cran: SAM | Projects | Ecosyste.ms: Papers

10.1093/bioinformatics/bty125

AltHapAlignR: improved accuracy of RNA-seq analyses through the use of alternative haplotypes
Cited by: 28
Author(s): Wanseon Lee, Katharine Plant, Peter Humburg, Julian C. Knight
Software Mentions: 4
Published: over 6 years ago

10.1007/s13205-020-02291-5

ddRAD-seq derived genome-wide SNPs, high density linkage map and QTLs for fruit quality traits in strawberry (Fragaria x ananassa)
Cited by: 3
Author(s): Sathishkumar Natarajan, Mohammad Rashed Hossain, Hoy‐Taek Kim, Denison Michael Immanuel Jesse, Mostari Jahan Ferdous, Hee-Jeong Jung, Jong-In Park, Ill Sup Nou
Software Mentions: 4
Published: over 4 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: about 8 years ago

10.18632/oncotarget.13025

Integrative analysis of DNA copy number, DNA methylation and gene expression in multiple myeloma reveals alterations related to relapse
Cited by: 10
Author(s): Patryk Krzemiński, Luis A. Corchete, Juan Luis Garcı́a, Lucía López-Corral, Encarnación Fermiñán, Ernesto Garcı́a, Ana A. Martín, Jesús M. Hernández-Rivas, Ramón García‐Sanz, Jesús F. San Miguel, Norma C. Gutiérrez
Software Mentions: 4
Published: about 8 years ago

10.1002/path.4886

Molecular classification of urothelial carcinoma: global mRNA classification versus tumour-cell phenotype classification
Cited by: 245
Author(s): Gottfrid Sjödahl, Pontus Eriksson, Fredrik Liedberg, Mattias Höglund
Software Mentions: 4
Published: over 7 years ago

10.1186/1471-2164-15-218

Deciphering gamma-decalactone biosynthesis in strawberry fruit using a combination of genetic mapping, RNA-Seq and eQTL analyses
Cited by: 60
Author(s): José F. Sánchez-Sevilla, Eduardo Cruz-Rus, Victoriano Valpuesta, Miguel A. Botella, Iraida Amaya
Software Mentions: 4
Published: over 10 years ago

10.1186/s12967-020-02372-2

Whole blood transcriptomic investigation identifies long non-coding RNAs as regulators in sepsis
Cited by: 38
Author(s): Lixin Cheng, Chuanchuan Nan, Lin Kang, Ning Zhang, Sheng Liu, Huaisheng Chen, Chengying Hong, Youlian Chen, Zhen Liang, Xueyan Liu
Software Mentions: 4
Published: over 4 years ago

10.18632/oncotarget.7442

Distinct lncRNA transcriptional fingerprints characterize progressive stages of multiple myeloma
Cited by: 75
Author(s): Domenica Ronchetti, Luca Agnelli, Elisa Taìana, S. Galletti, Martina Manzoni, Katia Todoerti, Pellegrino Musto, Francesco Strozzi, Antonino Neri
Software Mentions: 4
Published: almost 9 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: over 13 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: over 7 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: about 9 years ago

10.1186/1471-2164-13-619

Molecular characterisation of cell line models for triple-negative breast cancers
Cited by: 63
Author(s): Anita Grigoriadis, Alan Mackay, Elodie Noël, Pei Jun Wu, Rachael Natrajan, Jessica Frankum, Jorge S. Reis‐Filho, Andrew Tutt
Software Mentions: 4
Published: almost 13 years ago

10.3390/ijms21144865

Cytological and Gene Profile Expression Analysis Reveals Modification in Metabolic Pathways and Catalytic Activities Induce Resistance in Botrytis cinerea Against Iprodione Isolated From Tomato
Cited by: 4
Author(s): Ambreen Maqsood, Chaorong Wu, Sunny Ahmar, Haiyan Wu
Software Mentions: 4
Published: over 4 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: over 10 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: almost 5 years ago

10.1186/1471-2105-12-29

Investigating the effect of paralogs on microarray gene-set analysis
Cited by: 0
Author(s): Aline Faure, Cathal Seoighe, Nicola Mulder
Software Mentions: 4
Published: almost 14 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: over 12 years ago

10.3390/ijms21186762

Changes in Nuclear Shape and Gene Expression in Response to Simulated Microgravity Are LINC Complex-Dependent
Cited by: 13
Author(s): Srujana Neelam, Brian Richardson, Richard Barker, Ceasar Udave, Simon Gilroy, Mark J. Cameron, Howard G. Levine, Ye Zhang
Software Mentions: 4
Published: about 4 years ago

10.1128/mSystems.00980-20

Elucidation of Regulatory Modes for Five Two-Component Systems in Escherichia coli Reveals Novel Relationships
Cited by: 22
Author(s): Kumari Sonal Choudhary, Julia A. Kleinmanns, Katherine Decker, Anand V. Sastry, Ye Gao, Richard Szubin, Yara Seif, Bernhard Ø. Palsson
Software Mentions: 4
Published: almost 4 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: over 6 years ago

10.1186/s40246-015-0042-2

Performance evaluation of indel calling tools using real short-read data
Cited by: 76
Author(s): Mohammad Shabbir Hasan, Xiaowei Wu, Liqing Zhang
Software Mentions: 4
Published: over 9 years ago

10.7150/thno.45989

LncRNA CSMD1-1 promotes the progression of Hepatocellular Carcinoma by activating MYC signaling
Cited by: 22
Author(s): Ji Liu, Rui Xu, Shi-Juan Mai, Yu‐Shui Ma, Mei‐Yin Zhang, Ping‐Sheng Cao, Nuoqing Weng, Ruiqi Wang, Di Cao, Wei Wei, Rong Guo, Yaojun Zhang, Li Xu, Minshan Chen, Huizhong Zhang, Long Huang, Da Fu, Huiyun Wang
Software Mentions: 4
Published: almost 5 years ago

10.1186/s12859-017-1816-4

mmquant: how to count multi-mapping reads?
Cited by: 29
Author(s): Matthias Zytnicki
Software Mentions: 4
Published: about 7 years ago

10.1128/mBio.01060-17

Genome-Wide Sensitivity Analysis of the Microsymbiont <i>Sinorhizobium meliloti</i> to Symbiotically Important, Defensin-Like Host Peptides
Cited by: 47
Author(s): Markus F. F. Arnold, Mohammed Shabab, Jon Penterman, Kevin L. Boehme, Joel S. Griffitts, Graham C. Walker
Software Mentions: 4
Published: about 7 years ago

10.1186/s40246-016-0068-0

A comparative study of k-spectrum-based error correction methods for next-generation sequencing data analysis
Cited by: 18
Author(s): Isaac Akogwu, Nan Wang, Chaoyang Zhang, Ping Gong
Software Mentions: 4
Published: over 8 years ago

10.1186/1751-0473-7-10

PathNet: a tool for pathway analysis using topological information
Cited by: 62
Author(s): Bhaskar Dutta, Anders Wallqvist, Jaques Reifman
Software Mentions: 4
Published: about 12 years ago

10.1186/s13287-021-02601-5

Longitudinal clonal tracking in humanized mice reveals sustained polyclonal repopulation of gene-modified human-HSPC despite vector integration bias
Cited by: 0
Author(s): Gajendra W. Suryawanshi, Hubert Arokium, Sanggu Kim, Wannisa Khamaikawin, Samantha Lin, Saki Shimizu, Koollawat Chupradit, Yoojin Lee, Yiming Xie, Xin Guan, Vasantika Suryawanshi, Angela P. Presson, Dong-Sung An, Irvin S. Y. Chen
Software Mentions: 4
Published: about 3 years ago

10.1371/journal.pone.0198120

Spatial patterns of medium and large size mammal assemblages in várzea and terra firme forests, Central Amazonia, Brazil
Cited by: 31
Author(s): Guilherme Costa Alvarenga, Emiliano Esterci Ramalho, Fabrício Beggiato Baccaro, Daniel Gomes da Rocha, Jefferson Ferreira-Ferreira, Paulo Estefano Dineli Bobrowiec
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pone.0110134

Integrated Exon Level Expression Analysis of Driver Genes Explain Their Role in Colorectal Cancer
Cited by: 20
Author(s): Mohammad Azhar Aziz, Sathish Periyasamy, Zeyad Yousef, Ibrahim AlAbdulkarim, Majed Al Otaibi, Abdulaziz Alfahed, Glowi Alasiri
Software Mentions: 4
Published: about 10 years ago

10.1186/s12864-015-1233-x

Sequence and analysis of a whole genome from Kuwaiti population subgroup of Persian ancestry
Cited by: 27
Author(s): Gaurav Thareja, Sumi Elsa John, Prashantha Hebbar, Kazem Behbehani, Thangavel Alphonse Thanaraj, Osama Alsmadi
Software Mentions: 4
Published: almost 10 years ago

10.1186/s12864-016-2524-6

Heritable gene expression differences between apomictic clone members in Taraxacum officinale: Insights into early stages of evolutionary divergence in asexual plants
Cited by: 16
Author(s): Julie Ferreira de Carvalho, Carla Oplaat, Nikolaos Pappas, Martijn F.L. Derks, Dick de Ridder, Koen J. F. Verhoeven
Software Mentions: 4
Published: over 8 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: almost 4 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: over 6 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: almost 5 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 4 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: over 5 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 5 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: over 5 years ago

10.1186/1471-2164-14-494

Cloud-based uniform ChIP-Seq processing tools for modENCODE and ENCODE
Cited by: 6
Author(s): Quang Trinh, Fei-Yang Arthur Jen, Ziru Zhou, Kar Ming Chu, Marc D. Perry, Ellen Kephart, Sergio Contrino, Peter Ruzanov, Lincoln Stein
Software Mentions: 4
Published: over 11 years ago

10.1186/s12859-015-0795-6

TOGGLE: toolbox for generic NGS analyses
Cited by: 20
Author(s): Cécile Monat, Christine Tranchant‐Dubreuil, Ayité Kougbeadjo, Cédric Farcy, Enrique Ortega-Abboud, Souhila Amanzougarene, Sébastien Ravel, Mawussé Agbessi, Julie Orjuela, Marilyne Summo, François Sabot
Software Mentions: 4
Published: about 9 years ago

10.1186/1471-2164-15-1081

Adaptive genomic structural variation in the grape powdery mildew pathogen, Erysiphe necator
Cited by: 137
Author(s): Laura M. Jones, Summaira Riaz, Abraham Morales‐Cruz, Katherine C. H. Amrine, Brianna McGuire, W. D. Gubler, Michael Walker, Dario Cantu
Software Mentions: 4
Published: almost 10 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: over 12 years ago

10.1186/1471-2164-12-402

BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons
Cited by: 2,222
Author(s): Nabil-Fareed Alikhan, Nicola K. Petty, Nouri L. Ben Zakour, Scott A. Beatson
Software Mentions: 4
Published: over 13 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: almost 7 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: over 6 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: over 4 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: over 17 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: over 7 years ago

10.1186/1471-2105-12-139

PeakRanger: A cloud-enabled peak caller for ChIP-seq data
Cited by: 146
Author(s): Xin Feng, Robert L. Grossman, Lincoln Stein
Software Mentions: 4
Published: over 13 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: over 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: over 7 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: almost 7 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: over 8 years ago

10.1186/1471-2164-11-138

Escherichia coli infection induces distinct local and systemic transcriptome responses in the mammary gland
Cited by: 114
Author(s): Simone Mitterhuemer, Wolfram Petzl, Stefan Krebs, Daniel Mehne, Andrea Klanner, Eckhard Wolf, Holm Zerbe, Helmut Blum
Software Mentions: 4
Published: over 14 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: over 8 years ago

10.1371/journal.pone.0215465

FDG PET based prediction of response in head and neck cancer treatment: Assessment of new quantitative imaging features
Cited by: 18
Author(s): Reinhard Beichel, Ethan Ulrich, Brian J. Smith, Christian Bauer, Bruce P. Brown, Thomas L. Casavant, John Sunderland, Michael M. Graham, John M. Buatti
Software Mentions: 4
Published: over 5 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: over 8 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: almost 7 years ago

10.18632/aging.101170

Metabolomic signature associated with reproduction-regulated aging in Caenorhabditis elegans
Cited by: 39
Author(s): Qin-Li Wan, Xiaohuo Shi, Jiangxin Liu, Aijun Ding, Yuan-Zhu Pu, Zhigang Li, Gui-Sheng Wu, Huai‐Rong Luo
Software Mentions: 4
Published: almost 8 years ago

10.1111/imb.12688

Jekyll or Hyde? The genome (and more) of <i>Nesidiocoris tenuis</i>, 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: almost 4 years ago

10.1186/s12864-016-2738-7

Structural and functional analysis of the finished genome of the recently isolated toxic Anabaena sp. WA102
Cited by: 22
Author(s): Nathan Brown, Robert F. Mueller, Jonathan W. Shepardson, Zachary C. Landry, Jeff Morré, Christoph Maier, F. Joan Hardy, Theo W. Dreher
Software Mentions: 4
Published: over 8 years ago

10.3390/plants9101355

Next Generation Sequencing Based Forward Genetic Approaches for Identification and Mapping of Causal Mutations in Crop Plants: A Comprehensive Review
Cited by: 36
Author(s): Parmeshwar K. Sahu, Richa Sao, Suvendu Mondal, Gautam Vishwakarma, Sudhir Kumar Gupta, Vinay Kumar, Sudhir Singh, Deepak Sharma, Bikram Das
Software Mentions: 4
Published: about 4 years ago

10.1186/1471-2164-12-5

The 'PUCE CAFE' Project: the First 15K Coffee Microarray, a New Tool for Discovering Candidate Genes correlated to Agronomic and Quality Traits
Cited by: 23
Author(s): Isabelle Privat, Amélie Bardil, Aureliano Bombarely, Dany Séverac, Christelle Le Dantec, Ivanna Fuentes, Lukas A. Mueller, Thierry Joët, David Pot, Séverine Foucrier, Stéphane Dussert, Thierry Leroy, Laurent Journot, Alexandre de Kochko, Claudine Campa, Marie‐Christine Combes, Philippe Lebailly, Benoît Bertrand
Software Mentions: 4
Published: almost 14 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: almost 10 years ago

10.7717/peerj.2478

Identify potential drugs for cardiovascular diseases caused by stress-induced genes in vascular smooth muscle cells
Cited by: 13
Author(s): Chien-Hung Huang, Jin-Shuei Ciou, Shun-Tsung Chen, Victor C. Kok, Yuan‐Chiang Chung, Jeffrey J. P. Tsai, Nilubon Kurubanjerdjit, Chi-Ying F. Huang, Ka-Lok Ng
Software Mentions: 4
Published: about 8 years ago

10.7717/peerj.2681

RGFA: powerful and convenient handling of assembly graphs
Cited by: 5
Author(s): Giorgio Gonnella, Stefan Kurtz
Software Mentions: 4
Published: about 8 years ago

10.3390/plants10020364

A Systems Biology Approach to Identify Essential Epigenetic Regulators for Specific Biological Processes in Plants
Cited by: 5
Author(s): Rachel M. McCoy, Russell Julian, Shoban R V Kumar, Rajeev Ranjan, Kranthi Varala, Ying Liu
Software Mentions: 4
Published: almost 4 years ago

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: almost 12 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: almost 9 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: about 4 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: almost 15 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: over 9 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: over 3 years ago

10.7717/peerj.5551

BioWorkbench: a high-performance framework for managing and analyzing bioinformatics experiments
Cited by: 11
Author(s): Maria Luiza Mondelli, Thiago Tavares Magalhães, Guilherme Loss, Michael Wilde, Ian Foster, Marta Mattoso, Daniel S. Katz, Hélio J. C. Barbosa, Ana Tereza Ribeiro de Vasconcelos, Kary Ocaña, Luiz M. R. Gadelha
Software Mentions: 4
Published: about 6 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: over 3 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: almost 11 years ago

10.1186/s12859-017-1849-8

MetaComp: comprehensive analysis software for comparative meta-omics including comparative metagenomics
Cited by: 11
Author(s): Peng Zhai, Longshu Yang, Xiao Guo, Zhe Wang, Jiangtao Guo, Xiaoqi Wang, Huaiqiu Zhu
Software Mentions: 4
Published: about 7 years ago

10.7717/peerj.606

Massively parallel read mapping on GPUs with theq-group index and PEANUT
Cited by: 5
Author(s): Johannes Köster, Sven Rahmann
Software Mentions: 4
Published: about 10 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: over 18 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: over 10 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: about 9 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: almost 16 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: over 18 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: almost 11 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: almost 20 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: almost 12 years ago

10.1186/1471-2164-12-589

Relative impact of key sources of systematic noise in Affymetrix and Illumina gene-expression microarray experiments
Cited by: 30
Author(s): Robert Kitchen, Victoria Sabine, Arthur A. Simen, JM Dixon, John M.S. Bartlett, Andrew H. Sims
Software Mentions: 4
Published: almost 13 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: over 5 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: about 5 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: almost 10 years ago

10.1186/s12859-021-04390-3

SamQL: a structured query language and filtering tool for the SAM/BAM file format
Cited by: 2
Author(s): Christopher T. Lee, Manolis Maragkakis
Software Mentions: 4
Published: about 3 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: almost 6 years ago

10.26508/lsa.201800283

Expanding the repertoire of glucocorticoid receptor target genes by engineering genomic response elements
Cited by: 13
Author(s): Verena Thormann, Laura V. Glaser, Maika C. Rothkegel, Marina Borschiwer, Melissa Bothe, Alisa Fuchs, Sebastiaan H. Meijsing
Software Mentions: 4
Published: over 5 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: over 3 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: about 3 years ago

10.1186/s12864-017-4391-1

Profiling the onset of somatic embryogenesis in Arabidopsis
Cited by: 37
Author(s): Enrico Magnani, José M. Jiménez‐Gómez, Ludivine Soubigou‐Taconnat, Loïc Lepiniec, Elisa Fiume
Software Mentions: 4
Published: almost 7 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: over 3 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: almost 15 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: almost 5 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: almost 11 years ago

Projects: cran: SAM

Papers Mentioning SAM 4,566