cran: SAM | Projects | Ecosyste.ms: Papers

10.1038/s41598-021-82731-1

Mating system evolution and genetic structure of diploid sexual populations of Cyrtomium falcatum in Japan
Cited by: 0
Author(s): Ryōsuke Imai, Yoshiaki Tsuda, Atsushi Ebihara, Sadamu Matsumoto, Ayumi Tezuka, Atsushi J. Nagano, Ryo Ootsuki, Yasuyuki Watano
Software Mentions: 4
Published: over 5 years ago

10.3390/ijms21144865

Cytological and Gene Profile Expression Analysis Reveals Modification in Metabolic Pathways and Catalytic Activities Induce Resistance in Botrytis cinerea Against Iprodione Isolated From Tomato
Cited by: 4
Author(s): Ambreen Maqsood, Chaorong Wu, Sunny Ahmar, Haiyan Wu
Software Mentions: 4
Published: about 6 years ago

10.1371/journal.pgen.0030087

Whole-Genome Cartography of Estrogen Receptor α Binding Sites
Cited by: 414
Author(s): Chin-Yo Lin, Vinsensius B. Vega, Jane S. Thomsen, Tao Zhang, Say Li Kong, Ming Xie, King-Wah Chiu, Leonard Lipovich, Daniel H. Barnett, Fabio Stossi, A. Yeo, Joshy George, Vladimir A. Kuznetsov, Yew Kok Lee, Tze Howe Charn, Nallasivam Palanisamy, Lance D. Miller, Edwin Cheung, Benita S. Katzenellenbogen, Yijun Ruan, Guillaume Bourque, Chia Lin Wei, Edison T. Liu
Software Mentions: 4
Published: about 19 years ago

10.18632/oncotarget.7442

Distinct lncRNA transcriptional fingerprints characterize progressive stages of multiple myeloma
Cited by: 75
Author(s): Domenica Ronchetti, Luca Agnelli, Elisa Taìana, S. Galletti, Martina Manzoni, Katia Todoerti, Pellegrino Musto, Francesco Strozzi, Antonino Neri
Software Mentions: 4
Published: over 10 years ago

10.1186/s12711-016-0257-2

Fine mapping of a QTL on bovine chromosome 6 using imputed full sequence data suggests a key role for the group-specific component (GC) gene in clinical mastitis and milk production
Cited by: 31
Author(s): Harald Olsen, Tim Martin Knutsen, Anna Lewandowska-Sabat, Harald Grove, Torfinn Nome, Mathias Tiedemann Svendsen, Mariann Árnyasi, Marte Sodeland, Kristil Kindem Sundsaasen, Sandra Rinne Dahl, B. Heringstad, Hanne Hellerud Hansen, I. Olsaker, Matthew Kent, Sigbjørn Lien
Software Mentions: 4
Published: almost 10 years ago

10.1186/s13058-019-1159-3

On-treatment biomarkers can improve prediction of response to neoadjuvant chemotherapy in breast cancer
Cited by: 32
Author(s): Richard J. Bownes, Arran Turnbull, Carlos Martínez-Pérez, David Cameron, Andrew H. Sims, Olga Oikonomidou
Software Mentions: 4
Published: about 7 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: over 6 years ago

10.1371/journal.pcbi.1009078

lra: A long read aligner for sequences and contigs
Cited by: 50
Author(s): Jimin Ren, Mark Chaisson
Software Mentions: 4
Published: about 5 years ago

10.1186/gb-2005-6-6-r54

Cited by: 148
Author(s): Nils Rostoks, Justin O. Borevitz, Pete E. Hedley, Joanne Russell, Sharon Mudie, Jenny Morris, Linda Cardle, David Marshall, Robbie Waugh
Software Mentions: 4
Published: over 21 years ago

10.1534/g3.119.400777

rmtA-Dependent Transcriptome and Its Role in Secondary Metabolism, Environmental Stress, and Virulence inAspergillus flavus
Cited by: 5
Author(s): Timothy Satterlee, Sarah Entwistle, Yanbin Yin, J. W. Cary, Matthew D. Lebar, Liliana Losada, Ana M. Calvo
Software Mentions: 4
Published: over 6 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

10.3389/fgene.2014.00312

Gene expression responses of threespine stickleback to salinity: implications for salt-sensitive hypertension
Cited by: 33
Author(s): Gang Wang, Ence Yang, Kerri J. Smith, Yong Zeng, Guoli Ji, Richard E. Connon, Nann A. Fangue, James J. Cai
Software Mentions: 4
Published: almost 12 years ago

10.1534/g3.117.300550

Genetic Loci Governing Androgenic Capacity in Perennial Ryegrass (Lolium perenne L.)
Cited by: 8
Author(s): Rachel F. Begheyn, Steven Yates, Timothy Sykes, Bruno Studer
Software Mentions: 4
Published: about 8 years ago

10.1186/s12944-018-0915-1

Genome-wide identification and characterization of long non-coding RNAs during postnatal development of rabbit adipose tissue
Cited by: 19
Author(s): Guoze Wang, Kun Du, Shiyan Hu, Shiyi Chen, Xianbo Jia, Mingcheng Cai, Yu Shi, Jie Wang, Songjia Lai
Software Mentions: 4
Published: over 7 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

10.3389/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: about 6 years ago

10.1534/g3.116.026914

Environmental Association Analyses Identify Candidates for Abiotic Stress Tolerance inGlycine soja, the Wild Progenitor of Cultivated Soybeans
Cited by: 39
Author(s): Justin Anderson, Thomas J. Y. Kono, Robert M. Stupar, Michael B. Kantar, Peter L. Morrell
Software Mentions: 4
Published: over 10 years ago

10.1371/journal.pone.0240474

Were domestic camelids present on the prehispanic South American agricultural frontier? An ancient DNA study
Cited by: 7
Author(s): Cinthia Carolina Abbona, Gustavo Adolfo, Jeff Johnson, Tracy Kim, Adolfo Gil, Steve Wolverton
Software Mentions: 4
Published: over 5 years ago

10.1186/bcr3672

A genomic analysis of mouse models of breast cancer reveals molecular features ofmouse models and relationships to human breast cancer
Cited by: 71
Author(s): Daniel P. Hollern, Eran R. Andrechek
Software Mentions: 3
Published: about 12 years ago

10.1371/journal.pone.0031490

The Gene Expression Analysis of Blood Reveals S100A11 and AQP9 as Potential Biomarkers of Infective Endocarditis
Cited by: 44
Author(s): Franck Thuny, Julien Textoris, Amira Ben Amara, Adil El Filali, Christian Capo, Gilbert Habib, Didier Raoult, Jean‐Louis Mège
Software Mentions: 3
Published: over 14 years ago

10.1371/journal.pone.0128845

Comparison of High-Level Microarray Analysis Methods in the Context of Result Consistency
Cited by: 37
Author(s): Kornel Chromiński, Magdalena Tkacz
Software Mentions: 3
Published: about 11 years ago

10.1186/s40168-017-0341-z

Associations among dietary non-fiber carbohydrate, ruminal microbiota and epithelium G-protein-coupled receptor, and histone deacetylase regulations in goats
Cited by: 39
Author(s): Hong Shen, Zhongyan Lu, Zhihui Xu, Zhan Chen, Zongzhuan Shen
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pone.0119448

Analyzing Large Gene Expression and Methylation Data Profiles Using StatBicRM: Statistical Biclustering-Based Rule Mining
Cited by: 28
Author(s): Ujjwal Maulik, Saurav Mallik, Anirban Mukhopadhyay, Sanghamitra Bandyopadhyay
Software Mentions: 3
Published: over 11 years ago

10.3389/fgene.2021.622886

Familial Psychosis Associated With a Missense Mutation at MACF1 Gene Combined With the Rare Duplications DUP3p26.3 and DUP16q23.3, Affecting the CNTN6 and CDH13 Genes
Cited by: 3
Author(s): Josep Pol-Fuster, Francesca Cañellas, Laura Ruiz-Guerra, Aina Medina-Dols, Bàrbara Bisbal-Carrió, Víctor J. Asensio, Bernat Ortega-Vila, Diego M. Marzese, Carme Vidal, Carmen Sofia Pedro dos Santos, Jerònia Lladó, Gabriel Olmos, Damián Heine-Suñer, Konstantin Strauch, Antònia Flaquer, Cristòfol Vives-Bauzà
Software Mentions: 3
Published: over 5 years ago

10.1007/s11356-018-3765-5

Inter-species and inter-colony differences in elemental concentrations in eggshells of sympatrically nesting great cormorants Phalacrocorax carbo and grey herons Ardea cinerea
Cited by: 2
Author(s): Dariusz Jakubas, Ignacy Kitowski, Dariusz Wiącek, Szymon Bzoma
Software Mentions: 3
Published: over 7 years ago

10.3389/fgene.2019.01260

Joint Transcriptomic Analysis of Lung Cancer and Other Lung Diseases
Cited by: 8
Author(s): Beatriz Andrea Otálora‐Otálora, Mauro Florez, Liliana López‐Kleine, Alejandra Cañas Arboleda, Diana Urrego, Alejandra Rojas
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0037108

Extensive Gene-Specific Translational Reprogramming in a Model of B Cell Differentiation and Abl-Dependent Transformation
Cited by: 10
Author(s): Jamie Bates, Julia Salzman, Damon May, Patty B. Garcia, Gregory J. Hogan, Martin W. McIntosh, Mark S. Schlissel, Pat Brown
Software Mentions: 3
Published: about 14 years ago

10.1371/journal.pone.0173664

The miR-200 family is increased in dysplastic lesions in ulcerative colitis patients
Cited by: 14
Author(s): Amy Lewis, Carla Felice, Tomoko Kumagai, Claudia K. Y. Lai, Kriti Singh, Rosemary Jeffery, Roger Feakins, Eleni Giannoulatou, Alessandro Armuzzi, Noor Jawad, James O. Lindsay, Andrew Silver
Software Mentions: 3
Published: over 9 years ago

10.1534/g3.111.000240

Stacks: Building and Genotyping Loci De Novo From Short-Read Sequences
Cited by: 1,474
Author(s): Julian M. Catchen, Angel Amores, Paul A. Hohenlohe, William A. Cresko, John H. Postlethwait
Software Mentions: 3
Published: almost 15 years ago

10.1371/journal.pntd.0008234

Whole genome sequencing of Plasmodium vivax isolates reveals frequent sequence and structural polymorphisms in erythrocyte binding genes
Cited by: 20
Author(s): Anthony M. Ford, Daniel Kepple, Beka Raya Abagero, Jordan Connors, Richard D. Pearson, Sarah Auburn, Sisay Getachew, Colby T. Ford, Karthigayan Gunalan, Louis H. Miller, Daniel Janies, Julian C. Rayner, Guiyun Yan, Delenasaw Yewhalaw, Eugenia Lo
Software Mentions: 3
Published: almost 6 years ago

10.1534/g3.116.032839

Transcriptome Analysis Reveals that Vitamin A Metabolism in the Liver Affects Feed Efficiency in Pigs
Cited by: 31
Author(s): Yi‐Fang Zhao, Ye Hou, Fei Liu, An Liu, Jing Lü, Changzhi Zhao, Yu Luan, Yuanxin Miao, Shuhong Zhao, Xinyun Li
Software Mentions: 3
Published: over 9 years ago

10.3389/fpsyg.2021.622433

Understanding the Multidimensional and Dynamic Nature of Facial Expressions Based on Indicators for Appraisal Components as Basis for Measuring Drivers' Fear
Cited by: 2
Author(s): Meng Zhang, Klas Ihme, Uwe Drewitz, Meike Jipp
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pntd.0003115

Stability of the wMel Wolbachia Infection following Invasion into Aedes aegypti Populations
Cited by: 261
Author(s): Ary A. Hoffmann, Iñaki Iturbe‐Ormaetxe, Ashley G. Callahan, Benjamin L. Phillips, Katrina Billington, Jason K. Axford, Brian L. Montgomery, Andrew P. Turley, Scott Leslie O'Neill
Software Mentions: 3
Published: almost 12 years ago

10.26508/lsa.201800082

Mitochondrial ubiquinone–mediated longevity is marked by reduced cytoplasmic mRNA translation
Cited by: 12
Author(s): Marte Molenaars, Georges E. Janssens, Toon Santermans, Marco Lezzerini, Rob Jelier, Alyson W. MacInnes, Riekelt H. Houtkooper
Software Mentions: 3
Published: almost 8 years ago

10.3390/genes11010053

SparkRA: Enabling Big Data Scalability for the GATK RNA-seq Pipeline with Apache Spark
Cited by: 7
Author(s): Zaid Al-Ars, Saiyi Wang, Hamid Mushtaq
Software Mentions: 3
Published: over 6 years ago

10.3390/genes11091000

Comparative Transcriptome Analysis of Pine Trees Treated with Resistance-Inducing Substances against the Nematode Bursaphelenchus xylophilus
Cited by: 6
Author(s): Jung–Wook Park, Hee Won Jeon, Hyejung Jung, Hyun‐Hee Lee, Junheon Kim, Ae Ran Park, Namgyu Kim, Gil Soo Han, Jin-Cheol Kim, Young-Su Seo
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12987-020-00207-2

Advancing brain barriers RNA sequencing: guidelines from experimental design to publication
Cited by: 14
Author(s): David Francisco, Luca Marchetti, Sabela Rodríguez‐Lorenzo, Eduardo Frías-Anaya, Ricardo Figueiredo, Marjolein Heymanns, Maxime Culot, Ana Raquel Santa-Maria, Mária A. Deli, Raoul Freitas Vale Germano, Benoît Vanhollebeke, Nikolaos Kakogiannos, Monica Giannotta, Elisabetta Dejana, Amaia Dominguez-Belloso, Stefan Liebner, Markus Schuster, Harm‐Anton Klok, Marie Wiatr, Horst Schroten, Tobias Tenenbaum, Gijs Kooij, Peter Winter, Ignacio A. Romero, Helga E. de Vries, Britta Engelhardt, Rémy Bruggmann
Software Mentions: 3
Published: almost 6 years ago

10.18632/oncotarget.10947

Integrated analysis miRNA and mRNA profiling in patients with severe oligozoospermia reveals miR-34c-3p downregulates PLCXD3 expression
Cited by: 22
Author(s): Zhiming Li, Zaozao Zheng, Jun Ruan, Zhi Li, Xuan Zhuang, Chi-Meng Tzeng
Software Mentions: 3
Published: almost 10 years ago

10.18632/oncotarget.15604

NUSAP1 promotes invasion and metastasis of prostate cancer
Cited by: 49
Author(s): Catherine A. Gordon, Xue Gong, Durga Ganesh, James D. Brooks
Software Mentions: 3
Published: over 9 years ago

10.3390/genes12071064

Genetic and Transcriptomic Analysis Reveal the Molecular Basis of Photoperiod-Regulated Flowering in Xishuangbanna Cucumber (Cucumis sativus L. var. xishuangbannesis Qi et Yuan)
Cited by: 7
Author(s): Zhen Tian, Molly Jahn, Xiaodong Qin, Hesbon Ochieng Obel, Fan Yang, Ji Li, Jinfeng Chen
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pgen.1005265

The Developmental Intestinal Regulator ELT-2 Controls p38-Dependent Immune Responses in Adult C. elegans
Cited by: 42
Author(s): Dena H. S. Block, Kwame Twumasi-Boateng, Hae Sung Kang, Jolie A Carlisle, Alexandru Hanganu, Ty Yu-Jen Lai, Michael Y. Shapira
Software Mentions: 3
Published: about 11 years ago

10.3390/ijms22179246

Overdominance at the Gene Expression Level Plays a Critical Role in the Hybrid Root Growth of Brassica napus
Cited by: 8
Author(s): Nesma Shalby, Ibrahim A. A. Mohamed, Jie Xiong, Kaining Hu, Yuting Yang, Elsayed Nishawy, Bin Yi, Jing Wen, Chaozhi Ma, Tingdong Fu, Jinxing Tu
Software Mentions: 3
Published: almost 5 years ago

10.3390/ijms22041837

Whole Exome Sequencing Identifies APCDD1 and HDAC5 Genes as Potentially Cancer Predisposing in Familial Colorectal Cancer
Cited by: 5
Author(s): Diamanto Skopelitou, Benchun Miao, Aayushi Srivastava, Abhishek Kumar, Magdalena Kuswick, Dagmara Dymerska, Nagarajan Paramasivam, Matthias Schlesner, Jan Lubiński, Kari Hemminki, Asta Försti, Obul Reddy Bandapalli
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0142864

Evolutionary Quantitative Genomics of Populus trichocarpa
Cited by: 24
Author(s): Ilga Porth, Jaroslav Klápště, Athena D. McKown, Jonathan La Mantia, Robert D. Guy, Pär K. Ingvarsson, Richard Hamelin, Shawn D. Mansfield, Jürgen Ehlting, Carl J. Douglas, Yousry A. El‐Kassaby
Software Mentions: 3
Published: over 10 years ago

10.3390/metabo11090627

Comparative Untargeted Metabolomic Profiling of Induced Mitochondrial Fusion in Pancreatic Cancer
Cited by: 0
Author(s): Nathalie Nguyen, Meifang Yu, Vinit Y. Reddy, Ariana Carolina Acevedo-Diaz, Enzo C. Mesarick, Joseph Abi Jaoude, Min Yuan, John M. Asara, Cullen M. Taniguchi
Software Mentions: 3
Published: almost 5 years ago

10.3390/ijms20235922

Transcriptomic and Co-Expression Network Profiling of Shoot Apical Meristem Reveal Contrasting Response to Nitrogen Rate between Indica and Japonica Rice Subspecies
Cited by: 10
Author(s): Xiaoxiang Zhang, Juan Zhou, Niansheng Huang, Lanjing Mo, Minjia Lv, Yujiao Gao, Chen Chen, Yin Su, Jianhua Ju, Guichun Dong, Yong Zhou, Zefeng Yang, Aihong Li, Yulong Wang, Jianye Huang, Youli Yao
Software Mentions: 3
Published: over 6 years ago

10.3390/ijms16035975

RNA-Seq Transcriptome Analysis of Maize Inbred Carrying Nicosulfuron-Tolerant and Nicosulfuron-Susceptible Alleles
Cited by: 26
Author(s): Xiaomin Liu, Xiaogang Xu, Binghua Li, Xueqing Wang, Guiqi Wang, Yaqian Li
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pone.0084231

Identification of the Third Binding Site of Arsenic in Human Arsenic (III) Methyltransferase
Cited by: 12
Author(s): Xiangli Li, Zhirong Geng, Jiayin Chang, Shuping Wang, Xiaoli Song, Xin Hu, Zhilin Wang
Software Mentions: 3
Published: over 12 years ago

10.3390/s18020474

Design and Implementation of Cloud-Centric Configuration Repository for DIY IoT Applications
Cited by: 37
Author(s): Shabir Ahmad, Hang Lei, Do‐Hyeun Kim
Software Mentions: 3
Published: over 8 years ago

10.3390/s18051465

Smart Waste Collection System with Low Consumption LoRaWAN Nodes and Route Optimization
Cited by: 48
Author(s): Álvaro Lozano, Javier Caridad, Juan F. De Paz, Gabriel Villarrubia González, Javier Bajo
Software Mentions: 3
Published: about 8 years ago

10.1038/srep32965

Predicting the synergy of multiple stress effects
Cited by: 157
Author(s): Matthias Liess, Kaarina Foit, Saskia Knillmann, Ralf B. Schäfer, Hans-Dieter Ließ
Software Mentions: 3
Published: almost 10 years ago

10.1038/s41598-021-95698-w

PCA-based unsupervised feature extraction for gene expression analysis of COVID-19 patients
Cited by: 9
Author(s): Kota Fujisawa, Mamoru Shimo, Y-h. Taguchi, Shinya Ikematsu, Ryota Miyata
Software Mentions: 3
Published: almost 5 years ago

10.3390/s18124330

Variational Pansharpening for Hyperspectral Imagery Constrained by Spectral Shape and Gram–Schmidt Transformation
Cited by: 10
Author(s): Z. J. Huang, Qihao Chen, Xiuguo Liu
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-021-91503-w

Colonisation dynamics of Listeria monocytogenes strains isolated from food production environments
Cited by: 12
Author(s): Jessica Gray, P. Scott Chandry, Mandeep Kaur, Chawalit Kocharunchitt, Séamus Fanning, John P. Bowman, Edward M. Fox
Software Mentions: 3
Published: about 5 years ago

10.1038/s41598-020-65724-4

Simultaneous identification of animal-derived components in meats using high-throughput sequencing in combination with a custom-built mitochondrial genome database
Cited by: 6
Author(s): Yinan Zhang, Qinfeng Qu, RAO Mingzhen, Zhang Nana, Yu Zhao, Fei Tao
Software Mentions: 3
Published: about 6 years ago

10.1038/s41598-021-92395-6

MULTICOM2 open-source protein structure prediction system powered by deep learning and distance prediction
Cited by: 1
Author(s): Tai Tsun Wu, Jian Liu, Zhiye Guo, Jie Hou, Jianlin Cheng
Software Mentions: 3
Published: about 5 years ago

10.1038/srep39487

Novel Therapeutics Identification for Fibrosis in Renal Allograft Using Integrative Informatics Approach
Cited by: 24
Author(s): Li Li, Ilana Greene, Benjamin Readhead, Madhav C. Menon, Brian Kidd, Andrew Uzilov, Chengguo Wei, Nimrod Philippe, Bernd Schröppel, John Cijiang He, Rong Chen, Joel T. Dudley, Barbara Murphy
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0022226

High Resolution Detection and Analysis of CpG Dinucleotides Methylation Using MBD-Seq Technology
Cited by: 70
Author(s): Xun Lan, Christopher M. Adams, Mark Landers, Miroslav Dudas, Daniel Krissinger, George Marnellos, Russell Bonneville, Maoxiong Xu, Junbai Wang, Tim H-M. Huang, Gavin Meredith, Victor X. Jin
Software Mentions: 3
Published: about 15 years ago

10.1371/journal.pgen.1007949

Parental legacy, demography, and admixture influenced the evolution of the two subgenomes of the tetraploid Capsella bursa-pastoris (Brassicaceae)
Cited by: 38
Author(s): Dmytro Kryvokhyzha, Adriana Salcedo, Mimmi C. Eriksson, Tianlin Duan, Nilesh R. Tawari, Jun Chen, Maria Guerrina, Julia M. Kreiner, Tyler V. Kent, Ulf Lagercrantz, John R. Stinchcombe, Sylvain Glémin, Stephen I. Wright, Martin Lascoux
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-020-76533-0

High definition transcranial direct current stimulation modulates abnormal neurophysiological activity in post-stroke aphasia
Cited by: 16
Author(s): Priyanka P. Shah-Basak, Gayatri Sivaratnam, Selina Teti, Alexander Francois-Nienaber, Maryam Yossofzai, Sabrina E M Armstrong, Sumiti Nayar, Regina Jokel, Jed A. Meltzer
Software Mentions: 3
Published: over 5 years ago

10.1038/s41598-020-77600-2

Genetic mapping and candidate gene analysis for melon resistance to Phytophthora capsici
Cited by: 4
Author(s): Pingyong Wang, Xiuhong Xu, Guangwei Zhao, Yue He, C. T. Hou, Weihu Kong, Jian Zhang, Shuimiao Liu, Yong Xu, Zhigao Xu
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0015595

A Novel Statistical Algorithm for Gene Expression Analysis Helps Differentiate Pregnane X Receptor-Dependent and Independent Mechanisms of Toxicity
Cited by: 8
Author(s): M. Ann Mongan, Robert T. Dunn, Steven Vonderfecht, Nancy E. Everds, Guang Chen, Cheng Su, Marnie Higgins-Garn, Yuan Chen, Cynthia A. Afshari, Toni Williamson, Linda L. Carlock, Christopher DiPalma, Suzanne T. Moss, Jeanine L. Bussiere, Charles W. Qualls, Yudong He, Hisham K. Hamadeh
Software Mentions: 3
Published: over 15 years ago

10.1038/s41598-021-93893-3

Microarray-based selection of a serum biomarker panel that can discriminate between latent and active pulmonary TB
Cited by: 6
Author(s): Zhihui Li, Jianjun Hu, Pengchong Liu, Dan Cui, Hongqin Di, Shucai Wu
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pgen.1000812

Altered Gene Expression and DNA Damage in Peripheral Blood Cells from Friedreich's Ataxia Patients: Cellular Model of Pathology
Cited by: 95
Author(s): Astrid C. Haugen, Nicholas A. Di Prospero, Joel S. Parker, Rick D. Fannin, Jeff W. Chou, Joel N. Meyer, Christopher Halweg, Jennifer B. Collins, Alexandra Dürr, Kenneth H. Fischbeck, Bennett Van Houten
Software Mentions: 3
Published: over 16 years ago

10.1371/journal.pone.0010770

Integrative Genome Comparison of Primary and Metastatic Melanomas
Cited by: 159
Author(s): Omar Kabbarah, Cristina Nogueira, Bin Feng, Rosalynn M. Nazarian, Marcus W. Bosenberg, Min Wu, Kenneth L. Scott, Lawrence N. Kwong, Yonghong Xiao, Carlos Cordón-Cardo, Scott R. Granter, Sridhar Ramaswamy, Todd R. Golub, Lyn M. Duncan, Stephan N. Wagner, Cameron Brennan, Lynda Chin
Software Mentions: 3
Published: about 16 years ago

10.1038/s41598-020-74877-1

Low E2F2 activity is associated with high genomic instability and PARPi resistance
Cited by: 4
Author(s): Jonathan Rennhack, Eran R. Andrechek
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pgen.1006571

Enhancer of polycomb coordinates multiple signaling pathways to promote both cyst and germline stem cell differentiation in the Drosophila adult testis
Cited by: 25
Author(s): Lijuan Feng, Zhen Shi, Xin Chen
Software Mentions: 3
Published: over 9 years ago

10.1038/srep38096

Whole-genome scanning for the litter size trait associated genes and SNPs under selection in dairy goat (Capra hircus)
Cited by: 81
Author(s): Fang-Nong Lai, Hong-Li Zhai, Ming Cheng, Jun‐Yu Ma, Shun‐Feng Cheng, Wei Ge, Guoliang Zhang, Junjie Wang, Ruiqian Zhang, Xue Wang, Min Liu, Jiuzhou Song, Wei Shen
Software Mentions: 3
Published: over 9 years ago

10.1038/s41598-021-90243-1

Metabolomics and computational analysis of the role of monoamine oxidase activity in delirium and SARS-COV-2 infection
Cited by: 17
Author(s): Miroslava Čuperlović-Culf, Emma Cunningham, Hossen Teimoorinia, Anuradha Surendra, Xiaobei Pan, Steffany A. L. Bennett, Mijin Jung, Bernadette McGuiness, Anthony Peter Passmore, David Beverland, Brian D. Green
Software Mentions: 3
Published: about 5 years ago

10.1038/srep37563

A novel process of viral vector barcoding and library preparation enables high-diversity library generation and recombination-free paired-end sequencing
Cited by: 21
Author(s): Marcus Davidsson, Paula Díaz-Fernández, Oliver D. Schwich, Marcos Torroba, Gang Wang, Tomas Björklund
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0238311

Length of stay to recover from severe acute malnutrition and associated factors among under-five years children admitted to public hospitals in Aksum, Ethiopia
Cited by: 10
Author(s): Wagnew Tesfay, Mebrahtu Abay, Solomon Hintsa, Tekia Zafu
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pgen.1004142

Genetic Basis of Metabolome Variation in Yeast
Cited by: 50
Author(s): J. Scott Breunig, Sean R. Hackett, Joshua D. Rabinowitz, Leonid Kruglyak
Software Mentions: 3
Published: over 12 years ago

10.1038/srep33262

Subpathway-CorSP: Identification of metabolic subpathways via integrating expression correlations and topological features between metabolites and genes of interest within pathways
Cited by: 13
Author(s): Chenchen Feng, Jian Zhang, Xuecang Li, Bo Ai, Junwei Han, Qiuyu Wang, Taiming Wei, Yong Xu, Meng Li, Shang Li, Chao Song, Chunquan Li
Software Mentions: 3
Published: almost 10 years ago

10.1186/2049-3002-2-13

Loss of HSulf-1 promotes altered lipid metabolism in ovarian cancer
Cited by: 27
Author(s): Debarshi Roy, Susmita Mondal, Chen Wang, Xiaoping He, Ashwani Khurana, Shailendra Giri, Robert Hoffmann, Deok‐Beom Jung, Sung Hyun Kim, Eduardo N. Chini, Juliana Camacho Periera, Clifford D.L. Folmes, Andrea Mariani, Sean C. Dowdy, Jamie N. Bakkum-Gamez, Shaun M. Riska, Ann L. Oberg, Edward D. Karoly, Lauren N. Bell, Jeremy Chien, Viji Shridhar
Software Mentions: 3
Published: almost 12 years ago

10.1371/journal.pgen.1009600

Antagonistic fungal enterotoxins intersect at multiple levels with host innate immune defences
Cited by: 10
Author(s): Xing Zhang, Benjamin W. Harding, Dina Aggad, Damien Courtine, Jia‐Xuan Chen, Nathalie Pujol, Jonathan J. Ewbank
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0163832

The Role of Vitamin D in the Transcriptional Program of Human Pregnancy
Cited by: 30
Author(s): Amal Al-Garawi, Vincent J. Carey, Divya Chhabra, Hooman Mirzakhani, Jarrett Morrow, Jessica Lasky‐Su, Weiliang Qiu, Nancy Laranjo, Augusto A. Litonjua, Scott T. Weiss
Software Mentions: 3
Published: almost 10 years ago

10.1038/srep27623

Multiplex giant magnetoresistive biosensor microarrays identify interferon-associated autoantibodies in systemic lupus erythematosus
Cited by: 31
Author(s): J. Lee, D. James Haddon, Hannah Wand, J. M. Price, Vivian K. Diep, Drew A. Hall, Michelle Petri, Emily C. Baechler, Imelda Balboni, Paul J. Utz, Shan X. Wang
Software Mentions: 3
Published: about 10 years ago

10.1371/journal.pgen.1001135

Analysis of the Basidiomycete Coprinopsis cinerea Reveals Conservation of the Core Meiotic Expression Program over Half a Billion Years of Evolution
Cited by: 34
Author(s): Claire Burns, Jason E. Stajich, Andreas Rechtsteiner, Lorna A. Casselton, Sean E. Hanlon, Sarah K. Wilke, Oleksandr P. Savytskyy, Allen C. Gathman, Walt W. Lilly, Jason D. Lieb, Miriam E. Zolan, Patricia J. Pukkila
Software Mentions: 3
Published: almost 16 years ago

10.1038/srep41238

Patient-specific hepatocyte-like cells derived from induced pluripotent stem cells model pazopanib-mediated hepatotoxicity
Cited by: 43
Author(s): Yukti Choudhury, Yi‐Chin Toh, Jiangwa Xing, Yinghua Qu, Jonathan Poh, Huan Li, Hui Shan Tan, Ravindran Kanesvaran, Hanry Yu, Min‐Han Tan
Software Mentions: 3
Published: over 9 years ago

10.1038/s41598-021-83459-8

Investigation of allele specific expression in various tissues of broiler chickens using the detection tool VADT
Cited by: 5
Author(s): M. Joseph Tomlinson, Shawn W. Polson, Jing Qiu, Juniper A. Lake, William Lee, Behnam Abasht
Software Mentions: 3
Published: over 5 years ago

10.3390/s17040777

A Review of Wetland Remote Sensing
Cited by: 247
Author(s): Meng Guo, Jing Li, Chunlei Sheng, Jiawei Xu, Li Wu
Software Mentions: 3
Published: over 9 years ago

10.3390/s17030578

Assessing the Spectral Properties of Sunlit and Shaded Components in Rice Canopies with Near-Ground Imaging Spectroscopy Data
Cited by: 21
Author(s): Kai Zhou, Xinqiang Deng, Xia Yao, Yongchao Tian, Weixing Cao, Yan Zhu, Susan L. Ustin, Tao Cheng
Software Mentions: 3
Published: over 9 years ago

10.3758/s13421-020-01082-w

The simultaneous recognition of multiple words: A process analysis
Cited by: 4
Author(s): Anne Voormann, Mikhail S. Spektor, Karl Christoph Klauer
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pgen.0010016

Glucocorticoid Receptor-Dependent Gene Regulatory Networks
Cited by: 194
Author(s): Panin Le, Joshua R. Friedman, Jonathan Schug, John Brestelli, J. Brandon Parker, Irina M. Bochkis, Klaus H. Kaestner
Software Mentions: 3
Published: almost 21 years ago

10.1038/s41598-021-93555-4

The conserved ASTN2/BRINP1 locus at 9q33.1–33.2 is associated with major psychiatric disorders in a large pedigree from Southern Spain
Cited by: 1
Author(s): Josep Pol-Fuster, Francesca Cañellas, Laura Ruiz-Guerra, Aina Medina-Dols, Bàrbara Bisbal-Carrió, Bernat Ortega-Vila, Jaume Llinàs, Jessica Hernández-Rodríguez, Jerònia Lladó, Gabriel Olmos, Konstantin Strauch, Damián Heine-Suñer, Cristòfol Vives-Bauzà, Antònia Flaquer
Software Mentions: 3
Published: about 5 years ago

10.3390/ijms20010016

Clinically Relevant Post-Translational Modification Analyses—Maturing Workflows and Bioinformatics Tools
Cited by: 34
Author(s): Dana Pascovici, Jemma X. Wu, Matthew J. McKay, Chitra Joseph, Zainab Noor, Karthik Shantharam Kamath, Yunqi Wu, Shoba Ranganathan, Vivek Gupta, Mehdi Mirzaei
Software Mentions: 3
Published: over 7 years ago

10.1038/s41597-020-0427-5

Gut microbiome diversity detected by high-coverage 16S and shotgun sequencing of paired stool and colon sample
Cited by: 35
Author(s): Joan Mas-Lloret, Mireia Obón-Santacana, Gemma Ibáñez‐Sanz, Elisabet Guinó, Miguel L Pato, Francisco Rodríguez-Moranta, Alfredo Mata, Ana García-Rodríguez, Vı́ctor Moreno, Ville N. Pimenoff
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0046847

lociNGS: A Lightweight Alternative for Assessing Suitability of Next-Generation Loci for Evolutionary Analysis
Cited by: 6
Author(s): Sarah M. Hird
Software Mentions: 3
Published: almost 14 years ago

10.1038/srep13245

Predictive habitat suitability models to aid conservation of elasmobranch diversity in the central Mediterranean Sea
Cited by: 52
Author(s): Valentina Lauria, Michele Gristina, Martin J. Attrill, Fabio Fiorentino, Germana Garofalo
Software Mentions: 3
Published: almost 11 years ago

10.3390/ijms17050696

Identification of More Feasible MicroRNA–mRNA Interactions within Multiple Cancers Using Principal Component Analysis Based Unsupervised Feature Extraction
Cited by: 31
Author(s): Y-h. Taguchi
Software Mentions: 3
Published: about 10 years ago

10.3390/s100301967

A Comparison of Spectral Angle Mapper and Artificial Neural Network Classifiers Combined with Landsat TM Imagery Analysis for Obtaining Burnt Area Mapping
Cited by: 102
Author(s): George P. Petropoulos, Krishna Prasad Vadrevu, Gavriil Xanthopoulos, G. Karantounias, Marko Scholze
Software Mentions: 3
Published: over 16 years ago

10.1371/journal.pgen.1003820

The Genome and Development-Dependent Transcriptomes of Pyronema confluens: A Window into Fungal Evolution
Cited by: 80
Author(s): Stefanie Traeger, Florian Altegoer, Michael Freitag, Toni Gabaldón, Frank Kempken, Abhishek Kumar, Marina Marcet‐Houben, Stefanie Pöggeler, Jason E. Stajich, Minou Nowrousian
Software Mentions: 3
Published: almost 13 years ago

10.3390/ijms22105231

Dual RNA-Sequencing Analysis of Resistant (Pinus pinea) and Susceptible (Pinus radiata) Hosts during Fusarium circinatum Challenge
Cited by: 12
Author(s): Cristina Zamora-Ballesteros, Glória Pinto, Joana Amaral, Luís Valledor, Artur Alves, Julio J. Diez, Jorge Martín‐García
Software Mentions: 3
Published: about 5 years ago

10.3390/ijms22169081

Modeling and Structure Determination of Homo-Oligomeric Proteins: An Overview of Challenges and Current Approaches
Cited by: 10
Author(s): Aljaž Gaber, Miha Pavšič
Software Mentions: 3
Published: almost 5 years ago

10.18632/oncotarget.5876

KIAA0101 is associated with human renal cell carcinoma proliferation and migration induced by erythropoietin
Cited by: 27
Author(s): Shengjun Fan, Xin Li, Lu Tie, Yan Pan, Xuejun Li
Software Mentions: 3
Published: over 10 years ago

10.1186/s12974-017-0858-x

Toll-like receptor 4 in glial inflammatory responses to air pollution in vitro and in vivo
Cited by: 99
Author(s): Nick Woodward, Morgan C. Levine, Amin Haghani, Farimah Shirmohammadi, Arian Saffari, Constantinos Sioutas, Todd E. Morgan, Caleb E. Finch
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.pone.0086214

Protection Genes in Nucleus Accumbens Shell Affect Vulnerability to Nicotine Self-Administration across Isogenic Strains of Adolescent Rat
Cited by: 10
Author(s): Hao Chen, Rui Luo, Shusheng Gong, Shannon G. Matta, Burt M. Sharp
Software Mentions: 3
Published: over 12 years ago

10.1111/1751-7915.13863

Transcriptome analysis reveals the roles of nitrogen metabolism and sedoheptulose bisphosphatase pathway in methanol‐dependent growth of Corynebacterium glutamicum
Cited by: 4
Author(s): Liwen Fan, Yu Wang, Jin Qian, Ning Gao, Zhihui Zhang, Xiaomeng Ni, Letian Sun, Qianqian Yuan, Ping Zheng, Jibin Sun
Software Mentions: 3
Published: about 5 years ago

10.18632/oncotarget.18162

Upregulation of long noncoding RNA HOXA-AS3 promotes tumor progression and predicts poor prognosis in glioma
Cited by: 53
Author(s): Fan Wu, Chuanbao Zhang, Jinquan Cai, Fan Yang, Tingyu Liang, Xiaoyan Yan, Haoyuan Wang, Wen Wang, Jing Chen, Tao Jiang
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pone.0103515

Characterisation of Adaptive Genetic Diversity in Environmentally Contrasted Populations of Eucalyptus camaldulensis Dehnh. (River Red Gum)
Cited by: 40
Author(s): Shannon Dillon, Rachel McEvoy, Darren S. Baldwin, Gavin N. Rees, Y. M. Parsons, Simon G. Southerton
Software Mentions: 3
Published: almost 12 years ago

Projects: cran: SAM

Science Score: 85/100

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Papers Mentioning SAM 4,566