cran: SAM | Projects | Ecosyste.ms: Papers

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: over 7 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: over 5 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: about 7 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: over 6 years ago

10.1038/srep27722

Genomic leftovers: identifying novel microsatellites, over-represented motifs and functional elements in the human genome
Cited by: 6
Author(s): Natalie C. Fonville, Karthik Raja Velmurugan, Hongseok Tae, Zalman Vaksman, Lauren J. McIver, Harold R. Garner
Software Mentions: 5
Published: over 10 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: over 6 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: almost 14 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: about 14 years ago

10.1371/journal.pcbi.0030026

Functional Impact of Missense Variants in BRCA1 Predicted by Supervised Learning
Cited by: 56
Author(s): Rachel Karchin, Alvaro N.A. Monteiro, Sean V. Tavtigian, Marcelo A. Carvalho, Andrej S̆ali
Software Mentions: 5
Published: over 19 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: about 7 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: over 15 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: over 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: about 5 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: over 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: about 6 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: about 9 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: over 16 years ago

10.1002/advs.201901672

Comparison of <i>Arachis monticola</i> 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: almost 7 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: about 9 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: about 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: almost 14 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: almost 16 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: almost 10 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: almost 15 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: almost 10 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: about 9 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: almost 13 years ago

10.18632/oncotarget.16417

Interaction of Epstein-Barr virus genes with human gastric carcinoma transcriptome
Cited by: 10
Author(s): Ruiyuan Zhang, Michael J. Strong, Melody Baddoo, Zhen Lin, Yuping Wang, Erik K. Flemington, Yaozhong Liu
Software Mentions: 5
Published: over 9 years ago

10.18632/oncotarget.20405

Cancer cell line specific co-factors modulate the FOXM1 cistrome
Cited by: 8
Author(s): Yue Wang, Matthew Ung, Tian Xia, Wenqing Cheng, Chao Cheng
Software Mentions: 5
Published: about 9 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: over 11 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: over 15 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

10.7554/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: over 6 years ago

10.1371/journal.pone.0101374

Assessment of the Impact of Using a Reference Transcriptome in Mapping Short RNA-Seq Reads
Cited by: 21
Author(s): Shanrong Zhao
Software Mentions: 5
Published: over 12 years ago

10.3390/ijms19010071

Transcriptome-Wide Identification and Characterization of Potato Circular RNAs in Response to Pectobacterium carotovorum Subspecies brasiliense Infection
Cited by: 42
Author(s): Ran Zhou, Yong‐Guan Zhu, Jiao Zhao, Zhengwu Fang, Shuping Wang, Jia Yin, Chu Zhang, Dongfang Ma
Software Mentions: 5
Published: almost 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: over 11 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: over 12 years ago

10.1371/journal.pone.0206844

Clustering-local-unique-enriched-signals (CLUES) promotes identification of novel regulators of ES cell self-renewal and pluripotency
Cited by: 1
Author(s): Chao Wu, Jiao Yang, Minhong Shen, Ci Pan, Cheng Guo, Danmei Jia, Jing Zhu, Long Zhang, Min Zheng, Junling Jia
Software Mentions: 5
Published: almost 8 years ago

10.1038/s41598-021-87779-7

Identification of genes associated with altered gene expression and m6A profiles during hypoxia using tensor decomposition based unsupervised feature extraction
Cited by: 10
Author(s): Sanjiban Sekhar Roy, Y-h. Taguchi
Software Mentions: 5
Published: over 5 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: almost 16 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

10.1371/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: over 5 years ago

10.1371/journal.pgen.1008261

Restricted and non-essential redundancy of RNAi and piRNA pathways in mouse oocytes
Cited by: 26
Author(s): Eliška Táborská, Josef Pasulka, Radek Malı́k, Filip Horvat, Irena Jenickova, Zoe Jelić Matošević, Petr Svoboda
Software Mentions: 5
Published: almost 7 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: almost 11 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: almost 11 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: about 12 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: over 8 years ago

10.1371/journal.pone.0123658

A Powerful Statistical Approach for Large-Scale Differential Transcription Analysis
Cited by: 4
Author(s): Ying Tan, Anita M. Chandler, Arindam Chaudhury, Joel R. Neilson
Software Mentions: 5
Published: over 11 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: about 9 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: about 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: almost 12 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: over 6 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.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: almost 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: over 10 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: about 5 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: 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

10.1093/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

10.1186/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: almost 7 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: about 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: about 11 years ago

10.1371/journal.pone.0229502

A background correction method to compensate illumination variation in hyperspectral imaging
Cited by: 6
Author(s): Jonghee Yoon, Alexandru Grigoroiu, Sarah E. Bohndiek
Software Mentions: 5
Published: over 6 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: 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

10.1038/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

10.1371/journal.pone.0092663

Towards Decrypting Cryptobiosis—Analyzing Anhydrobiosis in the Tardigrade Milnesium tardigradum Using Transcriptome Sequencing
Cited by: 48
Author(s): Chong Wang, Markus A. Grohme, Brahim Mali, Ralph O. Schill, Marcus Frohme
Software Mentions: 5
Published: over 12 years ago

10.1111/eva.12278

Patterns of differential gene expression in adult rotation‐resistant and wild‐type western corn rootworm digestive tracts
Cited by: 10
Author(s): Chia‐Ching Chu, Jorge A. Zavala, Joseph L. Spencer, M. Curzi, Christopher J. Fields, Jenny Drnevich, Blair D. Siegfried, Manfredo J. Seufferheld
Software Mentions: 5
Published: over 11 years ago

10.1093/bib/bbz018

CAFU: a Galaxy framework for exploring unmapped RNA-Seq data
Cited by: 11
Author(s): Siyuan Chen, Chengzhi Ren, Jingjing Zhai, Jinxin Yu, Xuyang Zhao, Zelong Li, Ting Zhang, Wenlong Ma, Zhaoxue Han, Chuang Ma
Software Mentions: 5
Published: over 7 years ago

10.3389/fbioe.2020.598392

Phenotypic and Genomic Analysis of Clostridium beijerinckii NRRL B-598 Mutants With Increased Butanol Tolerance
Cited by: 6
Author(s): Maryna Vasylkivska, Barbora Branská, Karel Sedlář, Katerina Jureckova, Ivo Provazník, Petra Patáková
Software Mentions: 5
Published: almost 6 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: over 5 years ago

10.3389/fgene.2020.591806

Genome-Wide Identification of Circular RNAs in Response to Low-Temperature Stress in Tomato Leaves
Cited by: 11
Author(s): Xuedong Yang, Yahui Liu, Hui Zhang, Jinyu Wang, Gaurav Zinta, Shangbo Xie, Weimin Zhu, Wen-Feng Nie
Software Mentions: 5
Published: almost 6 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: about 7 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: over 10 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: over 6 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: almost 10 years ago

10.1186/bcr3116

Gene expression profiling of primary male breast cancers reveals two unique subgroups and identifies N-acetyltransferase-1 (NAT1) as a novel prognostic biomarker
Cited by: 102
Author(s): Ida Johansson, Cecilia Nilsson, Pontus Berglund, Martin Lauss, Markus Ringnér, Håkan Olsson, Lena Luts, Edith Sim, Sten Thorstensson, Marie-Louise Fjällskog, Ingrid Hedenfalk
Software Mentions: 5
Published: over 14 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: almost 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: about 6 years ago

10.1111/jfb.14349

Identification of male heterogametic sex‐determining regions on the Atlantic herring <scp><i>Clupea harengus</i></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: over 6 years ago

10.1186/s40168-021-01110-0

Prevotella copri increases fat accumulation in pigs fed with formula diets
Cited by: 70
Author(s): Congying Chen, Shouguo Fang, Hong Wei, Maozhang He, Hao Fu, Xinwei Xiong, Yunyan Zhou, Jingyuan Wu, Jun Gao, Hui Yang, Lusheng Huang
Software Mentions: 5
Published: about 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

10.7717/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

10.1186/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: about 9 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

10.4056/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: almost 17 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

10.1371/journal.pone.0033575

Genetic Dissection of Acute Ethanol Responsive Gene Networks in Prefrontal Cortex: Functional and Mechanistic Implications
Cited by: 78
Author(s): Aaron R. Wolen, Charles Phillips, Michael A. Langston, Alex H. Putman, Paul J. Vorster, Nathan A. Bruce, Timothy P. York, Robert W. Williams, Michael F. Miles
Software Mentions: 4
Published: over 14 years ago

10.1155/2013/270362

A Case Report and Genetic Characterization of a Massive Acinic Cell Carcinoma of the Parotid with Delayed Distant Metastases
Cited by: 5
Author(s): Anthony C. Nichols, Michelle Chan-Seng-Yue, John Yoo, Sumit Agrawal, Maud H.W. Starmans, Daryl Waggott, Nicholas J. Harding, Samuel Dowthwaite, David A. Palma, Kevin Fung, Bret Wehrli, Danielle MacNeil, Philippe Lambin, Eric Winquist, James Koropatnick, Joe S. Mymryk, Paul C. Boutros, John W. Barrett
Software Mentions: 4
Published: almost 14 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/life11080862

Comparative Analysis of PacBio and Oxford Nanopore Sequencing Technologies for Transcriptomic Landscape Identification of Penaeus monodon
Cited by: 6
Author(s): Zulema Udaondo, Kanchana Sittikankaew, Tanaporn Uengwetwanit, Thidathip Wongsurawat, Chutima Sonthirod, Piroon Jenjaroenpun, Wirulda Pootakham, Nitsara Karoonuthaisiri, Intawat Nookaew
Software Mentions: 4
Published: about 5 years ago

10.26508/lsa.201900561

Refining the adipose progenitor cell landscape in healthy and obese visceral adipose tissue using single-cell gene expression profiling
Cited by: 40
Author(s): Dong Seong Cho, Bolim Lee, Jason D. Doles
Software Mentions: 4
Published: almost 7 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

10.1038/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

10.3390/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

10.1371/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.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

10.1186/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

10.1007/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.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

Projects: cran: SAM

Science Score: 85/100

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Penalties:

Papers Mentioning SAM 4,566