-Seq to Identify Genes in Response to Plant Cadmium Stress
Cited by: 32
Author(s): Zhaoyang Hu, Yufei Zhang, Yue Ping He, Qingqing Cao, Ting Zhang, Laiqing Lou, Qingqing Cai
Software Mentions: 5
Published: over 4 years ago
10.3390/ijms22020678
JAZF1, A Novel p400/TIP60/NuA4 Complex Member, Regulates H2A.Z Acetylation at Regulatory Regions
Cited by: 15
Author(s): Tara Procida, Tobias Friedrich, Antonia Jack, Martina Peritore, Clemens Bönisch, H. Christian Eberl, Nadine Daus, Konstantin Kletenkov, Andrea Nist, Thorsten Stiewe, Tilman Borggrefe, Matthias Mann, Marek Bartkuhn, Sandra B. Hake
Software Mentions: 5
Published: over 3 years ago
10.1186/s12864-019-5561-0
In silico analysis of fungal small RNA accumulation reveals putative plant mRNA targets in the symbiosis between an arbuscular mycorrhizal fungus and its host plant
Cited by: 42
Author(s): Alessandro Silvestri, Valentina Fiorilli, Laura Miozzi, G. P. Accotto, Massimo Turina, Luisa Lanfranco
Software Mentions: 5
Published: about 5 years ago
10.1111/pbi.12615
A comprehensive draft genome sequence for lupin (<i>Lupinus angustifolius</i>), an emerging health food: insights into plant–microbe interactions and legume evolution
Cited by: 149
Author(s): James K. Hane, Ming Yao, Lars G. Kamphuis, Matthew N. Nelson, Gagan Garg, Craig A. Atkins, Philipp E. Bayer, Armando Bravo, Scott Bringans, Steven B. Cannon, David Edwards, Rhonda C. Foley, Ling Gao, Maria J. Harrison, Wei Huang, Bhavna Hurgobin, Sean Li, Cheng-Wu Liu, Annette McGrath, Grant Morahan, Jeremy D. Murray, James L. Weller, Jianbo Jian, Karam B. Singh
Software Mentions: 5
Published: over 7 years ago
10.3390/ijms17060956
Human Milk Cells Contain Numerous miRNAs that May Change with Milk Removal and Regulate Multiple Physiological Processes
Cited by: 58
Author(s): Mohammed Alsaweed, Ching Tat Lai, Peter Hartmann, Donna T. Geddes, Foteini Kakulas
Software Mentions: 5
Published: almost 8 years ago
10.1093/bib/bbab055
RNA2HLA: HLA-based quality control of RNA-seq datasets
Cited by: 9
Author(s): Irina Chelysheva, Andrew J. Pollard, Daniel O’Connor
Software Mentions: 5
Published: about 3 years ago
10.1038/s41598-021-93297-3
Zfp57 inactivation illustrates the role of ICR methylation in imprinted gene expression during neural differentiation of mouse ESCs
Cited by: 7
Author(s): Basilia Acurzio, Ankit Verma, Alessia Polito, Carlo Giaccari, Francesco Cecere, Salvatore Fioriniello, Floriana Della Ragione, Annalisa Fico, Flavia Cerrato, Claudia Angelini, Robert Feil, Andrea Riccio
Software Mentions: 5
Published: almost 3 years ago
10.1038/s41598-021-81297-2
CROP: a CRISPR/Cas9 guide selection program based on mapping guide variants
Cited by: 3
Author(s): Victor Aprilyanto, Redi Aditama, Zulfikar Achmad Tanjung, Condro Utomo, Tony Liwang
Software Mentions: 5
Published: over 3 years ago
10.1038/s41598-021-82136-0
A high-throughput RNA-Seq approach to elucidate the transcriptional response of Piriformospora indica to high salt stress
Cited by: 13
Author(s): Nivedita, Abdul Rawoof, Nirala Ramchiary, M. Z. Abdin
Software Mentions: 5
Published: over 3 years ago
10.1186/s12864-016-3118-z
Web-based bioinformatics workflows for end-to-end RNA-seq data computation and analysis in agricultural animal species
Cited by: 10
Author(s): Weizhong Li, René Richter, Yunsup Jung, Quanyin Zhu, Robert W. Li
Software Mentions: 5
Published: over 7 years ago
10.1371/journal.pone.0159093
Molecular Mechanism for Stress-Induced Depression Assessed by Sequencing miRNA and mRNA in Medial Prefrontal Cortex
Cited by: 57
Author(s): Ke Ma, Li Guo, Aiping Xu, Shan Cui, Jinhui Wang
Software Mentions: 5
Published: almost 8 years ago
10.1186/s40478-017-0414-z
Serum microRNA miR-501-3p as a potential biomarker related to the progression of Alzheimer’s disease
Cited by: 118
Author(s): Norikazu Hara, Masataka Kikuchi, Akinori Miyashita, Hiroyuki Hatsuta, Yuko Saito, Kensaku Kasuga, Shigeo Murayama, Takeshi Ikeuchi, Ryozo Kuwano
Software Mentions: 5
Published: over 7 years ago
10.1371/journal.pone.0151917
Classification of Promoters Based on the Combination of Core Promoter Elements Exhibits Different Histone Modification Patterns
Cited by: 9
Author(s): Yayoi Natsume-Kitatani, Hiroshi Mamitsuka
Software Mentions: 5
Published: about 8 years ago
10.1371/journal.pone.0105097
Transcriptome of American Oysters, Crassostrea virginica, in Response to Bacterial Challenge: Insights into Potential Mechanisms of Disease Resistance
Cited by: 64
Author(s): Ian C. McDowell, Chamilani Nikapitiya, Derek Aguiar, Christopher E. Lane, Sorin Istrail, Marta Gómez-Chiarri
Software Mentions: 5
Published: almost 10 years ago
10.1038/s41598-021-86919-3
Accessible chromatin reveals regulatory mechanisms underlying cell fate decisions during early embryogenesis
Cited by: 3
Author(s): Tongqiang Fan, Yajiang Huang
Software Mentions: 5
Published: about 3 years ago
10.1371/journal.pone.0119027
Comparative Transcriptome Analysis of Anthurium “Albama” and Its Anthocyanin-Loss Mutant
Cited by: 17
Author(s): Zhiying Li, Jiabin Wang, Xuequan Zhang, Li Xu
Software Mentions: 5
Published: about 9 years ago
10.1371/journal.pone.0184471
Genome-wide miRNA response to anacardic acid in breast cancer cells
Cited by: 14
Author(s): David J. Schultz, Penn Muluhngwi, Negin Alizadeh-Rad, Madelyn A. Green, Eric C. Rouchka, Sabine Waigel, Carolyn M. Klinge
Software Mentions: 5
Published: over 6 years ago
10.1371/journal.pone.0078316
Deep Sequencing Identification of Novel Glucocorticoid-Responsive miRNAs in Apoptotic Primary Lymphocytes
Cited by: 15
Author(s): Lydia Smith, Arpit Tandon, Ruchir Shah, Deepak Mav, Alyson B. Scoltock, John A. Cidlowski
Software Mentions: 5
Published: over 10 years ago
10.1186/s13071-015-0772-y
Dynamic expression of miRNAs across immature and adult stages of the malaria mosquito Anopheles stephensi
Cited by: 26
Author(s): Shanu Jain, Vandita Rana, T. Adak, Sujatha Sunil, Raj K. Bhatnagar
Software Mentions: 5
Published: about 9 years ago
10.3390/v13061129
Evidence of Transcriptional Shutoff by Pathogenic Viral Haemorrhagic Septicaemia Virus in Rainbow Trout
Cited by: 4
Author(s): Irene Cano, Eduarda M. Santos, Karen Moore, Audrey Farbos, Ronny van Aerle
Software Mentions: 5
Published: almost 3 years ago
10.1016/j.cell.2021.03.062
Splice site m6A methylation prevents binding of U2AF35 to inhibit RNA splicing
Cited by: 88
Author(s): Mateusz Mendel, Kamila Delaney, Radha Raman Pandey, Kuan-Ming Chen, Joanna M. Wenda, Cathrine Broberg Vågbø, Florian Steiner, David Homolka, Ramesh S. Pillai
Software Mentions: 5
Published: almost 3 years ago
10.7717/peerj.6660
Music-performance regulates microRNAs in professional musicians
Cited by: 7
Author(s): Preethy Sasidharan Nair, Tuire Kuusi, Minna Ahvenainen, Anju K. Philips, Irma Järvelä
Software Mentions: 5
Published: about 5 years ago
10.1371/journal.pone.0206844
Clustering-local-unique-enriched-signals (CLUES) promotes identification of novel regulators of ES cell self-renewal and pluripotency
Cited by: 1
Author(s): Chao Wu, Jiao Yang, Minhong Shen, Ci Pan, Cheng Guo, Danmei Jia, Jing Zhu, Long Zhang, Min Zheng, Junling Jia
Software Mentions: 5
Published: over 5 years ago
10.1371/journal.pone.0139868
NGS-QCbox and Raspberry for Parallel, Automated and Rapid Quality Control Analysis of Large-Scale Next Generation Sequencing (Illumina) Data
Cited by: 31
Author(s): Mohan A. V. S. K. Katta, Aamir W. Khan, Dadakhalandar Doddamani, Mahendar Thudi, Rajeev K. Varshney
Software Mentions: 5
Published: over 8 years ago
10.1038/s41598-018-19984-w
Comparative transcriptome analysis reveals molecular response to salinity stress of salt-tolerant and sensitive genotypes of indica rice at seedling stage
Cited by: 51
Author(s): Jun Wang, Zhu Jun, Yadong Zhang, Fangjun Fan, Wenqi Li, Fangquan Wang, Zhong WeiGong, Cailin Wang, Jie Yang
Software Mentions: 5
Published: over 6 years ago
10.1038/s41598-021-92448-w
Focused CRISPR-Cas9 genetic screening reveals USO1 as a vulnerability in B-cell acute lymphoblastic leukemia
Cited by: 8
Author(s): Amit Jaiswal, Hellen Truong, Tiffany Tran, Tasha Lin, David Casero, Michael O. Alberti, Dinesh S. Rao
Software Mentions: 5
Published: almost 3 years ago
10.18632/oncotarget.8192
Integrated analysis of long non-coding RNAs in human colorectal cancer
Cited by: 32
Author(s): Xiaohua Chen, Binjian Liu, Rui Yang, Yong Guo, Feng Li, Lin Wang, Hanyang Hu
Software Mentions: 5
Published: about 8 years ago
10.1038/srep43793
Hybrid sequencing and map finding (HySeMaFi): optional strategies for extensively deciphering gene splicing and expression in organisms without reference genome
Cited by: 24
Author(s): Guogui Ning, Cheng Xu, Ping Luo, Fan Liang, Zhen Wang, Guoliang Yu, Xin Li, Depeng Wang, Manzhu Bao
Software Mentions: 5
Published: about 7 years ago
10.1371/journal.pone.0097277
GPU-BSM: A GPU-Based Tool to Map Bisulfite-Treated Reads
Cited by: 6
Author(s): Andrea Manconi, Alessandro Orro, Elias Manca, Giuliano Armano, Luciano Milanesi
Software Mentions: 5
Published: about 10 years ago
10.1186/1756-0500-4-171
CloudAligner: A fast and full-featured MapReduce based tool for sequence mapping
Cited by: 101
Author(s): Tung Nguyen, Wei Shi, Douglas M. Ruden
Software Mentions: 5
Published: almost 13 years ago
10.1371/journal.ppat.1009217
EBV miRNAs are potent effectors of tumor cell transcriptome remodeling in promoting immune escape
Cited by: 14
Author(s): Nathan Ungerleider, Whitney Bullard, Mehmet Kara, Xia Wang, Claire Roberts, Rolf Renne, Scott A. Tibbetts, Erik K. Flemington
Software Mentions: 5
Published: about 3 years ago
10.1186/s12859-016-0902-3
NEAT: a framework for building fully automated NGS pipelines and analyses
Cited by: 7
Author(s): Patrick Schorderet
Software Mentions: 5
Published: over 8 years ago
10.1093/gigascience/giz145
Benchmark of long non-coding RNA quantification for RNA sequencing of cancer samples
Cited by: 31
Author(s): Hong Zheng, Kevin Brennan, Mikel Hernáez, Olivier Gevaert
Software Mentions: 5
Published: over 4 years ago
10.1186/1471-2164-15-704
Establishment and analysis of a reference transcriptome for Spodoptera frugiperda
Cited by: 26
Author(s): Fabrice Legeai, Sylvie Gimenez, Bernard Duvic, Jean-Michel Escoubas, Anne-Sophie Gosselin-Grenet, Florence Blanc, Clément François, Imène Séninet, Anthony Bretaudeau, Doriane Mutuel, Pierre-Alain Girard, Christelle Monsempès, Ghislaine Magdelenat, Frédérique Hilliou, René Feyereisen, Mylène Ogliastro, Anne-Nathalie Volkoff, Emmanuelle Jacquin‐Joly, Emmanuelle d’Alençon, Nicolas Nègre, Philippe Fournier
Software Mentions: 5
Published: over 9 years ago
10.1186/gm377
Digital transcriptome profiling of normal and glioblastoma-derived neural stem cells identifies genes associated with patient survival
Cited by: 47
Author(s): Pär G. Engström, Diva Tommei, Stefan H. Stricker, Christine Ender, Steven M. Pollard, Paul Bertone
Software Mentions: 5
Published: over 12 years ago
10.1186/s12864-015-1739-2
De novo assembly of a transcriptome from juvenile blue crabs (Callinectes sapidus) following exposure to surrogate Macondo crude oil
Cited by: 20
Author(s): Bree K. Yednock, Timothy J. Sullivan, Joseph E. Neigel
Software Mentions: 5
Published: almost 9 years ago
10.1186/s12859-018-2019-3
Closha: bioinformatics workflow system for the analysis of massive sequencing data
Cited by: 15
Author(s): Gun Hwan Ko, Pan Gyu Kim, Jong-Cheol Yoon, Gukhee Han, Seong-Jin Park, Wangho Song, Byung-Wook Lee
Software Mentions: 5
Published: over 6 years ago
10.1093/gbe/evz150
Evolution of Phototransduction Genes in Lepidoptera
Cited by: 26
Author(s): Aide Macias-Muñoz, Aline G. Rangel Olguin, Adriana D. Briscoe
Software Mentions: 5
Published: almost 5 years ago
10.1371/journal.pgen.1009010
Candidate variants in TUB are associated with familial tremor
Cited by: 2
Author(s): M. Reza Sailani, Fereshteh Jahanbani, Charles W. Abbott, Hayan Lee, Amin Zia, Shannon Rego, Juliane Winkelmann, Franziska Hopfner, Tahir Naeem Khan, Nicholas Katsanis, Stefanie H. Müller, Daniela Berg, Katherine M. Lyman, Christian Mychajliw, G. Deuschl, Jonathan A. Bernstein, Gregor Kuhlenbäumer, M Snyder
Software Mentions: 5
Published: over 3 years ago
10.1111/mec.13550
Bs<scp>RAD</scp>seq: screening <scp>DNA</scp> methylation in natural populations of non‐model species
Cited by: 95
Author(s): Emiliano Trucchi, Anna B. Mazzarella, Gregor D. Gilfillan, María Teresa Cáceres Lorenzo, Peter Schönswetter, Ovidiu Paun
Software Mentions: 5
Published: about 8 years ago
10.1186/s12859-019-3219-1
uap: reproducible and robust HTS data analysis
Cited by: 12
Author(s): Christoph Kämpf, Michael Specht, Alexander Scholz, Sven-Holger Puppel, Gero Doose, Kristin Reiche, Jana Schor, Jörg Hackermüller
Software Mentions: 5
Published: over 4 years ago
10.1186/s13059-021-02263-9
Optimized RNA-targeting CRISPR/Cas13d technology outperforms shRNA in identifying functional circRNAs
Cited by: 62
Author(s): Yang Zhang, Tuan M. Nguyen, Xiao‐Ou Zhang, Limei Wang, Tin Phan, John G. Clohessy, Pier Paolo Pandolfi
Software Mentions: 5
Published: over 3 years ago
10.1186/s13059-021-02464-2
Systematic functional interrogation of human pseudogenes using CRISPRi
Cited by: 11
Author(s): Ming Sun, Yunfei Wang, Caishang Zheng, Yanjun Wei, Jiakai Hou, Peng Zhang, Wei He, Xiangdong Lv, Yao Ding, Han Liang, Chung-Chau Hon, Xi Chen, Xu Han, Yiwen Chen
Software Mentions: 5
Published: over 2 years ago
10.1002/1878-0261.12853
Genome‐scale CRISPR screening identifies cell cycle and protein ubiquitination processes as druggable targets for erlotinib‐resistant lung cancer
Cited by: 10
Author(s): Jieun Lee, Ahyoung Choi, Sung Yup Cho, Yukyung Jun, Deukchae Na, Ahra Lee, Giyong Jang, Jee Young Kwon, Jaesang Kim, Sanghyuk Lee, Charles Lee
Software Mentions: 5
Published: over 3 years ago
10.1186/s12870-021-03193-1
The GRAS gene family and its roles in seed development in litchi (Litchi chinensis Sonn)
Cited by: 7
Author(s): Jingwen Chen, Qian Yan, Jiawei Li, Lei Feng, Yi Zhang, Jing Xu, Rui Xia, Zaohai Zeng, Yuanlong Liu
Software Mentions: 5
Published: over 2 years ago
10.1371/journal.pone.0207531
The conservation landscape of the human ribosomal RNA gene repeats
Cited by: 50
Author(s): Saumya Agrawal, Austen R. D. Ganley
Software Mentions: 5
Published: over 5 years ago
10.1016/j.molcel.2018.09.033
Exon Junction Complex Shapes the Transcriptome by Repressing Recursive Splicing
Cited by: 73
Author(s): Lorea Blázquez, Warren Emmett, Rupert Faraway, Jose Mario Bello Pineda, Simon Bajew, André Gohr, Nejc Haberman, Christopher R. Sibley, Robert K. Bradley, Manuel Irimia, Jernej Ule
Software Mentions: 5
Published: over 5 years ago
10.1186/s12870-018-1316-3
UGbS-Flex, a novel bioinformatics pipeline for imputation-free SNP discovery in polyploids without a reference genome: finger millet as a case study
Cited by: 43
Author(s): Peng Qi, Davis Gimode, Dipnarayan Saha, Stephan Schröder, Debkanta Chakraborty, Xuewen Wang, Mathews M. Dida, Russell L. Malmberg, Katrien M. Devos
Software Mentions: 5
Published: almost 6 years ago