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: cran: SAM
https://packages.ecosyste.ms/registries/cran.r-project.org/packages/SAM
Sparse Additive Modelling
9 versions
Latest release: almost 3 years ago
4 dependent packages
341 downloads last month
Papers Mentioning SAM 4,566
10.1186/1471-2105-13-270
Combining multiple hypothesis testing and affinity propagation clustering leads to accurate, robust and sample size independent classification on gene expression dataCited by: 11
Author(s): Αλέξανδρος Σακελλαρίου, Despina Sanoudou, George M. Spyrou
Software Mentions: 7
Published: over 11 years ago
10.7554/eLife.45403
The dynamic conformational landscape of the protein methyltransferase SETD8Cited by: 37
Author(s): Shi Chen, Rafal Wiewiora, Fanwang Meng, Nicolas Babault, Anqi Ma, Wenyu Yu, Kun Qian, Hao Hu, Hua Zou, Junyi Wang, Shijie Fan, Gil Blum, Fábio Pittella Silva, Kyle A. Beauchamp, W. Tempel, Hualiang Jiang, Kaixian Chen, R.J. Skene, Y. George Zheng, Peter J. Brown, Jian Jin, Cheng Luo, John D. Chodera, Minkui Luo
Software Mentions: 7
Published: about 5 years ago
10.1186/1471-2105-12-267
SeqGene: a comprehensive software solution for mining exome- and transcriptome- sequencing dataCited by: 39
Author(s): Xutao Deng
Software Mentions: 7
Published: almost 13 years ago
10.1186/s12864-019-6155-6
A framework using topological pathways for deeper analysis of transcriptome dataCited by: 0
Author(s): Yue Zhao, Stephanie Piekos, Tham H. Hoang, Dong-Guk Shin
Software Mentions: 7
Published: about 4 years ago
10.1186/1471-2164-15-178
seqCNA: an R package for DNA copy number analysis in cancer using high-throughput sequencingCited by: 12
Author(s): David Mósen-Ansorena, Naiara Tellería, Silvia Veganzones, Virginia de la Orden, M.L. Maestro, Ana M. Aransay
Software Mentions: 7
Published: over 10 years ago
10.3389/fimmu.2018.01553
Single Cell RNA Sequencing of Rare Immune Cell PopulationsCited by: 88
Author(s): Akira Nguyen, Weng Hua Khoo, Imogen Moran, Peter I. Croucher, Tri Giang Phan
Software Mentions: 7
Published: almost 6 years ago
10.1186/1471-2105-9-46
EzArray: A web-based highly automated Affymetrix expression array data management and analysis systemCited by: 16
Author(s): Yuerong Zhu, Yuelin J. Zhu, Wei Xu
Software Mentions: 7
Published: over 16 years ago
10.3390/cancers11060759
Detection of Epstein-Barr Virus Infection in Non-Small Cell Lung CancerCited by: 31
Author(s): Fayez Kheir, Mengmeng Zhao, Michael J. Strong, Yi Yu, Asuka Nanbo, Erik K. Flemington, Gilbert F. Morris, Krzysztof Reiss, Li Li, Zhen Lin
Software Mentions: 7
Published: almost 5 years ago
10.1186/s13059-020-1930-x
CUBIC: an atlas of genetic architecture promises directed maize improvementCited by: 49
Author(s): Haijun Liu, Xiaqing Wang, Yingjie Xiao, Jingyun Luo, Feng Qiao, Wenyu Yang, Ruyang Zhang, Yijiang Meng, Jiamin Sun, Shijuan Yan, Yong Peng, Luyao Niu, Liumei Jian, Wei Song, Jiali Yan, Chunhui Li, Yanxin Zhao, Liu Ya, Marilyn L. Warburton, Jiuran Zhao
Software Mentions: 7
Published: over 4 years ago
10.1186/s40168-017-0387-y
In-depth resistome analysis by targeted metagenomicsCited by: 103
Author(s): Val F. Lanza, Fernando Baquero, José Luis Martínez, Ricardo Ramos-Ruíz, Bruno González‐Zorn, Antoine Andremont, Antonio Sánchez-Valenzuela, S. Dusko Ehrlich, Sean Kennedy, Étienne Ruppé, Willem van Schaik, Rob J. L. Willems, Fernando de la Cruz, Teresa M. Coque
Software Mentions: 7
Published: over 6 years ago
10.1186/s12864-018-4805-8
Transcription profiling of butanol producer Clostridium beijerinckii NRRL B-598 using RNA-SeqCited by: 14
Author(s): Karel Sedlář, Pavlína Koščová, Maryna Vasylkivska, Barbora Branská, Jan Kolek, Kristyna Kupkova, Petra Patáková, Ivo Provazník
Software Mentions: 7
Published: almost 6 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
10.1038/s41598-020-73376-7
RNA oxidation in chromatin modification and DNA-damage response following exposure to formaldehydeCited 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
10.1371/journal.pone.0149891
Identification and Characterization of msf, a Novel Virulence Factor in Haemophilus influenzaeCited by: 15
Author(s): Jennifer M. Kress-Bennett, N. Luisa Hiller, Rory Eutsey, Evan Powell, Mark Longwell, Todd A. Hillman, Tenisha Blackwell, Barbara Byers, Joshua Chang Mell, J. Christopher Post, Fang Hu, Garth D. Ehrlich, Benjamin Janto
Software Mentions: 6
Published: about 8 years ago
10.1038/s41598-020-74567-y
Impact of RNA-seq data analysis algorithms on gene expression estimation and downstream predictionCited by: 11
Author(s): Tong Li, Po-Yen Wu, John H. Phan, Hamid R Hassazadeh, Weida Tong, May D. Wang
Software Mentions: 6
Published: over 3 years ago
10.1038/srep32753
HIPSTR and thousands of lncRNAs are heterogeneously expressed in human embryos, primordial germ cells and stable cell linesCited by: 35
Author(s): Dinar Yunusov, Letícia Anderson, Luis DaSilva, Joanna Wysocka, Toshihiko Ezashi, R. M. Roberts, Sérgio Verjovski-Almeida
Software Mentions: 6
Published: over 7 years ago
10.1371/journal.pcbi.1004393
Informatics for RNA Sequencing: A Web Resource for Analysis on the CloudCited by: 73
Author(s): Malachi Griffith, Jason Walker, Nicholas C. Spies, Benjamin J. Ainscough, Obi L. Griffith
Software Mentions: 6
Published: almost 9 years ago
10.1038/s41597-019-0261-9
A 2D hyperspectral library of mineral reflectance, from 900 to 2500 nmCited by: 7
Author(s): Laurent Fasnacht, Marie-Louise Vogt, Philippe Renard, Philip Brunner
Software Mentions: 6
Published: over 4 years ago
10.1371/journal.pcbi.1005515
Mixture models reveal multiple positional bias types in RNA-Seq data and lead to accurate transcript concentration estimatesCited by: 17
Author(s): Andreas Tuerk, Gregor Wiktorin, Serhat Güler
Software Mentions: 6
Published: about 7 years ago
10.1186/1471-2105-10-201
A-MADMAN: Annotation-based microarray data meta-analysis toolCited by: 35
Author(s): Andrea Bisognin, Alessandro Coppe, Francesco Ferrari, Davide Risso, Chiara Romualdi, Silvio Bicciato, Stefania Bortoluzzi
Software Mentions: 6
Published: almost 15 years ago
10.1186/s12862-020-01679-4
Multi-model seascape genomics identifies distinct environmental drivers of selection among sympatric marine speciesCited by: 9
Author(s): Erica S. Nielsen, Romina Henriques, Maria Beger, Robert J. Toonen, Sophie von der Heyden
Software Mentions: 6
Published: over 3 years ago
10.1186/1477-5956-8-66
A comparison of imputation procedures and statistical tests for the analysis of two-dimensional electrophoresis dataCited by: 7
Author(s): Jeffrey C. Miecznikowski, Srinivasan Damodaran, Kimberly F. Sellers, Richard A. Rabin
Software Mentions: 6
Published: over 14 years ago
10.1038/sdata.2016.8
Transcriptome regulation and chromatin occupancy by E2F3 and MYC in miceCited by: 8
Author(s): Xing Tang, Huayang Liu, Arunima Srivastava, Thierry Pécot, Zhong Chen, Qianben Wang, Kun Huang, Maria Teresa Sáenz-Robles, Paul G. Cantalupo, James M. Pipas, Gustavo Leone
Software Mentions: 6
Published: over 8 years ago
10.1111/pbi.12834
Conversion of array‐based single nucleotide polymorphic markers for use in targeted genotyping by sequencing in hexaploid wheat (<i>Triticum aestivum</i>)Cited by: 21
Author(s): Amanda Burridge, Paul Wilkinson, Mark Winfield, Gary Barker, Alexandra M. Allen, Jane A. Coghill, Christy Waterfall, Keith J. Edwards
Software Mentions: 6
Published: over 6 years ago
10.1093/gbe/evaa143
The Genome of the Softshell Clam Mya arenaria and the Evolution of ApoptosisCited by: 5
Author(s): David C. Plachetzki, M. Sabrina Pankey, Matthew D. MacManes, Michael P. Lesser, Charles W. Walker
Software Mentions: 6
Published: almost 4 years ago
10.1186/s13059-021-02423-x
GRIDSS2: comprehensive characterisation of somatic structural variation using single breakend variants and structural variant phasingCited by: 58
Author(s): Daniel Cameron, Jonathan Baber, Charles Shale, Jose Espejo Valle-Inclán, Nicolle Besselink, Arne van Hoeck, Roel Janssen, Edwin Cuppen, Peter Priestley, Anthony T. Papenfuss
Software Mentions: 6
Published: almost 3 years ago
10.1186/s13059-020-02216-8
Histone modifications during the life cycle of the brown alga EctocarpusCited by: 21
Author(s): Simon Bourdareau, Leïla Tirichine, Bérangère Lombard, Damarys Loew, Delphine Scornet, Yue Wu, Susana M. Coelho, J. Mark Cock
Software Mentions: 6
Published: over 3 years ago
10.1371/journal.ppat.1008754
JNK pathway restricts DENV2, ZIKV and CHIKV infection by activating complement and apoptosis in mosquito salivary glandsCited by: 37
Author(s): Avisha Chowdhury, Cassandra M. Modahl, Siok Thing Tan, Benjamin Wong Wei Xiang, Dorothée Missé, Thomas Vial, R. Manjunatha Kini, Julien Pompon
Software Mentions: 6
Published: almost 4 years ago
10.1371/journal.pcbi.1005950
HaSAPPy: A tool for candidate identification in pooled forward genetic screens of haploid mammalian cellsCited by: 9
Author(s): Giulio Di Minin, Andreas Postlmayr, Anton Wutz
Software Mentions: 6
Published: over 6 years ago
10.1186/1471-2105-12-92
Statistical Test of Expression Pattern (STEPath): a new strategy to integrate gene expression data with genomic information in individual and meta-analysis studiesCited by: 5
Author(s): Paolo Martini, Davide Risso, Gabriele Sales, Chiara Romualdi, Gerolamo Lanfranchi, Stefano Cagnin
Software Mentions: 6
Published: about 13 years ago
10.1038/sdata.2016.25
Extensive sequencing of seven human genomes to characterize benchmark reference materialsCited by: 535
Author(s): Justin M. Zook, David Catoe, Jennifer McDaniel, Lindsay K. Vang, Noah Spies, Arend Sidow, Ziming Weng, Yuling Liu, Christopher E. Mason, Noah Alexander, Elizabeth Hénaff, Alexa B. R. McIntyre, Dhruva Chandramohan, Feng Chen, Erich B. Jaeger, Ali Moshrefi, Khoa Pham, William Stedman, Tiffany Y. Liang, Michael Saghbini, Željko Džakula, Alex Hastie, Han Cao, Gintaras Deikus, Eric E. Schadt, Robert Sebra, Ali Kashif Bashir, Rebecca Truty, Christopher Chang, Natali Gulbahce, Keyan Zhao, Srinka Ghosh, Fiona Hyland, Yutao Fu, Mark Chaisson, Chunlin Xiao, Jonathan Trow, Stephen T. Sherry, Alexander Wait Zaranek, Madeleine Ball, Jason Bobe, Preston W. Estep, George M. Church, Patrick Marks, Sofia Kyriazopoulou-Panagiotopoulou, Grace Zheng, Michael Schnall-Levin, Heather Ordonez, Patrice A Mudivarti, Kristina Giorda, Ying Sheng, Karoline Bjarnesdatter Rypdal, Marc Salit
Software Mentions: 6
Published: almost 8 years ago
10.1186/s13059-017-1367-z
MICRA: an automatic pipeline for fast characterization of microbial genomes from high-throughput sequencing dataCited by: 9
Author(s): Ségolène Caboche, Gaël Even, Alexandre Loywick, Christophe Audebert, David Hot
Software Mentions: 6
Published: over 6 years ago
10.1186/s12864-020-07013-y
Optimizing performance of GATK workflows using Apache Arrow In-Memory data frameworkCited by: 3
Author(s): Tanveer Ahmad, Nauman Ahmed, Zaid Al-Ars, H. Peter Hofstee
Software Mentions: 6
Published: over 3 years ago
10.3389/fmicb.2019.01408
Chromatin Profiles of Chromosomally Integrated Human Herpesvirus-6ACited by: 19
Author(s): Anthony J. Saviola, Cosima Zimmermann, Michael Mariani, Sylvia Signorelli, Diana L. Gerrard, Joseph R. Boyd, Darren J. Wight, Guillaume Morissette, Annie Gravel, Isabelle Dubuc, Louis Flamand, Benedikt B. Kaufer, Seth Frietze
Software Mentions: 6
Published: almost 5 years ago
10.15252/msb.20156520
Environment‐induced epigenetic reprogramming in genomic regulatory elements in smoking mothers and their childrenCited by: 93
Author(s): Tobias Bauer, Saskia Trump, Naveed Ishaque, Loreen Thürmann, Lei Gu, Mario Bauer, Matthias Bieg, Zuguang Gu, Dieter Weichenhan, Jan‐Philipp Mallm, Stefan Röder, Gunda Herberth, Eiko Takada, Oliver Mücke, Marcus Winter, Kristin M. Junge, Konrad Grützmann, Ulrike Rolle-Kampczyk, Qi Wang, Christian Lawerenz, Michael Borte, Tobias Polte, Matthias Schlesner, Michaela Schanné, Stefan Wiemann, Christina Geörg, Hendrik G. Stunnenberg, Christoph Plass, Karsten Rippe, Junichiro Mizuguchi, Carl Herrmann, Roland Eils, Irina Lehmann
Software Mentions: 6
Published: about 8 years ago
10.1186/s12859-018-2437-2
Adaptively capturing the heterogeneity of expression for cancer biomarker identificationCited by: 1
Author(s): Xueping Xie, Yufeng Xie, Yitong Liu, Hongqiang Wang
Software Mentions: 6
Published: over 5 years ago
10.3389/fmicb.2018.01888
Infection-Induced Changes Within the Endocytic Recycling Compartment Suggest a Roadmap of Human Cytomegalovirus EgressCited by: 16
Author(s): William L. Close, James Glassbrook, Stephen J. Gurczynski, Philip E. Pellett
Software Mentions: 6
Published: over 5 years ago
10.1186/s40168-021-01136-4
Longitudinal study on the effects of growth-promoting and therapeutic antibiotics on the dynamics of chicken cloacal and litter microbiomes and resistomesCited by: 24
Author(s): Chhedi Lal Gupta, Shlomo E. Blum, Karuppasamy Kattusamy, Tali Daniel, S. Druyan, Roni Shapira, O. Krifucks, Yan Zhu, Xinyuan Zhou, Jian‐Qiang Su, Eddie Cytryn
Software Mentions: 6
Published: over 2 years ago
10.1186/1471-2105-11-279
Importance of replication in analyzing time-series gene expression data: Corticosteroid dynamics and circadian patterns in rat liverCited by: 12
Author(s): Tung Nguyen, Richard R. Almon, Debra C. DuBois, William J. Jusko, Ioannis P. Androulakis
Software Mentions: 6
Published: almost 14 years ago
10.1093/gbe/evu133
Settling Down: The Genome of Serratia symbiotica from the Aphid Cinara tujafilina Zooms in on the Process of Accommodation to a Cooperative Intracellular LifeCited by: 77
Author(s): Alejandro Manzano-Marı́n, Amparo Latorre
Software Mentions: 6
Published: almost 10 years ago
10.15252/embj.2019102808
HNF1A recruits KDM6A to activate differentiated acinar cell programs that suppress pancreatic cancerCited by: 36
Author(s): Jorge Ferrer, Edgar Bernardo, Anthony Beucher, Miguel A. Maestro, Natalia del Pozo, I.R. Hernández Millán, Lena Haeberle, Martin Schlensog, Sami-Alexander Safi, Wolfram Trudo Knoefel, Vanessa Grau, Matías De Vas, Karl B. Shpargel, Eva C. Vaquero, Terry Magnuson, Sagrario Ortega, Irene Espósito, Francisco X. Real, Jorge Ferrer
Software Mentions: 6
Published: about 4 years ago
10.1371/journal.pone.0072614
DistMap: A Toolkit for Distributed Short Read Mapping on a Hadoop ClusterCited by: 46
Author(s): Ram Vinay Pandey, Christian Schlötterer
Software Mentions: 6
Published: over 10 years ago
10.1038/s42003-021-01673-6
Glacial melt disturbance shifts community metabolism of an Antarctic seafloor ecosystem from net autotrophy to heterotrophyCited by: 11
Author(s): Ulrike Braeckman, Francesca Pasotti, Ralf Hoffmann, Susana Vázquez, Angela Wulff, Irene R Schloss, Ulrike Falk, Dolores Deregibus, Nene Lefaible, Anders Torstensson, Adil Y. Al-Handal, Frank Wenzhöfer, Ann Vanreusel
Software Mentions: 6
Published: over 3 years ago
10.1093/database/baaa082
Siberian sturgeon multi-tissue reference transcriptome databaseCited by: 2
Author(s): Christophe Klopp, Cédric Cabau, Gonzalo Greif, André Lasalle, Santiago Di Landro, Denise Vizziano-Cantonnet
Software Mentions: 6
Published: over 4 years ago
10.1186/2045-9769-3-1
glbase: a framework for combining, analyzing and displaying heterogeneous genomic and high-throughput sequencing dataCited by: 52
Author(s): Andrew P. Hutchins, Ralf Jauch, Mateusz Dyla, Diego Miranda‐Saavedra
Software Mentions: 6
Published: over 10 years ago
10.3390/ijms21249622
Novel Liver X Receptor Ligand GAC0001E5 Disrupts Glutamine Metabolism and Induces Oxidative Stress in Pancreatic Cancer CellsCited by: 7
Author(s): Shivangi Srivastava, Scott Widmann, Charles Ho, Donovan Nguyen, Alexis Nguyen, Asitha Premaratne, Jan‐Åke Gustafsson, Chin-Yo Lin
Software Mentions: 6
Published: over 3 years ago
10.7554/eLife.11491
Localized JNK signaling regulates organ size during developmentCited by: 37
Author(s): Helen Rankin Willsey, Xiaoyan Zheng, José Carlos Pastor-Pareja, A. Jeremy Willsey, Philip A. Beachy, Tian Xu
Software Mentions: 6
Published: about 8 years ago
10.1186/s12859-015-0664-3
Confident difference criterion: a new Bayesian differentially expressed gene selection algorithm with applicationsCited by: 5
Author(s): Fang Yu, Ming Hui Chen, Lynn Kuo, Heather Talbott, John S. Davis
Software Mentions: 6
Published: almost 9 years ago
10.1371/journal.pone.0116095
ICan: An Integrated Co-Alteration Network to Identify Ovarian Cancer-Related GenesCited by: 9
Author(s): Yuanshuai Zhou, Yongjing Liu, Kening Li, Rui Zhang, Fujun Qiu, Ning Zhao, Yan Xu
Software Mentions: 6
Published: about 9 years ago
10.7554/eLife.53933
Heterogeneous T cell motility behaviors emerge from a coupling between speed and turning in vivoCited by: 33
Author(s): Elizabeth R. Jerison, Stephen R. Quake
Software Mentions: 6
Published: about 4 years ago
10.1186/s12859-016-1195-2
A fuzzy method for RNA-Seq differential expression analysis in presence of multireadsCited by: 16
Author(s): Arianna Consiglio, Corrado Mencar, Giorgio Grillo, Flaviana Marzano, Mariano Francesco Caratozzolo, Sabino Liuni
Software Mentions: 6
Published: over 7 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 positionsCited 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
10.1371/journal.pone.0151895
Patterns of Species Richness and Turnover for the South American Rodent FaunaCited by: 57
Author(s): Renan Maestri, Bruce D. Patterson
Software Mentions: 6
Published: about 8 years ago
10.1007/s12275-020-9536-2
STATR: A simple analysis pipeline of Ribo-Seq in bacteriaCited by: 7
Author(s): Donghui Choe, Bernhard Ø. Palsson, Byung-Kwan Cho
Software Mentions: 6
Published: over 4 years ago
10.1371/journal.pone.0190279
pyPaSWAS: Python-based multi-core CPU and GPU sequence alignmentCited by: 12
Author(s): Sven Warris, N. Roshan N. Timal, Marcel Kempenaar, Arne M. Poortinga, Henri van de Geest, Ana Lucia Vărbănescu, Jan-Peter Nap
Software Mentions: 6
Published: over 6 years ago
10.1371/journal.pone.0003415
Gene Expression Profiling of Two Distinct Neuronal Populations in the Rodent Spinal CordCited by: 10
Author(s): Jesper Ryge, Ann-Charlotte Westerdahl, Preben Alstrøm, Ole Kiehn
Software Mentions: 6
Published: over 15 years ago
10.1371/journal.pone.0025279
GENE-Counter: A Computational Pipeline for the Analysis of RNA-Seq Data for Gene Expression DifferencesCited by: 62
Author(s): Jason S. Cumbie, Jeffrey A. Kimbrel, Yanming Di, Daniel W. Schafer, Larry J. Wilhelm, Samuel E. Fox, Christopher Sullivan, Aron D. Curzon, James C. Carrington, Todd C. Mockler, Jeff H. Chang
Software Mentions: 6
Published: over 12 years ago
10.1371/journal.pone.0251354
Altering mammalian transcription networking with ADAADi: An inhibitor of ATP-dependent chromatin remodelingCited by: 3
Author(s): Ramalingam Radhakrishnan, Upasana Bedi Chanana, Saddam Hussain, Soni Sharma, Kaveri Goel, Deepa Bisht, Ketki Patne, Pynskhem Bok Swer, Joel W. Hockensmith, Rohini Muthuswami
Software Mentions: 6
Published: about 3 years ago
10.1111/febs.13690
Structural and kinetic studies on RosA, the enzyme catalysing the methylation of 8-demethyl-8-amino-<scp>d</scp> -riboflavin to the antibiotic roseoflavinCited by: 13
Author(s): Chanakan Tongsook, M. Uhl, Frank Jankowitsch, Matthias Mack, Karl Gruber, Peter Macheroux
Software Mentions: 6
Published: about 8 years ago
10.3389/fgene.2021.647653
DysPIA: A Novel Dysregulated Pathway Identification Analysis MethodCited by: 1
Author(s): Limei Wang, Weixin Xie, Kongning Li, Zhenzhen Wang, Xia Li, Weixing Feng, Li Jin
Software Mentions: 6
Published: almost 3 years ago
10.3390/genes10100734
Developmental and Molecular Changes Underlying the Vernalization-Induced Transition to Flowering in Aquilegia coerulea (James)Cited by: 4
Author(s): Bharti Sharma, Timothy A. Batz, Rakesh Kaundal, Elena M. Kramer, Uriah R. Sanders, Valerie J. Mellano, Naveen Duhan, Rousselene B. Larson
Software Mentions: 6
Published: over 4 years ago
10.1186/1745-6150-7-44
Harnessing the complexity of gene expression data from cancer: from single gene to structural pathway methodsCited by: 21
Author(s): Frank Emmert‐Streib, Shailesh Tripathi, Ricardo de Matos Simoes
Software Mentions: 6
Published: over 12 years ago
10.12688/f1000research.6157.2
ViennaNGS: A toolbox for building efficient next- generation sequencing analysis pipelinesCited by: 21
Author(s): Michael T. Wolfinger, Jörg Fallmann, Florian Eggenhofer, Fabian Amman
Software Mentions: 6
Published: almost 9 years ago
10.3390/genes11121465
Plant TDP1 (Tyrosyl-DNA Phosphodiesterase 1): A Phylogenetic Perspective and Gene Expression Data MiningCited by: 2
Author(s): Giacomo Mutti, Alessandro Raveane, Andrea Pagano, Francesco Bertolini, Ornella Semino, Alma Balestrazzi, Anca Macovei
Software Mentions: 6
Published: over 3 years ago
10.1371/journal.pone.0012657
A Comprehensive and Universal Method for Assessing the Performance of Differential Gene Expression AnalysesCited by: 13
Author(s): Mikhail G. Dozmorov, Joel M. Guthridge, Robert E. Hurst, Igor Dozmorov
Software Mentions: 6
Published: over 13 years ago
10.1371/journal.pgen.1008905
Active transcription and Orc1 drive chromatin association of the AAA+ ATPase Pch2 during meiotic G2/prophaseCited by: 5
Author(s): Richard Silva, María Ascensión Villar-Fernández, Gerben Vader
Software Mentions: 6
Published: almost 4 years ago
10.1371/journal.pone.0086536
Dual Targeting of MEK and PI3K Pathways Attenuates Established and Progressive Pulmonary FibrosisCited by: 22
Author(s): Satish K. Madala, Ramakrishna Edukulla, Mukta Phatak, Stephanie Schmidt, Cynthia Davidson, Thomas H. Acciani, Thomas R. Korfhagen, Mario Medvedovic, Timothy D. Le Cras, Kimberly Wagner, William D. Hardie
Software Mentions: 6
Published: over 10 years ago
10.1038/s41598-018-22488-2
Profiles of miRNA Isoforms and tRNA Fragments in Prostate CancerCited by: 55
Author(s): Rogan Magee, Aristeidis G. Telonis, Phillipe Loher, Eric Londin, Isidore Rigoutsos
Software Mentions: 6
Published: about 6 years ago
10.3390/genes11060655
Transcriptional Basis for Differential Thermosensitivity of Seedlings of Various Tomato GenotypesCited by: 5
Author(s): Yangjie Hu, Sotirios Fragkostefanakis, Enrico Schleiff, Stefan Simm
Software Mentions: 6
Published: almost 4 years ago
10.1371/journal.pone.0164542
IGSA: Individual Gene Sets Analysis, including Enrichment and ClusteringCited by: 3
Author(s): Lingxiang Wu, Xiujie Chen, Denan Zhang, Wubing Zhang, Lei Liu, Hongzhe Ma, Jingbo Yang, Hongbo Xie, Bo Liu, Qing Jin
Software Mentions: 6
Published: over 7 years ago
10.1534/g3.117.300152
Heterogeneous Patterns of Genetic Diversity and Differentiation in European and Siberian Chiffchaff (<i>Phylloscopus collybita abietinus/P. tristis</i>)Cited by: 4
Author(s): Venkat Talla, Faheema Kalsoom, Daria Shipilina, И. М. Марова, Niclas Backström
Software Mentions: 6
Published: over 6 years ago
10.18632/oncotarget.22942
S-adenosyl-methionine (SAM) alters the transcriptome and methylome and specifically blocks growth and invasiveness of liver cancer cellsCited by: 33
Author(s): Yan Wang, Zhong Sheng Sun, Moshe Szyf
Software Mentions: 6
Published: over 6 years ago
10.1371/journal.pone.0015581
Therapeutic Implications of GIPC1 Silencing in CancerCited by: 21
Author(s): Thomas Chittenden, Jane Pak, Renee Rubio, Hai‐Ling Margaret Cheng, Kristina M. Holton, Niall Prendergast, Vladimir Glinskii, Yi Cai, Aedín C. Culhane, Stefan Bentink, Mathew Schwede, Jessica C. Mar, Eleanor Howe, Martin J. Aryee, Răzvan Sultana, Anthony A. Lanahan, Jennifer Taylor, Chris Holmes, William C. Hahn, Jean J. Zhao, J. Dirk Iglehart, John Quackenbush
Software Mentions: 6
Published: over 13 years ago
10.12688/f1000research.28608.2
ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy frameworkCited by: 6
Author(s): Subina Mehta, Marie Crane, Emma Leith, Bérénice Batut, Saskia Hiltemann, Magnus Ø. Arntzen, Benoît J. Kunath, Phillip B. Pope, Francesco Delogu, Ray Sajulga, Praveen Kumar, James E. Johnson, Timothy J. Griffin, Pratik Jagtap
Software Mentions: 6
Published: about 3 years ago
10.1101/2020.07.19.210955
Interferons and viruses induce a novel primate-specific isoform dACE2 and not the SARS-CoV-2 receptor ACE2Cited by: 19
Author(s): Olusegun O. Onabajo, Abdul Rouf Banday, Wusheng Yan, Adeola Obajemu, Megan L. Stanifer, Deanna M. Santer, Óscar Flórez-Vargas, Helen Piontkivska, Joselin M. Vargas, Carmon Kee, D. Lorne Tyrrell, Juan L. Mendoza, Steeve Boulant, Ludmila Prokunina‐Olsson
Software Mentions: 6
Published: almost 4 years ago
10.1371/journal.pone.0147426
Transcriptomic Profile of Whole Blood Cells from Elderly Subjects Fed Probiotic Bacteria Lactobacillus rhamnosus GG ATCC 53103 (LGG) in a Phase I Open Label StudyCited by: 16
Author(s): Gloria Solano‐Aguilar, Aleksey Molokin, Christine Botelho, Anne‐Maria Fiorino, Bryan T. Vinyard, Robert Li, Celine Chen, Joseph F. Urban, Harry Dawson, Irina Andreyeva, Miriam Haverkamp, Patricia L. Hibberd
Software Mentions: 6
Published: over 8 years ago
10.1186/s13072-018-0250-9
Chromatin changes in Anopheles gambiae induced by Plasmodium falciparum infectionCited by: 29
Author(s): José Luis Ruiz, Rakiswendé Serge Yerbanga, Thierry Léfèvre, Jean-Bosco Ouédraogo, Victor G. Corcés, Elena Gómez-Díaz
Software Mentions: 6
Published: over 5 years ago
10.1155/2014/248090
MultiRankSeq: Multiperspective Approach for RNAseq Differential Expression Analysis and Quality ControlCited by: 49
Author(s): Yan Guo, Shilin Zhao, Fei Ye, Quanhu Sheng, Yu Shyr
Software Mentions: 6
Published: over 10 years ago
10.3389/fvets.2021.733357
Chytridiomycosis Outbreak in a Chilean Giant Frog (Calyptocephalella gayi) Captive Breeding Program: Genomic Characterization and Pathological FindingsCited by: 5
Author(s): Mario Alvarado‐Rybak, Paz Acuña, Alexandra Peñafiel‐Ricaurte, Thomas R. Sewell, Simon J. O’Hanlon, Matthew C. Fisher, Andrés Valenzuela‐Sánchez, Andrew A. Cunningham, Claudio Soto‐Azat
Software Mentions: 6
Published: over 2 years ago
10.1128/mBio.02079-16
Merkel Cell Polyomavirus Exhibits Dominant Control of the Tumor Genome and Transcriptome in Virus-Associated Merkel Cell CarcinomaCited by: 87
Author(s): Gabriel J. Starrett, Christina Marcelus, Paul G. Cantalupo, Joshua P. Katz, Jingwei Cheng, Keiko Akagi, Manisha Thakuria, Guilherme Rabinowits, Linda C. Wang, David E. Symer, James M. Pipas, Reuben S. Harris, James A. DeCaprio
Software Mentions: 5
Published: about 7 years ago
10.1093/bioinformatics/btt016
Grape RNA-Seq analysis pipeline environmentCited by: 28
Author(s): David G. Knowles, Maik Röder, Angelika Merkel, Roderic Guigó
Software Mentions: 5
Published: over 11 years ago
10.1111/eva.12278
Patterns of differential gene expression in adult rotation‐resistant and wild‐type western corn rootworm digestive tractsCited by: 10
Author(s): Chia‐Ching Chu, Jorge A. Zavala, Joseph L. Spencer, M. Curzi, Christopher J. Fields, Jenny Drnevich, Blair D. Siegfried, Manfredo J. Seufferheld
Software Mentions: 5
Published: almost 9 years ago
10.1371/journal.pgen.1008261
Restricted and non-essential redundancy of RNAi and piRNA pathways in mouse oocytesCited by: 26
Author(s): Eliška Táborská, Josef Pasulka, Radek Malı́k, Filip Horvat, Irena Jenickova, Zoe Jelić Matošević, Petr Svoboda
Software Mentions: 5
Published: over 4 years ago
10.3389/fbioe.2020.598392
Phenotypic and Genomic Analysis of Clostridium beijerinckii NRRL B-598 Mutants With Increased Butanol ToleranceCited by: 6
Author(s): Maryna Vasylkivska, Barbora Branská, Karel Sedlář, Katerina Jureckova, Ivo Provazník, Petra Patáková
Software Mentions: 5
Published: over 3 years ago
10.1093/bioinformatics/btv634
EMDomics: a robust and powerful method for the identification of genes differentially expressed between heterogeneous classesCited by: 54
Author(s): Sheida Nabavi, Daniel Schmolze, Mayinuer Maitituoheti, Sadhika Malladi, Andrew H. Beck
Software Mentions: 5
Published: over 8 years ago
10.3389/fgene.2019.00772
Polycystic Ovary Syndrome: Novel and Hub lncRNAs in the Insulin Resistance-Associated lncRNA–mRNA NetworkCited by: 22
Author(s): Jun Zhao, Jiayu Huang, Xue Geng, Weiwei Chu, Shang Li, Zi‐Jiang Chen, Yanzhi Du
Software Mentions: 5
Published: over 4 years ago
10.1371/journal.pone.0206844
Clustering-local-unique-enriched-signals (CLUES) promotes identification of novel regulators of ES cell self-renewal and pluripotencyCited 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.0101374
Assessment of the Impact of Using a Reference Transcriptome in Mapping Short RNA-Seq ReadsCited by: 21
Author(s): Shanrong Zhao
Software Mentions: 5
Published: almost 10 years ago
10.6026/97320630013327
Robust Feature Selection Approach for Patient Classification using Gene Expression DataCited by: 6
Author(s): Shahjaman, Nishith Kumar, Shakil Ahmed, AnjumanAra Begum, S. M. Shahinul Islam, Md. Nurul Haque Mollah
Software Mentions: 5
Published: over 6 years ago
10.3389/fgene.2021.695124
Folate Deficiency Triggers the Abnormal Segregation of a Region With Large Cluster of CG-Rich Trinucleotide Repeats on Human Chromosome 2Cited by: 1
Author(s): Lorenza Garribba, Ivan Vogel, Mads Lerdrup, Marisa M Gonçalves Dinis, Liqun Ren, Ying Liu
Software Mentions: 5
Published: almost 3 years ago
10.1186/s13293-015-0056-4
Spatial sexual dimorphism of X and Y homolog gene expression in the human central nervous system during early male developmentCited by: 24
Author(s): Martin M. Johansson, E. Lundin, Xiaoyan Qian, Mohammadreza Mirzazadeh, Jonatan Halvardson, Elisabeth Darj, Lars Feuk, Mats Nilsson, Elena Jazin
Software Mentions: 5
Published: over 8 years ago
10.1084/jem.20171738
A broad atlas of somatic hypermutation allows prediction of activation-induced deaminase targetsCited by: 75
Author(s): Ángel F. Álvarez-Prado, Pablo Pérez-Durán, Arantxa Pérez-García, Alberto Benguría, Carlos Torroja, Virginia G. de Yébenes, Almudena R. Ramiro
Software Mentions: 5
Published: over 6 years ago
10.1111/jfb.14349
Identification of male heterogametic sex‐determining regions on the Atlantic herring <scp><i>Clupea harengus</i></scp> genomeCited by: 5
Author(s): Sunnvør í Kongsstovu, Hans Atli Dahl, Hannes Gislason, Eydna í Homrum, Jan Arge Jacobsen, Paul Flicek, Svein‐Ole Mikalsen
Software Mentions: 5
Published: almost 4 years ago
10.1038/s41598-017-03478-2
Diet-induced reconstruction of mucosal microbiota associated with alterations of epithelium lectin expression and regulation in the maintenance of rumen homeostasisCited by: 5
Author(s): Hong Shen, Zhongyan Lu, Zhihui Xu, Zongzhuan Shen
Software Mentions: 5
Published: almost 7 years ago
10.1371/journal.pone.0229502
A background correction method to compensate illumination variation in hyperspectral imagingCited by: 6
Author(s): Jonghee Yoon, Alexandru Grigoroiu, Sarah E. Bohndiek
Software Mentions: 5
Published: about 4 years ago
10.1371/journal.pcbi.0030026
Functional Impact of Missense Variants in BRCA1 Predicted by Supervised LearningCited by: 56
Author(s): Rachel Karchin, Alvaro N.A. Monteiro, Sean V. Tavtigian, Marcelo A. Carvalho, Andrej S̆ali
Software Mentions: 5
Published: over 17 years ago
10.1371/journal.pone.0092663
Towards Decrypting Cryptobiosis—Analyzing Anhydrobiosis in the Tardigrade Milnesium tardigradum Using Transcriptome SequencingCited by: 48
Author(s): Chong Wang, Markus A. Grohme, Brahim Mali, Ralph O. Schill, Marcus Frohme
Software Mentions: 5
Published: about 10 years ago
10.1371/journal.pone.0123658
A Powerful Statistical Approach for Large-Scale Differential Transcription AnalysisCited by: 4
Author(s): Ying Tan, Anita M. Chandler, Arindam Chaudhury, Joel R. Neilson
Software Mentions: 5
Published: about 9 years ago
10.1038/s41598-018-37679-0
Acidogenesis, solventogenesis, metabolic stress response and life cycle changes in Clostridium beijerinckii NRRL B-598 at the transcriptomic levelCited by: 46
Author(s): Petra Patáková, Barbora Branská, Karel Sedlář, Maryna Vasylkivska, Katerina Jureckova, Jan Kolek, Pavlína Koščová, Ivo Provazník
Software Mentions: 5
Published: over 5 years ago
10.1038/s41598-020-61158-0
Combining short and long read sequencing to characterize antimicrobial resistance genes on plasmids applied to an unauthorized genetically modified BacillusCited by: 46
Author(s): Bas Berbers, Assia Saltykova, Cristina Garcı́a-Graells, Patrick Philipp, F Arella, Kathleen Marchal, Raf Winand, Kevin Vanneste, Nancy Roosens, Sigrid C. J. De Keersmaecker
Software Mentions: 5
Published: about 4 years ago