cran: SAM | Projects | Ecosyste.ms: Papers

10.7554/eLife.46566

The transcription factor odd-paired regulates temporal identity in transit-amplifying neural progenitors via an incoherent feed-forward loop
Cited by: 29
Author(s): Merve Deniz Abdusselamoglu, Elif Eroğlu, Thomas R Burkard, Juergen A. Knoblich
Software Mentions: 4
Published: about 7 years ago

10.1186/s12859-016-1312-2

InDel marker detection by integration of multiple softwares using machine learning techniques
Cited by: 8
Author(s): Jin Yang, Xinyi Shi, Lun Hu, Daipeng Luo, Jing Peng, Shengwu Xiong, Fankai Kong, Baohui Liu, Xiaohui Yuan
Software Mentions: 4
Published: over 9 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: almost 12 years ago

10.7554/eLife.51109

Herpes simplex viral nucleoprotein creates a competitive transcriptional environment facilitating robust viral transcription and host shut off
Cited by: 47
Author(s): Sarah E Dremel, Neal A. DeLuca
Software Mentions: 4
Published: almost 7 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 9 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

10.1186/1471-2105-15-198

CIRCUS: a package for Circos display of structural genome variations from paired-end and mate-pair sequencing data
Cited by: 35
Author(s): Delphine Naquin, Yves d’Aubenton-Carafa, Claude Thermes, Maud Silvain
Software Mentions: 4
Published: about 12 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: about 14 years ago

10.1186/1471-2164-15-982

Retinal transcriptome profiling at transcription start sites: a cap analysis of gene expression early after axonal injury
Cited by: 19
Author(s): Masayuki Yasuda, Yuji Tanaka, Koji M. Nishiguchi, Morin Ryu, S. Tsuda, Kouichi Maruyama, Toru Nakazawa
Software Mentions: 4
Published: over 11 years ago

10.1186/1471-2105-11-465

Parallel multiplicity and error discovery rate (EDR) in microarray experiments
Cited by: 4
Author(s): Wayne Xu, Clay J. Carter
Software Mentions: 4
Published: almost 16 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 7 years ago

10.1186/1471-2105-8-446

Novel definition files for human GeneChips based on GeneAnnot
Cited by: 110
Author(s): Francesco Ferrari, Stefania Bortoluzzi, Alessandro Coppe, Alexandra Sirota, Marilyn Safran, Michael Shmoish, Sérgio Ferrari, Doron Lancet, Gian Antonio Danieli, Silvio Bicciato
Software Mentions: 4
Published: over 18 years ago

10.1186/1471-2105-12-468

openBIS: a flexible framework for managing and analyzing complex data in biology research
Cited by: 105
Author(s): Angela Bauch, Izabela Adamczyk, Piotr Buczek, Franz-Josef Elmer, Kaloyan Enimanev, Pawel Glyzewski, Manuel Kohler, Tomasz Pylak, Andreas Quandt, Chandrasekhar Ramakrishnan, Christian Beisel, Lars Malmström, Ruedi Aebersold, Bernd Rinn
Software Mentions: 4
Published: over 14 years ago

10.1186/1471-2164-11-365

Transcriptional regulation of gene expression clusters in motor neurons following spinal cord injury
Cited by: 39
Author(s): Jesper Ryge, Ole Winther, Jacob Wienecke, Albin Sandelin, Ann-Charlotte Westerdahl, Hans Hultborn, Ole Kiehn
Software Mentions: 4
Published: over 16 years ago

10.7554/eLife.36666

Neolithic and medieval virus genomes reveal complex evolution of hepatitis B
Cited by: 94
Author(s): Ben Krause‐Kyora, Julian Susat, Felix M. Key, Denise Kühnert, Esther Bosse, Alexander Immel, Christoph Rinne, Sabin-Christin Kornell, Diego Yepes, Sören Franzenburg, Henrike O. Heyne, Thomas Meier, Sandra Lösch, Harald Meller, Susanne Friederich, Nicole Nicklisch, Kurt W. Alt, Stefan Schreiber, Andreas Tholey, Alexander Herbig, Almut Nebel, Johannes Krause
Software Mentions: 4
Published: about 8 years ago

10.18632/aging.102754

The whole transcriptome regulation as a function of mitochondrial polymorphisms and aging in Caenorhabditis elegans
Cited by: 9
Author(s): Yuanjian Song, Yuechen Wang, Ying Liu, Liang Wang, WenDa Zhang, Jing Cheng, Yushan Zhu, Haoyu Zhang, Qiang Zhang, Haichen Niu, Yingwei Zheng, Mengyu Liang, Mengqiong Deng, Hao Shi, Hao Wang, Fang Zhang
Software Mentions: 4
Published: over 6 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

10.1186/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: about 6 years ago

10.1186/1471-2105-11-408

Comparison study of microarray meta-analysis methods
Cited by: 85
Author(s): Anna Campain, Jean Yee Hwa Yang
Software Mentions: 4
Published: almost 16 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: about 8 years ago

10.7554/eLife.60833

Novel LOTUS-domain proteins are organizational hubs that recruit C. elegans Vasa to germ granules
Cited by: 9
Author(s): Patricia Giselle Cipriani, Olivia Bay, John Zinno, Michelle Gutwein, Hin Hark Gan, Vinay K. Mayya, George Chung, Jia‐Xuan Chen, Hala Fahs, Yu Guan, Thomas F. Duchaîne, Matthias Selbach, Fabio Piano, Kristin C. Gunsalus
Software Mentions: 4
Published: about 5 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 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: over 6 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 12 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: almost 11 years ago

10.1186/1471-2164-12-S3-S9

UASIS: Universal Automatic SNP Identification System
Cited by: 5
Author(s): Danny Chiang Choon Poo, Shaojiang Cai, James T. L. Mah
Software Mentions: 4
Published: over 15 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 9 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: over 5 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: about 10 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: about 8 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: almost 9 years ago

10.1371/journal.pone.0045084

A Peak-Clustering Method for MEG Group Analysis to Minimise Artefacts Due to Smoothness
Cited by: 5
Author(s): Jessica R. Gilbert, Laura Shapiro, Gareth R. Barnes
Software Mentions: 4
Published: almost 14 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: almost 16 years ago

10.1128/mSphere.00231-18

Kinome Expansion in the Fusarium oxysporum Species Complex Driven by Accessory Chromosomes
Cited by: 28
Author(s): Gregory A. DeIulio, Li Guo, Yong Zhang, Jonathan M. Goldberg, H. Corby Kistler, Lijun Ma
Software Mentions: 4
Published: about 8 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: almost 5 years ago

10.1186/1471-2105-5-197

Cited by: 43
Author(s): Sara Cheek, Yuan Qi, S. Sri Krishna, Lisa N. Kinch, Nick V. Grishin
Software Mentions: 4
Published: over 22 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

10.1371/journal.pone.0255952

Vegan vs. omnivore diets paradox: A whole-metagenomic approach for defining metabolic networks during the race in ultra-marathoners- a before and after study design
Cited by: 1
Author(s): Aslı Devrim-Lanpir, Havvanur Yoldaş İlktaç, Katharina Wirnitzer, Lee Hill, Thomas Rosemann, Beat Knechtle
Software Mentions: 4
Published: almost 5 years ago

10.1371/journal.pone.0100250

Novel Method for Analysis of Allele Specific Expression in Triploid Oryzias latipes Reveals Consistent Pattern of Allele Exclusion
Cited by: 8
Author(s): Tzintzuni Garcia, Isa Matos, Yingjia Shen, Vagmita Pabuwal, M. M. Coelho, Yuko Wakamatsu, Manfred Schartl, Ronald B. Walter
Software Mentions: 4
Published: about 12 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: over 14 years ago

10.1371/journal.pone.0117818

mRNA Profiling Reveals Determinants of Trastuzumab Efficiency in HER2-Positive Breast Cancer
Cited by: 33
Author(s): Silvia von der Heyde, Sven Wagner, Czerny Alexander, M. Nietert, Fabian Ludewig, Gabriela Salinas-Riester, Dorit Arlt, Tim Beißbarth
Software Mentions: 4
Published: over 11 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: almost 14 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: 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: over 6 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/s41598-020-60595-1

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

10.1186/s12885-021-08218-4

MACE-Seq-based coding RNA and TrueQuant-based small RNA profile in breast cancer: tumor-suppressive miRNA-1275 identified as a novel marker
Cited by: 5
Author(s): Sevan Omer Majed, Suhad Asad Mustafa
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0102398

JAGuaR: Junction Alignments to Genome for RNA-Seq Reads
Cited by: 51
Author(s): Yaron S.N. Butterfield, Maayan Kreitzman, Nina Thiessen, Richard Corbett, Yisu Li, Johnson Pang, P. Yussanne, Steven J.M. Jones, İnanç Birol
Software Mentions: 4
Published: almost 12 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

10.1038/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

10.1038/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

10.1186/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: over 11 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

10.1007/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: almost 6 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 7 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 6 years ago

10.7554/eLife.21052

Embryonic origin of adult stem cells required for tissue homeostasis and regeneration
Cited by: 66
Author(s): Erin L. Davies, Kai Y. Lei, Christopher Seidel, Amanda E Kroesen, Sean A. McKinney, Longhua Guo, Sofia Robb, E. J. Ross, Kirsten Gotting, Alejandro Sánchez Alvarado
Software Mentions: 4
Published: over 9 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: over 5 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: almost 15 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

10.1186/2041-1480-5-42

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

10.1186/1471-2164-15-1081

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: over 11 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: almost 6 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 16 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

10.1186/1471-2105-9-164

A comprehensive re-analysis of the Golden Spike data: Towards a benchmark for differential expression methods
Cited by: 32
Author(s): Richard D. Pearson
Software Mentions: 4
Published: over 18 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: over 9 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: over 15 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

10.1111/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: over 5 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: about 10 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: almost 12 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: over 15 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/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

10.7717/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: almost 8 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: over 13 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: almost 10 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

10.1038/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: about 9 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: almost 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

10.1186/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/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/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

10.1186/1471-2105-9-548

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/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: over 10 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: about 5 years ago

10.3390/vaccines5040037

Elucidating the Role of Host Long Non-Coding RNA during Viral Infection: Challenges and Paths Forward
Cited by: 8
Author(s): David J. Lemler, Hayden Brochu, Fang Yang, Erin Harrell, Xinxia Peng
Software Mentions: 4
Published: almost 9 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: almost 9 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

10.1186/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

10.3389/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

10.1186/1471-2105-12-139

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: about 15 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

10.1074/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: about 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: over 8 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: almost 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: over 6 years ago

Projects: cran: SAM

Science Score: 85/100

Bonuses:

Penalties:

Papers Mentioning SAM 4,566