cran: SAM | Projects | Ecosyste.ms: Papers

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

10.1186/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 12 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/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

10.1371/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: about 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

10.1186/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

10.3389/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: about 8 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: about 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: 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

10.3389/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: about 8 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

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 14 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: over 7 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

10.7717/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 10 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

10.7717/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

10.7717/peerj.2681

RGFA: powerful and convenient handling of assembly graphs
Cited by: 5
Author(s): Giorgio Gonnella, Stefan Kurtz
Software Mentions: 4
Published: almost 10 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 11 years ago

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 8 years ago

10.3390/cells10061291

Innate and Adaptive Immune Genes Associated with MERS-CoV Infection in Dromedaries
Cited by: 6
Author(s): Sara Lado, Jean P. Elbers, Martin Plášil, Tom Loney, Pia Weidinger, Jeremy V. Camp, Jolanta Kolodziejek, Ján Futas, Dafalla A. Kannan, Pablo Orozco‐terWengel, Petr Hořín, Norbert Nowotny, Pamela A. Burger
Software Mentions: 4
Published: over 5 years ago

10.1016/j.stem.2019.09.008

Sphingolipid Modulation Activates Proteostasis Programs to Govern Human Hematopoietic Stem Cell Self-Renewal
Cited by: 71
Author(s): Stephanie Z. Xie, Laura García‐Prat, Véronique Voisin, Raffaele Ferrari, Olga I. Gan, Elvin Wagenblast, Kerstin B. Kaufmann, Andy G.X. Zeng, Shin‐ichiro Takayanagi, Ishita Patel, Esther K. Lee, Joseph Jargstorf, Gareth D. Holmes, Guy Romm, Kristele Pan, Michelle Shoong, Aditi Vedi, Chiara Luberto, Mark D. Minden, Gary D. Bader, Elisa Laurenti, John E. Dick
Software Mentions: 4
Published: almost 7 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 6 years ago

10.3390/cancers13051079

EphB6 Regulates TFEB-Lysosomal Pathway and Survival of Disseminated Indolent Breast Cancer Cells
Cited by: 10
Author(s): Manuela Zangrossi, Patrizia Romani, Probir Chakravarty, Colin D.H. Ratcliffe, Steven Hooper, Martina Dori, Mattia Forcato, Silvio Bicciato, Sirio Dupont, Erik Sahai, Marco Montagner
Software Mentions: 4
Published: over 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: almost 6 years ago

10.1016/j.cell.2018.11.041

The Implication of Early Chromatin Changes in X Chromosome Inactivation
Cited by: 188
Author(s): J. Ż̷ylicz, Aurélie Bousard, Kristina Žumer, François Dossin, Eusra Mohammad, Simão Teixeira da Rocha, Björn Schwalb, Laurène Syx, Florent Dingli, Damarys Loew, Patrick Cramer, Edith Heard
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pone.0224644

Transcriptomic profiling of PBDE-exposed HepaRG cells unveils critical lncRNA- PCG pairs involved in intermediary metabolism
Cited by: 5
Author(s): Angela Zhang, Cindy Yanfei Li, Edward J. Kelly, Lianne Sheppard, Julia Yue Cui
Software Mentions: 4
Published: over 6 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

10.1128/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 6 years ago

10.1371/journal.pone.0065598

diffReps: Detecting Differential Chromatin Modification Sites from ChIP-seq Data with Biological Replicates
Cited by: 292
Author(s): Li Shen, Ning‐Yi Shao, Xiaochuan Liu, Ian Maze, Jian Feng, Eric J. Nestler
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: 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: almost 5 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 10 years ago

10.1186/s13040-015-0052-6

DNA microarray integromics analysis platform
Cited by: 11
Author(s): Tomasz Waller, Tomasz Gubała, Krzysztof Sarapata, Monika Piwowar, Wiktor Jurkowski
Software Mentions: 4
Published: over 11 years ago

10.1371/journal.pone.0067134

Global Identification of EVI1 Target Genes in Acute Myeloid Leukemia
Cited by: 57
Author(s): Carolyn Glass, Charles A. Wuertzer, Xiaohui Cui, Yingtao Bi, Ramana V. Davuluri, Ying Yi Xiao, Michael P. Wilson, Kristina M. Owens, Yi Zhang, Archibald S. Perkins
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 9 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 6 years ago

10.1371/journal.pone.0126911

Recommendations for Accurate Resolution of Gene and Isoform Allele-Specific Expression in RNA-Seq Data
Cited by: 18
Author(s): David Wood, Kátia Nones, Anita L Steptoe, Angelika N. Christ, Ivon Harliwong, Felicity Newell, Timothy J. C. Bruxner, David Miller, Nicole Cloonan, Sean M. Grimmond
Software Mentions: 4
Published: over 11 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: over 8 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 7 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

10.1371/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: over 12 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 8 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

10.1371/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: about 5 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 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

10.1371/journal.pone.0206665

Identification of highly connected and differentially expressed gene subnetworks in metastasizing endometrial cancer
Cited by: 11
Author(s): Kanthida Kusonmano, Mari K. Halle, Elisabeth Wik, Erling A. Høivik, Camilla Krakstad, Karen Klepsland Mauland, Ingvild L. Tangen, Ansgar Berg, Henrica M.J. Werner, Jone Trovik, Anne Margrete Øyan, Karl‐Henning Kalland, Inge Jonassen, Helga B. Salvesen, Kjell Petersen
Software Mentions: 4
Published: almost 8 years ago

10.1371/journal.pone.0166721

A Genetic Algorithm for Diploid Genome Reconstruction Using Paired-End Sequencing
Cited by: 3
Author(s): Chuan-Kang Ting, Chun-Shin Lin, Ming-Tsai Chan, Jeremy J.W. Chen, Sheng-Yu Chuang, Yao‐Ting Huang
Software Mentions: 4
Published: almost 10 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: about 9 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

10.1371/journal.pone.0181463

DUDE-Seq: Fast, flexible, and robust denoising for targeted amplicon sequencing
Cited by: 49
Author(s): Byunghan Lee, Taesup Moon, Sungroh Yoon, Tsachy Weissman
Software Mentions: 4
Published: about 9 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 9 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 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: about 7 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 9 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: over 7 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

10.1371/journal.pone.0122339

The Active Tamoxifen Metabolite Endoxifen (4OHNDtam) Strongly Down-Regulates Cytokeratin 6 (CK6) in MCF-7 Breast Cancer Cells
Cited by: 4
Author(s): Thomas Helland, Jennifer Gjerde, Simon N. Dankel, Ingvild S. Fenne, Linn Skartveit, Andreas Drangevåg, Olivera Bozickovic, Marianne Hauglid Flågeng, Håvard Søiland, Gunnar Mellgren, Ernst A. Lien
Software Mentions: 4
Published: over 11 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

10.1007/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 12 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

10.3390/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 6 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 8 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

10.1038/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

10.1186/1751-0473-7-10

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 14 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

10.1186/1471-2164-15-948

Evaluation of variant identification methods for whole genome sequencing data in dairy cattle
Cited by: 41
Author(s): C.F. Baes, Marlies Dolezal, James E. Koltes, Beat Bapst, Eric R. Fritz-Waters, Sandra Jansen, Christine Flury, Heidi Signer-Hasler, Christine Stricker, Rohan L. Fernando, R. Fries, J. Moll, Dorian J. Garrick, James M. Reecy, Birgit Gredler
Software Mentions: 4
Published: over 12 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 19 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: over 9 years ago

10.1186/1471-2105-12-497

Partition decoupling for multi-gene analysis of gene expression profiling data
Cited by: 10
Author(s): Rosemary Braun, Gregory Leibon, Scott D. Pauls, Daniel N. Rockmore
Software Mentions: 4
Published: almost 15 years ago

10.1186/s12864-020-07260-z

Temporal salt stress-induced transcriptome alterations and regulatory mechanisms revealed by PacBio long-reads RNA sequencing in Gossypium hirsutum
Cited by: 18
Author(s): Delong Wang, Xuke Lu, Xiugui Chen, Shuai Wang, Junjuan Wang, Lixue Guo, Zujun Yin, Quanjia Chen, Wuwei Ye
Software Mentions: 4
Published: almost 6 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: over 12 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

10.1186/1471-2164-12-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

10.1186/1471-2105-15-180

PBHoney: identifying genomic variants via long-read discordance and interrupted mapping
Cited by: 135
Author(s): Adam C. English, William Salerno, Jeffrey G. Reid
Software Mentions: 4
Published: over 12 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: about 6 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

10.1371/journal.pone.0104504

Identification of Significant Features by the Global Mean Rank Test
Cited by: 17
Author(s): Martin Klammer, J. Nikolaj Dybowski, Daniel Hoffmann, Christoph Schaab
Software Mentions: 4
Published: about 12 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: about 16 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: almost 10 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.0013954

A Role for the Retinoblastoma Protein As a Regulator of Mouse Osteoblast Cell Adhesion: Implications for Osteogenesis and Osteosarcoma Formation
Cited by: 30
Author(s): Bernadette Sosa‐García, Volkan Gündüz, Viviana Vázquez‐Rivera, W. Douglas Cress, Gabriëla Wright, Haikuo Bian, Philip W. Hinds, Pedro G. Santiago‐Cardona
Software Mentions: 4
Published: almost 16 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: 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

10.1186/1471-2164-15-982

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: almost 12 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: about 16 years ago

10.1371/journal.pone.0155461

SparkBWA: Speeding Up the Alignment of High-Throughput DNA Sequencing Data
Cited by: 69
Author(s): José Manuel Abuín, Juan C. Pichel, Tomás F. Pena, Jorge Amigo
Software Mentions: 4
Published: over 10 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: almost 19 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

10.1186/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

10.1186/1471-2105-12-468

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: almost 15 years ago

10.1371/journal.pone.0098404

Deep Sequencing Reveals New Aspects of Progesterone Receptor Signaling in Breast Cancer Cells
Cited by: 12
Author(s): Anastasia Kougioumtzi, Panayiotis Tsaparas, Angeliki Magklara
Software Mentions: 4
Published: over 12 years ago

10.1371/journal.pone.0166358

Accelerating Information Retrieval from Profile Hidden Markov Model Databases
Cited by: 0
Author(s): A. Faleh Tamimi, Yaqoub Ashhab, Hashem Tamimi
Software Mentions: 4
Published: almost 10 years ago

10.1371/journal.pone.0121558

Mapping and Characterizing Selected Canopy Tree Species at the Angkor World Heritage Site in Cambodia Using Aerial Data
Cited by: 36
Author(s): Minerva Singh, Damian Evans, Boun Suy Tan, Chan Samean Nin
Software Mentions: 4
Published: over 11 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

10.1371/journal.pone.0119254

Goodness-of-Fit Tests and Model Diagnostics for Negative Binomial Regression of RNA Sequencing Data
Cited by: 12
Author(s): Gu Mi, Yanming Di, Daniel W. Schafer
Software Mentions: 4
Published: over 11 years ago

Projects: cran: SAM

Science Score: 85/100

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Papers Mentioning SAM 4,566