cran: SAM | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0134031

Genomic Resources for Water Yam (Dioscorea alata L.): Analyses of EST-Sequences, De Novo Sequencing and GBS Libraries
Cited by: 27
Author(s): Christopher Saski, Ranjana Bhattacharjee, Brian E. Scheffler, Robert Asiedu
Software Mentions: 2
Published: about 11 years ago

10.3390/cancers13153755

Transcription/Replication Conflicts in Tumorigenesis and Their Potential Role as Novel Therapeutic Targets in Multiple Myeloma
Cited by: 6
Author(s): Laure Dutrieux, Yea-Lih Lin, Malik Lutzmann, Raphaël Rodriguez, Michel Cogné, Philippe Pasero, Jérôme Moreaux
Software Mentions: 2
Published: about 5 years ago

10.3390/cancers13010001

Incorporating the Patient Voice in Sarcoma Research: How Can We Assess Health-Related Quality of Life in This Heterogeneous Group of Patients? A Study Protocol
Cited by: 11
Author(s): Dide den Hollander, Marco Fiore, Javier Martin‐Broto, Bernd Kasper, Antonio Casado Herráez, Danijela Kuliš, Ioanna Nixon, Samantha Sodergren, Martin Eichler, Winan J. van Houdt, Ingrid M.E. Desar, Isabelle Ray‐Coquard, Claire Piccinin, Hanna Koseła-Paterczyk, Aisha Miah, Leopold Hentschel, Susanne Schnittger, Roger Wilson, Winette T.A. van der Graaf, Olga Husson
Software Mentions: 2
Published: over 5 years ago

10.3390/cancers12061355

The Possible Influence of Mediterranean Diet on Extracellular Vesicle miRNA Expression in Breast Cancer Survivors
Cited by: 8
Author(s): Yu‐Jin Kwon, Young-Eun Cho, A-Ra Cho, Won-Jun Choi, Sijung Yun, Hyunki Park, Hyung-Suk Kim, Ann K. Cashion, Jessica Gill, Hyangkyu Lee, Jiwon Lee
Software Mentions: 2
Published: over 6 years ago

10.3390/cancers12123695

Functional Screening Techniques to Identify Long Non-Coding RNAs as Therapeutic Targets in Cancer
Cited by: 10
Author(s): Kathleen M Lucere, Megan M R O'Malley, Sarah D. Diermeier
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41419-018-0476-2

Inhibition of cancer progression by a novel trans-stilbene derivative through disruption of microtubule dynamics, driving G2/M arrest, and p53-dependent apoptosis
Cited by: 35
Author(s): Pravat Kumar Parida, Barun Mahata, Abhisek Santra, Sohini Chakraborty, Zhumur Ghosh, Sanghamitra Raha, Anup Kumar Misra, Kaushik Biswas, Kuladip Jana
Software Mentions: 2
Published: over 8 years ago

10.1038/cddis.2016.148

A ribosome-related signature in peripheral blood CLL B cells is linked to reduced survival following treatment
Cited by: 24
Author(s): Thomas Sbarrato, Emilie Horvilleur, Tuija Pöyry, Kirsti Hill, L C Chaplin, R V Spriggs, Mark Stoneley, Lindsay A. Wilson, Sandrine Jayne, Tom Vulliamy, Daniel Beck, Inderjeet Dokal, Martin J. S. Dyer, Alison Yeomans, Graham Packham, Martin Bushell, Simon D. Wagner, Anne E. Willis
Software Mentions: 2
Published: over 10 years ago

10.1038/s41419-021-03523-z

Long noncoding RNA LINC00518 induces radioresistance by regulating glycolysis through an miR-33a-3p/HIF-1α negative feedback loop in melanoma
Cited by: 28
Author(s): Yan Liu, Dong He, Mengqing Xiao, Yuxing Zhu, Jianda Zhou, Ke Cao
Software Mentions: 2
Published: over 5 years ago

10.1186/1747-1028-4-20

Proteomics, pathway array and signaling network-based medicine in cancer
Cited by: 56
Author(s): David Y. Zhang, Fei Ye, Ling Gao, Xiaoliang Liu, Xin Zhao, Yufang Che, Hongxia Wang, Libo Wang, Josephine W. Wu, Dong Eun Song, Wei Liu, Hong Xu, Bo Jiang, Weijia Zhang, Jinhua Wang, Peng Lee
Software Mentions: 2
Published: over 17 years ago

10.1007/s00018-020-03695-5

Human RNase3 immune modulation by catalytic-dependent and independent modes in a macrophage-cell line infection model
Cited by: 8
Author(s): Lu Lu, Ranlei Wei, Guillem Prats-Ejarque, Maria Goetz, Gang Wang, M. C. Torrent, Ester Boix
Software Mentions: 2
Published: almost 6 years ago

10.1016/j.celrep.2018.04.044

mTOR Senses Environmental Cues to Shape the Fibroblast-like Synoviocyte Response to Inflammation
Cited by: 46
Author(s): Thomas Karonitsch, Richard K. Kandasamy, Felix Kartnig, Barbara Herdy, K Dalwigk, Birgit Niederreiter, Johannes Holinka, Florian Sevelda, Reinhard Windhager, Martin Bilban, Thomas Weichhart, Marcus D. Säemann, Thomas Pap, Günter Steiner, Josef S Smolen, Hans P. Kiener, Giulio Superti‐Furga
Software Mentions: 2
Published: over 8 years ago

10.1016/j.stem.2013.09.003

Dynamic Analysis of Gene Expression and Genome-wide Transcription Factor Binding during Lineage Specification of Multipotent Progenitors
Cited by: 84
Author(s): Gillian May, Shamit Soneji, Alex J. Tipping, José Teles, Simon J. McGowan, Mengchu Wu, Yanping Guo, Cristina Fugazza, John Brown, Göran Karlsson, Cristina Pina, Victor Olariu, Stephen Taylor, Daniel G. Tenen, Carsten Peterson, Tariq Enver
Software Mentions: 2
Published: almost 13 years ago

10.1016/j.tcsw.2021.100051

Mycobacterium abscessus biofilms produce an extracellular matrix and have a distinct mycolic acid profile
Cited by: 20
Author(s): Anja Dokic, Eliza J.R. Peterson, Mario L. Arrieta-Ortiz, Min Pan, Alessandro Di Maio, Nitin S. Baliga, Apoorva Bhatt
Software Mentions: 2
Published: almost 5 years ago

10.1016/j.tcsw.2020.100043

Biofilms of the non-tuberculous Mycobacterium chelonae form an extracellular matrix and display distinct expression patterns
Cited by: 8
Author(s): Perla Jazmín Vega-Domínguez, Eliza J.R. Peterson, Min Pan, Alessandro Di Maio, Saumya Singh, Siva Umapathy, Deepak Kumar Saini, Nitin S. Baliga, Apoorva Bhatt
Software Mentions: 2
Published: almost 6 years ago

10.3390/cells9081864

S-Adenosylmethionine Treatment of Colorectal Cancer Cell Lines Alters DNA Methylation, DNA Repair and Tumor Progression-Related Gene Expression
Cited by: 15
Author(s): Sára Zsigrai, Alexandra Kalmár, Zsófia Brigitta Nagy, Barbara Kinga Barták, Gábor Valcz, Krisztina Andrea Szigeti, Orsolya Galamb, Titanilla Dankó, Anna Sebestyén, Gábor Barna, V. Szabó, Orsolya Pipek, Anna Medgyes-Horváth, István Csabai, Zsolt Tulassay, Péter Igaz, István Takács, Béla Molnár
Software Mentions: 2
Published: about 6 years ago

10.1289/ehp.11229

Murine Lung Responses to Ambient Particulate Matter: Genomic Analysis and Influence on Airway Hyperresponsiveness
Cited by: 55
Author(s): Ting Wang, Liliana Moreno‐Vinasco, Yong Huang, Gabriel Lang, Jered Linares, Sascha N. Goonewardena, Alayna Grabavoy, Jonathan M. Samet, Alison S. Geyh, Patrick N. Breysse, Yves A. Lussier, Viswanathan Natarajan, Joe G.N. Garcia
Software Mentions: 2
Published: almost 18 years ago

10.1289/ehp.10216

Nanosize Titanium Dioxide Stimulates Reactive Oxygen Species in Brain Microglia and Damages Neurons in Vitro
Cited by: 399
Author(s): Thomas Long, Julianne Tajuba, Preethi Sama, Navid B. Saleh, Carol D. Swartz, Joel Parker, Susan Hester, Gregory V. Lowry, Bellina Veronesi
Software Mentions: 2
Published: almost 19 years ago

10.1289/ehp.10861

Drinking-Water Arsenic Exposure Modulates Gene Expression in Human Lymphocytes from a U.S. Population
Cited by: 128
Author(s): Angeline S. Andrew, Dianne V. Jewell, Rebecca A. Mason, Michael L. Whitfield, Jason H. Moore, Margaret R. Karagas
Software Mentions: 2
Published: over 18 years ago

10.1111/1462-2920.14590

Riding the wave of genomics to investigate aquatic coliphage diversity and activity
Cited by: 25
Author(s): Slawomir Michniewski, Tamsin Redgwell, Aurelija Grigonyte, Branko Rihtman, Maria del Mar Aguiló-Ferretjans, Joseph Alexander Christie-Oleza, Eleanor Jameson, David J. Scanlan, Andrew Millard
Software Mentions: 2
Published: over 7 years ago

10.1186/s40793-020-00354-x

Impact of process temperature and organic loading rate on cellulolytic / hydrolytic biofilm microbiomes during biomethanation of ryegrass silage revealed by genome-centered metagenomics and metatranscriptomics
Cited by: 12
Author(s): Irena Maus, Michael Klocke, Jaqueline Derenkó, Yvonne Stolze, Michael Beckstette, Carsten Jost, Daniel Wibberg, Jochen Blom, Christian Henke, Katharina Willenbücher, Madis Rumming, Antje Rademacher, Alfred Pühler, Alexander Sczyrba, Andreas Schlüter
Software Mentions: 2
Published: over 6 years ago

10.1007/s11356-017-0515-z

Transcriptional changes measured in rice roots after exposure to arsenite-contaminated sediments
Cited by: 7
Author(s): Alexandra Brinke, Georg Reifferscheid, Roland Klein, Ute Feiler, Sebastian Buchinger
Software Mentions: 2
Published: almost 9 years ago

10.1186/1756-8935-4-10

Genome-wide mapping of imprinted differentially methylated regions by DNA methylation profiling of human placentas from triploidies
Cited by: 74
Author(s): Ryan K. C. Yuen, Ruiwei Jiang, Maria S. Peñaherrera, Deborah E. McFadden, Wendy P. Robinson
Software Mentions: 2
Published: about 15 years ago

10.1002/eji.200838232

Fibroblasts from different sites may promote or inhibit recruitment of flowing lymphocytes by endothelial cells
Cited by: 81
Author(s): Helen M. McGettrick, Emily Smith, Andrew Filer, Stephen Kissane, M Salmon, Christopher D. Buckley, G. Ed Rainger, Gerard B. Nash
Software Mentions: 2
Published: over 17 years ago

10.1186/s40001-014-0052-x

RETRACTED ARTICLE: Ranking candidate genes of esophageal squamous cell carcinomas based on differentially expressed genes and the topological properties of the co-expression network
Cited by: 3
Author(s): Yi Shen, Jicheng Tantai, Heng Zhao
Software Mentions: 2
Published: almost 12 years ago

10.1155/2020/5859023

Quyushengxin Formula Causes Differences in Bacterial and Phage Composition in Ulcerative Colitis Patients
Cited by: 7
Author(s): Haojie Yang, Dan Gan, Ying Li, Xiaosu Wang, Lan Jin, Kaijian Qin, Can Cui, Jiong Wu, Zhenyi Wang
Software Mentions: 2
Published: over 6 years ago

10.1111/eva.12890

Restoration‐mediated secondary contact leads to introgression of alewife ecotypes separated by a colonial‐era dam
Cited by: 10
Author(s): Kerry Reid, John Carlos Garza, Steven R. Gephard, Adalgisa Caccone, David M. Post, Eric P. Palkovacs
Software Mentions: 2
Published: almost 7 years ago

10.1002/evl3.39

Male-biased gene expression resolves sexual conflict through the evolution of sex-specific genetic architecture
Cited by: 62
Author(s): Alison E. Wright, Matteo Fumagalli, Christopher R. Cooney, Natasha I. Bloch, Filipe Garrett Vieira, Séverine D. Buechel, Niclas Kolm, Judith E. Mank
Software Mentions: 2
Published: over 8 years ago

10.12688/f1000research.2-217.v2

MethylExtract: High-Quality methylation maps and SNV calling from whole genome bisulfite sequencing data
Cited by: 16
Author(s): Guillermo Barturen, Antonio Rueda, José Luis Tejera Oliver, Michael Hackenberg
Software Mentions: 2
Published: over 12 years ago

10.12688/f1000research.8382.2

Closing gaps between open software and public data in a hackathon setting: User-centered software prototyping
Cited by: 12
Author(s): Ben Busby, Matthew Lesko, August, January Hackathon participants, Lisa Federer
Software Mentions: 2
Published: over 10 years ago

10.12688/f1000research.21142.2

Falco: high-speed FastQC emulation for quality control of sequencing data
Cited by: 104
Author(s): Guilherme de Sena Brandine, Andrew D. Smith
Software Mentions: 2
Published: over 5 years ago

10.12688/f1000research.22954.3

QUARTIC: QUick pArallel algoRithms for high-Throughput sequencIng data proCessing
Cited by: 3
Author(s): Frédéric Jarlier, Nicolas Joly, Nicolas Fedy, Thomas Magalhaes, Leonor Sirotti, Paul Paganiban, F. Elizabeth Martin, Michael T. McManus, Philippe Hupé
Software Mentions: 2
Published: almost 6 years ago

10.3389/fbioe.2020.00882

Cell Reprogramming With CRISPR/Cas9 Based Transcriptional Regulation Systems
Cited by: 26
Author(s): K. M. Shakirova, Viktoriia Y. Ovchinnikova, Э. Б. Дашинимаев
Software Mentions: 2
Published: about 6 years ago

10.3389/fbioe.2021.731247

Rapid Enabling of Gluconobacter oxydans Resistance to High D-Sorbitol Concentration and High Temperature by Microdroplet-Aided Adaptive Evolution
Cited by: 3
Author(s): Li Liu, Weizhu Zeng, Shiqin Yu, Jianghua Li, Jingwen Zhou
Software Mentions: 2
Published: about 5 years ago

10.3389/fbioe.2020.00711

Development and Application of CRISPR/Cas in Microbial Biotechnology
Cited by: 36
Author(s): Wentao Ding, Zhipeng Yang, Shuobo Shi
Software Mentions: 2
Published: about 6 years ago

10.3389/fcell.2020.00242

Detection of Allosteric Effects of lncRNA Secondary Structures Altered by SNPs in Human Diseases
Cited by: 7
Author(s): Xiaoyan Lu, Yu Ding, Yu Bai, Jing Li, Guosi Zhang, Siyu Wang, Wenyan Gao, Liangde Xu, Hong Wang
Software Mentions: 2
Published: over 6 years ago

10.3389/fcell.2021.715275

Identification of Somatic Mutation-Driven Immune Cells by Integrating Genomic and Transcriptome Data
Cited by: 2
Author(s): Ying Jiang, Buhong Zheng, Yang Yang, Xiangmei Li, Junwei Han
Software Mentions: 2
Published: about 5 years ago

10.3389/fcell.2021.607782

Hypermethylation and Downregulation of UTP6 Are Associated With Stemness Properties, Chemoradiotherapy Resistance, and Prognosis in Rectal Cancer: A Co-expression Network Analysis
Cited by: 1
Author(s): Yiyi Zhang, Qun Gao, Yong Wu, Yong Peng, Jinfu Zhuang, Yuanfeng Yang, Weizhong Jiang, Xing Liu, Guoxian Guan
Software Mentions: 2
Published: about 5 years ago

10.3389/fcell.2020.628222

Structural and Biochemical Characterization of EFhd1/Swiprosin-2, an Actin-Binding Protein in Mitochondria
Cited by: 6
Author(s): Sang A Mun, Jongseo Park, Kyoung Ryoung Park, Youngjin Lee, Jung Youn Kang, Tae‐In Park, Minho Jin, Jamie O. Yang, Chang‐Duk Jun, Soo Hyun Eom
Software Mentions: 2
Published: over 5 years ago

10.3389/fncom.2016.00077

ARTIE: An Integrated Environment for the Development of Affective Robot Tutors
Cited by: 7
Author(s): Luis-Eduardo Imbernón Cuadrado, Ángeles Manjarrés Riesco, Félix de la Paz López
Software Mentions: 2
Published: about 10 years ago

10.3389/fendo.2012.00133

Thyroid cancer cell lines: an overview
Cited by: 104
Author(s): Manuel Saiselet, Sébastien Floor, Maxime Tarabichi, Geert Dom, Aline Hébrant, Wilma C.G. van Staveren, Carine Maenhaut
Software Mentions: 2
Published: over 14 years ago

10.3389/fgene.2017.00231

Using RNA Sequence and Structure for the Prediction of Riboswitch Aptamer: A Comprehensive Review of Available Software and Tools
Cited by: 29
Author(s): Deborah Antunes, Natasha Andressa Nogueira Jorge, Ernesto R. Caffarena, Fábio Passetti
Software Mentions: 2
Published: over 8 years ago

10.3389/fgene.2019.00296

Mining Magnaporthe oryzae sRNAs With Potential Transboundary Regulation of Rice Genes Associated With Growth and Defense Through Expression Profile Analysis of the Pathogen-Infected Rice
Cited by: 7
Author(s): Hao Zhang, Sifei Liu, Haowu Chang, Mengping Zhan, Qing‐Ming Qin, Borui Zhang, Zhi Li, Yuanning Liu
Software Mentions: 2
Published: over 7 years ago

10.3389/fgene.2019.01190

Whole Genome Resequencing Reveals Selection Signatures Associated With Important Traits in Ethiopian Indigenous Goat Populations
Cited by: 6
Author(s): Haile Berihulay, Yefang Li, Berihu Gebrekidan, Gebremedhin Gebreselassie, Xuexue Liu, Lin Jiang, Yue Ma
Software Mentions: 2
Published: almost 7 years ago

10.3389/fgene.2021.634635

Research on the Mechanism of Soybean Resistance to Phytophthora Infection Using Machine Learning Methods
Cited by: 5
Author(s): Junxia Chi, Shizeng Song, Hao Zhang, Yuanning Liu, Hengyi Zhao, Liyan Dong
Software Mentions: 2
Published: over 5 years ago

10.3389/fgene.2020.603093

Detection of Pathogenic Microbe Composition Using Next-Generation Sequencing Data
Cited by: 0
Author(s): Huijing Zhao, Shuang Wang, Xiguo Yuan
Software Mentions: 2
Published: almost 6 years ago

10.3389/fgene.2020.00113

FBXW4 Acts as a Protector of FOLFOX-Based Chemotherapy in Metastatic Colorectal Cancer Identified by Co-Expression Network Analysis
Cited by: 6
Author(s): Yiyi Zhang, Lijun Sun, Xiaojie Wang, Yanwu Sun, Ying Chen, Meifang Xu, Pan Chi, Xingrong Lu, Zongbin Xu
Software Mentions: 2
Published: over 6 years ago

10.3389/fgene.2020.00830

Insights Into the Albinism Mechanism for Two Distinct Color Morphs of Northern Snakehead, Channa argus Through Histological and Transcriptome Analyses
Cited by: 2
Author(s): Aiguo Zhou, Shaolin Xie, Feng Yuan, Dan Sun, Shulin Liu, Zhuolin Sun, Mingzhi Li, Chaonan Zhang
Software Mentions: 2
Published: almost 6 years ago

10.3389/fgene.2020.00406

Analysis of the Mouse Y Chromosome by Single-Molecule Sequencing With Y Chromosome Enrichment
Cited by: 9
Author(s): Yuki Yano, Tomoki Chiba, Hiroshi Asahara
Software Mentions: 2
Published: over 6 years ago

10.3389/fgene.2015.00163

Hidden among the crowd: differential DNA methylation-expression correlations in cancer occur at important oncogenic pathways
Cited by: 12
Author(s): Adrián Mosquera Orgueira
Software Mentions: 2
Published: over 11 years ago

10.3389/fnhum.2018.00322

Mapping the Spatiotemporal Evolution of Emotional Processing: An MEG Study Across Arousal and Valence Dimensions
Cited by: 11
Author(s): Charis Styliadis, Andreas A. Ioannides, Panagiotis D. Bamidis, Christos Papadelis
Software Mentions: 2
Published: about 8 years ago

10.3389/fimmu.2021.625586

The Effects of Helicobacter pylori Infection on Microbiota Associated With Gastric Mucosa and Immune Factors in Children
Cited by: 9
Author(s): Wei Zheng, Miao Jin, Lingling Luo, Long Gao, Bin Chen, Xiaoli Shu, Weizhong Gu, Kui Peng, Fubang Li, Hong Zhao, Benson O. A. Botchway, Marong Fang, Mizu Jiang
Software Mentions: 2
Published: over 5 years ago

10.3389/fimmu.2017.01288

Helicobacter pylori Affects the Antigen Presentation Activity of Macrophages Modulating the Expression of the Immune Receptor CD300E through miR-4270
Cited by: 34
Author(s): Matteo Pagliari, Fabio Munari, Marta Toffoletto, Silvia Lonardi, Francesco Chemello, Gaia Codolo, Caterina Millino, Chiara Della Bella, Beniamina Pacchioni, William Vermi, Matteo Fassan, Marina de Bernard, Stefano Cagnin
Software Mentions: 2
Published: almost 9 years ago

10.3389/fimmu.2021.709910

Transcriptome Profiling of Atlantic Salmon Adherent Head Kidney Leukocytes Reveals That Macrophages Are Selectively Enriched During Culture
Cited by: 4
Author(s): Nicole C. Smith, Navaneethaiyer Umasuthan, Surendra Kumar, Nardos Tesfaye Woldemariam, Rune Andreassen, Sherri L. Christian, Matthew L. Rise
Software Mentions: 2
Published: about 5 years ago

10.3389/fimmu.2019.00468

CD117 (c-Kit) Is Expressed During CD8+ T Cell Priming and Stratifies Sensitivity to Apoptosis According to Strength of TCR Engagement
Cited by: 19
Author(s): Guido Frumento, Jianmin Zuo, Kriti Verma, Wayne Croft, Pradeep Ramagiri, Frederick Chen, Paul Moss
Software Mentions: 2
Published: over 7 years ago

10.3389/fnint.2012.00113

The Interplay between Emotion and Cognition in Autism Spectrum Disorder: Implications for Developmental Theory
Cited by: 91
Author(s): Sebastian Gaigg
Software Mentions: 2
Published: over 14 years ago

10.3389/fmicb.2019.00107

Survival Mechanisms of Campylobacter hepaticus Identified by Genomic Analysis and Comparative Transcriptomic Analysis of in vivo and in vitro Derived Bacteria
Cited by: 19
Author(s): Thi Thu Hao Van, Jake A. Lacey, Ben Vezina, Canh Phung, Arif Anwar, Peter C. Scott, Robert J. Moore
Software Mentions: 2
Published: over 7 years ago

10.3389/fmicb.2020.00863

The Mitochondrial Genome of the Phytopathogenic Fungus Bipolaris sorokiniana and the Utility of Mitochondrial Genome to Infer Phylogeny of Dothideomycetes
Cited by: 14
Author(s): Nan Song, Yuehua Geng, Xinghao Li
Software Mentions: 2
Published: over 6 years ago

10.3389/fmicb.2020.00202

Full Transcriptomic Response of Pseudomonas aeruginosa to an Inulin-Derived Fructooligosaccharide
Cited by: 11
Author(s): José Manuel Rubio-Gómez, Carlos Molina-Santiago, Zulema Udaondo, Mireia Tena-Garitaonaindia, Tino Krell, Juan L. Ramos, Abdelali Daddaoua
Software Mentions: 2
Published: over 6 years ago

10.3389/fmicb.2014.00530

Perturbations in small molecule synthesis uncovers an iron-responsive secondary metabolite network in Aspergillus fumigatus
Cited by: 44
Author(s): Philipp Wiemann, Beatrix E. Lechner, Joshua A. Baccile, Thomas Velk, Wen‐Bing Yin, Jin Woo Bok, Suman B. Pakala, Liliana Losada, William C. Nierman, Frank C. Schroeder, Hubertus Haas, Nancy P. Keller
Software Mentions: 2
Published: almost 12 years ago

10.3389/fmicb.2020.01467

Marine Oomycetes of the Genus Halophytophthora Harbor Viruses Related to Bunyaviruses
Cited by: 19
Author(s): Leticia Botella, Jan Janoušek, Cristiana Maia, Marília Horta Jung, Milica Raco, Thomas S. Jung
Software Mentions: 2
Published: about 6 years ago

10.3389/fmicb.2017.02394

Secretome Characterization and Correlation Analysis Reveal Putative Pathogenicity Mechanisms and Identify Candidate Avirulence Genes in the Wheat Stripe Rust Fungus Puccinia striiformis f. sp. tritici
Cited by: 25
Author(s): Chongjing Xia, Meinan Wang, Omar E. Cornejo, Derick Jiwan, Deven R. See, Xianming Chen
Software Mentions: 2
Published: almost 9 years ago

10.3389/fmicb.2021.640054

Identification and Validation of Reference Genes in Clostridium beijerinckii NRRL B-598 for RT-qPCR Using RNA-Seq Data
Cited by: 4
Author(s): Katerina Jureckova, Hana Raschmanová, Jan Kolek, Maryna Vasylkivska, Barbora Branská, Petra Patáková, Ivo Provazník, Karel Sedlář
Software Mentions: 2
Published: over 5 years ago

10.3389/fmicb.2020.591778

Brd/BET Proteins Influence the Genome-Wide Localization of the Kaposi’s Sarcoma-Associated Herpesvirus and Murine Gammaherpesvirus Major Latency Proteins
Cited by: 5
Author(s): Rishikesh Lotke, Ulrike Schneeweiß, Marcel Pietrek, Thomas Guenther, Adam Grundhoff, Magdalena Weidner-Glunde, Thomas F. Schulz
Software Mentions: 2
Published: almost 6 years ago

10.3389/fmicb.2017.01672

Complete Circular Genome Sequence and Temperature Independent Adaptation to Anaerobiosis of Listeria weihenstephanensis DSM 24698
Cited by: 0
Author(s): Elena Ferrari, Mathias C. Walter, Christopher Huptas, Siegfried Scherer, Stefanie Müller-Herbst
Software Mentions: 2
Published: about 9 years ago

10.3389/fmicb.2018.02827

BAC-BROWSER: The Tool for Visualization and Analysis of Prokaryotic Genomes
Cited by: 12
Author(s): Irina Garanina, Gleb Y. Fisunov, Vadim M. Govorun
Software Mentions: 2
Published: almost 8 years ago

10.3389/fmicb.2018.00882

Transcriptome Changes of Escherichia coli, Enterococcus faecalis, and Escherichia coli O157:H7 Laboratory Strains in Response to Photo-Degraded DOM
Cited by: 6
Author(s): Adelumola Oladeinde, Erin K. Lipp, Chiaying Chen, Richard W. Muirhead, Travis C. Glenn, Kyle DeMeo Cook, Marirosa Molina
Software Mentions: 2
Published: over 8 years ago

10.3389/fmolb.2021.724947

LZerD Protein-Protein Docking Webserver Enhanced With de novo Structure Prediction
Cited by: 16
Author(s): Charles Christoffer, Vijay Bharadwaj, Ryan Luu, Daisuke Kihara
Software Mentions: 2
Published: about 5 years ago

10.3389/fnmol.2021.651355

Single-Nucleus Chromatin Accessibility Landscape Reveals Diversity in Regulatory Regions Across Distinct Adult Rat Cortex
Cited by: 7
Author(s): Yeya Yu, Xiaoyü Wei, Qiuting Deng, Qing Lan, Yiping Guo, Lei Han, Yue Yuan, Peng Fan, Peng Wu, Shuncheng Shangguan, Yang Liu, Yiwei Lai, Giacomo Volpe, Miguel A. Esteban, Chuanyu Liu, Yong Hou, Longqi Liu
Software Mentions: 2
Published: over 5 years ago

10.3389/fnmol.2018.00290

Salivary MicroRNAs: Diagnostic Markers of Mild Traumatic Brain Injury in Contact-Sport
Cited by: 68
Author(s): Valentina Di Pietro, Edoardo Porto, Marco Ragusa, Cristina Barbagallo, David Davies, Mario Forcione, Ann Logan, Cinzia Di Pietro, Michele Purrello, Michael J. Grey, Douglas Hammond, Vijay Sawlani, Aron K. Barbey, Antonio Belli
Software Mentions: 2
Published: about 8 years ago

10.3389/fnmol.2017.00248

Translational Identification of Transcriptional Signatures of Major Depression and Antidepressant Response
Cited by: 26
Author(s): Mylène Hervé, Aurélie Bergon, Anne-Marie Le Guisquet, Samuel Leman, Julia-Lou Consoloni, Nicolas Fernandez-Nunez, Marie-Noëlle Lefebvre, Wissam El‐Hage, Raoul Belzeaux, Catherine Belzung, El Chérif Ibrahim
Software Mentions: 2
Published: about 9 years ago

10.3389/fninf.2019.00066

Exploring EEG Effective Connectivity Network in Estimating Influence of Color on Emotion and Memory
Cited by: 25
Author(s): Meei Tyng Chai, Hafeez Ullah Amin, Lila Iznita Izhar, Mohamad Naufal Mohamad Saad, Mohammad Abdul Rahman, Aamir Saeed Malik, Tong Boon Tang
Software Mentions: 2
Published: almost 7 years ago

10.3389/fnins.2016.00601

Variation in Gene Expression in Autism Spectrum Disorders: An Extensive Review of Transcriptomic Studies
Cited by: 62
Author(s): Ashley Ansel, Joshua P. Rosenzweig, Philip D. Zisman, Michal L. Melamed, Benjamin Gesundheit
Software Mentions: 2
Published: over 9 years ago

10.3389/fnins.2020.616802

A Sextuple Knockout Cell Line System to Study the Differential Roles of CRY, PER, and NR1D in the Transcription-Translation Feedback Loop of the Circadian Clock
Cited by: 4
Author(s): Yi Ying Chiou, Tzu-Ying Li, Yanyan Yang, Aziz Sancar
Software Mentions: 2
Published: almost 6 years ago

10.3389/fnins.2020.580970

Expected Valence Predicts Choice in a Recurrent Decision Task
Cited by: 1
Author(s): Daniel Thomas Jäger, Melanie Boltzmann, Jens D. Rollnik, Jascha Rüsseler
Software Mentions: 2
Published: almost 6 years ago

10.3389/fonc.2021.631056

Development of a Gene-Based Prediction Model for Recurrence of Colorectal Cancer Using an Ensemble Learning Algorithm
Cited by: 10
Author(s): Han-Ching Chan, Amrita Chattopadhyay, Eric Y. Chuang, Tzu-Pin Lu
Software Mentions: 2
Published: over 5 years ago

10.3389/fvets.2021.732129

Identification of Multiple Blastocystis Subtypes in Domestic Animals From Colombia Using Amplicon-Based Next Generation Sequencing
Cited by: 49
Author(s): Adriana Higuera, Giovanny Herrera, Paula Andrea Jiménez, Diego García-Corredor, Martín Orlando Pulido-Medellín, Diana María Bulla-Castañeda, Juan Carlos Pinilla, Darwin A. Moreno-Pérez, Jenny G. Maloney, Mónica Santı́n, Juan David Ramírez
Software Mentions: 2
Published: about 5 years ago

10.1186/1742-9994-10-9

Habitat productivity constrains the distribution of social spiders across continents – case study of the genus Stegodyphus
Cited by: 26
Author(s): Marija Majer, Jens‐Christian Svenning, Trine Bilde
Software Mentions: 2
Published: over 13 years ago

10.1534/g3.115.017921

Endogenous Small RNA Mediates Meiotic Silencing of a Novel DNA Transposon
Cited by: 33
Author(s): Yizhou Wang, Kristina M. Smith, John W. Taylor, Michael Freitag, Jason E. Stajich
Software Mentions: 2
Published: almost 11 years ago

10.1534/g3.116.036673

Genome Report: Identification and Validation of Antigenic Proteins from Pajaroellobacter abortibovis Using De Novo Genome Sequence Assembly and Reverse Vaccinology
Cited by: 8
Author(s): Bryan T. Welly, Michael R. Miller, Jeffrey L Stott, M Blanchard, Alma Islas–Trejo, Sean O’Rourke, Amy Young, Juan F. Medrano, Alison L. Van Eenennaam
Software Mentions: 2
Published: over 9 years ago

10.1534/g3.118.200134

Programmable Single and Multiplex Base-Editing in Bombyx mori Using RNA-Guided Cytidine Deaminases
Cited by: 14
Author(s): Yufeng Li, Sanyuan Ma, Le Sun, Tong Zhang, Jiasong Chang, Wei Lu, Xiaoxu Chen, Yue Liu, Xiaogang Wang, Run Shi, Ping Zhao, Qingyou Xia
Software Mentions: 2
Published: over 8 years ago

10.1534/g3.118.200417

Development of Diagnostic SNP Markers To Monitor Hybridization Between Sika Deer (Cervus nippon) and Wapiti (Cervus elaphus)
Cited by: 3
Author(s): Hengxing Ba, Zhipeng Li, Yumei Yang, Chunyi Li
Software Mentions: 2
Published: about 8 years ago

10.1534/g3.118.200481

Genomics-Assisted Identification and Characterization of the Genetic Variants Underlying Differential Nitrogen Use Efficiencies in Allotetraploid Rapeseed Genotypes
Cited by: 12
Author(s): Yingpeng Hua, Ting Zhou, Qiong Liao, Haixing Song, Chunyun Guan, Zhenhua Zhang
Software Mentions: 2
Published: about 8 years ago

10.1534/g3.118.200171

RAD Sequencing and a Hybrid Antarctic Fur Seal Genome Assembly Reveal Rapidly Decaying Linkage Disequilibrium, Global Population Structure and Evidence for Inbreeding
Cited by: 28
Author(s): Emily Humble, Kanchon K. Dasmahapatra, Alvaro Martinez-Barrio, Inês Gregório, Jaume Forcada, Ann-Christin Polikeit, Simon Goldsworthy, Michael E. Goebel, Jörn Kalinowski, Jochen B. W. Wolf, Joseph I. Hoffman
Software Mentions: 2
Published: about 8 years ago

10.1534/g3.120.401402

Training Population Optimization for Genomic Selection in Miscanthus
Cited by: 21
Author(s): Marcus O. Olatoye, Lindsay V. Clark, Nicholas R. LaBonte, Hongxu Dong, Maria Stefanie Dwiyanti, Kossonou Guillaume Anzoua, Joe E. Brummer, Bimal Kumar Ghimire, Elena Dzyubenko, N. I. Dzyubenko, Л. В. Багмет, Andrey Sabitov, Pavel Chebukin, Katarzyna Głowacka, Kweon Heo, Xiaoli Jin, Hironori Nagano, Junhua Peng, Chang Yeon Yu, Ji Hye Yoo, Hua Zhao, Stephen P. Long, Toshihiko Yamada, Erik J. Sacks, Alexander E. Lipka
Software Mentions: 2
Published: about 6 years ago

10.1534/g3.120.401460

Characterization and Fine Mapping of a Yellow-Virescent Gene Regulating Chlorophyll Biosynthesis and Early Stage Chloroplast Development in Brassica napus
Cited by: 16
Author(s): Chuanji Zhao, Lijiang Liu, Luqman Bin Safdar, Meili Xie, Xiaohui Cheng, Yueying Liu, Yu‐Tao Xiang, Chaobo Tong, Jinxing Tu, Junyan Huang, Liu S
Software Mentions: 2
Published: about 6 years ago

10.1093/g3journal/jkaa053

Multivariate linear mixed model enhanced the power of identifying genome-wide association to poplar tree heights in a randomized complete block design
Cited by: 13
Author(s): Yuhua Chen, Hualong Wu, Wenguo Yang, Wei Zhao, Chunfa Tong
Software Mentions: 2
Published: over 5 years ago

10.1093/g3journal/jkab076

Evidence of gene nucleotide composition favoring replication and growth in a fastidious plant pathogen
Cited by: 5
Author(s): Andreína I. Castillo, Rodrigo P. P. Almeida
Software Mentions: 2
Published: over 5 years ago

10.3390/genes5020366

Characterization of the Genomic Architecture and Mutational Spectrum of a Small Cell Prostate Carcinoma
Cited by: 9
Author(s): Alan F. Scott, David Mohr, Hua Ling, Robert B. Scharpf, Peng Zhang, Gregory S. Liptak
Software Mentions: 2
Published: over 12 years ago

10.3390/genes9060313

CoreProbe: A Novel Algorithm for Estimating Relative Abundance Based on Metagenomic Reads
Cited by: 2
Author(s): Dongmei Ai, Hongfei Pan, Ruocheng Huang, Xia Li
Software Mentions: 2
Published: about 8 years ago

10.3390/genes9090452

Recent Selection on a Class I ADH Locus Distinguishes Southwest Asian Populations Including Ashkenazi Jews
Cited by: 9
Author(s): Shuangshuang Gu, Hui Li, Andrew J. Pakstis, William C. Speed, David Genevieve, Judith R. Kidd, Kenneth K. Kídd
Software Mentions: 2
Published: about 8 years ago

10.3390/genes10030219

DNA Methylation Patterns in the Round Goby Hypothalamus Support an On-The-Spot Decision Scenario for Territorial Behavior
Cited by: 10
Author(s): Vincent Somerville, Michaela Schwaiger, Philipp Hirsch, Jean‐Claude Walser, Karen Bussmann, Alexandra Weyrich, Patricia Burkhardt‐Holm, Irene Adrian‐Kalchhauser
Software Mentions: 2
Published: over 7 years ago

10.3390/genes10090650

Affinity Purification of NF1 Protein–Protein Interactors Identifies Keratins and Neurofibromin Itself as Binding Partners
Cited by: 11
Author(s): Rachel M. Carnes, Robert A. Kesterson, Bruce R. Korf, James A. Mobley, Deeann Wallis
Software Mentions: 2
Published: about 7 years ago

10.3390/genes11050534

Investigating Human Mitochondrial Genomes in Single Cells
Cited by: 8
Author(s): Maria Angela Diroma, Angelo Sante Varvara, Marcella Attimonelli, Graziano Pesole, Ernesto Picardi
Software Mentions: 2
Published: over 6 years ago

10.3390/genes12010046

DIANA-mAP: Analyzing miRNA from Raw NGS Data to Quantification
Cited by: 8
Author(s): Αθανάσιος Αλεξίου, Dimitrios Zisis, Ioannis Kavakiotis, Marios Miliotis, Antonis Koussounadis, Dimitra Karagkouni, Artemis G. Hatzigeorgiou
Software Mentions: 2
Published: over 5 years ago

10.3390/genes12020167

Leishmania Sexual Reproductive Strategies as Resolved through Computational Methods Designed for Aneuploid Genomes
Cited by: 10
Author(s): Jahangheer Shaik, Deborah E. Dobson, David L. Sacks, Stephen M. Beverley
Software Mentions: 2
Published: over 5 years ago

10.1590/1678-4685-GMB-2017-0031

Ecological drivers of plant genetic diversity at the southern edge of geographical distributions: Forestal vines in a temperate region
Cited by: 7
Author(s): Michel J. F. Barros, José Alexandre Felizola Diniz‐Filho, Loreta B. Freitas
Software Mentions: 2
Published: over 8 years ago

Projects: cran: SAM

Science Score: 85/100

Bonuses:

Penalties:

Papers Mentioning SAM 4,566