cran: SAM | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0045178

An Accurate Prostate Cancer Prognosticator Using a Seven-Gene Signature Plus Gleason Score and Taking Cell Type Heterogeneity into Account
Cited by: 30
Author(s): Xin Chen, Shizhong Xu, Michael McClelland, Farah Rahmatpanah, Anne Sawyers, Zhenyu Jia, Dan Mercola
Software Mentions: 3
Published: almost 14 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

10.1186/s12859-018-2318-8

Identification of differentially expressed genes by means of outlier detection
Cited by: 5
Author(s): Itziar Irigoien, C. Arenas
Software Mentions: 3
Published: about 8 years ago

10.1186/s12859-019-2683-y

RIP-Chip analysis supports different roles for AGO2 and GW182 proteins in recruiting and processing microRNA targets
Cited by: 17
Author(s): Giovanni Perconti, Patrizia Rubino, Flavia Contino, Serena Bivona, Giorgio Bertolazzi, Michele Tumminello, Salvatore Feo, Agata Giallongo, Claudia Coronnello
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0031490

The Gene Expression Analysis of Blood Reveals S100A11 and AQP9 as Potential Biomarkers of Infective Endocarditis
Cited by: 44
Author(s): Franck Thuny, Julien Textoris, Amira Ben Amara, Adil El Filali, Christian Capo, Gilbert Habib, Didier Raoult, Jean‐Louis Mège
Software Mentions: 3
Published: over 14 years ago

10.1371/journal.pone.0083723

Function of GATA Factors in the Adult Mouse Liver
Cited by: 39
Author(s): Rena Zheng, Boris Rebolledo‐Jaramillo, Yiwei Zong, Liqing Wang, Pierre Russo, Wayne W. Hancock, Ben Z. Stanger, Ross C. Hardison, Gerd A. Blobel
Software Mentions: 3
Published: over 12 years ago

10.1002/evl3.122

Molecular evolution across developmental time reveals rapid divergence in early embryogenesis
Cited by: 16
Author(s): Asher D. Cutter, Rose H. Garrett, Stephanie Mark, Wei Wang, Lei Sun
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pone.0204100

Biologically anchored knowledge expansion approach uncovers KLF4 as a novel insulin signaling regulator
Cited by: 3
Author(s): Annamalai Muthiah, Morgan S. Angulo, Natalie N. Walker, Susanna R. Keller, Jae K. Lee
Software Mentions: 3
Published: almost 8 years ago

10.1186/1756-0500-3-298

KC-SMARTR: An R package for detection of statistically significant aberrations in multi-experiment aCGH data
Cited by: 22
Author(s): Jorma J. de Ronde, Christiaan Klijn, Arno Velds, Henne Holstege, Marcel J. T. Reinders, Jos Jonkers, Lodewyk Wessels
Software Mentions: 3
Published: almost 16 years ago

10.1186/1756-0500-1-80

Advanced spot quality analysis in two-colour microarray experiments
Cited by: 10
Author(s): Mikalai M. Yatskou, Eugene Novikov, Guillaume Vetter, Arnaud Muller, Emmanuel Barillot, Laurent Vallar, Evelyne Friederich
Software Mentions: 3
Published: over 18 years ago

10.1186/s12987-020-00207-2

Advancing brain barriers RNA sequencing: guidelines from experimental design to publication
Cited by: 14
Author(s): David Francisco, Luca Marchetti, Sabela Rodríguez‐Lorenzo, Eduardo Frías-Anaya, Ricardo Figueiredo, Marjolein Heymanns, Maxime Culot, Ana Raquel Santa-Maria, Mária A. Deli, Raoul Freitas Vale Germano, Benoît Vanhollebeke, Nikolaos Kakogiannos, Monica Giannotta, Elisabetta Dejana, Amaia Dominguez-Belloso, Stefan Liebner, Markus Schuster, Harm‐Anton Klok, Marie Wiatr, Horst Schroten, Tobias Tenenbaum, Gijs Kooij, Peter Winter, Ignacio A. Romero, Helga E. de Vries, Britta Engelhardt, Rémy Bruggmann
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pmed.0030047

Gene Expression Programs in Response to Hypoxia: Cell Type Specificity and Prognostic Significance in Human Cancers
Cited by: 549
Author(s): Jen‐Tsan Chi, Zhen Wang, Dimitry S.A. Nuyten, Edwin H. Rodriguez, Marci E. Schaner, Ali Salim, Yun Wang, Gunnar B. Kristensen, Åslaug Helland, Anne Lise Børresen-Dale, Amato J. Giaccia, Michael T. Longaker, Trevor Hastie, George P. Yang, Marc J. van de Vijver, Patrick O. Brown
Software Mentions: 3
Published: over 20 years ago

10.1371/journal.pntd.0003115

Stability of the wMel Wolbachia Infection following Invasion into Aedes aegypti Populations
Cited by: 261
Author(s): Ary A. Hoffmann, Iñaki Iturbe‐Ormaetxe, Ashley G. Callahan, Benjamin L. Phillips, Katrina Billington, Jason K. Axford, Brian L. Montgomery, Andrew P. Turley, Scott Leslie O'Neill
Software Mentions: 3
Published: about 12 years ago

10.1186/s12859-015-0812-9

QQ-SNV: single nucleotide variant detection at low frequency by comparing the quality quantiles
Cited by: 5
Author(s): Koen Van der Borght, Kim Thys, Yves Wetzels, Lieven Clement, Bie Verbist, Joke Reumers, Herman van Vlijmen, Jeroen Aerssens
Software Mentions: 3
Published: almost 11 years ago

10.18632/oncotarget.19733

Overexpression of COL3A1 confers a poor prognosis in human bladder cancer identified by co-expression analysis
Cited by: 59
Author(s): Lushun Yuan, Bo Shu, Changhong Liang, Kaiyu Qian, Yongzhi Wang, Guofeng Qian, Yuan Zhu, Xinyue Cao, Conghua Xie, Yu Xiao, Xinghuan Wang
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pgen.0010016

Glucocorticoid Receptor-Dependent Gene Regulatory Networks
Cited by: 194
Author(s): Panin Le, Joshua R. Friedman, Jonathan Schug, John Brestelli, J. Brandon Parker, Irina M. Bochkis, Klaus H. Kaestner
Software Mentions: 3
Published: about 21 years ago

10.18632/oncotarget.15604

NUSAP1 promotes invasion and metastasis of prostate cancer
Cited by: 49
Author(s): Catherine A. Gordon, Xue Gong, Durga Ganesh, James D. Brooks
Software Mentions: 3
Published: over 9 years ago

10.18632/oncotarget.10947

Integrated analysis miRNA and mRNA profiling in patients with severe oligozoospermia reveals miR-34c-3p downregulates PLCXD3 expression
Cited by: 22
Author(s): Zhiming Li, Zaozao Zheng, Jun Ruan, Zhi Li, Xuan Zhuang, Chi-Meng Tzeng
Software Mentions: 3
Published: about 10 years ago

10.1371/journal.pgen.1009600

Antagonistic fungal enterotoxins intersect at multiple levels with host innate immune defences
Cited by: 10
Author(s): Xing Zhang, Benjamin W. Harding, Dina Aggad, Damien Courtine, Jia‐Xuan Chen, Nathalie Pujol, Jonathan J. Ewbank
Software Mentions: 3
Published: about 5 years ago

10.1186/s12859-019-2903-5

A comparison of three programming languages for a full-fledged next-generation sequencing tool
Cited by: 10
Author(s): Pascal Costanza, Charlotte Herzeel, Wilfried Verachtert
Software Mentions: 3
Published: over 7 years ago

10.18632/oncotarget.18162

Upregulation of long noncoding RNA HOXA-AS3 promotes tumor progression and predicts poor prognosis in glioma
Cited by: 53
Author(s): Fan Wu, Chuanbao Zhang, Jinquan Cai, Fan Yang, Tingyu Liang, Xiaoyan Yan, Haoyuan Wang, Wen Wang, Jing Chen, Tao Jiang
Software Mentions: 3
Published: over 9 years ago

10.3390/ijms22179246

Overdominance at the Gene Expression Level Plays a Critical Role in the Hybrid Root Growth of Brassica napus
Cited by: 8
Author(s): Nesma Shalby, Ibrahim A. A. Mohamed, Jie Xiong, Kaining Hu, Yuting Yang, Elsayed Nishawy, Bin Yi, Jing Wen, Chaozhi Ma, Tingdong Fu, Jinxing Tu
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pgen.1007949

Parental legacy, demography, and admixture influenced the evolution of the two subgenomes of the tetraploid Capsella bursa-pastoris (Brassicaceae)
Cited by: 38
Author(s): Dmytro Kryvokhyzha, Adriana Salcedo, Mimmi C. Eriksson, Tianlin Duan, Nilesh R. Tawari, Jun Chen, Maria Guerrina, Julia M. Kreiner, Tyler V. Kent, Ulf Lagercrantz, John R. Stinchcombe, Sylvain Glémin, Stephen I. Wright, Martin Lascoux
Software Mentions: 3
Published: over 7 years ago

10.1186/s12974-017-0858-x

Toll-like receptor 4 in glial inflammatory responses to air pollution in vitro and in vivo
Cited by: 99
Author(s): Nick Woodward, Morgan C. Levine, Amin Haghani, Farimah Shirmohammadi, Arian Saffari, Constantinos Sioutas, Todd E. Morgan, Caleb E. Finch
Software Mentions: 3
Published: over 9 years ago

10.1186/1471-2164-10-361

Genomic analysis of a sexually-selected character: EST sequencing and microarray analysis of eye-antennal imaginal discs in the stalk-eyed fly Teleopsis dalmanni (Diopsidae)
Cited by: 18
Author(s): Richard H. Baker, Jenna Morgan, Xianhui Wang, Jeffrey L. Boore, Gerald S. Wilkinson
Software Mentions: 3
Published: over 17 years ago

10.1186/1471-2105-14-143

Investigating the concordance of Gene Ontology terms reveals the intra- and inter-platform reproducibility of enrichment analysis
Cited by: 23
Author(s): Lifang Zhang, Juan Zhang, Gang Yang, Di Wu, Lina Jiang, Zhining Wen, Menglong Li
Software Mentions: 3
Published: over 13 years ago

10.1371/journal.pgen.1006571

Enhancer of polycomb coordinates multiple signaling pathways to promote both cyst and germline stem cell differentiation in the Drosophila adult testis
Cited by: 25
Author(s): Lijuan Feng, Zhen Shi, Xin Chen
Software Mentions: 3
Published: over 9 years ago

10.18632/oncotarget.5876

KIAA0101 is associated with human renal cell carcinoma proliferation and migration induced by erythropoietin
Cited by: 27
Author(s): Shengjun Fan, Xin Li, Lu Tie, Yan Pan, Xuejun Li
Software Mentions: 3
Published: almost 11 years ago

10.3390/ijms22105231

Dual RNA-Sequencing Analysis of Resistant (Pinus pinea) and Susceptible (Pinus radiata) Hosts during Fusarium circinatum Challenge
Cited by: 12
Author(s): Cristina Zamora-Ballesteros, Glória Pinto, Joana Amaral, Luís Valledor, Artur Alves, Julio J. Diez, Jorge Martín‐García
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pgen.1001135

Analysis of the Basidiomycete Coprinopsis cinerea Reveals Conservation of the Core Meiotic Expression Program over Half a Billion Years of Evolution
Cited by: 34
Author(s): Claire Burns, Jason E. Stajich, Andreas Rechtsteiner, Lorna A. Casselton, Sean E. Hanlon, Sarah K. Wilke, Oleksandr P. Savytskyy, Allen C. Gathman, Walt W. Lilly, Jason D. Lieb, Miriam E. Zolan, Patricia J. Pukkila
Software Mentions: 3
Published: almost 16 years ago

10.3390/ijms22041837

Whole Exome Sequencing Identifies APCDD1 and HDAC5 Genes as Potentially Cancer Predisposing in Familial Colorectal Cancer
Cited by: 5
Author(s): Diamanto Skopelitou, Benchun Miao, Aayushi Srivastava, Abhishek Kumar, Magdalena Kuswick, Dagmara Dymerska, Nagarajan Paramasivam, Matthias Schlesner, Jan Lubiński, Kari Hemminki, Asta Försti, Obul Reddy Bandapalli
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pgen.1000812

Altered Gene Expression and DNA Damage in Peripheral Blood Cells from Friedreich's Ataxia Patients: Cellular Model of Pathology
Cited by: 95
Author(s): Astrid C. Haugen, Nicholas A. Di Prospero, Joel S. Parker, Rick D. Fannin, Jeff W. Chou, Joel N. Meyer, Christopher Halweg, Jennifer B. Collins, Alexandra Dürr, Kenneth H. Fischbeck, Bennett Van Houten
Software Mentions: 3
Published: over 16 years ago

10.1371/journal.pntd.0001512

Multiple Mutations in Heterogeneous Miltefosine-Resistant Leishmania major Population as Determined by Whole Genome Sequencing
Cited by: 85
Author(s): Adriano C. Coelho, Sébastien Boisvert, Avinaba Mukherjee, Philippe Leprohon, Jacques Corbeil, Marc Ouellette
Software Mentions: 3
Published: over 14 years ago

10.3390/ijms22169081

Modeling and Structure Determination of Homo-Oligomeric Proteins: An Overview of Challenges and Current Approaches
Cited by: 10
Author(s): Aljaž Gaber, Miha Pavšič
Software Mentions: 3
Published: about 5 years ago

10.3390/ijms17050696

Identification of More Feasible MicroRNA–mRNA Interactions within Multiple Cancers Using Principal Component Analysis Based Unsupervised Feature Extraction
Cited by: 31
Author(s): Y-h. Taguchi
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pgen.1003820

The Genome and Development-Dependent Transcriptomes of Pyronema confluens: A Window into Fungal Evolution
Cited by: 80
Author(s): Stefanie Traeger, Florian Altegoer, Michael Freitag, Toni Gabaldón, Frank Kempken, Abhishek Kumar, Marina Marcet‐Houben, Stefanie Pöggeler, Jason E. Stajich, Minou Nowrousian
Software Mentions: 3
Published: almost 13 years ago

10.3390/ijms20010016

Clinically Relevant Post-Translational Modification Analyses—Maturing Workflows and Bioinformatics Tools
Cited by: 34
Author(s): Dana Pascovici, Jemma X. Wu, Matthew J. McKay, Chitra Joseph, Zainab Noor, Karthik Shantharam Kamath, Yunqi Wu, Shoba Ranganathan, Vivek Gupta, Mehdi Mirzaei
Software Mentions: 3
Published: over 7 years ago

10.1186/1471-2105-9-144

Empirical Bayes analysis of single nucleotide polymorphisms
Cited by: 21
Author(s): Holger Schwender, Katja Ickstadt
Software Mentions: 3
Published: over 18 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

10.3390/ijms16035975

RNA-Seq Transcriptome Analysis of Maize Inbred Carrying Nicosulfuron-Tolerant and Nicosulfuron-Susceptible Alleles
Cited by: 26
Author(s): Xiaomin Liu, Xiaogang Xu, Binghua Li, Xueqing Wang, Guiqi Wang, Yaqian Li
Software Mentions: 3
Published: over 11 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

10.1101/2021.07.09.21260221

Genetic regulation ofOAS1nonsense-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: about 5 years ago

10.1186/ar2855

Insights in to the pathogenesis of axial spondyloarthropathy based on gene expression profiles
Cited by: 45
Author(s): Srilakshmi M Sharma, Dongseok Choi, Stephen R. Planck, Christina A. Harrington, Carrie R. Austin, J. A. Lewis, Tessa N. Diebel, Tammy M. Martin, Justine R. Smith, James T. Rosenbaum
Software Mentions: 3
Published: over 17 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: about 6 years ago

10.1186/1471-2105-14-220

NURD: an implementation of a new method to estimate isoform expression from non-uniform RNA-seq data
Cited by: 15
Author(s): Xinyun Ma, Xuegong Zhang
Software Mentions: 3
Published: about 13 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: almost 6 years ago

10.3390/ijms20235922

Transcriptomic and Co-Expression Network Profiling of Shoot Apical Meristem Reveal Contrasting Response to Nitrogen Rate between Indica and Japonica Rice Subspecies
Cited by: 10
Author(s): Xiaoxiang Zhang, Juan Zhou, Niansheng Huang, Lanjing Mo, Minjia Lv, Yujiao Gao, Chen Chen, Yin Su, Jianhua Ju, Guichun Dong, Yong Zhou, Zefeng Yang, Aihong Li, Yulong Wang, Jianye Huang, Youli Yao
Software Mentions: 3
Published: almost 7 years ago

10.1186/1471-2164-11-134

Correcting for intra-experiment variation in Illumina BeadChip data is necessary to generate robust gene-expression profiles
Cited by: 32
Author(s): Robert Kitchen, Victoria Sabine, Andrew H. Sims, E.J. Macaskill, Lorna Renshaw, Jeremy Thomas, Jano van Hemert, JM Dixon, John M.S. Bartlett
Software Mentions: 3
Published: over 16 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: almost 13 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/s12864-015-1975-5

Jitterbug: somatic and germline transposon insertion detection at single-nucleotide resolution
Cited by: 32
Author(s): Elizabeth Hénaff, Luís Zapata, Josep M. Casacuberta, Stephan Ossowski
Software Mentions: 3
Published: almost 11 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

10.1186/2193-1801-3-130

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: over 12 years ago

10.1186/1471-2105-9-85

Statistical issues in the analysis of Illumina data
Cited by: 91
Author(s): Mark J. Dunning, Nuno L. Barbosa‐Morais, Andy G. Lynch, Simon Tavaré, Matthew E. Ritchie
Software Mentions: 3
Published: over 18 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

10.1371/journal.pcbi.1003345

Next-Generation Sequence Assembly: Four Stages of Data Processing and Computational Challenges
Cited by: 120
Author(s): Sara El-Metwally, Taher Hamza, Magdi Zakaria, Mohamed Helmy
Software Mentions: 3
Published: almost 13 years ago

10.1186/s12859-020-03726-9

IonCRAM: a reference-based compression tool for ion torrent sequence files
Cited by: 2
Author(s): Moustafa Shokrof, Mohamed Abouelhoda
Software Mentions: 3
Published: about 6 years ago

10.1186/s12859-020-3388-y

ECFS-DEA: an ensemble classifier-based feature selection for differential expression analysis on expression profiles
Cited by: 64
Author(s): Xudong Zhao, Qing Jiao, Hangyu Li, Yiming Wu, Hanxu Wang, Shan Huang, Guohua Wang
Software Mentions: 3
Published: over 6 years ago

10.3389/fimmu.2019.01384

The Rheumatoid Arthritis Risk Gene AIRE Is Induced by Cytokines in Fibroblast-Like Synoviocytes and Augments the Pro-inflammatory Response
Cited by: 12
Author(s): Beatrice Bergström, Christina Lundqvist, Georgios K. Vasileiadis, Hans Carlsten, Olov Ekwall, Anna-Karin Hultgård Ekwall
Software Mentions: 3
Published: about 7 years ago

10.1128/mBio.02096-17

The Essential Genome of Escherichia coli 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: over 8 years ago

10.3390/s18020474

Design and Implementation of Cloud-Centric Configuration Repository for DIY IoT Applications
Cited by: 37
Author(s): Shabir Ahmad, Hang Lei, Do‐Hyeun Kim
Software Mentions: 3
Published: over 8 years ago

10.1186/s12864-015-1670-6

NanoCAGE-XL and CapFilter: an approach to genome wide identification of high confidence transcription start sites
Cited by: 31
Author(s): Jason S. Cumbie, Maria G. Ivanchenko, Molly Megraw
Software Mentions: 3
Published: about 11 years ago

10.3389/fimmu.2020.595877

Gene Networks Underlying the Resistance of Bifidobacterium longum to Inflammatory Factors
Cited by: 5
Author(s): Vladimir A. Veselovsky, Marina S. Dyachkova, Egor Menyailo, Polina S. Polyaeva, Evgenii I. Olekhnovich, Egor Shitikov, Dmitry Bespiatykh, Tatiana A. Semashko, Artem S. Kasianov, Elena N. Ilina, В Н Даниленко, Ksenia M. Klimina
Software Mentions: 3
Published: almost 6 years ago

10.3390/s18051465

Smart Waste Collection System with Low Consumption LoRaWAN Nodes and Route Optimization
Cited by: 48
Author(s): Álvaro Lozano, Javier Caridad, Juan F. De Paz, Gabriel Villarrubia González, Javier Bajo
Software Mentions: 3
Published: over 8 years ago

10.3390/s100301967

A Comparison of Spectral Angle Mapper and Artificial Neural Network Classifiers Combined with Landsat TM Imagery Analysis for Obtaining Burnt Area Mapping
Cited by: 102
Author(s): George P. Petropoulos, Krishna Prasad Vadrevu, Gavriil Xanthopoulos, G. Karantounias, Marko Scholze
Software Mentions: 3
Published: over 16 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: almost 10 years ago

10.1038/s41598-021-95698-w

PCA-based unsupervised feature extraction for gene expression analysis of COVID-19 patients
Cited by: 9
Author(s): Kota Fujisawa, Mamoru Shimo, Y-h. Taguchi, Shinya Ikematsu, Ryota Miyata
Software Mentions: 3
Published: about 5 years ago

10.3390/s18124330

Variational Pansharpening for Hyperspectral Imagery Constrained by Spectral Shape and Gram–Schmidt Transformation
Cited by: 10
Author(s): Z. J. Huang, Qihao Chen, Xiuguo Liu
Software Mentions: 3
Published: almost 8 years ago

10.1038/s41598-021-94396-x

Niche partitioning among dead wood-dependent beetles
Cited by: 1
Author(s): Jakub Horák
Software Mentions: 3
Published: about 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: almost 17 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

10.1186/1471-2164-11-315

A simple optimization can improve the performance of single feature polymorphism detection by Affymetrix expression arrays
Cited by: 3
Author(s): Youko Horiuchi, Yoshiaki Harushima, Hironori Fujisawa, Takako Mochizuki, Masanori Kawakita, Takayuki Sakaguchi, Nori Kurata
Software Mentions: 3
Published: over 16 years ago

10.1186/1471-2164-12-293

RNA-seq: technical variability and sampling
Cited by: 250
Author(s): Lauren M. McIntyre, Kenneth K. Lopiano, Alison M. Morse, V. Amin, Ann L. Oberg, Linda J. Young, Sergey V. Nuzhdin
Software Mentions: 3
Published: over 15 years ago

10.1038/s41598-021-91503-w

Colonisation dynamics of Listeria monocytogenes strains isolated from food production environments
Cited by: 12
Author(s): Jessica Gray, P. Scott Chandry, Mandeep Kaur, Chawalit Kocharunchitt, Séamus Fanning, John P. Bowman, Edward M. Fox
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2105-15-79

The characteristic direction: a geometrical approach to identify differentially expressed genes
Cited by: 142
Author(s): Neil R. Clark, Kevin Hu, Axel S. Feldmann, Yan Kou, Edward Y. Chen, Qiaonan Duan, Avi Ma’ayan
Software Mentions: 3
Published: over 12 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: about 7 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: over 6 years ago

10.1038/s41598-021-90243-1

Metabolomics and computational analysis of the role of monoamine oxidase activity in delirium and SARS-COV-2 infection
Cited by: 17
Author(s): Miroslava Čuperlović-Culf, Emma Cunningham, Hossen Teimoorinia, Anuradha Surendra, Xiaobei Pan, Steffany A. L. Bennett, Mijin Jung, Bernadette McGuiness, Anthony Peter Passmore, David Beverland, Brian D. Green
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-021-92395-6

MULTICOM2 open-source protein structure prediction system powered by deep learning and distance prediction
Cited by: 1
Author(s): Tai Tsun Wu, Jian Liu, Zhiye Guo, Jie Hou, Jianlin Cheng
Software Mentions: 3
Published: about 5 years ago

10.1186/1471-2105-15-S1-S2

Integrated Bio-Search: challenges and trends for the integration, search and comprehensive processing of biological information
Cited by: 11
Author(s): Marco Masseroli, Barend Mons, Erik Bongcam‐Rudloff, Stefano Ceri, Alexander Kel, François Rechenmann, Frédérique Lisacek, Paolo Romano
Software Mentions: 3
Published: over 12 years ago

10.1038/s41598-020-77600-2

Genetic mapping and candidate gene analysis for melon resistance to Phytophthora capsici
Cited by: 4
Author(s): Pingyong Wang, Xiuhong Xu, Guangwei Zhao, Yue He, C. T. Hou, Weihu Kong, Jian Zhang, Shuimiao Liu, Yong Xu, Zhigao Xu
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-020-76533-0

High definition transcranial direct current stimulation modulates abnormal neurophysiological activity in post-stroke aphasia
Cited by: 16
Author(s): Priyanka P. Shah-Basak, Gayatri Sivaratnam, Selina Teti, Alexander Francois-Nienaber, Maryam Yossofzai, Sabrina E M Armstrong, Sumiti Nayar, Regina Jokel, Jed A. Meltzer
Software Mentions: 3
Published: almost 6 years ago

10.1038/s41598-021-83459-8

Investigation of allele specific expression in various tissues of broiler chickens using the detection tool VADT
Cited by: 5
Author(s): M. Joseph Tomlinson, Shawn W. Polson, Jing Qiu, Juniper A. Lake, William Lee, Behnam Abasht
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-021-93893-3

Microarray-based selection of a serum biomarker panel that can discriminate between latent and active pulmonary TB
Cited by: 6
Author(s): Zhihui Li, Jianjun Hu, Pengchong Liu, Dan Cui, Hongqin Di, Shucai Wu
Software Mentions: 3
Published: about 5 years ago

10.1186/1471-2105-9-415

BATS: a Bayesian user-friendly software for Analyzing Time Series microarray experiments
Cited by: 53
Author(s): Claudia Angelini, Luisa Cutillo, Daniela De Canditiis, Margherita Mutarelli, Marianna Pensky
Software Mentions: 3
Published: almost 18 years ago

10.1038/s41598-020-65724-4

Simultaneous identification of animal-derived components in meats using high-throughput sequencing in combination with a custom-built mitochondrial genome database
Cited by: 6
Author(s): Yinan Zhang, Qinfeng Qu, RAO Mingzhen, Zhang Nana, Yu Zhao, Fei Tao
Software Mentions: 3
Published: over 6 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: over 11 years ago

10.7717/peerj.7156

Spread of the non-native anemone Anemonia alicemartinae Häussermann & 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: about 7 years ago

10.1038/srep41238

Patient-specific hepatocyte-like cells derived from induced pluripotent stem cells model pazopanib-mediated hepatotoxicity
Cited by: 43
Author(s): Yukti Choudhury, Yi‐Chin Toh, Jiangwa Xing, Yinghua Qu, Jonathan Poh, Huan Li, Hui Shan Tan, Ravindran Kanesvaran, Hanry Yu, Min‐Han Tan
Software Mentions: 3
Published: over 9 years ago

10.1038/srep37563

A novel process of viral vector barcoding and library preparation enables high-diversity library generation and recombination-free paired-end sequencing
Cited by: 21
Author(s): Marcus Davidsson, Paula Díaz-Fernández, Oliver D. Schwich, Marcos Torroba, Gang Wang, Tomas Björklund
Software Mentions: 3
Published: almost 10 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: about 10 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: almost 10 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: over 12 years ago

10.1186/s13071-016-1341-8

Reconstruction of the insulin-like signalling pathway of Haemonchus contortus
Cited by: 14
Author(s): Namitha Mohandas, Min Hu, Andreas J. Stroehlein, Neil D. Young, Paul W. Sternberg, James B. Lok, Robin B. Gasser
Software Mentions: 3
Published: over 10 years ago

10.1186/1471-2105-8-346

A framework for significance analysis of gene expression data using dimension reduction methods
Cited by: 41
Author(s): Lars Gidskehaug, Endre Anderssen, Arnar Flatberg, Bjørn K. Alsberg
Software Mentions: 3
Published: almost 19 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

10.1038/srep27623

Multiplex giant magnetoresistive biosensor microarrays identify interferon-associated autoantibodies in systemic lupus erythematosus
Cited by: 31
Author(s): J. Lee, D. James Haddon, Hannah Wand, J. M. Price, Vivian K. Diep, Drew A. Hall, Michelle Petri, Emily C. Baechler, Imelda Balboni, Paul J. Utz, Shan X. Wang
Software Mentions: 3
Published: over 10 years ago

10.1186/1471-2164-9-333

Structure and properties of transcriptional networks driving selenite stress response in yeasts
Cited by: 74
Author(s): Hélène Salin, Vivienne Fardeau, Eugenia Piccini, Gaëlle Lelandais, Véronique Tanty, Sophie Lemoine, Claude Jacq, Frédéric Devaux
Software Mentions: 3
Published: about 18 years ago

10.1038/srep13245

Predictive habitat suitability models to aid conservation of elasmobranch diversity in the central Mediterranean Sea
Cited by: 52
Author(s): Valentina Lauria, Michele Gristina, Martin J. Attrill, Fabio Fiorentino, Germana Garofalo
Software Mentions: 3
Published: about 11 years ago

Projects: cran: SAM

Science Score: 85/100

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Papers Mentioning SAM 4,566