Ecosyste.ms: Papers

10.1186/1751-0473-6-3

WebGimm: An integrated web-based platform for cluster analysis, functional analysis, and interactive visualization of results
Cited by: 5
Author(s): Vineet K Joshi, Johannes M. Freudenberg, Zhen Hu, Mario Medvedovic
Software Mentions: 3
Published: almost 14 years ago

10.1128/mBio.00233-17

Deciphering the Regulatory Network between the SREBP Pathway and Protein Secretion in <i>Neurospora crassa</i>
Cited by: 17
Author(s): Lu‐Ping Qin, V. Wu, N. Louise Glass
Software Mentions: 3
Published: over 7 years ago

10.1128/mBio.02785-19

Influence of Plant Fraction, Soil, and Plant Species on Microbiota: a Multikingdom Comparison
Cited by: 96
Author(s): Andrzej Tkacz, Eloïne Bestion, Zhiyan Bo, Marion Hortala, Philip S. Poole
Software Mentions: 3
Published: over 4 years ago

10.1186/s13068-021-01908-y

Accurate determination of genotypic variance of cell wall characteristics of a Populus trichocarpa pedigree using high-throughput pyrolysis-molecular beam mass spectrometry
Cited by: 4
Author(s): Anne E. Harman‐Ware, David Macaya‐Sanz, Chanaka Roshan Abeyratne, Crissa Doeppke, Kathleen Haiby, Gerald A. Tuskan, Brian J. Stanton, Stephen P. DiFazio, Mark F. Davis
Software Mentions: 3
Published: over 3 years ago

10.1186/1471-2105-10-S1-S26

Principal component tests: applied to temporal gene expression data
Cited by: 3
Author(s): Wensheng Zhang, Hong-Bin Fang, Jiuzhou Song
Software Mentions: 3
Published: almost 16 years ago

10.3390/ijerph16224526

Expressiveness and Instrumentality of Crime Scene Behavior in Spanish Homicides
Cited by: 7
Author(s): María del Mar Pecino-Latorre, María del Carmen Pérez Fuentes, Rosa María Patró-Hernández, Jorge Santos‐Hermoso
Software Mentions: 3
Published: almost 5 years ago

10.1007/s00442-016-3608-3

Moss stable isotopes (carbon-13, oxygen-18) and testate amoebae reflect environmental inputs and microclimate along a latitudinal gradient on the Antarctic Peninsula
Cited by: 33
Author(s): Jessica Royles, Matthew J. Amesbury, Thomas P. Roland, Glyn Jones, Peter Convey, Howard Griffiths, Dominic A. Hodgson, Dan J. Charman
Software Mentions: 3
Published: over 8 years ago

10.1002/1878-0261.12505

Increased expression of the <scp>HDAC</scp>9 gene is associated with antiestrogen resistance of breast cancers
Cited by: 30
Author(s): Aurélien Linarès, Saïd Assou, Marion Lapierre, Erwan Thouënnon, Céline Duraffourd, Carole Fromaget, Abdelhay Boulahtouf, Tian Gao, Jiafu Ji, Özgür Şahin, Éric Badia, Nathalie Boulle, Vincent Cavaillès
Software Mentions: 3
Published: over 5 years ago

10.3390/bs10030066

Schwartz Value Clusters in Modern University Students
Cited by: 4
Author(s): О В Маслова, Dmitriy A. Shlyakhta, Mikhail S. Yanitskiy
Software Mentions: 3
Published: over 4 years ago

10.1186/1746-6148-9-88

Defining syndromes using cattle meat inspection data for syndromic surveillance purposes: a statistical approach with the 2005–2010 data from ten French slaughterhouses
Cited by: 51
Author(s): Céline Dupuy, Eric Morignat, Xavier Maugey, Jean-Luc Vinard, Pascal Hendrikx, Christian Ducrot, Didier Calavas
Software Mentions: 3
Published: almost 12 years ago

10.1186/s12870-020-02797-3

Comparative analysis of powdery mildew resistant and susceptible cultivated cucumber (Cucumis sativus L.) varieties to reveal the metabolic responses to Sphaerotheca fuliginea infection
Cited by: 16
Author(s): Peng Zhang, Youyong Zhu, Shanshan Zhou
Software Mentions: 3
Published: almost 4 years ago

10.1371/journal.pone.0151309

Genetic Relationships among Tall Coconut Palm (Cocos nucifera L.) Accessions of the International Coconut Genebank for Latin America and the Caribbean (ICG-LAC), Evaluated Using Microsatellite Markers (SSRs)
Cited by: 18
Author(s): C. M. Loiola, Alinne Oliveira Nunes Azevedo, Leandro Eugênio Cardamone Diniz, W. M. Aragão, Carlos Diego de Oliveira Azevedo, Pedro Henrique Araújo Diniz Santos, Helaine Christine Cancela Ramos, Messias Gonzaga Pereira, S. R. R. Ramos
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0231753

Genome-wide assessment of population structure and genetic diversity of Chinese Lou onion using specific length amplified fragment (SLAF) sequencing
Cited by: 9
Author(s): Haitian Fang, Huiyan Liu, Ruoshuang Ma, Yuxuan Liu, Jinna Li, Xiaoyan Yu, Haoyu Zhang, Yali Yang, Zhang Guang-di
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0106349

Modulation of ErbB2 Blockade in ErbB2-Positive Cancers: The Role of ErbB2 Mutations and PHLDA1
Cited by: 26
Author(s): Guangyuan Li, Xiaoqi Wang, Hanina Hibshoosh, Cheng Jin, Balázs Halmos
Software Mentions: 3
Published: about 10 years ago

10.1371/journal.pone.0141613

Gene Expression Profiles in Rice Developing Ovules Provided Evidence for the Role of Sporophytic Tissue in Female Gametophyte Development
Cited by: 15
Author(s): Ya Fang Wu, Liyu Yang, Aqin Cao, Jianbo Wang
Software Mentions: 3
Published: about 9 years ago

10.3390/ijms19103169

Multiple Regulatory Networks Are Activated during Cold Stress in Medicago sativa L.
Cited by: 23
Author(s): Qiang Zhou, Dong Luo, Xutian Chai, Yuguo Wu, Yanrong Wang, Nan Zhang, Qingchuan Yang, Wenxian Liu
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pone.0099517

Optimized Cryopreservation of Mixed Microbial Communities for Conserved Functionality and Diversity
Cited by: 69
Author(s): Frederiek‐Maarten Kerckhof, Emilie Courtens, Annelies Geirnaert, Sven Hoefman, Adrian Ho, Ramiro Vílchez-Vargas, Dietmar H. Pieper, Ruy Jáuregui, Siegfried E. Vlaeminck, Tom Van de Wiele, Peter Vandamme, Kim Heylen, Nico Boon
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0150293

The Blurred Line between Form and Process: A Comparison of Stream Channel Classification Frameworks
Cited by: 76
Author(s): Alan Kasprak, Nate Hough‐Snee, Timothy J. Beechie, Nicolaas Bouwes, Gary Brierley, Reid Camp, Kirstie Fryirs, Hiroo Imaki, Martha L. Jensen, Gary O'Brien, David L. Rosgen, Joseph M. Wheaton
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0143768

Studies on the Coordination of Ribosomal Protein Assembly Events Involved in Processing and Stabilization of Yeast Early Large Ribosomal Subunit Precursors
Cited by: 15
Author(s): Uli Ohmayer, Álvaro Gil-Hernández, Martina Sauert, Pilar Martín-Marcos, Mercedes Tamame, Herbert Tschochner, Joachim Griesenbeck, Philipp Milkereit
Software Mentions: 2
Published: almost 9 years ago

10.1002/2211-5463.12556

The potential roles of long non‐coding RNAs in lipopolysaccharide‐induced human peripheral blood mononuclear cells as determined by microarray analysis
Cited by: 4
Author(s): Anqiang Zhang, Hongxiang Lu, Dalin Wen, Jianhui Sun, Juan Du, Xu Wang, Wei Gu, Jianxin Jiang
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0153093

RNA-Seq Profiling of Intact and Enucleated Oocyte SCNT Embryos Reveals the Role of Pig Oocyte Nucleus in Somatic Reprogramming
Cited by: 5
Author(s): Lin Bai, Mengqi Li, Jie Sun, Xiaogan Yang, Yangqing Lu, Sen Lu, LU Ke-huan
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0068412

Studies on the Assembly Characteristics of Large Subunit Ribosomal Proteins in S. cerevisae
Cited by: 50
Author(s): Uli Ohmayer, Michael Gamalinda, Martina Sauert, Julius Ossowski, Gisela Pöll, Jan Linnemann, Thomas Hierlmeier, Jorge Pérez-Fernández, Beril Kumcuoglu, Isabelle Léger-Silvestre, Marlène Faubladier, Joachim Griesenbeck, John L. Woolford, Herbert Tschochner, Philipp Milkereit
Software Mentions: 2
Published: over 11 years ago

10.1007/s00394-015-0966-2

Effects of high doses of vitamin D3 on mucosa-associated gut microbiome vary between regions of the human gastrointestinal tract
Cited by: 178
Author(s): Mina Bashir, Barbara Prietl, Martin Tauschmann, Selma Mautner, Patrizia Kump, Gerlies Treiber, Philipp Wurm, Gregor Gorkiewicz, Christoph Högenauer, Thomas R. Pieber
Software Mentions: 2
Published: over 9 years ago

10.1186/1471-2164-15-417

De novo assembly and transcriptome characterization: novel insights into the natural resistance mechanisms of Microtus fortis against Schistosoma japonicum
Cited by: 10
Author(s): Yuan Hu, Yaobo Xu, Wei-yuan Lu, Zhongying Yuan, Quan Hong, Yujuan Shen, Jianping Cao
Software Mentions: 2
Published: over 10 years ago

10.1038/srep31814

Plasma Membrane Intrinsic Proteins SlPIP2;1, SlPIP2;7 and SlPIP2;5 Conferring Enhanced Drought Stress Tolerance in Tomato
Cited by: 58
Author(s): Li Ren, Jinfang Wang, Shuangtao Li, Lei Zhang, Chuandong Qi, Sarah Weeda, Bing Zhao, Shuxin Ren, Yang‐Dong Guo
Software Mentions: 2
Published: about 8 years ago

10.1038/s41598-017-00214-8

Community-Associated Staphylococcus aureus from Sub-Saharan Africa and Germany: A Cross-Sectional Geographic Correlation Study
Cited by: 26
Author(s): Ulla Ruffing, Abraham Alabi, Theckla Kazimoto, Delfino Vubil, Ruslan Akulenko, Salim Abdulla, Pedro L. Alonso, Markus Bischoff, Anja Germann, Martin P. Grobusch, Volkhard Helms, Jonas Hoffmann, Winfried V. Kern, Peter G. Kremsner, Inácio Mandomando, Alexander Mellmann, Georg Peters, Frieder Schaumburg, Sabine Schubert, Lena Strauß, Marcel Tanner, Hagen von Briesen, Laura Wende, Lutz von Müller, Mathias Herrmann
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0086671

CD9 Negatively Regulates CD26 Expression and Inhibits CD26-Mediated Enhancement of Invasive Potential of Malignant Mesothelioma Cells
Cited by: 25
Author(s): Toshihiro Okamoto, Satoshi Iwata, Hiroto Yamazaki, Ryo Hatano, Eriko Komiya, Nam H. Dang, Kei Ohnuma, Chikao Morimoto
Software Mentions: 2
Published: almost 11 years ago

10.1371/journal.pone.0100946

De Novo Sequencing-Based Transcriptome and Digital Gene Expression Analysis Reveals Insecticide Resistance-Relevant Genes in Propylaea japonica (Thunberg) (Coleoptea: Coccinellidae)
Cited by: 23
Author(s): Liang-De Tang, Xingmin Wang, Fengliang Jin, Bao‐Li Qiu, Jing Wu, Sumei Ren
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0060771

Transcript and Protein Profiling Analysis of the Destruxin A-Induced Response in Larvae of Plutella xylostella
Cited by: 26
Author(s): Pengfei Han, Fengliang Jin, Xiaolin Dong, Jiqiao Fan, Bao‐Li Qiu, Sumei Ren
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0210948

Acid-base assessment of post-parturient German Holstein dairy cows from jugular venous blood and urine: A comparison of the strong ion approach and traditional blood gas analysis
Cited by: 11
Author(s): Tanja Gärtner, Veit Zoche-Golob, Stefanie Redlberger, Petra Reinhold, Karsten Donat
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-017-11298-7

Identification of immunity-related genes in Plutella xylostella in response to fungal peptide destruxin A: RNA-Seq and DGE analysis
Cited by: 15
Author(s): Muhammad Shakeel, Xi Xu, Jin Xu, Xun Zhu, Shuzhong Li, Xianqiang Zhou, Jia Yu, Xingye Xu, Qiongbo Hu, Xiao‐Qiang Yu, Fengliang Jin
Software Mentions: 2
Published: about 7 years ago

10.1186/s12863-015-0169-0

Differentially penalized regression to predict agronomic traits from metabolites and markers in wheat
Cited by: 16
Author(s): Jane L. Ward, Marianna Rakszegi, Z. Bedő, Peter R. Shewry, Ian Mackay
Software Mentions: 2
Published: over 9 years ago

10.3390/ani9110949

Classification of Pigs with Tail Lesions from Different Farrowing and Rearing Systems during Rearing and Fattening Period
Cited by: 7
Author(s): Maria Gentz, Anita Lange, Sebastian Zeidler, Imke Traulsen
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0203415

Impact of two neighbouring ribosomal protein clusters on biogenesis factor binding and assembly of yeast late small ribosomal subunit precursors
Cited by: 12
Author(s): Jan Linnemann, Gisela Pöll, Steffen Jakob, Sébastien Ferreira-Cerca, Joachim Griesenbeck, Herbert Tschochner, Philipp Milkereit
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0125355

Transcriptome Profiling Reveals the Regulatory Mechanism Underlying Pollination Dependent and Parthenocarpic Fruit Set Mainly Mediated by Auxin and Gibberellin
Cited by: 46
Author(s): Ning Tang, Wei Deng, Guojian Hu, Nan Hu, Zhengguo Li
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0089101

Image-Derived Input Function Derived from a Supervised Clustering Algorithm: Methodology and Validation in a Clinical Protocol Using [11C](R)-Rolipram
Cited by: 12
Author(s): Chul Hyoung Lyoo, Paolo Zanotti‐Fregonara, Sami S. Zoghbi, Jeih San Liow, Rong Xu, Victor W. Pike, Carlos A. Zarate, Masahiro Fujita, Robert B. Innis
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0217711

Climate vulnerability assessment for Pacific salmon and steelhead in the California Current Large Marine Ecosystem
Cited by: 87
Author(s): Lisa G. Crozier, Michelle McClure, Timothy J. Beechie, Steven J. Bograd, David A. Boughton, Mark H. Carr, Tom Cooney, Jason B. Dunham, Correigh M. Greene, Melissa A. Haltuch, Elliott L. Hazen, Damon M. Holzer, David D. Huff, Rachel C. Johnson, Chris E. Jordan, Issac C Kaplan, Steven T. Lindley, Nathan J. Mantua, Peter B. Moyle, James M. Myers, Mark W. Nelson, Brian C. Spence, Laurie A. Weitkamp, Thomas H. Williams, Ellen Willis‐Norton
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-018-34193-1

Using patient-derived iPSCs to develop humanized mouse models for chronic myelomonocytic leukemia and therapeutic drug identification, including liposomal clodronate
Cited by: 24
Author(s): Kazuki Taoka, Shunya Arai, Keisuke Kataoka, Masataka Hosoi, Mutsumi Miyauchi, Sho Yamazaki, Akira Honda, Wei Aixinjueluo, Takashi Kobayashi, Keiki Kumano, Akihide Yoshimi, Makoto Otsu, Akira Niwa, Tatsutoshi Nakahata, Hiromitsu Nakauchi, Mineo Kurokawa
Software Mentions: 2
Published: about 6 years ago

10.1038/s41598-018-35569-z

Description of a personality syndrome in a common and invasive ground beetle (Coleoptera: Carabidae)
Cited by: 14
Author(s): Sophie Labaude, Niamh O'Donnell, Christine T. Griffin
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pgen.1008368

Telomere dysfunction impairs epidermal stem cell specification and differentiation by disrupting BMP/pSmad/P63 signaling
Cited by: 16
Author(s): Na Liu, Yu Yin, Haiying Wang, Zhongli Zhou, Xiaoyan Sheng, Haifeng Fu, Renpeng Guo, Hua Wang, Jiao Yang, Peng Gong, Wen Ning, Zhenyu Ju, Yifei Liu, Lin Liu
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pone.0150904

MicroRNAs hsa-miR-99b, hsa-miR-330, hsa-miR-126 and hsa-miR-30c: Potential Diagnostic Biomarkers in Natural Killer (NK) Cells of Patients with Chronic Fatigue Syndrome (CFS)/ Myalgic Encephalomyelitis (ME)
Cited by: 37
Author(s): Robert Petty, Neil E. McCarthy, Rifca Le Dieu, Jonathan Kerr
Software Mentions: 2
Published: over 8 years ago

10.3390/ijms17060778

Effects of Endobacterium (Stenotrophomonas maltophilia) on Pathogenesis-Related Gene Expression of Pine Wood Nematode (Bursaphelenchus xylophilus) and Pine Wilt Disease
Cited by: 19
Author(s): He Li, Xiao‐Qin Wu, Qi Xue, Xiuwen Qiu
Software Mentions: 2
Published: over 8 years ago

10.18632/oncotarget.26485

Pan-cancer analysis of intratumor heterogeneity associated with patient prognosis using multidimensional measures
Cited by: 5
Author(s): Chie Kikutake, Minako Yoshihara, Tetsuya Sato, Daisuke Saito, Mikita Suyama
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0174824

Transcriptome analysis of Corynebacterium glutamicum in the process of recombinant protein expression in bioreactors
Cited by: 5
Author(s): Yan Sun, Wenwen Guo, Fen Wang, Cheng Zhan, Yankun Yang, Xiuxia Liu, Zhonghu Bai
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0148204

Cth2 Protein Mediates Early Adaptation of Yeast Cells to Oxidative Stress Conditions
Cited by: 8
Author(s): Laia Castells‐Roca, Jordi Pijuan, Francisco Ferrezuelo, Gemma Bellı́, Enrique Herrero
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0139588

Exploration of Novel Inhibitors for Class I Histone Deacetylase Isoforms by QSAR Modeling and Molecular Dynamics Simulation Assays
Cited by: 14
Author(s): Zainab Noor, Afzal Noreen, Sajid Rashid
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0149352

Identification of Differentially Expressed Genes Related to Dehydration Resistance in a Highly Drought-Tolerant Pear, Pyrus betulaefolia, as through RNA-Seq
Cited by: 34
Author(s): Kong-Qing Li, Xiaogang Xu, Xiaosan Huang
Software Mentions: 2
Published: over 8 years ago

10.1186/s12872-019-01322-1

A novel TAB2 nonsense mutation (p.S149X) causing autosomal dominant congenital heart defects: a case report of a Chinese family
Cited by: 15
Author(s): Jia Chen, Huizhen Yuan, Kang Xie, Xinrong Wang, Tan Liu, Ying Zou, Yan Yang, Pan Lu, Junfang Xiao, Ge Chen, Yanqiu Li
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pone.0048819

Uncovering the Salt Response of Soybean by Unraveling Its Wild and Cultivated Functional Genomes Using Tag Sequencing
Cited by: 28
Author(s): Zulfiqar Ali, Da Yong Zhang, Zhonghui Xu, Ling Xu, Jin Yi, Xiao Lan He, Yifan Huang, Xiao Qing Liu, Asif Ali Khan, Richard Trethowan, Hong Xiang
Software Mentions: 2
Published: almost 12 years ago

10.1038/s41598-020-77673-z

Emotional well-being and gut microbiome profiles by enterotype
Cited by: 32
Author(s): Sung Ha Lee, Seok-Hwan Yoon, Yeon Jae Jung, Namil Kim, Ui-Gi Min, Jongsik Chun, Incheol Choi
Software Mentions: 2
Published: almost 4 years ago

10.3892/mmr.2015.3308

Identification of genes and transcription factors associated with glucocorticoid response in lens epithelial cells
Cited by: 3
Author(s): Ding Zhou, Yi Zhang, Lishan Wang, Yunduan Sun, Ping Liu
Software Mentions: 2
Published: over 9 years ago

10.1186/s12885-021-08417-z

The lipid-lowering drug fenofibrate combined with si-HOTAIR can effectively inhibit the proliferation of gliomas
Cited by: 2
Author(s): Wei Zhu, Hongyang Zhao, Fengming Xu, Bin Huang, Xiaojing Dai, Jikui Sun, Alphonce M K Nyalali, Kailiang Zhang, Shilei Ni
Software Mentions: 2
Published: over 3 years ago

10.3390/ijms21228857

Transcriptome Analysis of Pyrus betulaefolia Seedling Root Responses to Short-Term Potassium Deficiency
Cited by: 12
Author(s): Yang Han, Yán Li, Yumeng Jin, Liping Kan, Changwei Shen, Anish Malladi, Savithri U. Nambeesan, Yangchun Xu, Caixia Dong
Software Mentions: 2
Published: almost 4 years ago

10.1186/s12859-020-3365-5

Unlocking the transcriptomic potential of formalin-fixed paraffin embedded clinical tissues: comparison of gene expression profiling approaches
Cited by: 29
Author(s): Arran Turnbull, Çiğdem Selli, Carlos Martínez-Pérez, Anu Fernando, Lorna Renshaw, J Keys, Jonine D. Figueroa, Xiaping He, Miki Tanioka, Alison F. Munro, Lee Murphy, Angie Fawkes, Richard Clark, Audrey Coutts, Charles M. Perou, Lisa A. Carey, JM Dixon, Andrew H. Sims
Software Mentions: 2
Published: almost 5 years ago

10.1186/s12866-015-0353-4

Transcriptome profiling of Bacillus subtilis OKB105 in response to rice seedlings
Cited by: 35
Author(s): Shanshan Xie, Huijun Wu, Lina Chen, Huadong Zang, Yun Xie, Xuewen Gao
Software Mentions: 2
Published: over 9 years ago

10.1371/journal.pone.0050376

Protective Effects of Acyl-coA Thioesterase 1 on Diabetic Heart via PPARα/PGC1α Signaling
Cited by: 36
Author(s): Shan Yang, Chen Chen, Hong Wang, Xiaoquan Rao, Feng Wang, Qing Duan, Fuqiong Chen, Guangwen Long, Wei Gong, Ming Zou, Dao Wen Wang
Software Mentions: 2
Published: almost 12 years ago

10.7717/peerj.3382

Transcriptome analysis reveals the regulation of brassinosteroids on petal growth in <i>Gerbera hybrida</i>
Cited by: 26
Author(s): Gan Huang, Meixiang Han, Wei Yao, Yaqin Wang
Software Mentions: 2
Published: over 7 years ago

10.1038/s41421-018-0020-7

Immortalized common marmoset (Callithrix jacchus) hepatic progenitor cells possess bipotentiality in vitro and in vivo
Cited by: 8
Author(s): Zhan Guo, Renwei Jing, Quan Rao, Ludi Zhang, Yimeng Gao, Fengyong Liu, Xin Wang, Lijian Hui, HaiFang Yin
Software Mentions: 2
Published: over 6 years ago

10.1186/s13058-017-0812-y

Integrative clustering reveals a novel split in the luminal A subtype of breast cancer with impact on outcome
Cited by: 83
Author(s): Miriam Ragle Aure, Valeria Vitelli, Sandra Jernstrøm, Surendra Kumar, Marit Krohn, Eldri Undlien Due, Tonje Husby Haukaas, Suvi‐Katri Leivonen, Hans Kristian Moen Vollan, Torben Lüders, Einar Andreas Rødland, Charles J. Vaske, Wei Zhao, Elen K. Møller, Silje Nord, Guro F. Giskeødegård, Tone Frost Bathen, Carlos Caldas, Trine Tramm, Jan Alsner, Jens Overgaard, Jürgen Geisler, Ida Rashida Khan Bukholm, Bjørn Naume, Ellen Schlichting, Torill Sauer, Gordon B. Mills, Rolf Kåresen, Gunhild Mari Mælandsmo, Ole Christian Lingjærde, Arnoldo Frigessi, Vessela N. Kristensen, Anne‐Lise Børresen‐Dale, Kristine Kleivi Sahlberg
Software Mentions: 2
Published: over 7 years ago

10.1038/s41419-021-03787-5

IL-26 mediates epidermal growth factor receptor-tyrosine kinase inhibitor resistance through endoplasmic reticulum stress signaling pathway in triple-negative breast cancer cells
Cited by: 9
Author(s): Takahiko Itoh, Ryo Hatano, Yoshiya Horimoto, Taketo Yamada, Dan Song, Haruna Otsuka, Yûki Shirakawa, Shuji Mastuoka, Noriaki Iwao, Thomas M. Aune, Nam H. Dang, Yutaro Kaneko, Ko Okumura, Chikao Morimoto, Kei Ohnuma
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0062704

Exploring Differentially Expressed Genes by RNA-Seq in Cashmere Goat (Capra hircus) Skin during Hair Follicle Development and Cycling
Cited by: 61
Author(s): Rong Geng, Chao Yuan, Yulin Chen
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0190221

Genomic alterations during p53-dependent apoptosis induced by γ-irradiation of Molt-4 leukemia cells
Cited by: 10
Author(s): Rouba Hage‐Sleiman, Hisham F. Bahmad, Hadile Kobeissy, Zeinab Dakdouk, Firas Kobeissy, Ghassan Dbaibo
Software Mentions: 2
Published: almost 7 years ago

10.1128/mBio.03482-20

Evolution of Antibiotic Tolerance Shapes Resistance Development in Chronic Pseudomonas aeruginosa Infections
Cited by: 51
Author(s): Isabella Santi, Pablo Manfredi, Enea Maffei, Adrian Egli, Urs Jenal
Software Mentions: 2
Published: over 3 years ago

10.1371/journal.pone.0068664

Comparison of Profile Similarity Measures for Genetic Interaction Networks
Cited by: 32
Author(s): Raamesh Deshpande, Benjamin VanderSluis, Chad L. Myers
Software Mentions: 2
Published: over 11 years ago

10.1371/journal.pone.0145532

Using RNA-seq to Profile Gene Expression of Spikelet Development in Response to Temperature and Nitrogen during Meiosis in Rice (Oryza sativa L.)
Cited by: 9
Author(s): Jun Yang, Xiaorong Chen, Zhu C, Xiaosong Peng, Xu He, Junru Fu, Liang Ouyang, Jianmin Bian, Lifang Hu, Xiaotang Sun, Jie Xu, Haohua He
Software Mentions: 2
Published: almost 9 years ago

10.1007/s41109-020-00317-8

Characterizing communities of hashtag usage on twitter during the 2020 COVID-19 pandemic by multi-view clustering
Cited by: 24
Author(s): Iain J. Cruickshank, Kathleen M. Carley
Software Mentions: 2
Published: about 4 years ago

10.3389/fpls.2017.00588

Genome-Wide Identification, Cloning and Functional Analysis of the Zinc/Iron-Regulated Transporter-Like Protein (ZIP) Gene Family in Trifoliate Orange (Poncirus trifoliata L. Raf.)
Cited by: 39
Author(s): Xing Zheng Fu, Xue Zhou, Fei Xing, Li Li Ling, Chang Pin Chun, Li Cao, Mark G. M. Aarts, Peng Liang
Software Mentions: 2
Published: over 7 years ago

10.1016/j.isci.2021.102795

3D single cell scale anatomical map of sex-dependent variability of the rat intrinsic cardiac nervous system
Cited by: 6
Author(s): Clara Leung, Shaina Robbins, Alison Moss, Maci Heal, Mahyar Osanlouy, Richard Christie, Navid Farahani, Corey Monteith, Jin Chen, Peter Hunter, Susan Tappan, Rajanikanth Vadigepalli, Zixi Cheng, James S. Schwaber
Software Mentions: 2
Published: over 3 years ago

10.1186/1471-2164-14-279

Transcriptome analysis of Cymbidium sinense and its application to the identification of genes associated with floral development
Cited by: 103
Author(s): Jianxia Zhang, Kunlin Wu, Songjun Zeng, Jaime A. Teixeira da Silva, Xiaolan Zhao, Chaoguang Tian, Haoqiang Xia, Jun Duan
Software Mentions: 2
Published: over 11 years ago

10.1186/1471-2164-14-197

Transcriptome-based discovery of pathways and genes related to resistance against Fusariumhead blight in wheat landrace Wangshuibai
Cited by: 124
Author(s): Jin Xiao, Xiahong Jin, Xiaoyun Jia, Haiyan Wang, Aizhong Cao, Weiming Zhao, Haiyan Pei, Zhaokun Xue, Ling He, Qiguang Chen, Xiue Wang
Software Mentions: 2
Published: over 11 years ago

10.3389/fpls.2017.00938

Transcriptome Analysis of Differentially Expressed Genes Induced by Low and High Potassium Levels Provides Insight into Fruit Sugar Metabolism of Pear
Cited by: 34
Author(s): Changwei Shen, Jie Wang, Xiaoqian Shi, Yalong Kang, Chaotian Xie, Lirun Peng, Caixia Dong, Qirong Shen, Yangchun Xu
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2105-12-S7-A13

MSCTrees: a mean-shift based toolkit for cluster analysis of phylogenetic trees
Cited by: 0
Author(s): Weixi Li, Jerzy W. Jaromczyk
Software Mentions: 2
Published: over 13 years ago

10.18632/oncotarget.11557

Identification of breast cancer recurrence risk factors based on functional pathways in tumor and normal tissues
Cited by: 11
Author(s): Xiujie Chen, Lei Liu, Yunfeng Wang, Bo Liu, Diheng Zeng, Qing Jin, Mengjian Li, Denan Zhang, Qiuqi Liu, Hongbo Xie
Software Mentions: 2
Published: about 8 years ago

10.18632/oncotarget.6993

Transcriptional profiling analysis and functional prediction of long noncoding RNAs in cancer
Cited by: 45
Author(s): Jiao Yuan, Haiyan Yue, Meiying Zhang, Jianjun Luo, Lihui Liu, Wei Wu, Tengfei Xiao, Xiaowei Chen, Xiaomin Chen, Dongdong Zhang, Rui Xing, Xin Tong, Nan Wu, Jian Zhao, Youyong Lü, Mingzhou Guo, Runsheng Chen
Software Mentions: 2
Published: almost 9 years ago

10.3390/ijms21031080

Differential Expression of Genes at Panicle Initiation and Grain Filling Stages Implied in Heterosis of Rice Hybrids
Cited by: 12
Author(s): Jawahar Lal Katara, Ram Lakhan Verma, Madhuchhanda Parida, Umakanta Ngangkham, Kutubuddin A. Molla, Kalyani M. Barbadikar, Mitadru Mukherjee, C. Parameswaran, Sanghamitra Samantaray, Nageswara Rao Ravi, O. N. Singh, Trilochan Mohapatra
Software Mentions: 2
Published: over 4 years ago

10.3389/fonc.2020.00546

The Altered Metabolic Molecular Signatures Contribute to the RAD001 Resistance in Gastric Neuroendocrine Tumor
Cited by: 2
Author(s): Jie Pan, Qiyu Bao, G. Enders
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pone.0088397

The Identification and Characteristics of Immune-Related MicroRNAs in Haemocytes of Oyster Crassostrea gigas
Cited by: 56
Author(s): Zhi Zhou, Lingling Wang, Linsheng Song, Rui Li, Huan Zhang, Mengmeng Huang, Hao Chen
Software Mentions: 2
Published: over 10 years ago

10.3389/fvets.2021.616774

Transcriptomic Analysis of High- and Low-Virulence Bovine Pasteurella multocida in vitro and in vivo
Cited by: 10
Author(s): Fang He, Zongling Zhao, Xiaoyan Wu, Lijie Duan, Nengzhang Li, Rendong Fang, Pan Li, Yuanyi Peng
Software Mentions: 2
Published: over 3 years ago

10.3389/fmicb.2019.03010

Construction of Simplified Microbial Consortia to Degrade Recalcitrant Materials Based on Enrichment and Dilution-to-Extinction Cultures
Cited by: 33
Author(s): Dingrong Kang, Samuel Jacquiod, Jakob Herschend, Wei Shi, Joseph Nesme, Søren J. Sørensen
Software Mentions: 2
Published: almost 5 years ago

10.3389/fmicb.2019.03133

Genome Sequencing and Comparative Analysis of Three Hanseniaspora uvarum Indigenous Wine Strains Reveal Remarkable Biotechnological Potential
Cited by: 12
Author(s): Nicoletta Guaragnella, Matteo De Chiara, Angela Capece, P. Romano, Rocchina Pietrafesa, Gabriella Siesto, Caterina Manzari, Graziano Pesole
Software Mentions: 2
Published: almost 5 years ago

10.3390/brainsci11080978

Restrained Eating Is Associated with Lower Cortical Thickness in the Inferior Frontal Gyrus in Adolescents
Cited by: 1
Author(s): Isabel García‐García, Maite Garolera, Jonatan Ottino‐González, Xavier Prats-Soteras, Anna Prunell-Castañé, Marı́a Ángeles Jurado
Software Mentions: 2
Published: over 3 years ago

10.1186/1743-422X-9-74

Evaluation of the immunogenicity of liposome encapsulated HVR1 and NS3 regions of genotype 3 HCV, either singly or in combination
Cited by: 11
Author(s): Gouri M. Gupte, Vidya A. Arankalle
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0032552

Interrelationships between Yeast Ribosomal Protein Assembly Events and Transient Ribosome Biogenesis Factors Interactions in Early Pre-Ribosomes
Cited by: 35
Author(s): Steffen Jakob, Uli Ohmayer, Andreas Neueder, Thomas Hierlmeier, Jorge Pérez-Fernández, Eduard Hochmuth, Rainer Deutzmann, Joachim Griesenbeck, Herbert Tschochner, Philipp Milkereit
Software Mentions: 2
Published: over 12 years ago

10.1186/gb-2007-8-9-r184

Transcriptomic and phenotypic analysis of murine embryonic stem cell derived BMP2+ lineage cells: an insight into mesodermal patterning
Cited by: 24
Author(s): Michael Xavier Doss, Shuhua Chen, Johannes Winkler, Hippler-Altenburg Rita, Odenthal Margareta, Claudia Wickenhauser, Sridevi Balaraman, Herbert Schulz, Oliver Hummel, Norbert Hübner, Nandini Ghosh‐Choudhury, Isaia Sotiriadou, Jürgen Hescheler, Agapios Sachinidis
Software Mentions: 2
Published: almost 18 years ago

10.1186/gb-2008-9-11-r159

ArrayPlex: distributed, interactive and programmatic access to genome sequence, annotation, ontology, and analytical toolsets
Cited by: 1
Author(s): Patrick J. Killion, Vishwanath R. Iyer
Software Mentions: 2
Published: almost 17 years ago

10.1186/gb-2008-9-4-r65

Histone deacetylase inhibition accelerates the early events of stem cell differentiation: transcriptomic and epigenetic analysis
Cited by: 87
Author(s): Efthimia Karantzali, Herbert Schulz, Oliver Hummel, Norbert Hübner, AK Hatzopoulos, Androniki Kretsovali
Software Mentions: 2
Published: almost 17 years ago

10.1371/journal.pone.0139794

Molecular Characterization and Expression Profiling of NAC Transcription Factors in Brachypodium distachyon L
Cited by: 30
Author(s): Guijie Zhu, Guanxing Chen, Jiantang Zhu, Yan Zhu, Xiaobing Lu, Xiaohui Li, Yingkao Hu, Yueming Yan
Software Mentions: 2
Published: about 9 years ago

10.1186/gb-2010-11-7-r79

Paternally biased X inactivation in mouse neonatal brain
Cited by: 43
Author(s): Xiaozhu Wang, Paul D. Soloway, Andrew G. Clark
Software Mentions: 2
Published: almost 15 years ago

10.1186/gb-2010-11-8-r85

Digital expression profiling of novel diatom transcripts provides insight into their biological functions
Cited by: 83
Author(s): Uma Maheswari, Kamel Jabbari, Jean-Louis Petit, Betina M. Porcel, Andrew E. Allen, Jean‐Paul Cadoret, Alessandra De Martino, Marc Heijde, Raymond Kaas, Pascal J. Lopez, Véronique Martin‐Jézéquel, Agnès Meichenin, Thomas Möck, Micaela S. Parker, Assaf Vardi, E. Virginia Armbrust, Jean Weissenbach, Michaël Katinka, Chris Bowler
Software Mentions: 2
Published: almost 15 years ago

10.18632/oncotarget.7514

Identification of long non-coding RNAs as novel biomarker and potential therapeutic target for atrial fibrillation in old adults
Cited by: 28
Author(s): Ying‐Jia Xu, Ruixuan Huang, Junjie Gu, Weifeng Jiang
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0031715

The Cryptosporidium Parvum Transcriptome during In Vitro Development
Cited by: 95
Author(s): Mary Jean Mauzy, Shinichiro Enomoto, Cheryl A. Lancto, Mitchell S. Abrahamsen, Mark S. Rutherford
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0187222

Ovarian carcinoma glyco-antigen targeted by human IgM antibody
Cited by: 1
Author(s): Yi Chen, Marcia M. Bieber, Neelima M. Bhat, Nelson N.H. Teng
Software Mentions: 2
Published: almost 7 years ago

10.18632/oncotarget.8702

Characterization of selective and potent PI3Kδ inhibitor (PI3KD-IN-015) for B-Cell malignances
Cited by: 7
Author(s): Xiaochuan Liu, Aoli Wang, Xiaofei Liang, Cheng Chen, Juanjuan Liu, Zheng Zhao, Hong Wu, Yunfei Deng, Li Wang, Beilei Wang, Jiaxin Wu, Feiyang Liu, Stacey M. Fernandes, Sophia Adamia, Richard Stone, Ilene Galinsky, Jennifer R. Brown, James D. Griffin, Shanchun Zhang, Teck Peng Loh, Xin Zhang, Qianqian Wang, Ellen Weisberg, Jing Liu, Qingsong Liu
Software Mentions: 2
Published: over 8 years ago

10.1093/gigascience/giw017

From reads to operational taxonomic units: an ensemble processing pipeline for MiSeq amplicon sequencing data
Cited by: 47
Author(s): Mohamed Mysara, Mercy Njima, Natalie Leys, Jeroen Raes, Pieter Monsieurs
Software Mentions: 2
Published: almost 8 years ago

10.18632/aging.101077

Aging dysregulates D- and E-series resolvins to modulate cardiosplenic and cardiorenal network following myocardial infarction
Cited by: 71
Author(s): Ganesh V. Halade, Vasundhara Kain, Laurence M. Black, Sumanth D. Prabhu, Kevin A. Ingle
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0082117

Deep Sequencing-Based Transcriptional Analysis of Bovine Mammary Epithelial Cells Gene Expression in Response to In Vitro Infection with Staphylococcus aureus Stains
Cited by: 15
Author(s): Wang Xiao, Lei Xiu, Qian-Nan Hu, Xinjie Cui, Bingchun Liu, Tao Lin, Ting Wang, Jingging Wu, Yuan Chen, Yan Chen
Software Mentions: 2
Published: almost 11 years ago

10.1186/s12864-015-2193-x

Differential expression profiling of the early response to Ustilaginoidea virens between false smut resistant and susceptible rice varieties
Cited by: 47
Author(s): Yanqing Han, Kang Zhang, Jun Yang, Nan Zhang, Anfei Fang, Yong Zhang, Yongfeng Liu, Zhiyi Chen, Tom Hsiang, Wenxian Sun
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0112375

Genome-Wide Classification and Evolutionary and Expression Analyses of Citrus MYB Transcription Factor Families in Sweet Orange
Cited by: 47
Author(s): Xiao-Jin Hou, Si-Bei Li, Shengrui Liu, Chun-Gen Hu, Jin‐Zhi Zhang
Software Mentions: 2
Published: almost 10 years ago

10.1186/1471-2164-13-700

Transcriptomic analysis of ‘Suli’ pear (Pyrus pyrifolia white pear group) buds during the dormancy by RNA-Seq
Cited by: 137
Author(s): Guoqin Liu, Wanshun Li, Ping Zheng, Tong Xu, Lijuan Chen, Dongfeng Liu, Sayed Hussain, Yuanwen Teng
Software Mentions: 2
Published: almost 12 years ago

10.1111/j.1365-2605.2009.01020.x

The effects of an in utero exposure to 2,3,7,8-tetrachloro-dibenzo-<i>p</i>-dioxin on male reproductive function: identification of Ccl5 as a potential marker
Cited by: 30
Author(s): Diane Rebourcet, Fanny Odet, Adélie Verot, Emmanuel Combe, Emmanuelle Meugnier, Sandra Pesenti, Patrick Leduque, H. Déchaud, Solange Magre, Brigitte Le Magueresse-Battistoni
Software Mentions: 2
Published: over 14 years ago