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

10.1371/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

10.1186/bcr3020

Genomic and phenotypic analysis of BRCA2mutated breast cancers reveals co-occurring changes linked to progression
Cited by: 22
Author(s): Olafur A. Stefansson, Jón G. Jonasson, Katrín Ólafsdóttir, Hörður Bjarnason, Óskar T. Jóhannsson, Sigrídur K. Bödvarsdóttir, Sigrı́dur Valgeirsdóttir, Jórunn E. Eyfjörd
Software Mentions: 3
Published: almost 15 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

10.3389/fbioe.2014.00064

Uncovering RNA Editing Sites in Long Non-Coding RNAs
Cited by: 41
Author(s): Ernesto Picardi, Anna Maria D’Erchia, Angela Gallo, Antonio Montalvo, Graziano Pesole
Software Mentions: 3
Published: over 11 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

10.3389/fbioe.2019.00427

A Novel Approach to Identify Enhancer lincRNAs by Integrating Genome, Epigenome, and Regulatome
Cited by: 1
Author(s): Liu Hui, Tiantongfei Jiang, Shuyuan Wang, Xiang Chen, Xiaoyan Jin, Qi Wang, Xinhui Li, Jiaqi Yin, Tingting Shao, Yongsheng Li, Juan Xu, Qiong Wu
Software Mentions: 3
Published: over 6 years ago

10.3389/fcvm.2021.658915

Common Variants Associated With OSMR Expression Contribute to Carotid Plaque Vulnerability, but Not to Cardiovascular Disease in Humans
Cited by: 3
Author(s): Daniëlle van Keulen, Ian D. van Koeverden, Arjan Boltjes, H.M.G. Princen, Alain J. van Gool, Gert J. de Borst, Folkert W. Asselbergs, Dennie Tempel, Gérard Pasterkamp, Sander W. van der Laan
Software Mentions: 3
Published: over 5 years ago

10.3389/fcvm.2021.693351

Plasma Testosterone Levels and Atherosclerotic Plaque Gene Expression in Men With Advanced Atherosclerosis
Cited by: 3
Author(s): Floor Groepenhoff, Ernest Diez Benavente, Arjan Boltjes, Nathalie Timmerman, Farahnaz Waissi, Robin Hartman, N. Charlotte Onland‐Moret, Gérard Pasterkamp, Hester M. den Ruijter
Software Mentions: 3
Published: about 5 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/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

10.3389/fcimb.2017.00186

RegA Plays a Key Role in Oxygen-Dependent Establishment of Persistence and in Isocitrate Lyase Activity, a Critical Determinant of In vivo Brucella suis Pathogenicity
Cited by: 10
Author(s): Elias Abdou, María Pilar Jiménez de Bagüés, Ignacio Martínez-Abadía, Safia Ouahrani‐Bettache, Véronique Pantesco, Alessandra Occhialini, Sascha Al Dahouk, Stephan Köhler, Véronique Jubier-Maurin
Software Mentions: 3
Published: about 9 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

10.1186/2049-3002-2-13

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

10.1186/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

10.3390/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.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

10.3389/fgene.2019.01268

Epigenetic and Transcriptomic Characterization of Pure Adipocyte Fractions From Obese Pigs Identifies Candidate Pathways Controlling Metabolism
Cited by: 10
Author(s): Mette Juul Jacobsen, Jakob Hull Havgaard, Christian Anthon, Caroline M. Junker Mentzel, Susanna Cirera, Poula Maltha Krogh, Sachin Pundhir, Peter Karlskov-Mortensen, Camilla S. Bruun, Philippe Lesnik, Maryse Guérin, Jan Gorodkin, Claus B. Jørgensen, Merete Fredholm, Romain Barrès
Software Mentions: 3
Published: over 6 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

10.3390/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

10.1371/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

10.3389/fgene.2014.00043

Quality assessment and control of tissue specific RNA-seq libraries of Drosophila transgenic RNAi models
Cited by: 12
Author(s): Andreia J. Amaral, Francisco Brito, Tamar Chobanyan, S. Yoshikawa, Takakazu Yokokura, David Van Vactor, Margarida Gama‐Carvalho
Software Mentions: 3
Published: over 12 years ago

10.3389/fgene.2014.00031

Multi-genome alignment for quality control and contamination screening of next-generation sequencing data
Cited by: 21
Author(s): James Hadfield, Matthew Eldridge
Software Mentions: 3
Published: over 12 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.pmed.0030047

Gene Expression Programs in Response to Hypoxia: Cell Type Specificity and Prognostic Significance in Human Cancers
Cited by: 549
Author(s): Jen‐Tsan Chi, Zhen Wang, Dimitry S.A. Nuyten, Edwin H. Rodriguez, Marci E. Schaner, Ali Salim, Yun Wang, Gunnar B. Kristensen, Åslaug Helland, Anne Lise Børresen-Dale, Amato J. Giaccia, Michael T. Longaker, Trevor Hastie, George P. Yang, Marc J. van de Vijver, Patrick O. Brown
Software Mentions: 3
Published: over 20 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

10.1371/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

10.18632/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

10.3389/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

10.3389/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

10.1371/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

10.3389/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.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

10.18632/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

10.3389/fvets.2019.00308

A Pine Enhanced Biochar Does Not Decrease Enteric CH4 Emissions, but Alters the Rumen Microbiota
Cited by: 24
Author(s): Stephanie A. Terry, Gabriel de Oliveira Ribeiro, Robert J. Gruninger, A. V. Chaves, K. A. Beauchemin, E. K. Okine, Tim A. McAllister
Software Mentions: 3
Published: almost 7 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.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

10.18632/oncotarget.19733

Overexpression of COL3A1 confers a poor prognosis in human bladder cancer identified by co-expression analysis
Cited by: 59
Author(s): Lushun Yuan, Bo Shu, Changhong Liang, Kaiyu Qian, Yongzhi Wang, Guofeng Qian, Yuan Zhu, Xinyue Cao, Conghua Xie, Yu Xiao, Xinghuan Wang
Software Mentions: 3
Published: almost 9 years ago

10.1534/g3.111.000240

<i>Stacks</i>: Building and Genotyping Loci <i>De Novo</i> 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

10.7554/eLife.29736

CDK9-dependent RNA polymerase II pausing controls transcription initiation
Cited by: 157
Author(s): Saskia Gressel, Björn Schwalb, Tim-Michael Decker, Weihua Qin, Heinrich Leonhardt, Dirk Eick, Patrick Cramer
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pone.0219551

Density distribution of gene expression profiles and evaluation of using maximal information coefficient to identify differentially expressed genes
Cited by: 16
Author(s): Han-Ming Liu, Dan Yang, Zhao-Fa Liu, Shengzhou Hu, Yan Shen-hai, Xian-Wen He
Software Mentions: 3
Published: about 7 years ago

10.7554/eLife.17903

A histone H3K9M mutation traps histone methyltransferase Clr4 to prevent heterochromatin spreading
Cited by: 32
Author(s): Chun-Min Shan, Jiyong Wang, Ke Xu, Huijie Chen, Jia-Xing Yue, Stuart Andrews, James J. Moresco, John R. Yates, Péter L. Nagy, Liang Tong, Songtao Jia
Software Mentions: 3
Published: almost 10 years ago

10.1186/1471-2105-12-382

Mulcom: a multiple comparison statistical test for microarray data in Bioconductor
Cited by: 5
Author(s): Claudio Isella, Tommaso Renzulli, Davide Corà, Enzo Medico
Software Mentions: 3
Published: almost 15 years ago

10.1186/s12864-015-1293-y

Genome-wide survey and expression analysis of F-box genes in chickpea
Cited by: 59
Author(s): Shefali Gupta, Vanika Garg, Chandra Kant, Sabhyata Bhatia
Software Mentions: 3
Published: over 11 years ago

10.1186/1471-2164-13-507

Surviving in a toxic world: transcriptomics and gene expression profiling in response to environmental pollution in the critically endangered European eel
Cited by: 67
Author(s): J. M. Pujolar, Ilaria A. M. Marino, Massimo Milan, Alessandro Coppe, Grégory E. Maes, Fabrizio Capoccioni, Eleonora Ciccotti, Lieven Bervoets, Adrian Covaci, Claude Belpaire, Gordon Cramb, Tomaso Patarnello, Luca Bargelloni, Stefania Bortoluzzi, Lorenzo Zane
Software Mentions: 3
Published: over 14 years ago

10.1186/s12859-017-1831-5

SimBA: A methodology and tools for evaluating the performance of RNA-Seq bioinformatic pipelines
Cited by: 8
Author(s): Jérôme Audoux, Mikaël Salson, Christophe Grosset, Sacha Beaumeunier, Jean-Marc Holder, Thérèse Commes, Philippe Naveilhan
Software Mentions: 3
Published: almost 9 years ago

10.1515/jib-2018-0080

Gene Expression Studies to Identify Significant Genes in AR, MTOR, MAPK Pathways and their Overlapping Regulatory Role in Prostate Cancer
Cited by: 0
Author(s): Nimisha Asati, Abhinav Mishra, Ayush Shukla, Tiratha Raj Singh
Software Mentions: 3
Published: about 7 years ago

10.1186/s12859-020-03726-9

IonCRAM: a reference-based compression tool for ion torrent sequence files
Cited by: 2
Author(s): Moustafa Shokrof, Mohamed Abouelhoda
Software Mentions: 3
Published: almost 6 years ago

10.1186/s12864-015-2112-1

Sequencing-based high throughput mutation detection in bread wheat
Cited by: 12
Author(s): Gaganjot Sidhu, Amita Mohan, Ping Zheng, Amandeep Kaur Dhaliwal, Dorrie Main, Kulvinder S. Gill
Software Mentions: 3
Published: over 10 years ago

10.1186/1471-2105-7-237

Components of the antigen processing and presentation pathway revealed by gene expression microarray analysis following B cell antigen receptor (BCR) stimulation
Cited by: 37
Author(s): Jamie A. Lee, Robert S. Sinkovits, Dennis Mock, Eva L Rab, Jennifer Cai, Peng Yang, Brian Saunders, Robert C. Hsueh, Sangdun Choi, Shankar Subramaniam, Richard H. Scheuermann
Software Mentions: 3
Published: about 20 years ago

10.1371/journal.pone.0028275

The Global Transcriptional Response of Fission Yeast to Hydrogen Sulfide
Cited by: 8
Author(s): Jianmin Xu, Weizhi He, Alastair I. H. Murchie, Dongrong Chen
Software Mentions: 3
Published: over 14 years ago

10.7150/ijms.51743

Identifying daily changes in circRNAs and circRNA-associated-ceRNA networks in the rat pineal gland
Cited by: 5
Author(s): Yi Zheng, Hao Jiang, Hao-Qi Wang, Haixiang Guo, Dong-Xu Han, Yongping Huang, Yan Gao, Bao Yuan
Software Mentions: 3
Published: over 5 years ago

10.1155/2013/924971

Gene Expression Profile Analysis of T1 and T2 Breast Cancer Reveals Different Activation Pathways
Cited by: 3
Author(s): Margit Riis, Xi Zhao, Fatemeh Kaveh, Hilde Synnøve Vollan, Anne-Jorunn Nesbakken, Hiroko Kato Solvang, Torben Lüders, Ida Rashida Khan Bukholm, Vessela N. Kristensen
Software Mentions: 3
Published: over 13 years ago

10.3892/ijo.2014.2648

Microarray phosphatome profiling of breast cancer patients unveils a complex phosphatase regulatory role of the MAPK and PI3K pathways in estrogen receptor-negative breast cancers
Cited by: 13
Author(s): Ramón González Manzano, E. Martinez-Navarro, Jerónimo Forteza, Antonio Brugarolas
Software Mentions: 3
Published: almost 12 years ago

10.1186/s12859-021-04267-5

Pheniqs 2.0: accurate, high-performance Bayesian decoding and confidence estimation for combinatorial barcode indexing
Cited by: 8
Author(s): Lior Galanti, Dennis Shasha, Kristin C. Gunsalus
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.pone.0085583

Consistent Errors in First Strand cDNA Due to Random Hexamer Mispriming
Cited by: 36
Author(s): Thomas P. van Gurp, Lauren M. McIntyre, Koen J. F. Verhoeven
Software Mentions: 3
Published: over 12 years ago

10.1371/journal.pone.0087499

Analysis of Global Gene Expression in Brachypodium distachyon Reveals Extensive Network Plasticity in Response to Abiotic Stress
Cited by: 80
Author(s): Henry D. Priest, Samuel E. Fox, Erik R. Rowley, Jessica R. Murray, Todd P. Michael, Todd C. Mockler
Software Mentions: 3
Published: over 12 years ago

10.1038/s41396-018-0332-5

Niche-directed evolution modulates genome architecture in freshwater Planctomycetes
Cited by: 55
Author(s): Adrian‐Ştefan Andrei, Michaela M. Salcher, Maliheh Mehrshad, Pavel Rychtecký, Petr Znachor, Rohit Ghai
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pone.0000242

Epigenetic Activation of a Subset of mRNAs by eIF4E Explains Its Effects on Cell Proliferation
Cited by: 203
Author(s): Yaël Mamane, Emmanuel Petroulakis, Yvan Martineau, Takaaki Sato, Ola Larsson, Vinagolu K. Rajasekhar, Nahum Sonenberg
Software Mentions: 3
Published: over 19 years ago

10.1186/s12859-020-03665-5

SimuSCoP: reliably simulate Illumina sequencing data based on position and context dependent profiles
Cited by: 11
Author(s): Zhenhua Yu, Fang Du, Rongjun Ban, Yuanwei Zhang
Software Mentions: 3
Published: about 6 years ago

10.1186/s40246-019-0194-6

vi-HMM: a novel HMM-based method for sequence variant identification in short-read data
Cited by: 1
Author(s): Man Lai Tang, Mohammad Shabbir Hasan, Hongxiao Zhu, Liqing Zhang, Xiaowei Wu
Software Mentions: 3
Published: over 7 years ago

10.18632/aging.103184

Plasma proteomic profiling of young and old mice reveals cadherin-13 prevents age-related bone loss
Cited by: 14
Author(s): Yong Ryoul Yang, Mohammad Humayun Kabir, Jin Hee Park, Jae-Il Park, Jae Sook Kang, Shinyeong Ju, Yeo Jin Shin, Seung Min Lee, Jaemin Lee, Seokho Kim, Kwang-Pyo Lee, Soo Young Lee, Cheolju Lee, Kideok D. Kwon
Software Mentions: 3
Published: about 6 years ago

10.1101/2021.07.09.21260221

Genetic regulation of<i>OAS1</i>nonsense-mediated decay underlies association with risk of severe COVID-19
Cited by: 8
Author(s): Abdul Rouf Banday, Megan L. Stanifer, Óscar Flórez-Vargas, Olusegun O. Onabajo, Muhammad Atif Zahoor, Brenen W. Papenberg, Timothy J. Ring, Chia-Han Lee, Evangelos Andreakos, Evgeny Arons, Greg Barsh, Leslie G. Biesecker, David L. Boyle, Andrea N. Burnett‐Hartman, Mary Carrington, Euijin Chang, Pyoeng Gyun Choe, Rex L Chrisholm, Clifton L. Dalgard, Jeff Edberg, Nathan Erdmann, Heather Spencer Feigelson, Gary S. Firestein, Adam J. Gehring, Michelle Ho, Steven M. Holland, Amy Hutchinson, Hogune Im, Michael G. Ison, Hong Bin Kim, Robert J. Kreitman, Bruce R. Korf, Lisa Mirabello, Jennifer A. Pacheco, Michael J. Peluso, Daniel J. Rader, David T. Redden, Marylyn D. Ritchie, Brooke Rosenbloom, Hanaisa P. Sant Anna, Sharon A. Savage, E. Siouti, Vasiliki Triantafyllia, Joselin M. Vargas, Anurag Verma, Vibha Vij, Duane R. Wesemann, Meredith Yeager, Xu G. Yu, Yu Zhang, Steeve Boulant, Stephen J. Chanock, Jordan J. Feld, Ludmila Prokunina–Olsson
Software Mentions: 3
Published: about 5 years ago

10.7554/eLife.22345

Stella modulates transcriptional and endogenous retrovirus programs during maternal-to-zygotic transition
Cited by: 83
Author(s): Yun Huang, Jong Kim, Dang Vinh, Caroline Lee, Christopher A. Penfold, J. Ż̷ylicz, John C. Marioni, Jim Hackett, M. Azim Surani
Software Mentions: 3
Published: over 9 years ago

10.1128/mBio.02096-17

The Essential Genome of <i>Escherichia coli</i> K-12
Cited by: 204
Author(s): Emily C. A. Goodall, Ashley Robinson, Iain G. Johnston, Sara Jabbari, A. Keith Turner, Adam F. Cunningham, Peter A. Lund, Jeffrey A. Cole, Ian R. Henderson
Software Mentions: 3
Published: over 8 years ago

10.1186/1471-2105-12-411

EPEPT: A web service for enhanced P-value estimation in permutation tests
Cited by: 5
Author(s): Theo Knijnenburg, Jake Lin, Hector Rovira, John P. Boyle, Ilya Shmulevich
Software Mentions: 3
Published: almost 15 years ago

10.1128/mBio.00731-20

Differential Alphavirus Defective RNA Diversity between Intracellular and Extracellular Compartments Is Driven by Subgenomic Recombination Events
Cited by: 11
Author(s): Rose M. Langsjoen, Antonio E. Muruato, S. R. Kunkel, Elizabeth Jaworski, Andrew Routh
Software Mentions: 3
Published: almost 6 years ago

10.1128/mBio.00684-13

Genes Required for Aerial Growth, Cell Division, and Chromosome Segregation Are Targets of WhiA before Sporulation in Streptomyces venezuelae
Cited by: 96
Author(s): Matthew J. Bush, Maureen J. Bibb, Govind Chandra, Kim Findlay, Mark J. Buttner
Software Mentions: 3
Published: over 12 years ago

10.1186/s12863-017-0568-5

IntroMap: a signal analysis based method for the detection of genomic introgressions
Cited by: 3
Author(s): Daniel J. Shea, Mitsuru Shimizu, Namiko Nishida, Eigo Fukai, Takashi Abe, Ryo Fujimoto, Keiichi Okazaki
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pcbi.1007543

Automated minute scale RNA-seq of pluripotent stem cell differentiation reveals early divergence of human and mouse gene expression kinetics
Cited by: 6
Author(s): Christopher Barry, Matthew T. Schmitz, Cara Argus, Jennifer M. Bolin, Mitchell D. Probasco, Ning Leng, Bret Duffin, John Steill, Scott Swanson, Brian E. McIntosh, Ron Stewart, Christina Kendziorski, James A. Thomson, Rhonda Bacher
Software Mentions: 3
Published: over 6 years ago

10.1128/mBio.01568-20

Decoding the Architecture of the Varicella-Zoster Virus Transcriptome
Cited by: 26
Author(s): Shirley E. Braspenning, Tomohiko Sadaoka, Judith Breuer, Georges M. G. M. Verjans, Werner J. D. Ouwendijk, Daniel P. Depledge
Software Mentions: 3
Published: over 5 years ago

10.1007/s00122-019-03517-8

Genetic analysis of wheat sensitivity to the ToxB fungal effector from Pyrenophora tritici-repentis, the causal agent of tan spot
Cited by: 22
Author(s): Beatrice Corsi, Lawrence Percival‐Alwyn, Rowena Downie, Luca Venturini, Elyce M. Iagallo, Camila Campos Mantello, Charlie McCormick-Barnes, Pao Theen See, Richard P. Oliver, Caroline S. Moffat, James Cockram
Software Mentions: 3
Published: over 6 years ago

10.1186/s12859-020-03658-4

Performance evaluation of lossy quality compression algorithms for RNA-seq data
Cited by: 1
Author(s): Rongshan Yu, Wenxian Yang, Wang Shun
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pbio.1000238

Concordant Regulation of Translation and mRNA Abundance for Hundreds of Targets of a Human microRNA
Cited by: 376
Author(s): David G. Hendrickson, Daniel J. Hogan, Heather McCullough, Jason W. Myers, Daniel Herschlag, James E. Ferrell, Patrick O. Brown
Software Mentions: 3
Published: over 16 years ago

10.1186/s12859-021-03980-5

ViR: a tool to solve intrasample variability in the prediction of viral integration sites using whole genome sequencing data
Cited by: 7
Author(s): Elisa Pischedda, Cristina M. Crava, Martina Carlassara, Susanna Zucca, Laila Gasmi, Mariangela Bonizzoni
Software Mentions: 3
Published: over 5 years ago

10.1186/s12862-019-1353-z

Origin and diversification of the plasminogen activation system among chordates
Cited by: 26
Author(s): Andrés Chana-Muñoz, Agnieszka Jendroszek, Malene Sønnichsen, Tobias Wang, Michael Ploug, Jan K. Jensen, Peter A. Andreasen, Christian Berthou, Frank Panitz
Software Mentions: 3
Published: over 7 years ago

10.1186/1751-0473-8-6

RECOT: a tool for the coordinate transformation of next-generation sequencing reads for comparative genomics and transcriptomics
Cited by: 1
Author(s): Izawa Akiko, Jun Sese
Software Mentions: 3
Published: over 13 years ago

10.3390/s21030888

R-YOLO: A Real-Time Text Detector for Natural Scenes with Arbitrary Rotation
Cited by: 16
Author(s): Xiqi Wang, Shunyi Zheng, Ce Zhang, Rui Li, Li Gui
Software Mentions: 3
Published: over 5 years ago

10.3390/s21041182

The New Hyperspectral Satellite PRISMA: Imagery for Forest Types Discrimination
Cited by: 56
Author(s): Elia Vangi, Giovanni D’Amico, Saverio Francini, Francesca Giannetti, Bruno Lasserre, Marco Marchetti, Gherardo Chirici
Software Mentions: 3
Published: over 5 years ago

10.1186/s12862-019-1522-0

RADseq population genomics confirms divergence across closely related species in blue coral (Heliopora coerulea)
Cited by: 11
Author(s): Akira Iguchi, Yuki Yoshioka, Zac H. Forsman, Ingrid S. Knapp, Robert J. Toonen, Yuki Hongo, Satoshi Nagai, Nina Yasuda
Software Mentions: 3
Published: almost 7 years ago

10.1186/2193-1801-3-130

ASTER, ALI and Hyperion sensors data for lithological mapping and ore minerals exploration
Cited by: 69
Author(s): Amin Beiranvand Pour, Mazlan Hashim
Software Mentions: 3
Published: over 12 years ago

10.1038/s41598-020-59541-y

Chronic circadian misalignment accelerates immune senescence and abbreviates lifespan in mice
Cited by: 78
Author(s): Hitoshi Inokawa, Yasuhiro Umemura, Akihiro Shimba, Eiryo Kawakami, Nobuya Koike, Yoshiki Tsuchiya, Masaru Ohashi, Yoichi Minami, Guangwei Cui, T. Asahi, Ryutaro Ono, Yuh Sasawaki, Eiichi Konishi, Seung-Hee Yoo, Chen Zheng, Satoshi Teramukai, Koichi Ikuta, Kazuhiro Yagita
Software Mentions: 3
Published: over 6 years ago

10.1186/s13007-020-00588-3

In-silico detection of aneuploidy and chromosomal deletions in wheat using genotyping-by-sequencing
Cited by: 2
Author(s): Narinder Singh, John Raupp, Dal‐Hoe Koo, Bernd Friebe, Bikram S. Gill, Jesse Poland
Software Mentions: 3
Published: over 6 years ago

10.1111/pbi.12685

Indel‐seq: a fast‐forward genetics approach for identification of trait‐associated putative candidate genomic regions and its application in pigeonpea (<i>Cajanus cajan</i>)
Cited by: 57
Author(s): Vikas K. Singh, Aamir W. Khan, Rachit K. Saxena, Pallavi Sinha, Sandip M. Kale, Swathi Parupalli, Vinay Kumar, Annapurna Chitikineni, Suryanarayana Vechalapu, C.V. Sameer Kumar, Mamta Sharma, G. Anuradha, K.N. Yamini, S. Muniswamy, Rajeev K. Varshney
Software Mentions: 3
Published: over 9 years ago

10.1111/tpj.14468

An ‘ <scp>eFP</scp> ‐Seq Browser’ for visualizing and exploring <scp>RNA</scp> sequencing data
Cited by: 31
Author(s): Alexander Sullivan, Priyank Purohit, Nowlan H. Freese, Asher Pasha, Eddi Esteban, Jamie Waese, Alison Wu, Michelle Chen, Chih Ying Chin, Richard Song, Sneha Ramesh Watharkar, Agnes P. Chan, Vivek Krishnakumar, Matthew Vaughn, Chris Town, Ann E. Loraine, Nicholas J. Provart
Software Mentions: 3
Published: almost 7 years ago

10.1111/tpj.12307

Resistance gene enrichment sequencing (<scp>R</scp>en<scp>S</scp>eq) enables reannotation of the <scp>NB</scp>‐<scp>LRR</scp> gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations
Cited by: 327
Author(s): Florian Jupe, Kamil Witek, Walter Verweij, Jadwiga Śliwka, Leighton Pritchard, Graham J. Etherington, Dan MacLean, Peter J. A. Cock, Richard M. Leggett, Glenn J. Bryan, Linda Cardle, Ingo Hein, Jonathan D. G. Jones
Software Mentions: 3
Published: almost 13 years ago

10.1186/1746-4811-8-12

Targeted parallel sequencing of large genetically-defined genomic regions for identifying mutations in Arabidopsis
Cited by: 18
Author(s): Kun-Hsiang Liu, Matthew McCormack, Jenq-Yunn Sheen
Software Mentions: 3
Published: over 14 years ago

10.1371/journal.pone.0191932

Integrated micro/messenger RNA regulatory networks in essential thrombocytosis
Cited by: 8
Author(s): Lu Zhao, Song Wu, Erya Huang, Dimitri Gnatenko, Wadie F. Bahou, Wei Zhu
Software Mentions: 3
Published: over 8 years ago

10.7554/eLife.27529

A viral protein promotes host SAMS1 activity and ethylene production for the benefit of virus infection
Cited by: 55
Author(s): Shanshan Zhao, Wei Hong, Jiang Wu, Yu Wang, Shaoyi Ji, Shuyi Zhu, Chunhong Wei, Jinsong Zhang, Yang Li
Software Mentions: 3
Published: almost 9 years ago

10.1038/s41598-019-43512-z

Melanoma proteomics suggests functional differences related to mutational status
Cited by: 9
Author(s): Lucía Trilla-Fuertes, Angelo Gámez‐Pozo, Guillermo Prado-Vázquez, Andrea Zapater-Moros, Mariana Díaz-Almirón, Claudia Fortes, María Ferrer-Gómez, Rocío López-Vacas, Verónica Parra Blanco, Iván Márquez-Rodas, Ainara Soria, Juan Ángel Fresno Vara, Enrique Espinosa
Software Mentions: 3
Published: about 7 years ago

10.1186/1472-6815-14-9

Combined examination of sequence and copy number variations in human deafness genes improves diagnosis for cases of genetic deafness
Cited by: 23
Author(s): Haiying Ji, Jingqiao Lü, Jianjun Wang, Huawei Li, Xiaobo Lin
Software Mentions: 3
Published: almost 12 years ago

10.1038/s41598-019-43141-6

CRISPR-Cas9 Editing in Maize: Systematic Evaluation of Off-target Activity and Its Relevance in Crop Improvement
Cited by: 62
Author(s): Joshua K. Young, Gina Zastrow-Hayes, Stéphane Deschamps, Sergei Svitashev, Mindaugas Zaremba, Ananta Acharya, Sushmitha Paulraj, Brooke D. Peterson-Burch, Chris Schwartz, Vesna Djukanovic, Brian Lenderts, Lanie Feigenbutz, Limin Wang, Clara M. Alarcon, Virginijus Šikšnys, Gregory D. May, N. Doane Chilcoat, Sandeep Kumar
Software Mentions: 3
Published: about 7 years ago

10.7717/peerj.382

Characterisation of the horse transcriptome from immunologically active tissues
Cited by: 6
Author(s): Joanna Moreton, Sunir Malla, A. Aziz Aboobaker, Rachael Tarlinton, Richard D. Emes
Software Mentions: 3
Published: about 12 years ago

10.7717/peerj.8275

Algorithms for efficiently collapsing reads with Unique Molecular Identifiers
Cited by: 9
Author(s): Daniel Liu
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-019-41625-z

Improved survival prognostication of node-positive malignant melanoma patients utilizing shotgun proteomics guided by histopathological characterization and genomic data
Cited by: 12
Author(s): Lázaro Betancourt, Krzysztof Pawłowski, Jonatan Eriksson, Attila Marcell Szász, Shamik Mitra, Indira Pla, Charlotte Welinder, Henrik Ekedahl, Per Broberg, Roger Appelqvist, Maria Yakovleva, Y. Sugita, Kenichi Miharada, Christian Ingvar, Lotta Lundgren, Bo Baldetorp, Håkan Olsson, Melinda Rezeli, Elisabet Wieslander, Péter Horvatovich, Johan Malm, Göran Jönsson, György Markó-Varga
Software Mentions: 3
Published: over 7 years ago

10.1038/s41598-019-45898-2

Transcriptional landscape of soybean (Glycine max) embryonic axes during germination in the presence of paclobutrazol, a gibberellin biosynthesis inhibitor
Cited by: 19
Author(s): Rajesh Kumar Gazara, Eduardo Alves Gamosa de Oliveira, B. Calderan Rodrigues, Rodrigo Nunes da Fonseca, Antônia Elenir Amâncio Oliveira, Thiago M. Venancio
Software Mentions: 3
Published: about 7 years ago

10.1038/s41598-019-39880-1

MicroRNAs from saliva of anopheline mosquitoes mimic human endogenous miRNAs and may contribute to vector-host-pathogen interactions
Cited by: 25
Author(s): Bruno Arcà, Alessio Colantoni, Carmine Fiorillo, Francesco Severini, Vladimír Beneš, Marco Di Luca, Raffaele Calogero, Fabrizio Lombardo
Software Mentions: 3
Published: over 7 years ago

10.7717/peerj.830

The effect of listening to music on human transcriptome
Cited by: 32
Author(s): Chakravarthi Kanduri, Pirre Raijas, Minna Ahvenainen, Anju K. Philips, Liisa Ukkola-Vuoti, Harri Lähdesmäki, Irma Järvelä
Software Mentions: 3
Published: over 11 years ago

10.1186/1471-2105-16-S18-S16

Identification of aberrant gene expression associated with aberrant promoter methylation in primordial germ cells between E13 and E16 rat F3 generation vinclozolin lineage
Cited by: 23
Author(s): Y-h. Taguchi
Software Mentions: 3
Published: over 10 years ago