10.3390/jpm11020062

Modified Significance Analysis of Microarrays in Heterogeneous Diseases
Cited by: 2
Author(s): I‐Shiang Tzeng
Software Mentions: 3
Published: over 5 years ago

10.1186/s41687-020-00193-x

Advances in Patient Reported Outcomes: Integration and Innovation
Cited by: 5
Author(s):
Software Mentions: 3
Published: about 6 years ago

10.3390/jpm11040262

A Novel Low-Risk Germline Variant in the SH2 Domain of the SRC Gene Affects Multiple Pathways in Familial Colorectal Cancer
Cited by: 0
Author(s): Diamanto Skopelitou, Benchun Miao, Aayushi Srivastava, Abhishek Kumar, Magdalena Kuświk, Dagmara Dymerska, Nagarajan Paramasivam, Matthias Schlesner, Jan Lubiński, Kari Hemminki, Asta Försti, Obul Reddy Bandapalli
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0160168

New Cell Adhesion Molecules in Human Ischemic Cardiomyopathy. PCDHGA3 Implications in Decreased Stroke Volume and Ventricular Dysfunction
Cited by: 14
Author(s): Ana Ortega, Carolina Gil-Cayuela, Estefanía Tarazón, María García‐Manzanares, José Montero, Juan Cinca, Manuel Portolés, Miguel Rivera, Esther Roselló‐Lletí
Software Mentions: 3
Published: almost 10 years ago

10.1128/JVI.01869-20

The Human Adenovirus 2 Transcriptome: an Amazing Complexity of Alternatively Spliced mRNAs
Cited by: 11
Author(s): Amanda Westergren Jakobsson, Bo Segerman, Ola Wallerman, Sara Bergström Lind, Hongxing Zhao, Carl-Johan Rubin, Ulf Pettersson, Göran Akusjärvi
Software Mentions: 3
Published: over 5 years ago

10.7554/eLife.23468

A lncRNA fine tunes the dynamics of a cell state transition involving Lin28, let-7 and de novo DNA methylation
Cited by: 29
Author(s): Meng Amy Li, Paulo Amaral, Priscilla Cheung, Jan H. Bergmann, Masaki Kinoshita, Tüzer Kalkan, Markus Ralser, Sam Robson, Ferdinand von Meyenn, Maike Paramor, Fengtang Yang, Caifu Chen, Jennifer Nichols, David L. Spector, Tony Kouzarides, Lin He, Austin Smith
Software Mentions: 3
Published: almost 9 years ago

10.7554/eLife.32920

Association mapping from sequencing reads using k-mers
Cited by: 82
Author(s): Atif Rahman, Ingileif B. Hallgrímsdóttir, Michael B. Eisen, Lior Pachter
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.pone.0117006

Spatial Transferability of Habitat Suitability Models of Nephrops norvegicus among Fished Areas in the Northeast Atlantic: Sufficiently Stable for Marine Resource Conservation?
Cited by: 24
Author(s): Valentina Lauria, Anne Marie Power, Colm Lordan, Adrian Weetman, Mark P. Johnson
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pone.0173094

Transgenic expression of fungal accessory hemicellulases in Arabidopsis thaliana triggers transcriptional patterns related to biotic stress and defense response
Cited by: 6
Author(s): Alex Yi‐Lin Tsai, Kin Chan, Chi-Yip Ho, Thomas Canam, Resmi Capron, Emma R. Master, Katharina Bräutigam
Software Mentions: 3
Published: over 9 years ago

10.3390/ani11071863

Differential Expression and Functional Analysis of CircRNA in the Ovaries of Low and High Fecundity Hanper Sheep
Cited by: 8
Author(s): Aiju Liu, Xiaoyong Chen, Menghe Liu, Limeng Zhang, Xiaofei Ma, Shujun Tian
Software Mentions: 3
Published: almost 5 years ago

10.7554/eLife.22345

Stella modulates transcriptional and endogenous retrovirus programs during maternal-to-zygotic transition
Cited by: 83
Author(s): Yun Huang, Jong Kim, Dang Vinh, Caroline Lee, Christopher A. Penfold, J. Ż̷ylicz, John C. Marioni, Jim Hackett, M. Azim Surani
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pone.0102185

Embryonic miRNA Profiles of Normal and Ectopic Pregnancies
Cited by: 30
Author(s): Francisco Domı́nguez, Juan Manuel Moreno-Moya, Teresa Lozoya, Ainhoa Romero, Sebastián Martínez, Mercedes Monterde, Marta Gurrea, Blanca Ferri, Marı́a José Núñez, Carlos Simón, António Pellicer
Software Mentions: 3
Published: almost 12 years ago

10.1186/s12859-018-2592-5

IMOS: improved Meta-aligner and Minimap2 On Spark
Cited by: 7
Author(s): Mostafa Hadadian Nejad Yousefi, Maziar Goudarzi, Seyed Abolfazl Motahari
Software Mentions: 3
Published: over 7 years ago

10.7554/eLife.27529

A viral protein promotes host SAMS1 activity and ethylene production for the benefit of virus infection
Cited by: 55
Author(s): Shanshan Zhao, Wei Hong, Jiang Wu, Yu Wang, Shaoyi Ji, Shuyi Zhu, Chunhong Wei, Jinsong Zhang, Yang Li
Software Mentions: 3
Published: over 8 years ago

10.1186/s12859-020-3491-0

Enhancing fragment-based protein structure prediction by customising fragment cardinality according to local secondary structure
Cited by: 6
Author(s): Jad Abbass, Jean‐Christophe Nebel
Software Mentions: 3
Published: about 6 years ago

10.7554/eLife.29736

CDK9-dependent RNA polymerase II pausing controls transcription initiation
Cited by: 157
Author(s): Saskia Gressel, Björn Schwalb, Tim-Michael Decker, Weihua Qin, Heinrich Leonhardt, Dirk Eick, Patrick Cramer
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0121730

Gene Expression Profiles Associated with Pediatric Relapsed AML
Cited by: 23
Author(s): Costa Bachas, Gerrit Jan Schuurhuis, C. Michel Zwaan, Marry M. van den Heuvel‐Eibrink, Monique L. den Boer, Eveline S.J.M. de Bont, Zinia J. Kwidama, Dirk Reinhardt, Ursula Creutzig, Valérie de Haas, Gertjan J. L. Kaspers, Jacqueline Cloos
Software Mentions: 3
Published: about 11 years ago

10.1371/journal.pone.0028275

The Global Transcriptional Response of Fission Yeast to Hydrogen Sulfide
Cited by: 8
Author(s): Jianmin Xu, Weizhi He, Alastair I. H. Murchie, Dongrong Chen
Software Mentions: 3
Published: over 14 years ago

10.1186/1471-2105-11-73

BABAR: an R package to simplify the normalisation of common reference design microarray-based transcriptomic datasets
Cited by: 11
Author(s): Mark Alston, John Seers, Jay C. D. Hinton, Sacha Lucchini
Software Mentions: 3
Published: over 16 years ago

10.1371/journal.pone.0191932

Integrated micro/messenger RNA regulatory networks in essential thrombocytosis
Cited by: 8
Author(s): Lu Zhao, Song Wu, Erya Huang, Dimitri Gnatenko, Wadie F. Bahou, Wei Zhu
Software Mentions: 3
Published: over 8 years ago

10.1515/jib-2018-0080

Gene Expression Studies to Identify Significant Genes in AR, MTOR, MAPK Pathways and their Overlapping Regulatory Role in Prostate Cancer
Cited by: 0
Author(s): Nimisha Asati, Abhinav Mishra, Ayush Shukla, Tiratha Raj Singh
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pone.0219551

Density distribution of gene expression profiles and evaluation of using maximal information coefficient to identify differentially expressed genes
Cited by: 16
Author(s): Han-Ming Liu, Dan Yang, Zhao-Fa Liu, Shengzhou Hu, Yan Shen-hai, Xian-Wen He
Software Mentions: 3
Published: almost 7 years ago

10.1371/journal.pone.0082638

Evaluation of Current and New Biomarkers in Severe Preeclampsia: A Microarray Approach Reveals the VSIG4 Gene as a Potential Blood Biomarker
Cited by: 33
Author(s): Julien Textoris, Delphine Ivorra, Amira Ben Amara, Florence Sabatier, Jean-Pierre Ménard, H. Heckenroth, Florence Bretelle, Jean‐Louis Mège
Software Mentions: 3
Published: over 12 years ago

10.3758/s13414-015-0860-2

The long and the short of priming in visual search
Cited by: 24
Author(s): Wouter Kruijne, Martijn Meeter
Software Mentions: 3
Published: about 11 years ago

10.1186/1476-9255-7-50

TNFRSF11B computational development network construction and analysis between frontal cortex of HIV encephalitis (HIVE) and HIVE-control patients
Cited by: 26
Author(s): Ju X Huang, Lin Wang, Meng Ji
Software Mentions: 3
Published: over 15 years ago

10.1186/1471-2407-14-64

Concerted down-regulation of immune-system related genes predicts metastasis in colorectal carcinoma
Cited by: 21
Author(s): Marion Fehlker, Matthew R. Huska, Thomas Jöns, Miguel A. Andrade‐Navarro, Wolfgang Kemmner
Software Mentions: 3
Published: over 12 years ago

10.3892/ijo.2014.2648

Microarray phosphatome profiling of breast cancer patients unveils a complex phosphatase regulatory role of the MAPK and PI3K pathways in estrogen receptor-negative breast cancers
Cited by: 13
Author(s): Ramón González Manzano, E. Martinez-Navarro, Jerónimo Forteza, Antonio Brugarolas
Software Mentions: 3
Published: over 11 years ago

10.7150/ijms.51743

Identifying daily changes in circRNAs and circRNA-associated-ceRNA networks in the rat pineal gland
Cited by: 5
Author(s): Yi Zheng, Hao Jiang, Hao-Qi Wang, Haixiang Guo, Dong-Xu Han, Yongping Huang, Yan Gao, Bao Yuan
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2407-7-61

Identification of a robust gene signature that predicts breast cancer outcome in independent data sets
Cited by: 37
Author(s): James E. Korkola, Ekaterini Blaveri, Sandy DeVries, Dan H. Moore, E. Shelley Hwang, Yunn Yi Chen, Anne L. Estep, Karen Chew, Ronald H. Jensen, Frederic M. Waldman
Software Mentions: 3
Published: about 19 years ago

10.1038/s41396-018-0332-5

Niche-directed evolution modulates genome architecture in freshwater Planctomycetes
Cited by: 55
Author(s): Adrian‐Ştefan Andrei, Michaela M. Salcher, Maliheh Mehrshad, Pavel Rychtecký, Petr Znachor, Rohit Ghai
Software Mentions: 3
Published: over 7 years ago

10.1155/2013/924971

Gene Expression Profile Analysis of T1 and T2 Breast Cancer Reveals Different Activation Pathways
Cited by: 3
Author(s): Margit Riis, Xi Zhao, Fatemeh Kaveh, Hilde Synnøve Vollan, Anne-Jorunn Nesbakken, Hiroko Kato Solvang, Torben Lüders, Ida Rashida Khan Bukholm, Vessela N. Kristensen
Software Mentions: 3
Published: over 13 years ago

10.7554/eLife.17903

A histone H3K9M mutation traps histone methyltransferase Clr4 to prevent heterochromatin spreading
Cited by: 32
Author(s): Chun-Min Shan, Jiyong Wang, Ke Xu, Huijie Chen, Jia-Xing Yue, Stuart Andrews, James J. Moresco, John R. Yates, Péter L. Nagy, Liang Tong, Songtao Jia
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0015617

A Dual Platform Approach to Transcript Discovery for the Planarian Schmidtea Mediterranea to Establish RNAseq for Stem Cell and Regeneration Biology
Cited by: 61
Author(s): Martin Blythe, Damian Kao, Sunir Malla, Joanna Rowsell, Reginald H. Wilson, Deborah Evans, Jamie Jowett, Amy Hall, Virginie Lemay, Sabrina Lam, A. Aziz Aboobaker
Software Mentions: 3
Published: over 15 years ago

10.1186/1471-2105-16-S7-S5

Heterozygous genome assembly via binary classification of homologous sequence
Cited by: 13
Author(s): Paul Bodily, Mao Fujimoto, Cameron Ortega, Nozomu Okuda, Joseph Price, Mark J. Clement, Quinn Snell
Software Mentions: 3
Published: about 11 years ago

10.1101/2021.07.09.21260221

Genetic regulation of<i>OAS1</i>nonsense-mediated decay underlies association with risk of severe COVID-19
Cited by: 8
Author(s): Abdul Rouf Banday, Megan L. Stanifer, Óscar Flórez-Vargas, Olusegun O. Onabajo, Muhammad Atif Zahoor, Brenen W. Papenberg, Timothy J. Ring, Chia-Han Lee, Evangelos Andreakos, Evgeny Arons, Greg Barsh, Leslie G. Biesecker, David L. Boyle, Andrea N. Burnett‐Hartman, Mary Carrington, Euijin Chang, Pyoeng Gyun Choe, Rex L Chrisholm, Clifton L. Dalgard, Jeff Edberg, Nathan Erdmann, Heather Spencer Feigelson, Gary S. Firestein, Adam J. Gehring, Michelle Ho, Steven M. Holland, Amy Hutchinson, Hogune Im, Michael G. Ison, Hong Bin Kim, Robert J. Kreitman, Bruce R. Korf, Lisa Mirabello, Jennifer A. Pacheco, Michael J. Peluso, Daniel J. Rader, David T. Redden, Marylyn D. Ritchie, Brooke Rosenbloom, Hanaisa P. Sant Anna, Sharon A. Savage, E. Siouti, Vasiliki Triantafyllia, Joselin M. Vargas, Anurag Verma, Vibha Vij, Duane R. Wesemann, Meredith Yeager, Xu G. Yu, Yu Zhang, Steeve Boulant, Stephen J. Chanock, Jordan J. Feld, Ludmila Prokunina–Olsson
Software Mentions: 3
Published: almost 5 years ago

10.1371/journal.pone.0151522

Genome-Wide Analysis and Characterization of Aux/IAA Family Genes in Brassica rapa
Cited by: 25
Author(s): Paul Pavlidis, Vignesh Dhandapani, Jana Jeevan Rameneni, Xiaonan Li, Ganesan Sivanandhan, Su Ryun Choi, Wenxing Pang, Subin Im, Yong Pyo Lim
Software Mentions: 3
Published: about 10 years ago

10.1186/1471-2164-11-592

Development and validation of a flax (Linum usitatissimum L.) gene expression oligo microarray
Cited by: 55
Author(s): Stéphane Fénart, Yves-Placide Assoumou Ndong, Jorge Duarte, Nathalie Rivière, Jeroen Wilmer, Olivier Van Wuytswinkel, Anca Lucau, Emmanuelle Cariou, Godfrey Neutelings, Laurent Gutierrez, Brigitte Chabbert, Xavier Guillot, Reynald Tavernier, Simon Hawkins, Brigitte Thomasset
Software Mentions: 3
Published: over 15 years ago

10.1186/s12859-018-2319-7

BrownieAligner: accurate alignment of Illumina sequencing data to de Bruijn graphs
Cited by: 21
Author(s): Mahdi Heydari, Giles Miclotte, Yves Van de Peer, Jan Fostier
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0063946

Predicting Species Cover of Marine Macrophyte and Invertebrate Species Combining Hyperspectral Remote Sensing, Machine Learning and Regression Techniques
Cited by: 26
Author(s): Jonne Kotta, Tiit Kutser, Karolin Teeveer, Ele Vahtmäe, Merli Pärnoja
Software Mentions: 3
Published: about 13 years ago

10.1186/s40246-019-0194-6

vi-HMM: a novel HMM-based method for sequence variant identification in short-read data
Cited by: 1
Author(s): Man Lai Tang, Mohammad Shabbir Hasan, Hongxiao Zhu, Liqing Zhang, Xiaowei Wu
Software Mentions: 3
Published: over 7 years ago

10.1128/mBio.00731-20

Differential Alphavirus Defective RNA Diversity between Intracellular and Extracellular Compartments Is Driven by Subgenomic Recombination Events
Cited by: 11
Author(s): Rose M. Langsjoen, Antonio E. Muruato, S. R. Kunkel, Elizabeth Jaworski, Andrew Routh
Software Mentions: 3
Published: almost 6 years ago

10.1128/mBio.02096-17

The Essential Genome of <i>Escherichia coli</i> K-12
Cited by: 204
Author(s): Emily C. A. Goodall, Ashley Robinson, Iain G. Johnston, Sara Jabbari, A. Keith Turner, Adam F. Cunningham, Peter A. Lund, Jeffrey A. Cole, Ian R. Henderson
Software Mentions: 3
Published: about 8 years ago

10.1371/journal.pone.0101754

An Integrated SNP Mining and Utilization (ISMU) Pipeline for Next Generation Sequencing Data
Cited by: 10
Author(s): Sarwar Azam, Abhishek Rathore, Trushar Shah, Mohan Telluri, BhanuPrakash Amindala, Pradeep Ruperao, Mohan A. V. S. K. Katta, Rajeev K. Varshney
Software Mentions: 3
Published: almost 12 years ago

10.1128/mBio.01568-20

Decoding the Architecture of the Varicella-Zoster Virus Transcriptome
Cited by: 26
Author(s): Shirley E. Braspenning, Tomohiko Sadaoka, Judith Breuer, Georges M. G. M. Verjans, Werner J. D. Ouwendijk, Daniel P. Depledge
Software Mentions: 3
Published: over 5 years ago

10.1128/mBio.00684-13

Genes Required for Aerial Growth, Cell Division, and Chromosome Segregation Are Targets of WhiA before Sporulation in Streptomyces venezuelae
Cited by: 96
Author(s): Matthew J. Bush, Maureen J. Bibb, Govind Chandra, Kim Findlay, Mark J. Buttner
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pone.0087499

Analysis of Global Gene Expression in Brachypodium distachyon Reveals Extensive Network Plasticity in Response to Abiotic Stress
Cited by: 80
Author(s): Henry D. Priest, Samuel E. Fox, Erik R. Rowley, Jessica R. Murray, Todd P. Michael, Todd C. Mockler
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pcbi.1005096

AlignerBoost: A Generalized Software Toolkit for Boosting Next-Gen Sequencing Mapping Accuracy Using a Bayesian-Based Mapping Quality Framework
Cited by: 10
Author(s): Qi Zheng, Elizabeth A. Grice
Software Mentions: 3
Published: over 9 years ago

10.1007/s00122-019-03517-8

Genetic analysis of wheat sensitivity to the ToxB fungal effector from Pyrenophora tritici-repentis, the causal agent of tan spot
Cited by: 22
Author(s): Beatrice Corsi, Lawrence Percival‐Alwyn, Rowena Downie, Luca Venturini, Elyce M. Iagallo, Camila Campos Mantello, Charlie McCormick-Barnes, Pao Theen See, Richard P. Oliver, Caroline S. Moffat, James Cockram
Software Mentions: 3
Published: over 6 years ago

10.1186/1751-0473-8-6

RECOT: a tool for the coordinate transformation of next-generation sequencing reads for comparative genomics and transcriptomics
Cited by: 1
Author(s): Izawa Akiko, Jun Sese
Software Mentions: 3
Published: over 13 years ago

10.1371/journal.pcbi.1007543

Automated minute scale RNA-seq of pluripotent stem cell differentiation reveals early divergence of human and mouse gene expression kinetics
Cited by: 6
Author(s): Christopher Barry, Matthew T. Schmitz, Cara Argus, Jennifer M. Bolin, Mitchell D. Probasco, Ning Leng, Bret Duffin, John Steill, Scott Swanson, Brian E. McIntosh, Ron Stewart, Christina Kendziorski, James A. Thomson, Rhonda Bacher
Software Mentions: 3
Published: over 6 years ago

10.1186/1471-2105-10-418

TransportTP: A two-phase classification approach for membrane transporter prediction and characterization
Cited by: 57
Author(s): Haiquan Li, Vagner A. Benedito, Michael K. Udvardi, Patrick Xuechun Zhao
Software Mentions: 3
Published: over 16 years ago

10.1186/2193-1801-3-130

ASTER, ALI and Hyperion sensors data for lithological mapping and ore minerals exploration
Cited by: 69
Author(s): Amin Beiranvand Pour, Mazlan Hashim
Software Mentions: 3
Published: about 12 years ago

10.1371/journal.pone.0132642

Spontaneous Deletion of an “ORFanage” Region Facilitates Host Adaptation in a “Photosynthetic” Cyanophage
Cited by: 12
Author(s): Richard John Puxty, Blanca Perez-Sepulveda, Branko Rihtman, David J. Evans, Andrew Millard, David J. Scanlan
Software Mentions: 3
Published: almost 11 years ago

10.1186/1471-2105-13-S14-S5

IBDsite: a Galaxy-interacting, integrative database for supporting inflammatory bowel disease high throughput data analysis
Cited by: 12
Author(s): Ivan Merelli, Federica Viti, Luciano Milanesi
Software Mentions: 3
Published: almost 14 years ago

10.1371/journal.pbio.0050057

Genome-Wide Profiling and Analysis of Arabidopsis siRNAs
Cited by: 501
Author(s): Kristin D. Kasschau, Noah Fahlgren, Elisabeth J. Chapman, Christopher Sullivan, Jason S. Cumbie, Scott A. Givan, James C. Carrington
Software Mentions: 3
Published: over 19 years ago

10.3390/s21041182

The New Hyperspectral Satellite PRISMA: Imagery for Forest Types Discrimination
Cited by: 56
Author(s): Elia Vangi, Giovanni D’Amico, Saverio Francini, Francesca Giannetti, Bruno Lasserre, Marco Marchetti, Gherardo Chirici
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pbio.1000238

Concordant Regulation of Translation and mRNA Abundance for Hundreds of Targets of a Human microRNA
Cited by: 376
Author(s): David G. Hendrickson, Daniel J. Hogan, Heather McCullough, Jason W. Myers, Daniel Herschlag, James E. Ferrell, Patrick O. Brown
Software Mentions: 3
Published: over 16 years ago

10.1186/1751-0473-6-2

SAMMate: a GUI tool for processing short read alignments in SAM/BAM format
Cited by: 55
Author(s): Guiyin Xu, Nan Deng, Zhiyu Zhao, Thair Judeh, Erik K. Flemington, Dongxiao Zhu
Software Mentions: 3
Published: over 15 years ago

10.3390/v12070782

High-Quality Resolution of the Outbreak-Related Zika Virus Genome and Discovery of New Viruses Using Ion Torrent-Based Metatranscriptomics
Cited by: 4
Author(s): Sílvia Inês Sardi, Renata Carvalho, Luis Gustavo Carvalho Pacheco, João Fernando Lourenço de Almeida, Emilia M M D A Belitardo, Carina S. Pinheiro, Gúbio Soares Campos, Eric Roberto Guimarães Rocha Aguiar
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12885-016-2453-4

Context dependent regulatory patterns of the androgen receptor and androgen receptor target genes
Cited by: 26
Author(s): Jan Roger Olsen, Waqas Azeem, Margrete R. Hellem, Kristo Marvyin, Yaping Hua, Yi Qu, Lisha Li, Biaoyang Lin, Xiaoting Ke, Anne Margrete Øyan, Karl H. Kalland
Software Mentions: 3
Published: almost 10 years ago

10.1111/pbi.12685

Indel‐seq: a fast‐forward genetics approach for identification of trait‐associated putative candidate genomic regions and its application in pigeonpea (<i>Cajanus cajan</i>)
Cited by: 57
Author(s): Vikas K. Singh, Aamir W. Khan, Rachit K. Saxena, Pallavi Sinha, Sandip M. Kale, Swathi Parupalli, Vinay Kumar, Annapurna Chitikineni, Suryanarayana Vechalapu, C.V. Sameer Kumar, Mamta Sharma, G. Anuradha, K.N. Yamini, S. Muniswamy, Rajeev K. Varshney
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0077396

The Pituitary Gland of the European Eel Reveals Massive Expression of Genes Involved in the Melanocortin System
Cited by: 15
Author(s): Eirill Ager-Wick, Ron P. Dirks, Erik Burgerhout, Rasoul Nourizadeh-Lillabadi, Daniëlle L. de Wijze, Herman P. Spaink, Guido E.E.J.M. van den Thillart, Katsumi Tsukamoto, Sylvie Dufour, Finn‐Arne Weltzien, Christiaan V. Henkel
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pone.0183128

Anguillicola crassus infection affects mRNA expression levels in gas gland tissue of European yellow and silver eel
Cited by: 16
Author(s): Gabriel Schneebauer, Ron P. Dirks, Bernd Pelster
Software Mentions: 3
Published: almost 9 years ago

10.1111/tpj.14468

An ‘ <scp>eFP</scp> ‐Seq Browser’ for visualizing and exploring <scp>RNA</scp> sequencing data
Cited by: 31
Author(s): Alexander Sullivan, Priyank Purohit, Nowlan H. Freese, Asher Pasha, Eddi Esteban, Jamie Waese, Alison Wu, Michelle Chen, Chih Ying Chin, Richard Song, Sneha Ramesh Watharkar, Agnes P. Chan, Vivek Krishnakumar, Matthew Vaughn, Chris Town, Ann E. Loraine, Nicholas J. Provart
Software Mentions: 3
Published: almost 7 years ago

10.1038/s41598-020-59541-y

Chronic circadian misalignment accelerates immune senescence and abbreviates lifespan in mice
Cited by: 78
Author(s): Hitoshi Inokawa, Yasuhiro Umemura, Akihiro Shimba, Eiryo Kawakami, Nobuya Koike, Yoshiki Tsuchiya, Masaru Ohashi, Yoichi Minami, Guangwei Cui, T. Asahi, Ryutaro Ono, Yuh Sasawaki, Eiichi Konishi, Seung-Hee Yoo, Chen Zheng, Satoshi Teramukai, Koichi Ikuta, Kazuhiro Yagita
Software Mentions: 3
Published: over 6 years ago

10.1186/1471-2164-14-666

Intronic Non-CG DNA hydroxymethylation and alternative mRNA splicing in honey bees
Cited by: 62
Author(s): Pablo Cingolani, Xiaoyi Cao, Radhika S. Khetani, Chieh Chun Chen, Melissa Coon, Alya’a Sammak, Aliccia Bollig‐Fischer, Susan Land, Yun Huang, Matthew E. Hudson, Mark D. Garfinkel, Sheng Zhong, Gene E. Robinson, Douglas M. Ruden
Software Mentions: 3
Published: over 12 years ago

10.1111/tpj.12307

Resistance gene enrichment sequencing (<scp>R</scp>en<scp>S</scp>eq) enables reannotation of the <scp>NB</scp>‐<scp>LRR</scp> gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations
Cited by: 327
Author(s): Florian Jupe, Kamil Witek, Walter Verweij, Jadwiga Śliwka, Leighton Pritchard, Graham J. Etherington, Dan MacLean, Peter J. A. Cock, Richard M. Leggett, Glenn J. Bryan, Linda Cardle, Ingo Hein, Jonathan D. G. Jones
Software Mentions: 3
Published: over 12 years ago

10.7717/peerj.382

Characterisation of the horse transcriptome from immunologically active tissues
Cited by: 6
Author(s): Joanna Moreton, Sunir Malla, A. Aziz Aboobaker, Rachael Tarlinton, Richard D. Emes
Software Mentions: 3
Published: about 12 years ago

10.1186/1471-2164-15-969

MaxSSmap: a GPU program for mapping divergent short reads to genomes with the maximum scoring subsequence
Cited by: 9
Author(s): Turki Turki, Usman Roshan
Software Mentions: 3
Published: over 12 years ago

10.1186/1471-2164-9-131

The Songbird Neurogenomics (SoNG) Initiative: Community-based tools and strategies for study of brain gene function and evolution
Cited by: 127
Author(s): Kirstin Replogle, Arthur P. Arnold, Gregory F. Ball, Mark Band, Staffan Bensch, Eliot A. Brenowitz, Shu Dong, Jenny Drnevich, Margaret Ferris, Julia M. George, George Gong, Dennis Hasselquist, Álvaro Gonzalez Hernández, Ryan Kim, Harris A. Lewin, Lei Liu, Peter V. Lovell, Claudio V. Mello, Sara Naurin, Sandra L. Rodriguez-Zas, Jyothi Thimmapuram, Juli Wade, David F. Clayton
Software Mentions: 3
Published: about 18 years ago

10.7717/peerj.8275

Algorithms for efficiently collapsing reads with Unique Molecular Identifiers
Cited by: 9
Author(s): Daniel Liu
Software Mentions: 3
Published: over 6 years ago

10.7717/peerj.2105

Constant and seasonal drivers of bird communities in a wind farm: implications for conservation
Cited by: 7
Author(s): Zuzanna M. Rosin, Piotr Skórka, Paweł Szymański, Marcin Tobółka, Andrzej Łuczak, Piotr Tryjanowski
Software Mentions: 3
Published: almost 10 years ago

10.1038/s41598-019-51645-4

Predicting low-concentration effects of pesticides
Cited by: 17
Author(s): Matthias Liess, Sebastian Henz, Saskia Knillmann
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-019-43141-6

CRISPR-Cas9 Editing in Maize: Systematic Evaluation of Off-target Activity and Its Relevance in Crop Improvement
Cited by: 62
Author(s): Joshua K. Young, Gina Zastrow-Hayes, Stéphane Deschamps, Sergei Svitashev, Mindaugas Zaremba, Ananta Acharya, Sushmitha Paulraj, Brooke D. Peterson-Burch, Chris Schwartz, Vesna Djukanovic, Brian Lenderts, Lanie Feigenbutz, Limin Wang, Clara M. Alarcon, Virginijus Šikšnys, Gregory D. May, N. Doane Chilcoat, Sandeep Kumar
Software Mentions: 3
Published: about 7 years ago

10.1038/s41598-019-43512-z

Melanoma proteomics suggests functional differences related to mutational status
Cited by: 9
Author(s): Lucía Trilla-Fuertes, Angelo Gámez‐Pozo, Guillermo Prado-Vázquez, Andrea Zapater-Moros, Mariana Díaz-Almirón, Claudia Fortes, María Ferrer-Gómez, Rocío López-Vacas, Verónica Parra Blanco, Iván Márquez-Rodas, Ainara Soria, Juan Ángel Fresno Vara, Enrique Espinosa
Software Mentions: 3
Published: about 7 years ago

10.7717/peerj.7156

Spread of the non-native anemone <i>Anemonia alicemartinae</i> Häussermann &amp; Försterra, 2001 along the Humboldt-current large marine ecosystem: an ecological niche model approach
Cited by: 7
Author(s): Javier Pinochet, Reinaldo Rivera, Paula E. Neill, Antonio Brante, Cristián E. Hernández
Software Mentions: 3
Published: almost 7 years ago

10.7717/peerj.830

The effect of listening to music on human transcriptome
Cited by: 32
Author(s): Chakravarthi Kanduri, Pirre Raijas, Minna Ahvenainen, Anju K. Philips, Liisa Ukkola-Vuoti, Harri Lähdesmäki, Irma Järvelä
Software Mentions: 3
Published: about 11 years ago

10.1038/s41598-019-39880-1

MicroRNAs from saliva of anopheline mosquitoes mimic human endogenous miRNAs and may contribute to vector-host-pathogen interactions
Cited by: 25
Author(s): Bruno Arcà, Alessio Colantoni, Carmine Fiorillo, Francesco Severini, Vladimír Beneš, Marco Di Luca, Raffaele Calogero, Fabrizio Lombardo
Software Mentions: 3
Published: over 7 years ago

10.7717/peerj.4040

I-ATAC: interactive pipeline for the management and pre-processing of ATAC-seq samples
Cited by: 19
Author(s): Zeeshan Ahmed, Duygu Ucar
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-018-31064-7

Unique Molecular Identifiers reveal a novel sequencing artefact with implications for RNA-Seq based gene expression analysis
Cited by: 33
Author(s): Johnny A. Sena, Giulia Galotto, Nico Devitt, Melanie C. Connick, Jennifer L. Jacobi, Pooja Umale, Luis Vidali, Callum J. Bell
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41598-018-21484-w

Systematic and stochastic influences on the performance of the MinION nanopore sequencer across a range of nucleotide bias
Cited by: 56
Author(s): Raga Krishnakumar, Anupama Sinha, Sara W. Bird, Harikrishnan Jayamohan, Harrison Edwards, Joseph S. Schoeniger, Kamlesh D. Patel, Steven S. Branda, Michael Bartsch
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-018-23641-7

Unbiased Strain-Typing of Arbovirus Directly from Mosquitoes Using Nanopore Sequencing: A Field-forward Biosurveillance Protocol
Cited by: 43
Author(s): Joseph A. Russell, Brittany Campos, Jennifer Stone, Erik M. Blosser, Nathan D. Burkett‐Cadena, Jonathan L. Jacobs
Software Mentions: 3
Published: about 8 years ago

10.1186/s13007-020-00588-3

In-silico detection of aneuploidy and chromosomal deletions in wheat using genotyping-by-sequencing
Cited by: 2
Author(s): Narinder Singh, John Raupp, Dal‐Hoe Koo, Bernd Friebe, Bikram S. Gill, Jesse Poland
Software Mentions: 3
Published: about 6 years ago

10.1038/s41598-018-31093-2

Population level mitogenomics of long-lived bats reveals dynamic heteroplasmy and challenges the Free Radical Theory of Ageing
Cited by: 23
Author(s): David Jebb, Nicole M. Foley, Conor V. Whelan, Frédéric Touzalin, Sébastien J. Puechmaille, Emma C. Teeling
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-45898-2

Transcriptional landscape of soybean (Glycine max) embryonic axes during germination in the presence of paclobutrazol, a gibberellin biosynthesis inhibitor
Cited by: 19
Author(s): Rajesh Kumar Gazara, Eduardo Alves Gamosa de Oliveira, B. Calderan Rodrigues, Rodrigo Nunes da Fonseca, Antônia Elenir Amâncio Oliveira, Thiago M. Venancio
Software Mentions: 3
Published: almost 7 years ago

10.1186/1471-2164-10-342

Gene expression profile of rat left ventricles reveals persisting changes following chronic mild exercise protocol: implications for cardioprotection
Cited by: 23
Author(s): Betti Giusti, Marina Marini, Luciana Rossi, Ilaria Lapini, Alberto Magi, Andrea Capalbo, Rosa Lapalombella, Simona di Tullio, Michele Samaja, Fabio Esposito, V. Margonato, Maria Boddi, Rosanna Abbate, Arsenio Veicsteinas
Software Mentions: 3
Published: over 17 years ago

10.1038/s41598-017-04786-3

sRNA and cis-antisense sRNA identification in Staphylococcus aureus highlights an unusual sRNA gene cluster with one encoding a secreted peptide
Cited by: 25
Author(s): Julie Bronsard, Gaëtan Pascreau, Mohamed Sassi, Tony Mauro, Yoann Augagneur, Brice Felden
Software Mentions: 3
Published: almost 9 years ago

10.1186/s12915-021-01108-y

Mutant resources for functional genomics in Dictyostelium discoideum using REMI-seq technology
Cited by: 14
Author(s): Nicole Gruenheit, Amy Baldwin, Balint Stewart, Sarah Jaques, Thomas Keller, Katie Parkinson, William Salvidge, Robert Baines, Chris Brimson, Jason B. Wolf, Rex L. Chisholm, Adrian J. Harwood, Christopher Thompson
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12915-021-01114-0

Profiling of chromatin accessibility identifies transcription factor binding sites across the genome of Aspergillus species
Cited by: 7
Author(s): Lianggang Huang, Xuejie Li, Lü Dong, Bin Wang, Li Pan
Software Mentions: 3
Published: over 4 years ago

10.1038/s41598-017-14418-5

Promoter-level transcriptome in primary lesions of endometrial cancer identified biomarkers associated with lymph node metastasis
Cited by: 10
Author(s): Emiko Yoshida, Yasuhisa Terao, Noriko Hayashi, Kaoru Mogushi, Atsushi Arakawa, Yuji Tanaka, Yoshiaki Ito, Hiroko Ohmiya, Yoshihide Hayashizaki, Satoru Takeda, Masayoshi Itoh, Hideya Kawaji
Software Mentions: 3
Published: over 8 years ago

10.1038/s41598-017-02329-4

Expression Profiling of mRNAs and Long Non-Coding RNAs in Aged Mouse Olfactory Bulb
Cited by: 11
Author(s): Ming Wang, Wei Liu, Jian Jiao, Jingyun Li, Chengshuo Wang, Luo Zhang
Software Mentions: 3
Published: about 9 years ago

10.1186/s12859-015-0775-x

A large-scale conformation sampling and evaluation server for protein tertiary structure prediction and its assessment in CASP11
Cited by: 21
Author(s): Jilong Li, Renzhi Cao, Jianlin Cheng
Software Mentions: 3
Published: over 10 years ago

10.1038/srep39487

Novel Therapeutics Identification for Fibrosis in Renal Allograft Using Integrative Informatics Approach
Cited by: 24
Author(s): Li Li, Ilana Greene, Benjamin Readhead, Madhav C. Menon, Brian Kidd, Andrew Uzilov, Chengguo Wei, Nimrod Philippe, Bernd Schröppel, John Cijiang He, Rong Chen, Joel T. Dudley, Barbara Murphy
Software Mentions: 3
Published: over 9 years ago

10.3390/v11010033

A Comprehensive RNA-seq Analysis of Human Bocavirus 1 Transcripts in Infected Human Airway Epithelium
Cited by: 5
Author(s): Wei Zou, Min Xiong, Xuefeng Deng, John F. Engelhardt, Ziying Yan, Jianming Qiu
Software Mentions: 3
Published: over 7 years ago

10.1038/srep38096

Whole-genome scanning for the litter size trait associated genes and SNPs under selection in dairy goat (Capra hircus)
Cited by: 81
Author(s): Fang-Nong Lai, Hong-Li Zhai, Ming Cheng, Jun‐Yu Ma, Shun‐Feng Cheng, Wei Ge, Guoliang Zhang, Junjie Wang, Ruiqian Zhang, Xue Wang, Min Liu, Jiuzhou Song, Wei Shen
Software Mentions: 3
Published: over 9 years ago

10.1038/s41598-017-02824-8

High-resolution promoter map of human limbal epithelial cells cultured with keratinocyte growth factor and rho kinase inhibitor
Cited by: 8
Author(s): Masahito Yoshihara, Yuzuru Sasamoto, Ryuhei Hayashi, Yuki Ishikawa, Motokazu Tsujikawa, Yoshihide Hayashizaki, Masayoshi Itoh, Hideya Kawaji, Kohji Nishida
Software Mentions: 3
Published: almost 9 years ago

10.1186/s12864-015-1860-2

ISMapper: identifying transposase insertion sites in bacterial genomes from short read sequence data
Cited by: 115
Author(s): Jane Hawkey, Mohammad Hamidian, Ryan R. Wick, D.J. Edwards, Helen Billman‐Jacobe, Ruth M. Hall, Kathryn E. Holt
Software Mentions: 3
Published: almost 11 years ago

10.1186/1743-422X-8-285

Cellular transcriptional profiling in human lung epithelial cells infected by different subtypes of influenza A viruses reveals an overall down-regulation of the host p53 pathway
Cited by: 38
Author(s): Benjamin Terrier, Laurence Josset, Julien Textoris, Virginie Marcel, Gaëlle Cartet, Olivier Ferraris, Catherine Nguyen, Bruno Lina, Jean‐Jacques Diaz, Jean-Christophe Bourdon, Manuel Rosa‐Calatrava
Software Mentions: 3
Published: almost 15 years ago

10.1038/srep32965

Predicting the synergy of multiple stress effects
Cited by: 157
Author(s): Matthias Liess, Kaarina Foit, Saskia Knillmann, Ralf B. Schäfer, Hans-Dieter Ließ
Software Mentions: 3
Published: over 9 years ago

10.1186/1471-2164-8-123

STATc is a key regulator of the transcriptional response to hyperosmotic shock
Cited by: 32
Author(s): Jianbo Na, Budi Tunggal, Ludwig M. Eichinger
Software Mentions: 3
Published: about 19 years ago