10.1186/1471-2164-15-765

Liver transcriptome analysis in gilthead sea bream upon exposure to low temperature
Cited by: 80
Author(s): Alba Nicoletta Mininni, Massimo Milan, Serena Ferraresso, T. Petochi, Patrizia Di Marco, G. Marino, Silvia Livi, Chiara Romualdi, Luca Bargelloni, Tomaso Patarnello
Software Mentions: 2
Published: about 12 years ago

10.1371/journal.pone.0013451

A Molecular Signature of Proteinuria in Glomerulonephritis
Cited by: 63
Author(s): Heather N. Reich, David Tritchler, Daniel C. Cattran, Andrew M. Herzenberg, Felix Eichinger, Anissa Boucherot, Anna Henger, Céline C. Berthier, Viji Nair, Clemens D. Cohen, James W. Scholey, Matthias Kretzler
Software Mentions: 2
Published: almost 16 years ago

10.1371/journal.pone.0074825

CEQer: A Graphical Tool for Copy Number and Allelic Imbalance Detection from Whole-Exome Sequencing Data
Cited by: 19
Author(s): Rocco Piazza, Vera Magistroni, Alessandra Pirola, Sara Redaelli, Roberta Spinelli, Serena Redaelli, Marta Galbiati, Simona Valletta, Giovanni Giudici, Giovanni Cazzaniga, Carlo Gambacorti‐Passerini
Software Mentions: 2
Published: almost 13 years ago

10.1371/journal.pone.0095481

Global Gene Expression Analysis of Canine Cutaneous Mast Cell Tumor: Could Molecular Profiling Be Useful for Subtype Classification and Prognostication?
Cited by: 21
Author(s): Mery Giantin, Anna Granato, Chiara Baratto, Laura Marconato, Marta Vascellari, Emanuela Morello, Alessandro Vercelli, Franco Mutinelli, Mauro Dacasto
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0065571

Peptidomic Identification of Serum Peptides Diagnosing Preeclampsia
Cited by: 36
Author(s): Qiaojun Wen, Linda Y. Liu, Ting Yang, Cantas Alev, Shao-Yi Wu, David K. Stevenson, Guojun Sheng, Atul J. Butte, Xuefeng B. Ling
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0071826

Transcript Profiling Identifies Iqgap2−/− Mouse as a Model for Advanced Human Hepatocellular Carcinoma
Cited by: 22
Author(s): Dmitri V. Gnatenko, Xiao Xu, Wei Zhu, Valentina A. Schmidt
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0072699

In-Depth Characterization of microRNA Transcriptome in Melanoma
Cited by: 111
Author(s): James Kozubek, Zhihai Ma, Elizabeth Fleming, Tatiana Duggan, Rong Wu, Dong-Guk Shin, Soheil S. Dadras
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0023204

Drug-Resistant Genotypes and Multi-Clonality in Plasmodium falciparum Analysed by Direct Genome Sequencing from Peripheral Blood of Malaria Patients
Cited by: 45
Author(s): Tim Robinson, Susana Campino, Sarah Auburn, Samuel Assefa, Spencer D. Polley, Magnus Manske, Bronwyn MacInnis, Kirk A. Rockett, G. Maslen, Mandy Sanders, Michael A. Quail, Peter L. Chiodini, Dominic P. Kwiatkowski, Taane G. Clark, Colin J. Sutherland
Software Mentions: 2
Published: about 15 years ago

10.1089/ast.2016.1551

The Mars Organic Molecule Analyzer (MOMA) Instrument: Characterization of Organic Material in Martian Sediments
Cited by: 164
Author(s): Fred Goesmann, W. B. Brinckerhoff, F. Raulin, W. Goetz, Ryan M. Danell, Stéphanie Getty, Sandra Siljeström, Helge Mißbach, Harald Steininger, Ricardo Arévalo, Arnaud Buch, Caroline Freissinet, Andrej Grubisic, Uwe J. Meierhenrich, V. Pinnick, Fabien Stalport, Cyril Szopa, Jorge L. Vago, Robert Lindner, Mitchell D. Schulte, J. R. Brucato, Daniel P. Glavin, N. Grand, Xiang Li, F. H. W. van Amerom
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0180469

Genome-wide analysis of the CCCH zinc finger family identifies tissue specific and stress responsive candidates in chickpea (Cicer arietinum L.)
Cited by: 27
Author(s): Seema Pradhan, Chandra Kant, Subodh Verma, Sabhyata Bhatia
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0041001

Transcriptome Profiling of the Cancer, Adjacent Non-Tumor and Distant Normal Tissues from a Colorectal Cancer Patient by Deep Sequencing
Cited by: 65
Author(s): Yanan Wu, Xuetao Wang, WU Fang-bo, Ruolei Huang, Fangqin Xue, Guantao Liang, Min Tao, Peng Cai, Yi Huang
Software Mentions: 2
Published: about 14 years ago

10.1371/journal.pone.0104709

Functional Networks of Nucleocytoplasmic Transport-Related Genes Differentiate Ischemic and Dilated Cardiomyopathies. A New Therapeutic Opportunity
Cited by: 26
Author(s): María Micaela Molina-Navarro, Juan Carlos Triviño, Luis Martínez‐Dolz, Francisca Lago, José Ramón González-Juanatey, Manuel Portolés, Miguel Rivera
Software Mentions: 2
Published: about 12 years ago

10.1186/1471-2164-15-540

Building the sugarcane genome for biotechnology and identifying evolutionary trends
Cited by: 97
Author(s): Nathalia de Setta, Cláudia Barros Monteiro-Vitorello, Cushla J. Metcalfe, Guilherme M. Q. Cruz, Luiz-Eduardo Del-Bem, Renato Vicentini, Fábio Tebaldi Silveira Nogueira, Roberto Augusto de Carvalho Campos, Sideny Lima Nunes, Paula Cristina Gasperazzo Turrini, Andréia Prata Vieira, Edgar Andrés Ochoa Cruz, Tatiana Caroline Silveira Corrêa, Carlos Takeshi Hotta, Alessandro de Mello Varani, Sonia Vautrin, Adilson Silva da Trindade, Mariane de Mendonça Vilela, Carolina Gimiliani Lembke, Paloma Mieko Sato, Rodrigo Fandiño de Andrade, Milton Yutaka Nishiyama, Cláudio Benício Cardoso-Silva, Kátia Castanho Scortecci, Antônio Augusto Franco Garcia, Monalisa Sampaio Carneiro, Changsoo Kim, Andrew H. Paterson, Hélène Bergès, Angélique D’Hont, Anete Pereira de Souza, Gláucia Mendes Souza, Michel Vincentz, João Paulo Kitajima, Marie‐Anne Van Sluys
Software Mentions: 2
Published: about 12 years ago

10.1186/s12885-019-5650-0

Association of pathway mutation with survival after recurrence in colorectal cancer patients treated with adjuvant fluoropyrimidine and oxaliplatin chemotherapy
Cited by: 2
Author(s): Dae Won Lee, Sae Won Han, Yongjun Cha, Jeong Mo Bae, Hwang Phill Kim, Jaemyun Lyu, Hyojun Han, Hyoki Kim, Hoon Jang, Duhee Bang, Jae Kyung Won, Seung Yong Jeong, Kyu Joo Park, Gyeong Hoon Kang, Tae You Kim
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2407-6-54

Cross-platform expression profiling demonstrates that SV40 small tumor antigen activates Notch, Hedgehog, and Wnt signaling in human cells
Cited by: 17
Author(s): Mohamed Ali-Seyed, Noelani Laycock, Suresh Karanam, Wenming Xiao, Eric T. Blair, Carlos S. Moreno
Software Mentions: 2
Published: over 20 years ago

10.1371/journal.pone.0025925

Diverting the Flux of the JA Pathway in Nicotiana attenuata Compromises the Plant's Defense Metabolism and Fitness in Nature and Glasshouse
Cited by: 38
Author(s): Michael Stitz, Ian Thomas Baldwin, Emmanuel Gaquerel
Software Mentions: 2
Published: almost 15 years ago

10.1371/journal.pone.0055368

Expression Profile of Ectopic Olfactory Receptors Determined by Deep Sequencing
Cited by: 219
Author(s): Caroline Flegel, Stavros Manteniotis, Sandra Osthold, Hanns Hatt, Günter Gisselmann
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0215908

Wild-type and SAMP8 mice show age-dependent changes in distinct stem cell compartments of the interfollicular epidermis
Cited by: 8
Author(s): Gopakumar Changarathil, Karina Ramírez, Hiroko Isoda, Aiko Sada, Hiromi Yanagisawa
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0251149

A robust method of nuclei isolation for single-cell RNA sequencing of solid tissues from the plant genus Populus
Cited by: 17
Author(s): Daniel Conde, Paolo M. Triozzi, Kelly M. Balmant, Andria Doty, Mariza Abreu Miranda, Anthony Boullosa, Henry W. Schmidt, Wendell Jacinto Pereira, Christopher Dervinis, Matias Kirst
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0031241

Genome-Wide Maps of Circulating miRNA Biomarkers for Ulcerative Colitis
Cited by: 92
Author(s): Radha Duttagupta, Sharon DiRienzo, Rong Jiang, Jessica Bowers, Jeremy Gollub, Jennifer L. Kao, Keith R. Kearney, David Rudolph, Noor Dawany, Michael K. Showe, Tom Stamato, Robert C. Getts, Keith Jones
Software Mentions: 2
Published: over 14 years ago

10.1186/1471-2164-15-20

Sex specific expression and distribution of small RNAs in papaya
Cited by: 21
Author(s): Rishi Aryal, Guru Jagadeeswaran, Yun Zheng, Qingyi Yu, Ramanjulu Sunkar, Ray Ming
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0039469

Deregulation of Rab and Rab Effector Genes in Bladder Cancer
Cited by: 94
Author(s): Joël Rainui Ho, Élodie Chapeaublanc, Lisa A. Kirkwood, Rémy Nicolle, Simone Benhamou, Thierry Lebrét, Yves Allory, Jennifer Southgate, François Radvanyi, Bruno Goud
Software Mentions: 2
Published: about 14 years ago

10.1371/journal.pone.0043012

ESSENTIALS: Software for Rapid Analysis of High Throughput Transposon Insertion Sequencing Data
Cited by: 125
Author(s): Aldert Zomer, Peter Burghout, Hester J. Bootsma, Peter W. M. Hermans, Sacha A. F. T. van Hijum
Software Mentions: 2
Published: about 14 years ago

10.1186/1471-2164-13-417

Improving mapping and SNP-calling performance in multiplexed targeted next-generation sequencing
Cited by: 6
Author(s): Abdou ElSharawy, Michael Förster, Nadine Schracke, Andreas Keller, Ingo Thomsen, Britt‐Sabina Petersen, Björn Stade, Peer F. Stähler, Stefan Schreiber, Philip Rosenstiel, André Franke
Software Mentions: 2
Published: about 14 years ago

10.1371/journal.pone.0197840

Analysis of the resistance mechanisms in sugarcane during Sporisorium scitamineum infection using RNA-seq and microscopy
Cited by: 31
Author(s): Meredith D. McNeil, Shamsul A. Bhuiyan, Paul J. Berkman, B. J. Croft, Karen S. Aitken
Software Mentions: 2
Published: over 8 years ago

10.1186/s12885-017-3226-4

Genome-wide methylation analysis identifies a core set of hypermethylated genes in CIMP-H colorectal cancer
Cited by: 27
Author(s): Tyler McInnes, Donghui Zou, Dasari S. Rao, Francesca Maree Munro, Vicky Phillips, John L. McCall, Michael A. Black, Anthony E. Reeve, Parry Guilford
Software Mentions: 2
Published: over 9 years ago

10.1186/1471-2164-10-196

Molecular profiles of Quadriceps muscle in myostatin-null mice reveal PI3K and apoptotic pathways as myostatin targets
Cited by: 78
Author(s): Ilham Chelh, Bruno Meunier, Brigitte Picard, Mark James Reecy, Catherine Chevalier, Jean-François Hocquette, Isabelle Cassar-Malek
Software Mentions: 2
Published: over 17 years ago

10.1186/1471-2164-9-580

Development and validation of a gene expression oligo microarray for the gilthead sea bream (Sparus aurata)
Cited by: 58
Author(s): Serena Ferraresso, Nicola Vitulo, Alba Nicoletta Mininni, Chiara Romualdi, Barbara Cardazzo, Enrico Negrisolo, Richard Reinhardt, Adelino V.M. Canário, Tomaso Patarnello, Luca Bargelloni
Software Mentions: 2
Published: almost 18 years ago

10.1089/ast.2016.1533

Habitability on Early Mars and the Search for Biosignatures with the ExoMars Rover
Cited by: 350
Author(s): Jorge L. Vago, Francès Westall, A. J. Coates, R. Jaumann, Oleg Korablev, Valérie Ciarletti, И. Г. Митрофанов, Jean-Luc Josset, M. C. De Sanctis, Jean‐Pierre Bibring, Fernando Rull, Fred Goesmann, Harald Steininger, W. Goetz, W. B. Brinckerhoff, Cyril Szopa, F. Raulin, Howell G. M. Edwards, Lyle G. Whyte, Alberto González Fairén, J. C. Bridges, Ernst Hauber, G. G. Ori, Stéphanie C. Werner, D. Loizeau, R. O. Kuzmin, R. M. E. Williams, J. Flahaut, F. Forget, D. Rodionov, H. Svedhem, E. Sefton‐Nash, Gerhard Kminek, L. Lorenzoni, Luc Joudrier, В. А. Михайлов, Alexander Zashchirinskiy, S. Alexashkin, F. Calantropio, Andrea Merlo, Pantelis Poulakis, Olivier Witasse, Olivier Bayle, Silvia Bayón, Uwe J. Meierhenrich, John Carter, Juan Manuel García‐Ruiz, P. Baglioni, A. F. C. Haldemann, Andrew Ball, A. Debus, Robert Lindner, Frédéric Haessig, D. Monteiro, R. Trautner, Christoph Voland, Pierre Rebeyre, D. Goulty, F. Didot, Stephen Durrant, Eric Zekri, D. Koschny, Andrea De Toni, Gianfranco Visentin, Martin Zwick, M. van Winnendael, Martín Azkarate, Christophe Carreau
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0222503

Genetic diversity and population structure of four Chinese rabbit breeds
Cited by: 13
Author(s): Anyong Ren, Kun Du, Xianbo Jia, Rui Yang, Jie Wang, Shiyi Chen, Songjia Lai
Software Mentions: 2
Published: about 7 years ago

10.1186/s12885-019-5786-y

miR-520d-5p can reduce the mutations in hepatoma cancer cells and iPSCs-derivatives
Cited by: 5
Author(s): Naruhisa Miura, Y. Ishihara, Yugo Miura, Mai Kimoto, Keigo Miura
Software Mentions: 2
Published: over 7 years ago

10.1186/s12885-016-2109-4

Regulation of the tumour suppressor PDCD4 by miR-499 and miR-21 in oropharyngeal cancers
Cited by: 49
Author(s): Xiaoying Zhang, Harriet E. Gee, Barbara Rose, Cheok Soon Lee, Jonathan Clark, Michael Elliott, Jennifer R. Gamble, Murray J. Cairns, Adrian L. Harris, Samantha Khoury, Nham Tran
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0028990

CrossQuery: A Web Tool for Easy Associative Querying of Transcriptome Data
Cited by: 1
Author(s): Toni U. Wagner, Andreas Fischer, Eva C. Thoma, Manfred Schartl
Software Mentions: 2
Published: almost 15 years ago

10.1371/journal.pone.0247047

Managing conflicting goals through prioritization? The role of age and relative goal importance
Cited by: 3
Author(s): Alexandra M. Freund, Martin J. Tomasik
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0091466

Transcriptome Profiling of a Multiple Recurrent Muscle-Invasive Urothelial Carcinoma of the Bladder by Deep Sequencing
Cited by: 34
Author(s): Shufang Zhang, Yan-Xuan Liu, Zhenxiang Liu, Chong Zhang, Hui Cao, Yongqing Ye, Shunlan Wang, Yingai Zhang, Sifang Xiao, Yang Peng, Jindong Li, Zhiming Bai
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0039158

An Ultra-Fast Metabolite Prediction Algorithm
Cited by: 1
Author(s): Zheng Yang, Murray Grant
Software Mentions: 2
Published: about 14 years ago

10.1371/journal.pone.0137748

Comparison of Hybrid Classifiers for Crop Classification Using Normalized Difference Vegetation Index Time Series: A Case Study for Major Crops in North Xinjiang, China
Cited by: 28
Author(s): Pengyu Hao, Li Wang, Zheng Niu
Software Mentions: 2
Published: about 11 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

10.3389/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

10.1371/journal.pone.0012362

Profiling and Functional Analyses of MicroRNAs and Their Target Gene Products in Human Uterine Leiomyomas
Cited by: 65
Author(s): Jiří Zavadil, Huihui Ye, Zhaojian Liu, Jingjing Wu, Peng Lee, Eva Hernando, Patricia Soteropoulos, Gokce Toruner, Jian Jun Wei
Software Mentions: 2
Published: about 16 years ago

10.1371/journal.pone.0215405

Large cortical bone pores in the tibia are associated with proximal femur strength
Cited by: 17
Author(s): Gianluca Iori, Johannes Schneider, Andreas Reisinger, Frans Heyer, Laura Peralta, Caroline E. Wyers, Melanie Gräsel, Reinhard Barkmann, Claus C. Glüer, Joop van den Bergh, Dieter H. Pahr, Kay Raum
Software Mentions: 2
Published: over 7 years ago

10.1186/1471-2407-11-332

Serum estradiol levels associated with specific gene expression patterns in normal breast tissue and in breast carcinomas
Cited by: 35
Author(s): Vilde Drageset Haakensen, Trine Bjøro, Torben Lüders, Margit Riis, Ida K. Bukholm, Vessela N. Kristensen, Melissa A. Troester, Marit M. Homen, Giske Ursin, Anne Lise Børresen-Dale, Åslaug Helland
Software Mentions: 2
Published: about 15 years ago

10.1371/journal.pone.0006146

Molecular Profiling of Breast Cancer Cell Lines Defines Relevant Tumor Models and Provides a Resource for Cancer Gene Discovery
Cited by: 647
Author(s): Jennifer L. Kao, Keyan Salari, Melanie Bocanegra, Yoon‐La Choi, Luc Girard, Jeet Gandhi, Kevin Kwei, Tina Hernandez‐Boussard, Pei Wang, Adi F. Gazdar, John D. Minna, Jonathan R. Pollack
Software Mentions: 2
Published: about 17 years ago

10.1371/journal.pone.0197539

Terrestrial mammal responses to oil palm dominated landscapes in Colombia
Cited by: 27
Author(s): Lain E. Pardo, Mason J. Campbell, Will Edwards, Gopalasamy Reuben Clements, William F. Laurance
Software Mentions: 2
Published: over 8 years ago

10.1371/journal.pone.0064829

Transcriptome Analysis Reveals New Insights into the Modulation of Endometrial Stromal Cell Receptive Phenotype by Embryo-Derived Signals Interleukin-1 and Human Chorionic Gonadotropin: Possible Involvement in Early Embryo Implantation
Cited by: 35
Author(s): Amélie Bourdiec, Ézéquiel Calvo, Ch.V. Rao, Ali Akoum
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0092202

A Microarray-Based Analysis of Gametogenesis in Two Portuguese Populations of the European Clam Ruditapes decussatus
Cited by: 14
Author(s): Joana Sousa, Massimo Milan, Luca Bargelloni, Marianna Pauletto, Domitília Matias, Sandra Joaquim, Ana Margarete Matias, Virgile Quillien, Alexandra Leitão, Arnaud Huvet
Software Mentions: 2
Published: over 12 years ago

10.1186/s12864-021-07456-x

Immune profiles of male giant panda (Ailuropoda melanoleuca) during the breeding season
Cited by: 3
Author(s): Hsin-Hsin Shen, Caiwu Li, Ming He, Yan Huang, Jing Wang, Minglei Wang, Bisong Yue, Xiuyue Zhang
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0000145

Heterologous Tissue Culture Expression Signature Predicts Human Breast Cancer Prognosis
Cited by: 8
Author(s): Eun Sung Park, Ju Seog Lee, Hyun Goo Woo, Fenghuang Zhan, Joanna H. Shih, John D. Shaughnessy, J. Frederic Mushinski
Software Mentions: 2
Published: over 19 years ago

10.1371/journal.pone.0091869

Upland Cotton Gene GhFPF1 Confers Promotion of Flowering Time and Shade-Avoidance Responses in Arabidopsis thaliana
Cited by: 21
Author(s): Xiaoyan Wang, Shuli Fan, Meizhen Song, Chaoyou Pang, Hengling Wei, Jie-Ae Yu, Qin Ma, Shuang Yu
Software Mentions: 2
Published: over 12 years ago

10.1186/s12864-015-1295-9

Inorganic Arsenic-induced cellular transformation is coupled with genome wide changes in chromatin structure, transcriptome and splicing patterns
Cited by: 39
Author(s): Caitlyn Riedmann, Ye Ma, Manana Melikishvili, Steven Grason Godfrey, Zhou Zhang, Kuey Chu Chen, Eric C. Rouchka, Yvonne Fondufe‐Mittendorf
Software Mentions: 2
Published: over 11 years ago

10.1007/s10456-016-9527-4

Identification of HIF-2α-regulated genes that play a role in human microvascular endothelial sprouting during prolonged hypoxia in vitro
Cited by: 40
Author(s): Tessa D. Nauta, Marloes van den Broek, S. Gibbs, Tineke C. T. M. van der Pouw‐Kraan, Cees B.M. Oudejans, Victor W.M. van Hinsbergh, Pieter Koolwijk
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pone.0106054

Extracellular Matrix Defects in Aneurysmal Fibulin-4 Mice Predispose to Lung Emphysema
Cited by: 17
Author(s): Natasja W. M. Ramnath, Koen M. van de Luijtgaarden, Ingrid van der Pluijm, Menno van Nimwegen, Paula M. van Heijningen, Sigrid Swagemakers, Bibi S. van Thiel, Ruziedi Y. Ridwan, Nicole van Vliet, Marcel Vermeij, Lukas J.A.C. Hawinkels, Anne de Munck, Oleh Dzyubachyk, Erik Meijering, Peter van der Spek, Robbert J. Rottier, Hiromi Yanagisawa, Rudi W. Hendriks, Roland Kanaar, Ellen V. Rouwet, Alex KleinJan, Jeroen Essers
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0091353

Natural Antisense Transcripts and Long Non-Coding RNA in Neurospora crassa
Cited by: 41
Author(s): Yamini Arthanari, Christian Heintzen, Sam Griffiths-Jones, Susan K. Crosthwaite
Software Mentions: 2
Published: over 12 years ago

10.1186/1471-2407-10-196

Genomic expression and single-nucleotide polymorphism profiling discriminates chromophobe renal cell carcinoma and oncocytoma
Cited by: 88
Author(s): Min‐Han Tan, Chin Fong Wong, Hwei Ling Tan, Ximing J. Yang, Jonathon A. Ditlev, Daisuke Matsuda, Sok Kean Khoo, Jun Sugimura, Tomoaki Fujioka, Kyle A. Furge, Eric J. Kort, Sophie Giraud, Sophie Ferlicot, Philippe Vielh, Delphine Amsellem-Ouazana, B Debré, T. Flam, Nicolas Thiounn, Marc Zerbib, Benoît Galand, S. Droupy, Vincent Molinié, Annick Vieillefond, Puay Hoon Tan, Stéphane Richard, Bin Tean Teh
Software Mentions: 2
Published: over 16 years ago

10.1186/1471-2164-7-114

Gene expression alterations in brains of mice infected with three strains of scrapie
Cited by: 81
Author(s): Pamela J. Skinner, H. Abbassi, Bruce Chesebro, Richard E. Race, Cavan Reilly, Ashley T. Haase
Software Mentions: 2
Published: over 20 years ago

10.1186/s12864-018-4890-8

A high-density genetic map of extra-long staple cotton (Gossypium barbadense) constructed using genotyping-by-sequencing based single nucleotide polymorphic markers and identification of fiber traits-related QTL in a recombinant inbred line population
Cited by: 24
Author(s): Fan Lü, Liping Wang, Xinyi Wang, Haiyan Zhang, Yanfei Zhu, Jiayan Guo, Wenwei Gao, Hao Geng, Quanjia Chen, Yanying Qu
Software Mentions: 2
Published: about 8 years ago

10.1186/1471-2407-10-490

Transcriptional profiling of ErbB signalling in mammary luminal epithelial cells - interplay of ErbB and IGF1 signalling through IGFBP3 regulation
Cited by: 17
Author(s): Jenny Worthington, Mariana Fianco Bertani, Hong‐Lin Chan, Bertran Gerrits, John F. Timms
Software Mentions: 2
Published: about 16 years ago

10.1371/journal.pone.0234759

Tunica intima compensation for reduced stiffness of the tunica media in aging renal arteries as measured with scanning acoustic microscopy
Cited by: 2
Author(s): Katsutoshi Miura
Software Mentions: 2
Published: almost 6 years ago

10.1371/journal.pone.0011310

The Gene Expression Profile in the Synovium as a Predictor of the Clinical Response to Infliximab Treatment in Rheumatoid Arthritis
Cited by: 84
Author(s): Johan Lindberg, Carla A. Wijbrandts, Lisa G. M. van Baarsen, Gustavo A. Nader, Lars Klareskog, Anca I. Catrina, Rogier M. Thurlings, Margriet J. Vervoordeldonk, Joakim Lundeberg, Paul P. Tak
Software Mentions: 2
Published: about 16 years ago

10.1371/journal.pone.0068167

Distinct Contributions of TNF Receptor 1 and 2 to TNF-Induced Glomerular Inflammation in Mice
Cited by: 24
Author(s): Anela Taubitz, M. A. Schwarz, Nuru Eltrich, Maja T. Lindenmeyer, Volker Vielhauer
Software Mentions: 2
Published: about 13 years ago

10.1371/journal.pone.0165543

Identification of Genes Discriminating Multiple Sclerosis Patients from Controls by Adapting a Pathway Analysis Method
Cited by: 4
Author(s): Lei Zhang, Linlin Wang, Pu Tian, Suyan Tian
Software Mentions: 2
Published: almost 10 years ago

10.1371/journal.pone.0000945

Transcriptional Program Induced by Wnt Protein in Human Fibroblasts Suggests Mechanisms for Cell Cooperativity in Defining Tissue Microenvironments
Cited by: 76
Author(s): Zach Klapholz-Brown, Graham G. Walmsley, Ysbrand Nusse, Roel Nusse, Patrick O. Brown
Software Mentions: 2
Published: almost 19 years ago

10.1371/journal.pone.0040399

Dynamic Changes in Ezh2 Gene Occupancy Underlie Its Involvement in Neural Stem Cell Self-Renewal and Differentiation towards Oligodendrocytes
Cited by: 56
Author(s): Falak Sher, Erik Boddeke, Marta Olah, Sjef Copray
Software Mentions: 2
Published: about 14 years ago

10.1371/journal.pone.0006971

Genomic Analysis Suggests that mRNA Destabilization by the Microprocessor Is Specialized for the Auto-Regulation of Dgcr8
Cited by: 45
Author(s): Archana Shenoy, Robert Blelloch
Software Mentions: 2
Published: about 17 years ago

10.1186/1471-2164-14-191

Multiphasic analysis of whole exome sequencing data identifies a novel mutation of ACTG1 in a nonsyndromic hearing loss family
Cited by: 33
Author(s): Gibeom Park, Jungsoo Gim, Ah Reum Kim, Kyou‐Sup Han, Hyosang Kim, Seung-Ha Oh, Taesung Park, Woong-Yang Park, Byung Yoon Choi
Software Mentions: 2
Published: over 13 years ago

10.1186/1471-2164-13-354

Genome-wide SNP discovery in walnut with an AGSNP pipeline updated for SNP discovery in allogamous organisms
Cited by: 37
Author(s): Frank M. You, Karin R. Deal, Jirui Wang, Monica Britton, Joseph Fass, Dazhen Lin, Abhaya M. Dandekar, Charles A. Leslie, Mallikarjuna K. Aradhya, Ming Luo, Jan Dvořák
Software Mentions: 2
Published: over 14 years ago

10.1186/s12915-020-00928-8

The transcriptional trajectories of pluripotency and differentiation comprise genes with antithetical architecture and repetitive-element content
Cited by: 5
Author(s): Aristeidis G. Telonis, Isidore Rigoutsos
Software Mentions: 2
Published: over 5 years ago

10.1186/s12864-018-4791-x

Identification of recombination events in outbred species with next-generation sequencing data
Cited by: 5
Author(s): Shentong Tao, Jiyan Wu, Dan Yao, Yuhua Chen, Wenguo Yang, Chunfa Tong
Software Mentions: 2
Published: over 8 years ago

10.1007/978-3-030-49392-9_15

Results from a Replicated Experiment on the Affective Reactions of Novice Developers When Applying Test-Driven Development
Cited by: 0
Author(s): Simone Romano, Giuseppe Scanniello, María Teresa Baldassarre, Davide Fucci, Danilo Caivano
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pone.0001821

Identification of Direct Target Genes Using Joint Sequence and Expression Likelihood with Application to DAF-16
Cited by: 10
Author(s): Ronald Yu, Jie Liu, Nick True, Wei Wang
Software Mentions: 2
Published: over 18 years ago

10.1371/journal.pone.0083028

Transcriptome Analysis in Prenatal IGF1-Deficient Mice Identifies Molecular Pathways and Target Genes Involved in Distal Lung Differentiation
Cited by: 31
Author(s): Rosete S. Pais, Nuria Moreno-Barriuso, Isabel Hernández-Porras, Icíar P. López, Javier De Las Rivas, José G. Pichel
Software Mentions: 2
Published: over 12 years ago

10.1186/s12915-020-0763-0

Ribosomal RNA fragmentation into short RNAs (rRFs) is modulated in a sex- and population of origin-specific manner
Cited by: 28
Author(s): Tess Cherlin, Rogan Magee, Jing Yi, Venetia Pliatsika, Phillipe Loher, Isidore Rigoutsos
Software Mentions: 2
Published: over 6 years ago

10.1186/s12864-017-4098-3

Biological networks in Parkinson’s disease: an insight into the epigenetic mechanisms associated with this disease
Cited by: 28
Author(s): Paulami Chatterjee, Dilip Roy, Malay Bhattacharyya, Sanghamitra Bandyopadhyay
Software Mentions: 2
Published: about 9 years ago

10.1371/journal.pone.0034291

Characterisation of Bovine Leukocyte Ig-like Receptors
Cited by: 19
Author(s): Louise E. Hogan, Sabin Bhuju, Des C. Jones, Ken Laing, John Trowsdale, Philip D. Butcher, Mahavir Singh, Martin Vordermeier, Rachel Allen
Software Mentions: 2
Published: over 14 years ago

10.1371/journal.pone.0097842

Impact of Gene Dosage on Gene Expression, Biological Processes and Survival in Cervical Cancer: A Genome-Wide Follow-Up Study
Cited by: 40
Author(s): Ingrid Medina-Martínez, Valeria Barrón, Edgar Román-Bassaure, Eligia Juárez-Torres, Mariano Guardado-Estrada, Ana Espinosa, Miriam Bermúdez, Fernando Fernández, Carlos Venegas-Vega, Lorena Orozco, Edgar Zenteno, Susana Kofman, Jaime Berumen
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0097255

Determinants of Spatial Distribution in a Bee Community: Nesting Resources, Flower Resources, and Body Size
Cited by: 74
Author(s): Anna Torné‐Noguera, Anselm Rodrigo, Xavier Arnán, Sergio Osorio, Helena Barril-Graells, Léo Correia da Rocha-Filho, Jordi Bosch
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0189999

HIV-1 envelope sequence-based diversity measures for identifying recent infections
Cited by: 8
Author(s): Alexis Kafando, Éric Fournier, Bouchra Serhir, Christine Martineau, Florence Doualla-Bell, Mohamed N'dongo Sangaré, Mohamed Sylla, Annie Chamberland, Mohamed El-Far, Hugues Charest, Cécile Tremblay
Software Mentions: 2
Published: over 8 years ago

10.1186/1471-2105-7-152

Domain-based small molecule binding site annotation
Cited by: 27
Author(s): Kevin A. Snyder, Hume A. Feldman, Michel Dumontier, John J. Salama, Christopher W. V. Hogue
Software Mentions: 2
Published: over 20 years ago

10.1186/1471-2164-14-270

Genome analyses of the wheat yellow (stripe) rust pathogen Puccinia striiformis f. sp. triticireveal polymorphic and haustorial expressed secreted proteins as candidate effectors
Cited by: 189
Author(s): Dario Cantu, Vanesa Segovia, Dan MacLean, R. A. Bayles, Xianming Chen, Sophien Kamoun, Jorge Dubcovsky, Diane G. O. Saunders, Cristóbal Uauy
Software Mentions: 2
Published: over 13 years ago

10.1107/S1744309109050416

Structures of the first representatives of Pfam family PF06938 (DUF1285) reveal a new fold with repeated structural motifs and possible involvement in signal transduction
Cited by: 7
Author(s): Gye Won Han, Constantina Bakolitsa, Mitchell D. Miller, Abhinav Kumar, Dennis Carlton, Rafaël Najmanovich, Polat Abdubek, Tamara Astakhova, Herbert L. Axelrod, Connie Chen, Hsiu Ju Chiu, Thomas Clayton, Debanu Das, Marc C. Deller, Lian Duan, Dustin C. Ernst, Julie Feuerhelm, Joanna C Grant, Anna Grzechnik, Lukasz Jaroszewski, Kevin K. Jin, Hope A. Johnson, Heath E. Klock, Mark W. Knuth, Piotr Koźbiał, Sanjeev Krishna, David Marciano, Daniel McMullan, Andrew Morse, Edward Nigoghossian, Linda Okach, Ron Reyes, Christopher L. Rife, Natasha Sefcovic, Henry J Tien, Christine B Trame, H. van den Bedem, Dana Weekes, Qingping Xu, Keith O. Hodgson, John Wooley, Marc‐André Elsliger, Ashley M. Deacon, Adam Godzik, Scott A. Lesley, Ian A. Wilson
Software Mentions: 2
Published: over 16 years ago

10.1186/1471-2164-8-294

Design and evaluation of Actichip, a thematic microarray for the study of the actin cytoskeleton
Cited by: 6
Author(s): Jean Muller, André Mehlen, Guillaume Vetter, Mikalai M. Yatskou, Arnaud Muller, Frédéric Chalmel, Olivier Poch, Evelyne Friederich, Laurent Vallar
Software Mentions: 2
Published: about 19 years ago

10.1371/journal.pone.0011109

Large-Scale Expression Analysis Reveals Distinct MicroRNA Profiles at Different Stages of Human Neurodevelopment
Cited by: 72
Author(s): Brandon Smith, Julie A. Treadwell, Dongling Zhang, Dao Ly, Iain W. McKinnell, P. Roy Walker, Marianna Sikorska
Software Mentions: 2
Published: over 16 years ago

10.1186/s12864-018-5277-6

Constructing tissue-specific transcriptional regulatory networks via a Markov random field
Cited by: 6
Author(s): Shuping Ma, Tao Jiang, Rui Jiang
Software Mentions: 2
Published: almost 8 years ago

10.1186/1471-2105-9-348

Gene Vector Analysis (Geneva): A unified method to detect differentially-regulated gene sets and similar microarray experiments
Cited by: 13
Author(s): Stephen Tanner, Pankaj Agarwal
Software Mentions: 2
Published: about 18 years ago

10.1186/1471-2105-8-285

miRAS: a data processing system for miRNA expression profiling study
Cited by: 2
Author(s): Feng Tian, Huayue Zhang, Xinyu Zhang, Chi Song, Yuanming Xia, Yiqing Wu, Xiangjun Liu
Software Mentions: 2
Published: about 19 years ago

10.1371/journal.pone.0060321

Biological Characteristics and Genetic Heterogeneity between Carcinoma-Associated Fibroblasts and Their Paired Normal Fibroblasts in Human Breast Cancer
Cited by: 67
Author(s): Qiongle Peng, Liuyang Zhao, Yixuan Hou, Yan Sun, Liyang Wang, Haojun Luo, Huimin Peng, Manran Liu
Software Mentions: 2
Published: over 13 years ago

10.1186/s12859-019-2791-8

DNAscan: personal computer compatible NGS analysis, annotation and visualisation
Cited by: 15
Author(s): Alfredo Iacoangeli, Ahmad Al Khleifat, William Sproviero, Aleksey Shatunov, Ashley Jones, Sarah Morgan, Alan Pittman, Richard Dobson, Stephen J. Newhouse, Ammar Al‐Chalabi
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0132868

elPrep: High-Performance Preparation of Sequence Alignment/Map Files for Variant Calling
Cited by: 23
Author(s): Charlotte Herzeel, Pascal Costanza, Dries Decap, Jan Fostier, Joke Reumers
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0004802

Human and Murine Kidneys Show Gender- and Species-Specific Gene Expression Differences in Response to Injury
Cited by: 61
Author(s): Han Si, Ramandeep S. Banga, Pinelopi P. Kapitsinou, Manjunath Ramaiah, Janis Lawrence, Ganesh Kambhampati, Antje Gruenwald, Erwin P. Böttinger, Daniel Glicklich, Vivian A. Tellis, Stuart Greenstein, David B. Thomas, James Pullman, Melissa Fazzari, Katalin Suszták
Software Mentions: 2
Published: over 17 years ago

10.1371/journal.pone.0202022

Rare gene deletions in genetic generalized and Rolandic epilepsies
Cited by: 4
Author(s): Kamel Jabbari, Dheeraj Reddy Bobbili, Dennis Lal, Eva M. Reinthaler, Julian Schubert, Stefan Wolking, Vishal Sinha, Susanne Motameny, Holger Thiele, Amit Kawalia, Janine Altmüller, Mohammad Reza Toliat, Robert Kraaij, Jeroen van Rooij, André G. Uitterlinden, M. Arfan Ikram, Federico Zara, Anna‐Elina Lehesjoki, Roland Krause, Fritz Zimprich, Thomas Sander, Bernd A. Neubauer, Patrick May, Holger Lerche, Peter Nürnberg
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0052249

FastUniq: A Fast De Novo Duplicates Removal Tool for Paired Short Reads
Cited by: 406
Author(s): Haibin Xu, Xiang Luo, Jun Qian, Xiaohui Pang, Jingyuan Song, Guang‐Rui Qian, Jinhui Chen, Shilin Chen
Software Mentions: 2
Published: over 13 years ago

10.1186/1471-2105-11-351

Identifying differentially regulated subnetworks from phosphoproteomic data
Cited by: 31
Author(s): Martin Klammer, Klaus Godl, Andreas Tebbe, Christoph Schaab
Software Mentions: 2
Published: about 16 years ago

10.1371/journal.pone.0242780

Discovering novel driver mutations from pan-cancer analysis of mutational and gene expression profiles
Cited by: 5
Author(s): Houriiyah Tegally, Kevin H. Kensler, Zahra Mungloo-Dilmohamud, Anisah W. Ghoorah, Timothy R. Rebbeck, Shakuntala Baichoo
Software Mentions: 2
Published: almost 6 years ago

10.1002/advs.201901380

Targeting YAP1/LINC00152/FSCN1 Signaling Axis Prevents the Progression of Colorectal Cancer
Cited by: 106
Author(s): Chunlin Ou, Zhenqiang Sun, Xiaoyun He, Xiaoling Li, Songqing Fan, Xiang Zheng, Ping Qiu, Guiyuan Li, Xiayu Li, Jian Ma
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pone.0020414

Blood Signature of Pre-Heart Failure: A Microarrays Study
Cited by: 21
Author(s): Fatima Smih, Franck Desmoulin, Matthieu Berry, Annie Turkieh, Romain Harmancey, Jason S. Iacovoni, Charlotte Trouillet, Clément Delmas, Atul Pathak, Olivier Lairez, François Koukoui, P Massabuau, Jean Ferrières, Michel Galinier, Philippe Rouet
Software Mentions: 2
Published: about 15 years ago

10.1371/journal.pone.0000594

Comprehensive Expression Profiling of Tumor Cell Lines Identifies Molecular Signatures of Melanoma Progression
Cited by: 240
Author(s): Byungwoo Ryu, Dave S. Kim, Amena M. DeLuca, Rhoda M. Alani
Software Mentions: 2
Published: about 19 years ago

10.1371/journal.pone.0093462

Arabidopsis Transcriptome Analysis Reveals Key Roles of Melatonin in Plant Defense Systems
Cited by: 262
Author(s): Sarah Weeda, Na Zhang, Xiaolei Zhao, Grace Ndip, Yang‐Dong Guo, Gregory A. Buck, Conggui Fu, Shuxin Ren
Software Mentions: 2
Published: over 12 years ago

10.1371/journal.pone.0111581

MiRNA Expression May Account for Chronic but Not for Acute Regulation of mRNA Expression in Human Thyroid Tumor Models
Cited by: 9
Author(s): Sébastien Floor, Aline Hébrant, Jaime Miguel Gomes Pita, Manuel Saiselet, Christophe Trésallet, Frédérick Libert, Guy Andry, Jacques Emile Dumont, Wilma Van Staveren, Carine Maenhaut
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0067142

Layered Signaling Regulatory Networks Analysis of Gene Expression Involved in Malignant Tumorigenesis of Non-Resolving Ulcerative Colitis via Integration of Cross-Study Microarray Profiles
Cited by: 13
Author(s): Shengjun Fan, Zhenyu Pan, Qiang Geng, Xin Li, Yefan Wang, Yu An, Yan Xu, Lu Tie, Yan Pan, Xuejun Li
Software Mentions: 2
Published: about 13 years ago

10.1186/1471-2164-8-193

Profiling of chicken adipose tissue gene expression by genome array
Cited by: 82
Author(s): Hongbao Wang, Hui Li, Qigui Wang, Xin Yu Zhang, Shouzhi Wang, Yuxiang Wang, Xiuping Wang
Software Mentions: 2
Published: about 19 years ago