10.1016/j.cell.2020.05.002

Metabolic Dynamics and Prediction of Gestational Age and Time to Delivery in Pregnant Women
Cited by: 127
Author(s): Liang Liang, Marie-Louise Hee Rasmussen, Brian D. Piening, Xiaotao Shen, Songjie Chen, Hannes L. Röst, John K. Snyder, Robert Tibshirani, Line Skotte, Norman Cy Lee, Kévin Contrepois, Bjarke Feenstra, Hanyah Zackriah, M Snyder, Mads Melbye
Software Mentions: 4
Published: over 6 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

10.1016/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

10.3390/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

10.1155/2019/2725192

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

10.3390/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

10.1186/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

10.3389/fbioe.2015.00028

G-CNV: A GPU-Based Tool for Preparing Data to Detect CNVs with Read-Depth Methods
Cited by: 8
Author(s): Andrea Manconi, Elias Manca, Marco Moscatelli, Matteo Gnocchi, Alessandro Orro, Giuliano Armano, Luciano Milanesi
Software Mentions: 4
Published: over 11 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

10.3390/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

10.1128/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 9 years ago

10.12688/f1000research.15604.1

Androgen-dependent alternative mRNA isoform expression in prostate cancer cells
Cited by: 14
Author(s): Jennifer Munkley, Teresa Maia, Jesús Ibarluzea, Karen E. Livermore, Daniel Vodák, Ingrid Ehrmann, Katherine James, Prabhakar Rajan, Nuno L. Barbosa‐Morais, David Elliott
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 9 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

10.1128/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

10.1186/1751-0473-7-10

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

10.3390/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

10.1093/biostatistics/kxu038

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

10.1038/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

10.3390/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

10.1038/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 10 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

10.1038/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

10.3389/fgene.2021.731515

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

10.3389/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 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 5 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

10.1371/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: about 13 years ago

10.1186/gb-2014-15-1-r4

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

10.1093/bioinformatics/bts458

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

10.1038/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

10.1186/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

10.1038/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

10.7717/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/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

10.1186/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 5 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

10.1093/bioinformatics/bty157

Integrating long-range connectivity information into de Bruijn graphs
Cited by: 56
Author(s): Isaac Turner, Kiran Garimella, Zamin Iqbal, Gil McVean
Software Mentions: 4
Published: over 8 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.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

10.7717/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 8 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.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

10.1186/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

10.1186/gm551

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

10.1186/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

10.1371/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

10.1186/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

10.1371/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

10.1186/gb-2014-15-1-r11

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

10.1371/journal.pone.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

10.1371/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

10.7717/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

10.1371/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/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/s13059-017-1290-3

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

10.1038/s41598-017-04300-9

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

10.1371/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 7 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.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/s41598-018-19554-0

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

10.1038/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/s41598-017-02110-7

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

10.1038/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

10.1371/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

10.3389/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: almost 10 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

10.1371/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

10.1186/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

10.1128/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

10.1111/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

10.3389/fcell.2020.00369

Coding and Non-coding RNAs: Molecular Basis of Forest-Insect Outbreaks
Cited by: 9
Author(s): Sufang Zhang, Sifan Shen, Zhihui Yang, Xiangbo Kong, Fu Liu, Zhen Zhang
Software Mentions: 4
Published: over 6 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: about 20 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: about 20 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

10.1186/1471-2164-12-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

10.1186/1471-2229-14-169

RNA-seq analyses of multiple meristems of soybean: novel and alternative transcripts, evolutionary and functional implications
Cited by: 190
Author(s): Lei Wang, Chenlong Cao, Qibin Ma, Qiaoying Zeng, Haifeng Wang, Zhihao Cheng, Genfeng Zhu, Ji Qi, Hong Mā, Hai Nian, Yingxiang Wang
Software Mentions: 4
Published: over 12 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

10.1371/journal.pone.0163106

Tanscriptomic Study of the Soybean-Fusarium virguliforme Interaction Revealed a Novel Ankyrin-Repeat Containing Defense Gene, Expression of Whose during Infection Led to Enhanced Resistance to the Fungal Pathogen in Transgenic Soybean Plants
Cited by: 21
Author(s): Micheline N. Ngaki, Bing Wang, Binod Bihari Sahu, Subodh Srivastava, Mohammad Samir Farooqi, Kondapalli Venkata Gowri Chandra Sekhar, Sundararaman Swaminathan, Madan K. Bhattacharyya
Software Mentions: 4
Published: almost 10 years ago

10.1371/journal.pone.0247028

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

10.1371/journal.pone.0223397

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

10.18632/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.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

10.1186/1471-2105-15-198

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.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

10.1186/1471-2164-15-982

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: almost 16 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

10.1371/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

10.1371/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