cran: SAM | Projects | Ecosyste.ms: Papers

10.1186/1471-2164-14-425

Rainbow: a tool for large-scale whole-genome sequencing data analysis using cloud computing
Cited by: 47
Author(s): Shanrong Zhao, Kurt Prenger, Lance Smith, Thomas Messina, Huiying Fan, Edward P. Jaeger, S. A. Stephens
Software Mentions: 4
Published: over 13 years ago

10.1155/2015/760423

HBS-Tools for Hairpin Bisulfite Sequencing Data Processing and Analysis
Cited by: 5
Author(s): Miao‐Kun Sun, Karthik Raja Velmurugan, David Keimig, Hehuang Xie
Software Mentions: 4
Published: over 10 years ago

10.1038/s41598-020-70757-w

Circadian regulation of chemotherapy-induced peripheral neuropathic pain and the underlying transcriptomic landscape
Cited by: 17
Author(s): Hee Kee Kim, Sun Yeul Lee, Nobuya Koike, Eunju Kim, Marvin Wirianto, Mark J. Burish, Kazuhiro Yagita, Hyun Kyoung Lee, Zheng Chen, Jin Mo Chung, Salahadin Abdi, Seung Hee Yoo
Software Mentions: 4
Published: almost 6 years ago

10.1038/srep29434

Tumour sampling method can significantly influence gene expression profiles derived from neoadjuvant window studies
Cited by: 13
Author(s): Dominic Pearce, Laura Arthur, Arran Turnbull, Lorna Renshaw, Victoria Sabine, Jeremy Thomas, John M.S. Bartlett, J. Michael Dixon, Andrew H. Sims
Software Mentions: 4
Published: almost 10 years ago

10.1038/srep26846

Transcriptome analysis of human ageing in male skin shows mid-life period of variability and central role of NF-κB
Cited by: 48
Author(s): Daniel Haustead, Andrew Stevenson, Vishal Saxena, Fiona Marriage, Martin J Firth, Robyn C Silla, Lisa W. Martin, Katharine F. Adcroft, Suzanne Rea, Philip J. Day, Phillip E. Melton, Fiona Wood, Mark W. Fear
Software Mentions: 4
Published: about 10 years ago

10.1186/s12864-015-1635-9

Identification of a putative quantitative trait nucleotide in guanylate binding protein 5 for host response to PRRS virus infection
Cited by: 72
Author(s): James E. Koltes, Eric R. Fritz-Waters, Christopher J. Eisley, Igseo Choi, Hua Bao, Arun Kommadath, Nick V. L. Serão, Nicholas Boddicker, Samuel M. Abrams, Martine Schroyen, Hyelee Loyd, Christopher K. Tuggle, Graham Plastow, Leluo Guan, Paul Stothard, Joan K. Lunney, Peng Liu, Susan Carpenter, Raymond R. R. Rowland, Jack C. M. Dekkers, James M. Reecy
Software Mentions: 4
Published: about 11 years ago

10.1186/s12859-017-1897-0

Identification of streptococcal small RNAs that are putative targets of RNase III through bioinformatics analysis of RNA sequencing data
Cited by: 6
Author(s): Ethan Rath, Stephanie Pitman, Kyu Hong Cho, Yongsheng Bai
Software Mentions: 4
Published: over 8 years ago

10.1038/s41597-020-00642-8

Large eQTL meta-analysis reveals differing patterns between cerebral cortical and cerebellar brain regions
Cited by: 65
Author(s): Solveig K. Sieberts, Thanneer M. Perumal, Minerva M. Carrasquillo, Mariet Allen, Joseph S. Reddy, Gabriel E. Hoffman, Kristen K. Dang, John N. Calley, Philip J. Ebert, James A. Eddy, X Wang, Anna K. Greenwood, Sara Mostafavi, Schahram Akbarian, Jaroslav Bendl, Michael S. Breen, Kristen J. Brennand, Leanne Brown, Andrew Browne, Joseph D. Buxbaum, Alex Charney, Andrew Chess, Lizette Couto, Greg Crawford, Olivia Devillers, Bernie Devlin, Amanda Dobbyn, Enrico Domenici, Michele Filosi, Elie Flatow, Nancy Francoeur, John F. Fullard, Sergio Espeso-Gil, Kiran Girdhar, Attila Gulyás-Kovács, Ruben C. Gur, Chang Gyu Hahn, Vahram Haroutunian, Mads E. Hauberg, Laura Huckins, Rivka Jacobov, Yonghua Jiang, Jessica Johnson, Bibi Kassim, Y Kim, Lambertus Klei, Robin Kramer, Mario Lauria, Thomas Lehner, David A. Lewis, Barbara K. Lipska, Kelsey S. Montgomery, Royce Park, Chaggai Rosenbluh, Panos Roussos, Douglas M. Ruderfer, Geetha Senthil, Hardik Shah, Laura Sloofman, Song Li, Eli Stahl, Patrick F. Sullivan, Roberto Visintainer, J Wang, Y C Wang, Jennifer Wiseman, Eva Xia, W Zhang, Elizabeth Zharovsky, Laura Addis, Sadiya N. Addo, David Airey, Matthias Arnold, David A. Bennett, Ying Bi, Knut Biber, Colette Blach, E Bradhsaw, Patrick McKinley Brennan, R Canet-Aviles, Shaolong Cao, A Cavalla, Yooree Chae, W W Chen, Joyce Cheng, David A. Collier, Jeffrey L. Dage, Eric B. Dammer, J Davis, J Davis, Derek Drake, Duc Duong, Brian J. Eastwood, Michelle E. Ehrlich, Benjamin M. Ellingson, Brett W. Engelmann, Sahar Esmaeeli-Nieh, Daniel Felsky, Cory C. Funk, Chris Gaiteri
Software Mentions: 4
Published: over 5 years ago

10.1038/srep13364

Chimeric peptide constructs comprising linear B-cell epitopes: application to the serodiagnosis of infectious diseases
Cited by: 26
Author(s): Yao Lu, Zhong Li, Huan Teng, Hongke Xu, Songnan Qi, Jianan He, Dayong Gu, Qijun Chen, Hongwei Ma
Software Mentions: 4
Published: almost 11 years ago

10.1186/1476-4598-6-64

Molecular signatures define two main classes of meningiomas
Cited by: 65
Author(s): Lucia Helena de Carvalho, Иван Смирнов, Gilson S. Baía, Zora Modrušan, Justin S. Smith, Peter Jun, J Costello, Michael W. McDermott, Scott R. VandenBerg, Anita Lal
Software Mentions: 4
Published: over 18 years ago

10.1074/mcp.RA119.001392

Cathepsin L Regulates Metabolic Networks Controlling Rapid Cell Growth and Proliferation
Cited by: 7
Author(s): Tommy Weiss-Sadan, Gal Itzhak, Farnusch Kaschani, Zhanru Yu, Mohamed Mahameed, Adi Anaki, Yael Ben-Nun, Emmanuelle Merquiol, Boaz Tirosh, Benedikt M. Kessler, Markus Kaiser, Galia Blum
Software Mentions: 4
Published: almost 7 years ago

10.1038/bcj.2016.77

lncRNA profiling in early-stage chronic lymphocytic leukemia identifies transcriptional fingerprints with relevance in clinical outcome
Cited by: 40
Author(s): Domenica Ronchetti, Martina Manzoni, Luca Agnelli, Cristina Vinci, Sonia Fabris, Giovanna Cutrona, Serena Matis, Monica Colombo, S. Galletti, Elisa Taìana, Anna Grazia Recchia, Sabrina Bossio, Massimo Gentile, Caterina Musolino, Francesco Di Raimondo, Andrea Grilli, Silvio Bicciato, Agostino Cortelezzi, Pierfrancesco Tassone, Fortunato Morabito, Manlio Ferrarini, Antonino Neri
Software Mentions: 4
Published: over 9 years ago

10.1186/gb-2005-6-6-r54

Cited by: 148
Author(s): Nils Rostoks, Justin O. Borevitz, Pete E. Hedley, Joanne Russell, Sharon Mudie, Jenny Morris, Linda Cardle, David Marshall, Robbie Waugh
Software Mentions: 4
Published: over 21 years ago

10.1093/biostatistics/kxu038

Joint analysis of differential gene expression in multiple studies using correlation motifs
Cited by: 29
Author(s): Yingying Wei, Toyoaki Tenzen, Hongkai Ji
Software Mentions: 4
Published: almost 12 years ago

10.1186/1471-2105-6-79

Cited by: 189
Author(s): Voichita D. Marinescu, Isaac S. Kohane, Alberto Riva
Software Mentions: 4
Published: over 21 years ago

10.1186/s12711-016-0257-2

Fine mapping of a QTL on bovine chromosome 6 using imputed full sequence data suggests a key role for the group-specific component (GC) gene in clinical mastitis and milk production
Cited by: 31
Author(s): Harald Olsen, Tim Martin Knutsen, Anna Lewandowska-Sabat, Harald Grove, Torfinn Nome, Mathias Tiedemann Svendsen, Mariann Árnyasi, Marte Sodeland, Kristil Kindem Sundsaasen, Sandra Rinne Dahl, B. Heringstad, Hanne Hellerud Hansen, I. Olsaker, Matthew Kent, Sigbjørn Lien
Software Mentions: 4
Published: over 9 years ago

10.1186/2041-1480-5-42

Executing SADI services in Galaxy
Cited by: 7
Author(s): Mikel Egaña Aranguren, Alejandro Rodríguez Gonzàlez, Mark D. Wilkinson
Software Mentions: 4
Published: over 12 years ago

10.1534/g3.117.300550

Genetic Loci Governing Androgenic Capacity in Perennial Ryegrass (Lolium perenne L.)
Cited by: 8
Author(s): Rachel F. Begheyn, Steven Yates, Timothy Sykes, Bruno Studer
Software Mentions: 4
Published: about 8 years ago

10.1186/1471-2164-13-131

VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data
Cited by: 31
Author(s): Elena S. Peterson, Lee Ann McCue, Alexandra C. Schrimpe‐Rutledge, Jeffrey L. Jensen, Hyunjoo Walker, Markus A. Kobold, Samantha R Webb, Samuel H. Payne, Charles Ansong, Joshua N. Adkins, W. Roger Cannon, Bobbie-Jo M. Webb-Robertson
Software Mentions: 4
Published: about 14 years ago

10.1186/1471-2105-7-359

Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data
Cited by: 321
Author(s): Ian B. Jeffery, Desmond G. Higgins, Aedín C. Culhane
Software Mentions: 4
Published: almost 20 years ago

10.1534/g3.119.400777

rmtA-Dependent Transcriptome and Its Role in Secondary Metabolism, Environmental Stress, and Virulence inAspergillus flavus
Cited by: 5
Author(s): Timothy Satterlee, Sarah Entwistle, Yanbin Yin, J. W. Cary, Matthew D. Lebar, Liliana Losada, Ana M. Calvo
Software Mentions: 4
Published: over 6 years ago

10.3390/genes9040180

Non-Pleiotropic Coupling of Daily and Seasonal Temporal Isolation in the European Corn Borer
Cited by: 29
Author(s): Rebecca C. Levy, Genevieve M. Kozak, Erik B. Dopman
Software Mentions: 4
Published: about 8 years ago

10.1186/1471-2105-9-548

GeneChaser: Identifying all biological and clinical conditions in which genes of interest are differentially expressed
Cited by: 34
Author(s): Rong Chen, Rohan Mallelwar, Ajit Thosar, Shivkumar Venkatasubrahmanyam, Atul J. Butte
Software Mentions: 4
Published: over 17 years ago

10.1186/1471-2105-7-335

AMDA: an R package for the automated microarray data analysis
Cited by: 35
Author(s): Mattia Pelizzola, Norman Pavelka, Maria Foti, Paola Ricciardi‐Castagnoli
Software Mentions: 4
Published: almost 20 years ago

10.3389/fpls.2021.632033

The Genomic Impact of Mycoheterotrophy in Orchids
Cited by: 8
Author(s): Marcin Jąkalski, Julita Minasiewicz, José Caïus, Michał May, Marc‐André Selosse, Étienne Delannoy
Software Mentions: 4
Published: almost 5 years ago

10.1186/1471-2164-11-23

Transcriptomic profiling of bovine IVF embryos revealed candidate genes and pathways involved in early embryonic development
Cited by: 37
Author(s): Wen Huang, Brian S. Yandell, Hasan Khatib
Software Mentions: 4
Published: over 16 years ago

10.1534/g3.116.026914

Environmental Association Analyses Identify Candidates for Abiotic Stress Tolerance inGlycine soja, the Wild Progenitor of Cultivated Soybeans
Cited by: 39
Author(s): Justin Anderson, Thomas J. Y. Kono, Robert M. Stupar, Michael B. Kantar, Peter L. Morrell
Software Mentions: 4
Published: about 10 years ago

10.3390/genes10070554

Chromatin Interaction Analysis with Updated ChIA-PET Tool (V3)
Cited by: 17
Author(s): Guoliang Li, Tongkai Sun, Huidan Chang, Liuyang Cai, Hong Pan, Qiangwei Zhou
Software Mentions: 4
Published: almost 7 years ago

10.1186/1471-2105-5-195

Cited by: 20
Author(s): Joachim Theilhaber, Anatoly Ulyanov, Anish Malanthara, Jack Cole, Dapeng Xu, Robert Nahf, Michael Heuer, Christoph Brockel, Steven Bushnell
Software Mentions: 4
Published: over 22 years ago

10.3389/fpls.2016.01651

Modeling the Morphometric Evolution of the Maize Shoot Apical Meristem
Cited by: 10
Author(s): Samuel Leiboff, Christopher K. DeAllie, Michael J. Scanlon
Software Mentions: 4
Published: over 9 years ago

10.3389/fpls.2021.664250

New Insights Into Lignification via Network and Multi-Omics Analyses of Arogenate Dehydratase Knock-Out Mutants in Arabidopsis thaliana
Cited by: 1
Author(s): Kim Hixson, Joaquim V. Marques, Jason P. Wendler, Jason McDermott, Karl K. Weitz, Therese RW Clauss, Matthew E. Monroe, Ronald J. Moore, Joseph N. Brown, Mary Lipton, Callum J. Bell, Ljiljana Paša‐Tolić, Laurence Davin, Norman Lewis
Software Mentions: 4
Published: about 5 years ago

10.1093/bioinformatics/btaa950

RepeatFS: a file system providing reproducibility through provenance and automation
Cited by: 0
Author(s): Anthony Westbrook, Elizabeth Varki, W. Kelley Thomas
Software Mentions: 4
Published: over 5 years ago

10.1186/1471-2164-11-26

1,25 dihydroxyvitamin D-mediated orchestration of anticancer, transcript-level effects in the immortalized, non-transformed prostate epithelial cell line, RWPE1
Cited by: 80
Author(s): Pavlo L. Kovalenko, Zhentao Zhang, Min Cui, S. Clinton, James C. Fleet
Software Mentions: 4
Published: over 16 years ago

10.1093/bioinformatics/bts458

MolBioLib: a C++11 framework for rapid development and deployment of bioinformatics tasks
Cited by: 9
Author(s): Toshiro K. Ohsumi, Mark Borowsky
Software Mentions: 4
Published: almost 14 years ago

10.1186/1471-2105-7-533

Effect of various normalization methods on Applied Biosystems expression array system data
Cited by: 44
Author(s): Cátálin Bárbácioru, Yulei Wang, Roger D. Canales, Yongming Sun, David Keys, Felix Hon-Wai Chan, Karen Poulter, Raymond R. Samaha
Software Mentions: 4
Published: over 19 years ago

10.1021/acssynbio.0c00637

Construction of DNA Tools for Hyperexpression in Marchantia Chloroplasts
Cited by: 8
Author(s): Eftychios Frangedakis, Fernando Guzman Chavez, Marius Rebmann, Kasey Markel, Ying Yu, Artemis Perraki, Sze Wai Tse, Yang Liu, Jenna Rever, Susanna Sauret-Güeto, Bernard Goffinet, Harald Schneider, Jim Haseloff
Software Mentions: 4
Published: almost 5 years ago

10.1155/2019/2725192

In Silico Integration Approach Reveals Key MicroRNAs and Their Target Genes in Follicular Thyroid Carcinoma
Cited by: 10
Author(s): Shengqing Hu, Yunfei Liao, Juan Zheng, Luoning Gou, Anita Regmi, Mohammad Ishraq Zafar, Lulu Chen
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.pcbi.1004884

A Network Biology Approach Identifies Molecular Cross-Talk between Normal Prostate Epithelial and Prostate Carcinoma Cells
Cited by: 5
Author(s): Víctor Treviño, Alberto Cassese, Zsuzsanna Nagy, Xiaodong Zhuang, John Herbert, Philipp Antzack, Kim Clarke, Nick Davies, Ayesha Rahman, Moray J. Campbell, Michele Guindani, Roy Bicknell, Marina Vannucci, Francesco Falciani
Software Mentions: 4
Published: about 10 years ago

10.3389/fgene.2021.731515

PanSVR: Pan-Genome Augmented Short Read Realignment for Sensitive Detection of Structural Variations
Cited by: 1
Author(s): Gaoyang Li, Tao Jiang, Junyi Li, Yadong Wang
Software Mentions: 4
Published: almost 5 years ago

10.1002/emmm.201201823

Functional genomics identifies five distinct molecular subtypes with clinical relevance and pathways for growth control in epithelial ovarian cancer
Cited by: 172
Author(s): Tuan Zea Tan, Qing Hao Miow, Ruby Yun‐Ju Huang, Ming Keong Wong, Jieru Ye, Jieying Amelia Lau, Meng Wu, Luqman Hakim Bin Abdul Hadi, Richie Soong, Mahesh Choolani, Ben Davidson, Jahn M. Nesland, Ling Zhi Wang, Noriomi Matsumura, Masaki Mandai, Ikuo Konishi, Boon Cher Goh, Jeffrey T. Chang, Jean Paul Thiery, Seiichi Mori
Software Mentions: 4
Published: about 13 years ago

10.1038/s41598-020-58969-6

Dramatic HIV DNA degradation associated with spontaneous HIV suppression and disease-free outcome in a young seropositive woman following her infection
Cited by: 2
Author(s): Philippe Colson, Catherine Dhiver, Catherine Tamalet, Jérémy Delerce, Olga O. Glazunova, Maxime Gaudin, Anthony Levasseur, Didier Raoult
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-019-44542-3

Plasmodium pseudo-Tyrosine Kinase-like binds PP1 and SERA5 and is exported to host erythrocytes
Cited by: 9
Author(s): Bénédicte Gnangnon, Aline Fréville, Kátia Cailliau, Catherine Leroy, Caroline De Witte, David Tulasne, Alain Martoriarti, Vincent Jung, Ida Chiara Guerrera, Sabrina Marion, Jamal Khalife, Christine Pierrot
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.pone.0089445

RNA CoMPASS: A Dual Approach for Pathogen and Host Transcriptome Analysis of RNA-Seq Datasets
Cited by: 38
Author(s): Guiyin Xu, Michael J. Strong, Michelle Lacey, Carl Baribault, Erik K. Flemington, Christopher M. Taylor
Software Mentions: 4
Published: over 12 years ago

10.1038/s41598-020-60595-1

Prediction of Alzheimer’s disease using blood gene expression data
Cited by: 55
Author(s): Taesic Lee, Hyunju Lee
Software Mentions: 4
Published: over 6 years ago

10.1002/ece3.5604

Contribution of rare and common species to subterranean species richness patterns
Cited by: 28
Author(s): Petra Bregović, Cene Fišer, Maja Zagmajster
Software Mentions: 4
Published: over 6 years ago

10.1002/ece3.7037

FastD: Fast detection of insecticide target‐site mutations and overexpressed detoxification genes in insect populations from RNA‐Seq data
Cited by: 1
Author(s): Longfei Chen, Kun Lang, Mei Yang, Zhanghong Shi, Kang He, Fei Li, Huamei Xiao, Gōngyín Yè, Zhaojun Han
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-018-26854-y

Transcriptome analysis in Hevea brasiliensis latex revealed changes in hormone signalling pathways during ethephon stimulation and consequent Tapping Panel Dryness
Cited by: 23
Author(s): Pascal Montoro, Shizhou Wu, Bénédicte Favreau, Eva Herlinawati, Cécile Labrune, Marie‐Laure Martin‐Magniette, Stéphanie Pointet, Maryannick Rio, Julie Leclercq, Sigit Ismawanto, Kuswanhadi
Software Mentions: 4
Published: about 8 years ago

10.1371/journal.pone.0090706

A Bulk Segregant Gene Expression Analysis of a Peach Population Reveals Components of the Underlying Mechanism of the Fruit Cold Response
Cited by: 36
Author(s): Clara Pons, Cristina Martí, Javier Forment, Carlos H. Crisosto, Abhaya M. Dandekar, Antonio Granell
Software Mentions: 4
Published: about 12 years ago

10.1186/s13058-019-1159-3

On-treatment biomarkers can improve prediction of response to neoadjuvant chemotherapy in breast cancer
Cited by: 32
Author(s): Richard J. Bownes, Arran Turnbull, Carlos Martínez-Pérez, David Cameron, Andrew H. Sims, Olga Oikonomidou
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41598-017-08386-z

Species distribution models of two critically endangered deep-sea octocorals reveal fishing impacts on vulnerable marine ecosystems in central Mediterranean Sea
Cited by: 37
Author(s): Valentina Lauria, Germana Garofalo, Fabio Fiorentino, D. Massi, Giacomo Milisenda, Stefano Piraino, Tommaso Russo, Michele Gristina
Software Mentions: 4
Published: almost 9 years ago

10.3389/fgene.2018.00328

Co-expression Network Analysis of Biomarkers for Adrenocortical Carcinoma
Cited by: 37
Author(s): Lushun Yuan, Guofeng Qian, Liang Chen, Chin‐Lee Wu, Dong Han, Yu Xiao, Xinghuan Wang
Software Mentions: 4
Published: almost 8 years ago

10.1007/s00251-014-0819-9

Different binding motifs of the celiac disease-associated HLA molecules DQ2.5, DQ2.2, and DQ7.5 revealed by relative quantitative proteomics of endogenous peptide repertoires
Cited by: 79
Author(s): Elin Bergseng, Siri Dørum, Magnus Ø. Arntzen, Morten Nielsen, Ståle Nygård, Søren Buus, Gustavo Souza, Ludvig M. Sollid
Software Mentions: 4
Published: over 11 years ago

10.1111/imb.12688

Jekyll or Hyde? The genome (and more) of Nesidiocoris tenuis, a zoophytophagous predatory bug that is both a biological control agent and a pest
Cited by: 11
Author(s): Kim Ferguson, Sako Visser, Martina Dalíková, Irena Provazníková, Alberto Urbaneja, František Marec, John H. Werren, Bas J. Zwaan, Bart A. Pannebakker, Eveline C. Verhulst
Software Mentions: 4
Published: over 5 years ago

10.3389/fmicb.2018.00280

Physiological and Metagenomic Characterizations of the Synergistic Relationships between Ammonia- and Nitrite-Oxidizing Bacteria in Freshwater Nitrification
Cited by: 14
Author(s): Mingwei Cai, Siu-Kin Ng, Chee Kent Lim, Hsu Feng Lu, Yangyang Jia, Patrick K. H. Lee
Software Mentions: 4
Published: over 8 years ago

10.3390/life11080862

Comparative Analysis of PacBio and Oxford Nanopore Sequencing Technologies for Transcriptomic Landscape Identification of Penaeus monodon
Cited by: 6
Author(s): Zulema Udaondo, Kanchana Sittikankaew, Tanaporn Uengwetwanit, Thidathip Wongsurawat, Chutima Sonthirod, Piroon Jenjaroenpun, Wirulda Pootakham, Nitsara Karoonuthaisiri, Intawat Nookaew
Software Mentions: 4
Published: almost 5 years ago

10.1186/gm551

Early aberrant DNA methylation events in a mouse model of acute myeloid leukemia
Cited by: 28
Author(s): Miriam Sonnet, Rainer Claus, Natália Becker, Manuela Zucknick, Jana Petersen, Daniel B. Lipka, Christopher C. Oakes, Mindaugas Andrulis, Amelie Lier, Michael D. Milsom, Tania Witte, Lei Gu, Soo Zin Kim-Wanner, Peter Schirmacher, Michael Wulfert, Norbert Gattermann, Michael Lübbert, Frank Rosenbauer, Michael Rehli, Lars Bullinger, Dieter Weichenhan, Christoph Plass
Software Mentions: 4
Published: over 12 years ago

10.1186/gb-2013-14-11-r125

Transcriptomic classification of genetically engineered mouse models of breast cancer identifies human subtype counterparts
Cited by: 176
Author(s): Adam D. Pfefferle, Jason I. Herschkowitz, Jerry Usary, J. Chuck Harrell, Benjamin T. Spike, Jessica R. Adams, Maria I. Torres-Arzayus, Myles Brown, Sean E. Egan, Geoffrey M. Wahl, Jeffrey M. Rosen, Charles M. Perou
Software Mentions: 4
Published: over 13 years ago

10.1186/s13073-014-0059-5

A systems biology approach reveals a link between systemic cytokines and skeletal muscle energy metabolism in a rodent smoking model and human COPD
Cited by: 21
Author(s): Peter K. Davidsen, John Herbert, Philipp Antczak, Kim Clarke, Elisabet Ferrer, Víctor I. Peinado, C. González, Josep Roca, Stuart Egginton, Joan Albert Barberà, Francesco Falciani
Software Mentions: 4
Published: almost 12 years ago

10.1371/journal.pone.0103441

Fast and Sensitive Alignment of Microbial Whole Genome Sequencing Reads to Large Sequence Datasets on a Desktop PC: Application to Metagenomic Datasets and Pathogen Identification
Cited by: 9
Author(s): Lőrinc Sándor Pongor, Roberto Vera, Balázs Ligeti
Software Mentions: 4
Published: almost 12 years ago

10.1038/s41598-020-61057-4

The ankyrin repeat gene family in Capsicum spp: Genome-wide survey, characterization and gene expression profile
Cited by: 19
Author(s): Carlos Lopez-Ortiz, Yadira Peña-Garcia, Purushothaman Natarajan, Menuka Bhandari, Venkata Lakshmi Abburi, Sunil Dutta, Lav K. Yadav, John R. Stommel, Padma Nimmakayala, Umesh K. Reddy
Software Mentions: 4
Published: about 6 years ago

10.1038/s41598-018-19554-0

Human migration and the spread of malaria parasites to the New World
Cited by: 65
Author(s): Priscila T. Rodrigues, Hugo O. Valdivia, Thaís Crippa de Oliveira, João M. P. Alves, Ana Maria Ribeiro de Castro Duarte, Crispim Cerutti-Junior, Julyana Cerqueira Buery, Cristiana Ferreira Alves de Brito, Júlio César de Souza, Zelinda Maria Braga Hirano, Marina Galvão Bueno, José Luiz Catão‐Dias, Rosely S. Malafronte, Simone Ladeia‐Andrade, Toshihiro Mita, Ana María Santamaría, Igor Calzada, Indah Setyawati Tantular, Fumihiko Kawamoto, Leonie R. J. Raijmakers, Ivo Müeller, M. Andreína Pacheco, Ananías A. Escalante, Ingrid Felger, Marcelo U. Ferreira
Software Mentions: 4
Published: over 8 years ago

10.1186/s13059-014-0555-3

Determining the quality and complexity of next-generation sequencing data without a reference genome
Cited by: 27
Author(s): Seyed Yahya Anvar, Lusine Khachatryan, Martijn Vermaat, M.A. van Galen, Irina Pulyakhina, Yavuz Ariyürek, Ken Kraaijeveld, Johan T. den Dunnen, Peter de Knijff, Peter A C ‘t Hoen, Jeroen F. J. Laros
Software Mentions: 4
Published: over 11 years ago

10.1371/journal.pone.0023581

Strategy to Find Molecular Signatures in a Small Series of Rare Cancers: Validation for Radiation-Induced Breast and Thyroid Tumors
Cited by: 16
Author(s): Nicolas Ugolin, Catherine Ory, Emilie Lefèvre, Nora Benhabilès, Paul Hofman, Martin Schlumberger, Sylvie Chevillard
Software Mentions: 4
Published: almost 15 years ago

10.1371/journal.pone.0038946

Profound Effect of Profiling Platform and Normalization Strategy on Detection of Differentially Expressed MicroRNAs – A Comparative Study
Cited by: 51
Author(s): Swanhild U. Meyer, Sebastian Kaiser, Carola Wagner, Christian Thirion, Michael W. Pfaffl
Software Mentions: 4
Published: almost 14 years ago

10.1186/gb-2014-15-1-r4

Global regulation of mRNA translation and stability in the early Drosophila embryo by the Smaug RNA-binding protein
Cited by: 93
Author(s): Li-Nan Chen, Jason G Dumelie, Xiao Li, Matthew Hong Kei Cheng, Zhiyong Yang, John Laver, Najeeb U. Siddiqui, J. Timothy Westwood, Quaid Morris, Howard D. Lipshitz, Craig Smibert
Software Mentions: 4
Published: over 12 years ago

10.1093/bib/bbw020

A review of bioinformatic pipeline frameworks
Cited by: 155
Author(s): Jeremy Leipzig
Software Mentions: 4
Published: about 10 years ago

10.3389/fmicb.2020.00495

Regulation of Bottromycin Biosynthesis Involves an Internal Transcriptional Start Site and a Cluster-Situated Modulator
Cited by: 7
Author(s): Natalia M. Vior, Eva Cea-Torrescassana, Tom H. Eyles, Govind Chandra, Andrew W. Truman
Software Mentions: 4
Published: about 6 years ago

10.1186/s13059-017-1290-3

A tandem simulation framework for predicting mapping quality
Cited by: 14
Author(s): Ben Langmead
Software Mentions: 4
Published: almost 9 years ago

10.1155/2013/270362

A Case Report and Genetic Characterization of a Massive Acinic Cell Carcinoma of the Parotid with Delayed Distant Metastases
Cited by: 5
Author(s): Anthony C. Nichols, Michelle Chan-Seng-Yue, John Yoo, Sumit Agrawal, Maud H.W. Starmans, Daryl Waggott, Nicholas J. Harding, Samuel Dowthwaite, David A. Palma, Kevin Fung, Bret Wehrli, Danielle MacNeil, Philippe Lambin, Eric Winquist, James Koropatnick, Joe S. Mymryk, Paul C. Boutros, John W. Barrett
Software Mentions: 4
Published: over 13 years ago

10.1371/journal.pone.0084212

Genome Wide Expression Profiling during Spinal Cord Regeneration Identifies Comprehensive Cellular Responses in Zebrafish
Cited by: 74
Author(s): Subhra Prakash Hui, Dhriti Sengupta, Serene Gek Ping Lee, Triparna Sen, Sudip Kundu, Sinnakaruppan Mathavan, Sukla Ghosh
Software Mentions: 4
Published: over 12 years ago

10.1186/gm122

Using transcriptomics to identify and validate novel biomarkers of human skeletal muscle cancer cachexia
Cited by: 105
Author(s): Nathan Stephens, Iain J. Gallagher, Olav Rooyackers, Richard J.E. Skipworth, Ben Tan, Troels Marstrand, James A. Ross, Denis C. Guttridge, Lars Lundell, Kenneth C. H. Fearon, James A. Timmons
Software Mentions: 4
Published: over 16 years ago

10.1371/journal.pone.0137171

Discovery of a Novel Immune Gene Signature with Profound Prognostic Value in Colorectal Cancer: A Model of Cooperativity Disorientation Created in the Process from Development to Cancer
Cited by: 22
Author(s): Ning An, Xiaoyu Shi, Yueming Zhang, Ning Lv, Feng Li, Di Xia, Ning Han, Guiqi Wang, Shujun Cheng, Kaitai Zhang
Software Mentions: 4
Published: almost 11 years ago

10.1038/s41598-017-17298-x

NSD1 inactivation defines an immune cold, DNA hypomethylated subtype in squamous cell carcinoma
Cited by: 59
Author(s): Kevin Brennan, June Ho Shin, Joshua K. Tay, Marcos Prunello, Andrew J. Gentles, John B. Sunwoo, Olivier Gevaert
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pgen.1007332

Genome-wide detection of conservative site-specific recombination in bacteria
Cited by: 37
Author(s): Ognjen Sekulović, Elizabeth M. Garrett, Jacob Bourgeois, Rita Tamayo, Aimee Shen, Andrew Camilli
Software Mentions: 4
Published: about 8 years ago

10.1186/s13059-021-02375-2

Highly recurrent CBS epimutations in gastric cancer CpG island methylator phenotypes and inflammation
Cited by: 8
Author(s): Nisha Padmanabhan, Kie Kyon Huang, Arnoud Boot, Kevin Lim, Supriya Srivastava, Shuwen Chen, Zhiyuan Wu, Hyung-O K Lee, Vineeth T. Mukundan, Charlene Chan, Yarn Kit Chan, Xuewen Ong, Jason J. Pitt, Zul Fazreen Adam Isa, Manjie Xing, Ming Hui Lee, Angie Lay Keng Tan, Shamaine Ho Wei Ting, Micah A. Luftig, Dennis Kappei, Warren D. Kruger, Jun Bian, Ying Swan Ho, Ming Teh, Steve Rozen, Patrick Tan
Software Mentions: 4
Published: about 5 years ago

10.1186/gb-2014-15-1-r11

dCLIP: a computational approach for comparative CLIP-seq analyses
Cited by: 46
Author(s): Tao Wang, Yang Xie, Guanghua Xiao
Software Mentions: 4
Published: over 12 years ago

10.1371/journal.pone.0170540

Avian Species and Functional Diversity in Agricultural Landscapes: Does Landscape Heterogeneity Matter?
Cited by: 33
Author(s): Myung Bok Lee, James A. Martin
Software Mentions: 4
Published: over 9 years ago

10.26508/lsa.201900561

Refining the adipose progenitor cell landscape in healthy and obese visceral adipose tissue using single-cell gene expression profiling
Cited by: 40
Author(s): Dong Seong Cho, Bolim Lee, Jason D. Doles
Software Mentions: 4
Published: over 6 years ago

10.3389/fimmu.2018.01626

Transcriptomic Profiles of Senegalese Sole Infected With Nervous Necrosis Virus Reassortants Presenting Different Degree of Virulence
Cited by: 23
Author(s): Alejandro M. Labella, Esther García-Rosado, Isabel Bandı́n, Carlos P. Dopazo, Dolores Castro, M. Carmen Alonso, Juan J. Borrego
Software Mentions: 4
Published: almost 8 years ago

10.1038/s41598-017-02110-7

Revealing genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles under osmotic stress in Escherichia coli K-12 MG1655
Cited by: 31
Author(s): Sang Woo Seo, Ye Gao, Donghyuk Kim, Richard Szubin, Joseph Yang, Byung-Kwan Cho, Bernhard Ø. Palsson
Software Mentions: 4
Published: about 9 years ago

10.1038/s41598-017-04300-9

Altered miRNA expression network in locus coeruleus of depressed suicide subjects
Cited by: 59
Author(s): Bhaskar Roy, Qingzhong Wang, M. Palkóvits, Gábor Faludi, Yogesh K. Dwivedi
Software Mentions: 4
Published: almost 9 years ago

10.1371/journal.pone.0229606

Postprandial transfer of colostral extracellular vesicles and their protein and miRNA cargo in neonatal calves
Cited by: 13
Author(s): Benedikt Kirchner, Dominik Buschmann, Vijay Paul, Michael W. Pfaffl
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0132448

A Quantitative Profiling Tool for Diverse Genomic Data Types Reveals Potential Associations between Chromatin and Pre-mRNA Processing
Cited by: 5
Author(s): Isaac Kremsky, Nicolás Bellora, Eduardo Eyras
Software Mentions: 4
Published: almost 11 years ago

10.1038/s41598-019-49915-2

RNAseq analysis reveals drought-responsive molecular pathways with candidate genes and putative molecular markers in root tissue of wheat
Cited by: 52
Author(s): Mir Asif Iquebal, Pradeep Sharma, Rahul Singh Jasrotia, Sarika Jaiswal, Amandeep Kaur, Monika Saroha, U. B. Angadi, Sonia Sheoran, Rajender Singh, Gyanendra Singh, Anil Rai, Ruchi Tiwari, Dinesh Kumar
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0223397

Brief communication: Long-term absence of Langerhans cells alters the gene expression profile of keratinocytes and dendritic epidermal T cells
Cited by: 10
Author(s): Qingtai Su, Aurélie Bouteau, Jacob Cardenas, Uthra Balaji, Yuanyaun Wang, Cynthia Smitherman, Jin Gu, Botond Z. Igyártó
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0013169

Gene Expression Signature-Based Screening Identifies New Broadly Effective Influenza A Antivirals
Cited by: 58
Author(s): Laurence Josset, Julien Textoris, Béatrice Loriod, Olivier Ferraris, Vincent Moulès, Bruno Lina, Catherine Nguyen, Jean‐Jacques Diaz, Manuel Rosa‐Calatrava
Software Mentions: 4
Published: over 15 years ago

10.3389/fmicb.2019.01400

Complete Assembly of the Genome of an Acidovorax citrulli Strain Reveals a Naturally Occurring Plasmid in This Species
Cited by: 11
Author(s): Rongzhi Yang, Diego Santos-García, Francisco Pérez‐Montaño, Gustavo Mateus da Silva, Mei Zhao, Irene Jiménez‐Guerrero, Tally Rosenberg, Gong Chen, Inbar Plaschkes, Shai Morin, R. R. Walcott, Saul Burdman
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41598-019-40495-9

Differential gene expression induced by Verteporfin in endometrial cancer cells
Cited by: 8
Author(s): Lisa Bang, Venkata Ramesh Dasari, Dokyoon Kim, Radhika Gogoi
Software Mentions: 4
Published: about 7 years ago

10.1186/s12944-018-0915-1

Genome-wide identification and characterization of long non-coding RNAs during postnatal development of rabbit adipose tissue
Cited by: 19
Author(s): Guoze Wang, Kun Du, Shiyan Hu, Shiyi Chen, Xianbo Jia, Mingcheng Cai, Yu Shi, Jie Wang, Songjia Lai
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pgen.0030087

Whole-Genome Cartography of Estrogen Receptor α Binding Sites
Cited by: 414
Author(s): Chin-Yo Lin, Vinsensius B. Vega, Jane S. Thomsen, Tao Zhang, Say Li Kong, Ming Xie, King-Wah Chiu, Leonard Lipovich, Daniel H. Barnett, Fabio Stossi, A. Yeo, Joshy George, Vladimir A. Kuznetsov, Yew Kok Lee, Tze Howe Charn, Nallasivam Palanisamy, Lance D. Miller, Edwin Cheung, Benita S. Katzenellenbogen, Yijun Ruan, Guillaume Bourque, Chia Lin Wei, Edison T. Liu
Software Mentions: 4
Published: about 19 years ago

10.15252/embj.2018100003

A common molecular logic determines embryonic stem cell self‐renewal and reprogramming
Cited by: 31
Author(s): Sara‐Jane Dunn, Meng Amy Li, Elena Carbognin, Austin Smith, Graziano Martello
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-019-48692-2

Efficient and specific oligo-based depletion of rRNA
Cited by: 41
Author(s): Amelie J. Kraus, Benedikt G. Brink, T. Nicolai Siegel
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41598-019-40080-0

Morphological, genetic and epigenetic aspects of homoploid hybridization between Salvia officinalis L. and Salvia fruticosa Mill.
Cited by: 15
Author(s): Ivan Radosavljević, Sandro Bogdanović, Ferhat Celep, Maja Filipović, Zlatko Šatović, Boštjan Surina, Zlatko Liber
Software Mentions: 4
Published: over 7 years ago

10.1099/mgen.0.000039

Whole-genome sequencing investigation of animal-skin-drum-associated UK anthrax cases reveals evidence of mixed populations and relatedness to a US case
Cited by: 9
Author(s): Steven T. Pullan, Talima Pearson, Jennie Latham, Joanne Mason, Barry Atkinson, Nigel Silman, Chung K. Marston, Jason W. Sahl, Dawn N. Birdsell, Alex R. Hoffmaster, Paul Keim, Richard Vipond
Software Mentions: 4
Published: over 10 years ago

10.1371/journal.pone.0247028

How similar is “similar,” or what is the best measure of soil spectral and physiochemical similarity?
Cited by: 2
Author(s): Rong Zeng, J P Zhang, Kaiyong Cai, Weichang Gao, Wenjie Pan, Chaoying Jiang, P Y Zhang, Bing Wu, C H Wang, Xing Jin, Daixun Li
Software Mentions: 4
Published: about 5 years ago

10.3390/s21010163

Personality-Based Affective Adaptation Methods for Intelligent Systems
Cited by: 4
Author(s): Krzysztof Kutt, Dominika Drążyk, Szymon Bobek, Grzegorz J. Nalepa
Software Mentions: 4
Published: over 5 years ago

10.1128/mSystems.00044-18

A Prospective Metagenomic and Metabolomic Analysis of the Impact of Exercise and/or Whey Protein Supplementation on the Gut Microbiome of Sedentary Adults
Cited by: 127
Author(s): Owen Cronin, Wiley Barton, Peter Skuse, Nicholas Penney, Isabel García-Pérez, Eileen F. Murphy, Trevor Woods, Helena Nugent, Áine Fanning, Silvia Melgar, Éanna Falvey, Elaine Holmes, Paul D. Cotter, Órla O’Sullivan, Michael G. Molloy, Fergus Shanahan
Software Mentions: 4
Published: almost 8 years ago

10.1371/journal.pcbi.1009078

lra: A long read aligner for sequences and contigs
Cited by: 50
Author(s): Jimin Ren, Mark Chaisson
Software Mentions: 4
Published: almost 5 years ago

10.3390/nu9040407

Prenatal Exposure to a Maternal High-Fat Diet Affects Histone Modification of Cardiometabolic Genes in Newborn Rats
Cited by: 24
Author(s): Bijaya Upadhyaya, Tricia D. Larsen, Shivon Barwari, Eli J. Louwagie, Michelle Baack, Moul Dey
Software Mentions: 4
Published: about 9 years ago

10.1371/journal.pone.0223680

Comprehensive analysis of chromosomal mobile genetic elements in the gut microbiome reveals phylum-level niche-adaptive gene pools
Cited by: 51
Author(s): Xiaofang Jiang, Andrew Brantley Hall, Ramnik J. Xavier, Eric J. Alm
Software Mentions: 4
Published: over 6 years ago

Projects: cran: SAM

Science Score: 85/100

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Penalties:

Papers Mentioning SAM 4,566