cran: SAM | Projects | Ecosyste.ms: Papers

10.1038/srep13135

Unique Toll-Like Receptor 4 Activation by NAMPT/PBEF Induces NFκB Signaling and Inflammatory Lung Injury
Cited by: 119
Author(s): Sara M. Camp, Ermelinda Ceco, Carrie Evenoski, Sergei M. Danilov, Tong Zhou, Eddie T. Chiang, Liliana Moreno‐Vinasco, Brandon Mapes, Jieling Zhao, Gamze Gürsoy, Mary Elizabeth Brown, Djanybek Adyshev, Shahid Siddiqui, Hector Quijada, Saad Sammani, Eleftheria Letsiou, Laleh Saadat, Mohammed Yousef, Ting Wang, Jie Liang, Joe G.N. Garcia
Software Mentions: 5
Published: almost 11 years ago

10.1186/s12284-019-0322-x

Signatures of differential selection in chloroplast genome between japonica and indica
Cited by: 17
Author(s): Lin Cheng, Jungrye Nam, Sang-Ho Chu, Rungnapa Phitaktansakul, Myeong-Hyeon Min, Cheng Yuan, Ji-Min Yoo, Jee-Su Kang, Kyu‐Won Kim, Yong‐Jin Park
Software Mentions: 5
Published: almost 7 years ago

10.3389/fgene.2019.00772

Polycystic Ovary Syndrome: Novel and Hub lncRNAs in the Insulin Resistance-Associated lncRNA–mRNA Network
Cited by: 22
Author(s): Jun Zhao, Jiayu Huang, Xue Geng, Weiwei Chu, Shang Li, Zi‐Jiang Chen, Yanzhi Du
Software Mentions: 5
Published: almost 7 years ago

10.3389/fgene.2021.695124

Folate Deficiency Triggers the Abnormal Segregation of a Region With Large Cluster of CG-Rich Trinucleotide Repeats on Human Chromosome 2
Cited by: 1
Author(s): Lorenza Garribba, Ivan Vogel, Mads Lerdrup, Marisa M Gonçalves Dinis, Liqun Ren, Ying Liu
Software Mentions: 5
Published: about 5 years ago

10.1186/s13058-016-0714-4

Intermittent energy restriction induces changes in breast gene expression and systemic metabolism
Cited by: 33
Author(s): Michelle Harvie, Andrew H. Sims, Mary Pegington, Katherine Spence, Adam Mitchell, Andrew A. Vaughan, J. William Allwood, Yun Xu, Nicholas J. W. Rattray, Royston Goodacre, D. Gareth Evans, Ellen Sullivan Mitchell, Debbie McMullen, Robert B. Clarke, Anthony Howell
Software Mentions: 5
Published: about 10 years ago

10.1186/s12934-020-01489-9

Translational landscape and protein biogenesis demands of the early secretory pathway in Komagataella phaffii
Cited by: 6
Author(s): Troy R Alva, Melanie Riera, J.W. Chartron
Software Mentions: 5
Published: over 5 years ago

10.1002/1878-0261.12726

Characterization of super‐enhancer‐associated functional lncRNAs acting as ceRNAs in ESCC
Cited by: 22
Author(s): Qiuyu Wang, Peng Liu, Chen Yang, Lian‐Di Liao, Jiaxin Chen, Meng Li, Yanyu Li, Fengcui Qian, Yuexin Zhang, Fan Wang, Chunquan Li, De–Chen Lin, Li‐Yan Xu, En‐Min Li
Software Mentions: 5
Published: about 6 years ago

10.1186/s13059-014-0579-8

Pancancer analysis of DNA methylation-driven genes using MethylMix
Cited by: 102
Author(s): Olivier Gevaert, Robert Tibshirani, Sylvia K. Plevritis
Software Mentions: 5
Published: over 11 years ago

10.1186/s13059-015-0734-x

Errors in RNA-Seq quantification affect genes of relevance to human disease
Cited by: 128
Author(s): Christelle Robert, Michael Watson
Software Mentions: 5
Published: almost 11 years ago

10.1242/dmm.034124

Epigenetic regulators Rbbp4 and Hdac1 are overexpressed in a zebrafish model of RB1 embryonal brain tumor, and are required for neural progenitor survival and proliferation
Cited by: 37
Author(s): Linda Schultz, Jeffrey A. Haltom, Maira P. Almeida, Wesley A. Wierson, Staci L. Solin, Trevor Weiss, Jordan A Helmer, Elizabeth J. Sandquist, Heather R. Shive, Maura McGrail
Software Mentions: 5
Published: about 8 years ago

10.3389/fmicb.2019.02075

Functional Characterization of a Global Virulence Regulator Hfq and Identification of Hfq-Dependent sRNAs in the Plant Pathogen Pantoea ananatis
Cited by: 14
Author(s): Gi Yoon Shin, Jeffrey K. Schachterle, Divine Yufetar Shyntum, Lucy N. Moleleki, Teresa A. Coutinho, George W. Sundin
Software Mentions: 5
Published: almost 7 years ago

10.6026/97320630013327

Robust Feature Selection Approach for Patient Classification using Gene Expression Data
Cited by: 6
Author(s): Shahjaman, Nishith Kumar, Shakil Ahmed, AnjumanAra Begum, S. M. Shahinul Islam, Md. Nurul Haque Mollah
Software Mentions: 5
Published: over 8 years ago

10.3389/fmicb.2020.587306

An Improved Sequencing-Based Bioinformatics Pipeline to Track the Distribution and Clonal Architecture of Proviral Integration Sites
Cited by: 4
Author(s): Nicolas Rosewick, Vincent Hahaut, Keith Durkin, Maria Artesi, Snehal D. Karpe, Jérôme Wayet, Philip Griebel, Natasa Arsic, Ambroise Marçais, Olivier Hermine, Arsène Burny, Michel Georges, Anne Van den Broeke
Software Mentions: 5
Published: almost 6 years ago

10.1093/molbev/msv282

Population Structure Shapes Copy Number Variation in Malaria Parasites
Cited by: 43
Author(s): Ian H. Cheeseman, Becky A. Miller, John C. Tan, Aiping Tan, Shalini Nair, Standwell C. Nkhoma, Marcos De Donato, Hectorina Rodulfo, Arjen M. Dondorp, OraLee H. Branch, Lastenia Ruiz Mesía, Paul N. Newton, Mayfong Mayxay, Alfred Amambua-Ngwa, David J. Conway, François Nosten, Michael T. Ferdig, Tim Anderson
Software Mentions: 5
Published: over 10 years ago

10.1093/ve/vex023

STEAK: A specific tool for transposable elements and retrovirus detection in high-throughput sequencing data
Cited by: 17
Author(s): Cindy G. Santander, Philippe Gambron, Emanuele Marchi, Timokratis Karamitros, Aris Katzourakis, Gkikas Magiorkinis
Software Mentions: 5
Published: about 9 years ago

10.1186/s13059-017-1285-0

Chromosome contacts in activated T cells identify autoimmune disease candidate genes
Cited by: 66
Author(s): Oliver S. Burren, Arcadio Rubio Garćıa, Biola M. Javierre, Daniel B. Rainbow, Jonathan Cairns, Nicholas Cooper, John Lambourne, Ellen Schofield, Xaquín Castro Dopico, Ricardo C. Ferreira, Richard M. R. Coulson, Frances Burden, Sophia Rowlston, Kate Downes, Steven W. Wingett, Mattia Frontini, Willem H. Ouwehand, Peter Fraser, Mikhail Spivakov, John A. Todd, Linda S. Wicker, Antony J. Cutler, Chris Wallace
Software Mentions: 5
Published: almost 9 years ago

10.1093/molbev/msaa309

A New Catalog of Structural Variants in 1,301 A. thaliana Lines from Africa, Eurasia, and North America Reveals a Signature of Balancing Selection at Defense Response Genes
Cited by: 22
Author(s): Mehmet Göktay, Andrea Fulgione, Angela M. Hancock
Software Mentions: 5
Published: over 5 years ago

10.3390/ani11082226

In Search of Species-Specific SNPs in a Non-Model Animal (European Bison (Bison bonasus))—Comparison of De Novo and Reference-Based Integrated Pipeline of STACKS Using Genotyping-by-Sequencing (GBS) Data
Cited by: 1
Author(s): Sazia Kunvar, Sylwia D. Czarnomska, Cino Pertoldi, Małgorzata Tokarska
Software Mentions: 5
Published: almost 5 years ago

10.1029/2020EA001343

An Interpolation Method to Reduce the Computational Time in the Stochastic Lagrangian Particle Dispersion Modeling of Spatially Dense XCO2 Retrievals
Cited by: 6
Author(s): Dustin Roten, Dien Wu, Benjamin Fasoli, T. Oda, John C. Lin
Software Mentions: 5
Published: over 5 years ago

10.1093/bioinformatics/btv634

EMDomics: a robust and powerful method for the identification of genes differentially expressed between heterogeneous classes
Cited by: 54
Author(s): Sheida Nabavi, Daniel Schmolze, Mayinuer Maitituoheti, Sadhika Malladi, Andrew H. Beck
Software Mentions: 5
Published: over 10 years ago

10.1016/j.ebiom.2019.06.041

Metabolomics in plasma of Malawian children 7 years after surviving severe acute malnutrition: “ChroSAM” a cohort study
Cited by: 14
Author(s): Céline Bourdon, Natasha Lelijveld, Debbie Thompson, Prasad S. Dalvi, Gerard Bryan Gonzales, Dominic Wang, Misagh Alipour, Eytan Wine, Emmanuel Chimwezi, Jonathan C. K. Wells, Marko Kerac, Robert Bandsma, Moffat Nyirenda
Software Mentions: 5
Published: about 7 years ago

10.1093/bioinformatics/btt016

Grape RNA-Seq analysis pipeline environment
Cited by: 28
Author(s): David G. Knowles, Maik Röder, Angelika Merkel, Roderic Guigó
Software Mentions: 5
Published: over 13 years ago

10.1186/s13293-015-0056-4

Spatial sexual dimorphism of X and Y homolog gene expression in the human central nervous system during early male development
Cited by: 24
Author(s): Martin M. Johansson, E. Lundin, Xiaoyan Qian, Mohammadreza Mirzazadeh, Jonatan Halvardson, Elisabeth Darj, Lars Feuk, Mats Nilsson, Elena Jazin
Software Mentions: 5
Published: over 10 years ago

10.3389/fgene.2021.661440

Extensive Variation in Drought-Induced Gene Expression Changes Between Loblolly Pine Genotypes
Cited by: 3
Author(s): Jingjia Li, Jason B. West, Alexander Hart, Jill L. Wegrzyn, Matthew A. Smith, Jean‐Christophe Domec, Carol A. Loopstra, Claudio Casola
Software Mentions: 5
Published: about 5 years ago

10.1002/ctm2.133

Analysis of single‐cell RNAseq identifies transitional states of T cells associated with hepatocellular carcinoma
Cited by: 12
Author(s): Yang Yz, Fangming Liu, Weiren Liu, Mingyue Ma, Jie Gao, Yan Lu, Li-Hao Huang, Xiaoying Li, Ying–Hong Shi, Xiangdong Wang, Duojiao Wu
Software Mentions: 5
Published: about 6 years ago

10.1186/s13059-015-0716-z

Genetic properties of the MAGIC maize population: a new platform for high definition QTL mapping in Zea mays
Cited by: 191
Author(s): Matteo Dell’Acqua, Daniel M. Gatti, G. Pea, Federica Cattonaro, Frederik Coppens, Gabriele Magris, Aye L. Hlaing, Htay Htay Aung, Hilde Nelissen, Joke Baute, Elisabetta Frascaroli, Gary A. Churchill, Dirk Inzé, Michèle Morgante, Mario Enrico Pè
Software Mentions: 5
Published: almost 11 years ago

10.1186/s13059-014-0577-x

Churchill: an ultra-fast, deterministic, highly scalable and balanced parallelization strategy for the discovery of human genetic variation in clinical and population-scale genomics
Cited by: 109
Author(s): Benjamin J. Kelly, James Fitch, Yangqiu Patrick Hu, Donald J. Corsmeier, Huachun Zhong, Amy Wetzel, Russell D Nordquist, David L. Newsom, Peter White
Software Mentions: 5
Published: over 11 years ago

10.15252/msb.156172

Comprehensive assembly of novel transcripts from unmapped human RNA‐Seq data and their association with cancer
Cited by: 17
Author(s): Majid Kazemian, Min Ren, Jian-Xin Lin, Wei Liao, Rosanne Spolski, Warren J. Leonard
Software Mentions: 5
Published: almost 11 years ago

10.1186/1471-2105-11-221

GATExplorer: Genomic and Transcriptomic Explorer; mapping expression probes to gene loci, transcripts, exons and ncRNAs
Cited by: 77
Author(s): Alberto Risueño, Celia Fontanillo, Marcel E. Dinger, Javier De Las Rivas
Software Mentions: 5
Published: about 16 years ago

10.1016/j.stem.2017.09.003

Chromatin and Single-Cell RNA-Seq Profiling Reveal Dynamic Signaling and Metabolic Transitions during Human Spermatogonial Stem Cell Development
Cited by: 190
Author(s): Jingtao Guo, Edward J. Grow, Chongil Yi, Hana Mlčochová, Geoffrey J. Maher, Cecilia Lindskog, Patrick J. Murphy, Candice L. Wike, Douglas T. Carrell, Anne Goriely, James M. Hotaling, Bradley R. Cairns
Software Mentions: 5
Published: almost 9 years ago

10.1186/s13059-017-1302-3

Extensive transcriptomic and epigenomic remodelling occurs during Arabidopsis thaliana germination
Cited by: 127
Author(s): Reena Narsai, Quentin Gouil, David Secco, Akanksha Srivastava, Yuliya V. Karpievitch, Lim Chee Liew, Ryan Lister, Mathew G. Lewsey, James Whelan
Software Mentions: 5
Published: almost 9 years ago

10.1186/1471-2164-14-100

A hybrid next generation transcript sequencing-based approach to identify allelic and homeolog-specific single nucleotide polymorphisms in allotetraploid white clover
Cited by: 19
Author(s): Istvàn Nagy, Susanne Barth, Jeanne Mehenni-Ciz, Michael T. Abberton, Dan Milbourne
Software Mentions: 5
Published: over 13 years ago

10.3389/fgene.2017.00147

An Algorithm for Template-Based Prediction of Secondary Structures of Individual RNA Sequences
Cited by: 2
Author(s): Josef Pánek, Martin Modrák, Marek Schwarz
Software Mentions: 5
Published: almost 9 years ago

10.1186/1471-2164-13-351

The RosR transcription factor is required for gene expression dynamics in response to extreme oxidative stress in a hypersaline-adapted archaeon
Cited by: 38
Author(s): Kusum Sharma, Nicholas Gillum, J Lomax Boyd, Amy K. Schmid
Software Mentions: 5
Published: almost 14 years ago

10.1186/s12870-018-1329-y

Distinct tissue-specific transcriptional regulation revealed by gene regulatory networks in maize
Cited by: 39
Author(s): Ji Huang, Jue-Fei Zheng, Hui Yuan, Karen M. McGinnis
Software Mentions: 5
Published: about 8 years ago

10.3390/cancers12082257

A Global Gene Body Methylation Measure Correlates Independently with Overall Survival in Solid Cancer Types
Cited by: 1
Author(s): Dietmar Pils, Elisabeth Steindl, Anna Bachmayr-Heyda, Sabine Dekan, Stefanie Aust
Software Mentions: 5
Published: almost 6 years ago

10.1186/1471-2229-10-150

Pathway analysis of the transcriptome and metabolome of salt sensitive and tolerant poplar species reveals evolutionary adaption of stress tolerance mechanisms
Cited by: 129
Author(s): Dennis Janz, Katja Behnke, Jörg‐Peter Schnitzler, Basem Kanawati, Philippe Schmitt‐Kopplin, Andrea Polle
Software Mentions: 5
Published: about 16 years ago

10.1186/s12864-017-3959-0

Transcriptomic analysis of the response of Acropora millepora to hypo-osmotic stress provides insights into DMSP biosynthesis by corals
Cited by: 19
Author(s): Catalina Aguilar, Jean-Baptiste Raina, Cherie A. Motti, Sylvain Forêt, David C. Hayward, Bruno Lapeyre, David G. Bourne, David J. Miller
Software Mentions: 5
Published: almost 9 years ago

10.1371/journal.pone.0016294

Plasmodium vivax Tryptophan-Rich Antigen PvTRAg33.5 Contains Alpha Helical Structure and Multidomain Architecture
Cited by: 12
Author(s): Hema Bora, Satpal Garg, Priyankar Sen, Deepak Kumar, Punit Kaur, Rizwan Hasan Khan, Yagya D. Sharma
Software Mentions: 5
Published: over 15 years ago

10.1371/journal.pone.0166067

Immunohistochemical Typing of Adenocarcinomas of the Pancreatobiliary System Improves Diagnosis and Prognostic Stratification
Cited by: 31
Author(s): Carlos Fernández Moro, Alejandro Fernandez-Woodbridge, Melroy D’Souza, Qianni Zhang, Benedek Bozóky, Senthil Vasan Kandaswamy, Piera Catalano, Rainer Heuchel, Sonia Shtembari, Marco Del Chiaro, Olof Danielsson, Mikael Björnstedt, Matthias Löhr, Bengt Isaksson, Caroline Verbeke, Béla Bozóky
Software Mentions: 5
Published: over 9 years ago

10.1186/1756-0500-4-171

CloudAligner: A fast and full-featured MapReduce based tool for sequence mapping
Cited by: 101
Author(s): Tung Nguyen, Wei Shi, Douglas M. Ruden
Software Mentions: 5
Published: about 15 years ago

10.1186/s12859-019-3017-9

Guide for library design and bias correction for large-scale transcriptome studies using highly multiplexed RNAseq methods
Cited by: 8
Author(s): Shintaro Katayama, Tiina Skoog, Cilla Söderhäll, Elisabet Einarsdottir, Kaarel Krjutškov, Juha Kere
Software Mentions: 5
Published: almost 7 years ago

10.1371/journal.pcbi.1007904

Restriction of S-adenosylmethionine conformational freedom by knotted protein binding sites
Cited by: 7
Author(s): Agata P. Perlinska, Adam Stasiulewicz, Ewa K. Nawrocka, Krzysztof Kazimierczuk, Piotr Setny, Joanna I. Sułkowska
Software Mentions: 5
Published: about 6 years ago

10.1186/s13075-015-0682-6

Autoantigen microarrays reveal autoantibodies associated with proliferative nephritis and active disease in pediatric systemic lupus erythematosus
Cited by: 42
Author(s): D. James Haddon, Vivian K. Diep, J. M. Price, Cindy Limb, Paul J. Utz, Imelda Balboni
Software Mentions: 5
Published: about 11 years ago

10.1016/j.cell.2021.06.007

Polyamine metabolism is a central determinant of helper T cell lineage fidelity
Cited by: 96
Author(s): Daniel J. Puleston, Francesc Baixauli, David E. Sanin, Joy Edwards-Hicks, Matteo Villa, Agnieszka M. Kabat, Marcin M. Kamiński, Michal Stanckzak, Hauke J. Weiss, Katarzyna M. Grzes, Klara Piletič, Cameron S. Field, Mauro Corrado, Fabian Haessler, Chao Wang, Yaarub Musa, L Schimmelpfennig, Lea J. Flachsmann, Gerhard Mittler, Nir Yosef, Vijay K. Kuchroo, Joerg M. Buescher, Stefan Balabanov, Edward J. Pearce, Douglas R. Green, Erika L. Pearce
Software Mentions: 5
Published: almost 5 years ago

10.1186/s12864-017-4031-9

unitas: the universal tool for annotation of small RNAs
Cited by: 83
Author(s): Daniel Gebert, Charlotte Hewel, David Rosenkranz
Software Mentions: 5
Published: almost 9 years ago

10.1002/advs.201901672

Comparison of Arachis monticola with Diploid and Cultivated Tetraploid Genomes Reveals Asymmetric Subgenome Evolution and Improvement of Peanut
Cited by: 38
Author(s): Dongmei Yin, Changmian Ji, Qingxin Song, Wan–Ke Zhang, Xingguo Zhang, Kunkun Zhao, Charles Y. Chen, Chuan Tang Wang, He Guo, Zhe Liang, Xingli Ma, Zhongfeng Li, Yueyi Tang, Yuejun Wang, Ké Li, Longlong Ning, Hui Zhang, Kai Zhao, Xuming Li, Haiyan Yu, Lei Yan, Mingcheng Wang, Liming Ma, Hongkun Zheng, Yijing Zhang, Jinsong Zhang, Wei Hu, Z Jeffrey Chen
Software Mentions: 5
Published: over 6 years ago

10.1186/1471-2105-15-14

Fold change rank ordering statistics: a new method for detecting differentially expressed genes
Cited by: 99
Author(s): Doulaye Dembélé, Philippe Kastner
Software Mentions: 5
Published: over 12 years ago

10.1186/s12864-018-4926-0

CircMarker: a fast and accurate algorithm for circular RNA detection
Cited by: 23
Author(s): Xin Li, Chong Chu, Jingwen Pei, Ion Măndoiu, Yufeng Wu
Software Mentions: 5
Published: almost 8 years ago

10.1186/1748-7188-8-25

Data compression for sequencing data
Cited by: 84
Author(s): Sebastian Deorowicz, Szymon Grabowski
Software Mentions: 5
Published: over 13 years ago

10.1371/journal.pone.0086299

Functional Module Connectivity Map (FMCM): A Framework for Searching Repurposed Drug Compounds for Systems Treatment of Cancer and an Application to Colorectal Adenocarcinoma
Cited by: 33
Author(s): Feng Hsiang Chung, Yun Ru Chiang, Ai Lun Tseng, Yung Chuan Sung, Jean Lu, Min Chang Huang, Nianhan Ma, Hoong Chien Lee
Software Mentions: 5
Published: over 12 years ago

10.1371/journal.pone.0134880

Heterozygous Mapping Strategy (HetMappS) for High Resolution Genotyping-By-Sequencing Markers: A Case Study in Grapevine
Cited by: 99
Author(s): Katie E. Hyma, Paola Barba, Minghui Wang, Jason P. Londo, Charlotte B. Acharya, Sharon E. Mitchell, Qi Sun, Bruce I. Reisch, Lance Cadle‐Davidson
Software Mentions: 5
Published: almost 11 years ago

10.1186/1471-2164-13-26

Postmortem cardiac tissue maintains gene expression profile even after late harvesting
Cited by: 35
Author(s): Saloni Gupta, Marc K. Halushka, Gina M. Hilton, Dan E. Arking
Software Mentions: 5
Published: over 14 years ago

10.7554/eLife.60326

Antagonistic roles for Ataxin-2 structured and disordered domains in RNP condensation
Cited by: 15
Author(s): Amanjot Singh, Joern Hulsmeier, Arvind Reddy Kandi, Sai Shruti Pothapragada, Jens Hillebrand, Arnas Petrauskas, Khushboo Agrawal, Krishnan Rt, Devasena Thiagarajan, Deepa Jayaprakashappa, K. VijayRaghavan, Mani Ramaswami, Baskar Bakthavachalu
Software Mentions: 5
Published: over 5 years ago

10.1186/s12859-016-1440-8

TTCA: an R package for the identification of differentially expressed genes in time course microarray data
Cited by: 15
Author(s): Marco Albrecht, Damian Stichel, Bettina Müller, Ruth Merkle, Carsten Sticht, Norbert Gretz, Ursula Klingmüller, Kai Breuhahn, Franziska Matthäus
Software Mentions: 5
Published: over 9 years ago

10.3892/or.2015.4023

Integrated analysis of DNA methylation and microRNA regulation of the lung adenocarcinoma transcriptome
Cited by: 20
Author(s): Jie Du, Lin Zhang
Software Mentions: 5
Published: about 11 years ago

10.7554/eLife.55832

Temporal integration of auxin information for the regulation of patterning
Cited by: 79
Author(s): Carlos Galván‐Ampudia, Guillaume Cerutti, Jonathan Legrand, Géraldine Brunoud, Raquel Martín-Arevalillo, Romain Azaïs, Vincent Bayle, Steven Moussu, Christian Wenzl, Yvon Jaillais, Jan U. Lohmann, Christophe Godin, Teva Vernoux
Software Mentions: 5
Published: about 6 years ago

10.1084/jem.20171738

A broad atlas of somatic hypermutation allows prediction of activation-induced deaminase targets
Cited by: 75
Author(s): Ángel F. Álvarez-Prado, Pablo Pérez-Durán, Arantxa Pérez-García, Alberto Benguría, Carlos Torroja, Virginia G. de Yébenes, Almudena R. Ramiro
Software Mentions: 5
Published: over 8 years ago

10.1371/journal.pone.0252457

Lack of parent-of-origin effects in Nasonia jewel wasp: A replication and extension study
Cited by: 1
Author(s): Kimberly C. Olney, Joshua D. Gibson, Heini M. Natri, Avery Underwood, Juergen Gadau, Melissa A. Wilson
Software Mentions: 5
Published: about 5 years ago

10.1111/jfb.14349

Identification of male heterogametic sex‐determining regions on the Atlantic herring <scp>Clupea harengus</scp> genome
Cited by: 5
Author(s): Sunnvør í Kongsstovu, Hans Atli Dahl, Hannes Gislason, Eydna í Homrum, Jan Arge Jacobsen, Paul Flicek, Svein‐Ole Mikalsen
Software Mentions: 5
Published: about 6 years ago

10.1371/journal.pone.0103207

A Comparative Study of Techniques for Differential Expression Analysis on RNA-Seq Data
Cited by: 195
Author(s): Zong Hong Zhang, Dhanisha J. Jhaveri, Vikki M. Marshall, Denis C. Bauer, Janette Edson, Ramesh Narayanan, Gregory J. Robinson, Andreas E. Lundberg, Perry F. Bartlett, Naomi R. Wray, Qiongyi Zhao
Software Mentions: 5
Published: almost 12 years ago

10.1186/s12859-015-0670-5

QoRTs: a comprehensive toolset for quality control and data processing of RNA-Seq experiments
Cited by: 211
Author(s): Stephen W. Hartley, James C. Mullikin
Software Mentions: 5
Published: about 11 years ago

10.1371/journal.pone.0244829

Whole-genome sequence analysis and comparisons between drug-resistance mutations and minimum inhibitory concentrations of Mycobacterium tuberculosis isolates causing M/XDR-TB
Cited by: 16
Author(s): Ditthawat Nonghanphithak, Orawee Kaewprasert, Pratchakan Chaiyachat, Wipa Reechaipichitkul, Angkana Chaiprasert, Kiatichai Faksri
Software Mentions: 5
Published: over 5 years ago

10.1128/mBio.02079-16

Merkel Cell Polyomavirus Exhibits Dominant Control of the Tumor Genome and Transcriptome in Virus-Associated Merkel Cell Carcinoma
Cited by: 87
Author(s): Gabriel J. Starrett, Christina Marcelus, Paul G. Cantalupo, Joshua P. Katz, Jingwei Cheng, Keiko Akagi, Manisha Thakuria, Guilherme Rabinowits, Linda C. Wang, David E. Symer, James M. Pipas, Reuben S. Harris, James A. DeCaprio
Software Mentions: 5
Published: over 9 years ago

10.1038/s41598-018-37679-0

Acidogenesis, solventogenesis, metabolic stress response and life cycle changes in Clostridium beijerinckii NRRL B-598 at the transcriptomic level
Cited by: 46
Author(s): Petra Patáková, Barbora Branská, Karel Sedlář, Maryna Vasylkivska, Katerina Jureckova, Jan Kolek, Pavlína Koščová, Ivo Provazník
Software Mentions: 5
Published: over 7 years ago

10.1186/1471-2164-12-326

Multiple platform assessment of the EGF dependent transcriptome by microarray and deep tag sequencing analysis
Cited by: 19
Author(s): Franc Llorens, Manuela Hummel, Xavier Pastor, Anna Ferrer, Raquel Pluvinet, Ana Vivancos, Ester Castillo, Susana Iraola, A.M. Mosquera, E. A. Gonzalez, Juan José Lozano, Matthew Ingham, Juliane C. Dohm, María Noguera, Robert Kofler, José Antonio del Rı́o, Mònica Bayés, Heinz Himmelbauer, Lauro Sumoy
Software Mentions: 5
Published: about 15 years ago

10.1038/s41598-017-03478-2

Diet-induced reconstruction of mucosal microbiota associated with alterations of epithelium lectin expression and regulation in the maintenance of rumen homeostasis
Cited by: 5
Author(s): Hong Shen, Zhongyan Lu, Zhihui Xu, Zongzhuan Shen
Software Mentions: 5
Published: about 9 years ago

10.1371/journal.pbio.1002585

Single-Cell-Based Analysis Highlights a Surge in Cell-to-Cell Molecular Variability Preceding Irreversible Commitment in a Differentiation Process
Cited by: 192
Author(s): Richard Angélique, Boullu Loïs, Ulysse Herbach, Bonnafoux Arnaud, Valérie Morin, Elodie Vallin, Anissa Guillemin, Nan Gao, Gunawan Rudiyanto, Jérémie Cosette, Ophélie Arnaud, Jean-Jacques Kupiec, Thibault Espinasse, Sandrine Gonin-Giraud, Olivier Gandrillon
Software Mentions: 5
Published: over 9 years ago

10.1038/s41598-020-61158-0

Combining short and long read sequencing to characterize antimicrobial resistance genes on plasmids applied to an unauthorized genetically modified Bacillus
Cited by: 46
Author(s): Bas Berbers, Assia Saltykova, Cristina Garcı́a-Graells, Patrick Philipp, F Arella, Kathleen Marchal, Raf Winand, Kevin Vanneste, Nancy Roosens, Sigrid C. J. De Keersmaecker
Software Mentions: 5
Published: over 6 years ago

10.1093/gigascience/giab057

VC@Scale: Scalable and high-performance variant calling on cluster environments
Cited by: 3
Author(s): Tanveer Ahmad, Zaid Al-Ars, Peter Hofstee
Software Mentions: 5
Published: almost 5 years ago

10.1186/1471-2105-15-144

MOIRAI: a compact workflow system for CAGE analysis
Cited by: 62
Author(s): Akira Hasegawa, Carsten O. Daub, Piero Carninci, Yoshihide Hayashizaki, Timo Lassmann
Software Mentions: 5
Published: about 12 years ago

10.1007/s13238-020-00720-y

Integrative analysis of in vivo recording with single-cell RNA-seq data reveals molecular properties of light-sensitive neurons in mouse V1
Cited by: 9
Author(s): Jianwei Liu, Mengdi Wang, Le Sun, Na Pan, Changjiang Zhang, Junjing Zhang, Zhentao Zuo, Sheng He, Qian Wu, Xiaoqun Wang
Software Mentions: 5
Published: about 6 years ago

10.1186/s13073-016-0319-7

Extracting a low-dimensional description of multiple gene expression datasets reveals a potential driver for tumor-associated stroma in ovarian cancer
Cited by: 20
Author(s): Safiye Çelik, Benjamin A. Logsdon, Stephanie L. Battle, Charles W. Drescher, Mara H. Rendi, R. David Hawkins, Su-In Lee
Software Mentions: 5
Published: about 10 years ago

10.1093/gigascience/giaa054

Fcirc: A comprehensive pipeline for the exploration of fusion linear and circular RNAs
Cited by: 5
Author(s): Zhaoqing Cai, Hongzhang Xue, Yue Xu, Jens Köhler, Xiaoyu Cheng, Yanjun Dai, Jie Zheng, Haiyun Wang
Software Mentions: 5
Published: about 6 years ago

10.7717/peerj.9777

Generalized Linear Models outperform commonly used canonical analysis in estimating spatial structure of presence/absence data
Cited by: 4
Author(s): Lélis Antonio Carlos-Júnior, Joel Christopher Creed, Rob H. Marrs, Rob J. Lewis, Timothy P. Moulton, Rafael Feijó‐Lima, Matthew Spencer
Software Mentions: 5
Published: almost 6 years ago

10.7717/peerj.10539

Composition and distribution of fish environmental DNA in an Adirondack watershed
Cited by: 2
Author(s): Robert S. Cornman, James E. McKenna, Jennifer A. Fike
Software Mentions: 5
Published: over 5 years ago

10.1186/s13059-019-1858-1

Evaluating nanopore sequencing data processing pipelines for structural variation identification
Cited by: 30
Author(s): Anbo Zhou, Timothy Lin, Jinchuan Xing
Software Mentions: 5
Published: over 6 years ago

10.1186/s12859-017-1462-x

Comparative network stratification analysis for identifying functional interpretable network biomarkers
Cited by: 5
Author(s): Chuanchao Zhang, Juan Liu, Qianqian Shi, Tao Zeng, Luonan Chen
Software Mentions: 5
Published: over 9 years ago

10.7717/peerj.3091

Effect of method of deduplication on estimation of differential gene expression using RNA-seq
Cited by: 20
Author(s): Anna V. Klepikova, Artem S. Kasianov, Mikhail S. Chesnokov, Н. Л. Лазаревич, Aleksey A. Penin, Maria D. Logacheva
Software Mentions: 5
Published: over 9 years ago

10.1002/wrna.1649

Evolutionary conservation of <scp>RNA</scp> sequence and structure
Cited by: 22
Author(s): Elena Rivas
Software Mentions: 5
Published: over 5 years ago

10.3897/zookeys.542.5975

Taxonomic revision of Afrotropical Laccophilus Leach, 1815 (Coleoptera, Dytiscidae)
Cited by: 10
Author(s): Olof Biström, Anders N. Nilsson, Johannes Bergsten
Software Mentions: 5
Published: over 10 years ago

10.1371/journal.pone.0016266

Whole Transcriptome Sequencing Reveals Gene Expression and Splicing Differences in Brain Regions Affected by Alzheimer's Disease
Cited by: 257
Author(s): Natalie A. Twine, Karolina Janitz, Marc R. Wilkins, Michał Janitz
Software Mentions: 5
Published: over 15 years ago

10.7717/peerj.10501

Recalibration of mapping quality scores in Illumina short-read alignments improves SNP detection results in low-coverage sequencing data
Cited by: 3
Author(s): Eliot Cline, Nuttachat Wisittipanit, Tossapon Boongoen, Ekachai Chukeatirote, D. Struss, A. Eungwanichayapant
Software Mentions: 5
Published: over 5 years ago

10.1186/s12864-015-2246-1

High-throughput transcriptomics reveals common and strain-specific responses of human macrophages to infection with Mycobacterium abscessus Smooth and Rough variants
Cited by: 12
Author(s): Anna Aulicino, Adam M. Dinan, Aleksandra A. Miranda-CasoLuengo, John A. Browne, Kévin Rue-Albrecht, David E. MacHugh, Brendan J. Loftus
Software Mentions: 5
Published: over 10 years ago

10.3390/v13081647

Monitoring SARS-CoV-2 Populations in Wastewater by Amplicon Sequencing and Using the Novel Program SAM Refiner
Cited by: 25
Author(s): Devon A. Gregory, Chris G. Wieberg, Jeff Wenzel, Chung‐Ho Lin, Marc C. Johnson
Software Mentions: 5
Published: almost 5 years ago

10.1093/gbe/evaa062

The Origin and Composition of Korean Ethnicity Analyzed by Ancient and Present-Day Genome Sequences
Cited by: 16
Author(s): Jung-Eun Kim, Sungwon Jeon, Jae-Pil Choi, Asta Blažytė, Yeonsu Jeon, Jong‐Il Kim, Jun Ohashi, Katsushi Tokunaga, Sumio Sugano, Suthat Fucharoen, Fahd Al-Mulla, Jong Bhak
Software Mentions: 5
Published: over 6 years ago

10.4056/sigs.1353455

Meeting Report from the Genomic Standards Consortium (GSC) Workshop 9
Cited by: 4
Author(s): Tanja Davidsen, Ramana Madupu, Peter J. Sterk, Dawn Field, George M Garrity, Jack A. Gilbert, Frank Oliver Glöckner, Lynette Hirschman, Eugene Kolker, Renzo Kottmann, Nikos C. Kyrpides, Patrick Meyer, Norman Morrison, Lynn M. Schriml, Tatiana Tatusova, John Wooley
Software Mentions: 5
Published: over 16 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

10.1186/1471-2105-12-497

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: over 14 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/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

10.3389/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

10.1186/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-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/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

10.1074/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

10.1186/1471-2105-15-180

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: 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: almost 9 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: about 7 years ago

Projects: cran: SAM

Science Score: 85/100

Bonuses:

Penalties:

Papers Mentioning SAM 4,566