10.1186/s12870-020-02809-2

Tight association of genome rearrangements with gene expression in conifer plastomes
Cited by: 5
Author(s): Ching‐Yi Wu, Edi Sudianto, Shu‐Miaw Chaw
Software Mentions: 3
Published: over 5 years ago

10.1186/s12870-017-1188-y

Physiological and transcriptomic responses in the seed coat of field-grown soybean (Glycine max L. Merr.) to abiotic stress
Cited by: 25
Author(s): Courtney P. Leisner, Craig R. Yendrek, Elizabeth A. Ainsworth
Software Mentions: 3
Published: almost 9 years ago

10.1186/s12870-014-0188-4

Metabolite and transcript profiling of berry skin during fruit development elucidates differential regulation between Cabernet Sauvignon and Shiraz cultivars at branching points in the polyphenol pathway
Cited by: 109
Author(s): Asfaw Degu, Uri Hochberg, Noga Sikron, Luca Venturini, Genny Buson, Ryan Ghan, Inbar Plaschkes, Albert Batushansky, Vered Chalifa‐Caspi, Fulvio Mattivi, Massimo Delledonne, Mario Pezzotti, Shimon Rachmilevitch, Grant R. Cramer, Aaron Fait
Software Mentions: 3
Published: about 12 years ago

10.1186/s12870-016-0775-7

B chromosome contains active genes and impacts the transcription of A chromosomes in maize (Zea mays L.)
Cited by: 53
Author(s): Wei Huang, Yan Du, Xin Zhao, Weiwei Jin
Software Mentions: 3
Published: over 10 years ago

10.1186/s12870-021-03129-9

Tomato transcriptomic response to Tuta absoluta infestation
Cited by: 11
Author(s): Daniela D’Esposito, Daniele Manzo, Alessandro Ricciardi, Antonio P. Garonna, Antonino De Natale, Luigi Frusciante, Francesco Pennacchio, Maria Raffaella Ercolano
Software Mentions: 3
Published: about 5 years ago

10.1186/s12870-021-02825-w

Transcriptional and proteomic insights into phytotoxic activity of interspecific potato hybrids with low glycoalkaloid contents
Cited by: 5
Author(s): Katarzyna Szajko, Jarosław Ciekot, Iwona Wasilewicz‐Flis, Waldemar Marczewski, Dorota Sołtys‐Kalina
Software Mentions: 3
Published: over 5 years ago

10.1186/s12870-019-1802-2

Transcript analyses reveal a comprehensive role of abscisic acid in modulating fruit ripening in Chinese jujube
Cited by: 8
Author(s): Zhang Zhong, C.K. Kang, Shuyi Zhang, Xingang Li
Software Mentions: 3
Published: over 7 years ago

10.1186/s12870-015-0468-7

Specific pools of endogenous peptides are present in gametophore, protonema, and protoplast cells of the moss Physcomitrella patens
Cited by: 37
Author(s): Igor Fesenko, Georgij Arapidi, Alexander Skripnikov, Dmitry Alexeev, Elena S. Kostryukova, Alexander I. Manolov, Ilya Altukhov, Regina Khazigaleeva, A. V. Seredina, Sergey I. Kovalchuk, Rustam H. Ziganshin, В. Г. Згода, Svetlana E. Novikova, Tatiana A. Semashko, D. K. Slizhikova, Vasilij V Ptushenko, A. Yu. Gorbachev, Vadim M. Govorun, В. Т. Иванов
Software Mentions: 3
Published: over 11 years ago

10.1186/s13104-018-3864-x

Transcriptomic evidence for distinct mechanisms underlying abscission deficiency in the Arabidopsis mutants haesa/haesa-like 2 and nevershed
Cited by: 6
Author(s): Isaiah Taylor, John C. Walker
Software Mentions: 3
Published: almost 8 years ago

10.1186/s12918-016-0366-0

Integrative transcriptome network analysis of iPSC-derived neurons from schizophrenia and schizoaffective disorder patients with 22q11.2 deletion
Cited by: 87
Author(s): Mingyan Lin, Erika Pedrosa, Anastasia Hrabovsky, Jian Chen, Benjamin R. Puliafito, Stephanie R. Gilbert, Deyou Zheng, Herbert M. Lachman
Software Mentions: 3
Published: almost 10 years ago

10.1186/s12917-017-1279-x

RNA sequencing reveals candidate genes and polymorphisms related to sperm DNA integrity in testis tissue from boars
Cited by: 14
Author(s): Maren van Son, Nina Hårdnes Tremoen, Ann Helen Gaustad, Frøydis Deinboll Myromslien, Dag Inge Våge, Else‐Berit Stenseth, Teklu T Zeremichael, Eli Grindflek
Software Mentions: 3
Published: almost 9 years ago

10.1186/1746-6148-10-146

Effect of photoperiod on the feline adipose transcriptome as assessed by RNA sequencing
Cited by: 5
Author(s): Akira Mori, Kelly Kappen, A. C. Dilger, Kelly S. Swanson
Software Mentions: 3
Published: about 12 years ago

10.15252/msb.20177754

<scp>RNA</scp> polymerase <scp>II</scp> primes Polycomb‐repressed developmental genes throughout terminal neuronal differentiation
Cited by: 39
Author(s): Carmelo Ferrai, Elena Torlai Triglia, Jessica R. Risner-Janiczek, Tiago Rito, Owen J. L. Rackham, Inês de Santiago, Alexander Kukalev, Mario Nicodemi, Altuna Akalin, Meng Li, Mark A. Ungless, Ana Pombo
Software Mentions: 3
Published: almost 9 years ago

10.1016/j.omto.2021.04.014

Induction of cell death in ovarian cancer cells by doxorubicin and oncolytic vaccinia virus is associated with CREB3L1 activation
Cited by: 8
Author(s): Anna Mistarz, Matthew A. Graczyk, M. Winkler, Prashant Singh, Eduardo Cortes, Anthony Miliotto, Song Liu, Mark D. Long, Yan Li, Aimee Stablewski, Kieran L. O’Loughlin, Hans Minderman, Kunle Odunsi, Hanna Rokita, AJ Robert McGray, Emese Zsíros, Danuta Kozbor
Software Mentions: 3
Published: almost 5 years ago

10.1186/1297-9716-42-114

Characterization of the abomasal transcriptome for mechanisms of resistance to gastrointestinal nematodes in cattle
Cited by: 40
Author(s): Robert W. Li, Manuela Rinaldi, Anthony Capuco
Software Mentions: 3
Published: over 15 years ago

10.1186/s13567-018-0545-7

Comparative liver transcriptome analysis in ducklings infected with duck hepatitis A virus 3 (DHAV-3) at 12 and 48 hours post-infection through RNA-seq
Cited by: 11
Author(s): Xuelian Zhang, Chen Cao, Yue Liu, Haihui Qi, Wenjing Zhang, Chunxue Hao, Haotian Chen, Qi Zhang, Wenlong Zhang, Mingchun Gao, Junwei Wang, Bo Ma
Software Mentions: 3
Published: about 8 years ago

10.1186/s12985-018-1044-1

Transcriptome analysis of Nicotiana benthamiana infected by Tobacco curly shoot virus
Cited by: 35
Author(s): Ke Li, Gentu Wu, Mingjun Li, Mingge Ma, Jie Du, Miao Sun, Xianchao Sun, Ling Qing
Software Mentions: 3
Published: about 8 years ago

10.1080/21505594.2020.1797274

Transcriptional remodeling during metacyclogenesis in <i>Trypanosoma cruzi</i> I
Cited by: 11
Author(s): Lissa Cruz-Saavedra, Gustavo Adolfo Calderón Vallejo, Felipe Guhl, Louisa A. Messenger, Juan David Ramírez
Software Mentions: 3
Published: about 6 years ago

10.1080/21505594.2020.1839231

A new regulator in the crossroads of oxidative stress resistance and virulence in <i>Candida glabrata</i>: The transcription factor CgTog1
Cited by: 5
Author(s): Pedro Pais, Susana Vagueiro, Dalila Mil‐Homens, Andreia I. Pimenta, Romeu Viana, Michiyo Okamoto, Hiroji Chibana, Arsénio M. Fialho, Miguel C. Teixeira
Software Mentions: 3
Published: almost 6 years ago

10.3390/v11010033

A Comprehensive RNA-seq Analysis of Human Bocavirus 1 Transcripts in Infected Human Airway Epithelium
Cited by: 5
Author(s): Wei Zou, Min Xiong, Xuefeng Deng, John F. Engelhardt, Ziying Yan, Jianming Qiu
Software Mentions: 3
Published: over 7 years ago

10.1186/s13071-019-3650-1

Evaluation of dynamic developmental processes and the molecular basis of the high body fat percentage of different proglottid types of Moniezia expansa
Cited by: 8
Author(s): Yi Liu, Zhengrong Wang, Shuai Pang, Wenjuan Zhao, Lichao Kang, Yanyan Zhang, Hui Zhang, Jingquan Yang, Zhixin Wang, Pingping Lu, Mengfei Xu, Weiyi Wang, Xiaochen Bo, Zhenzhen Li
Software Mentions: 3
Published: about 7 years ago

10.1186/s13071-020-04125-y

Slight temperature changes cause rapid transcriptomic responses in Trypanosoma cruzi metacyclic trypomastigotes
Cited by: 10
Author(s): Lissa Cruz-Saavedra, Marina Muñoz, Luz Helena Patiño, Gustavo Adolfo Calderón Vallejo, Felipe Guhl, Juan David Ramírez
Software Mentions: 3
Published: over 6 years ago

10.1186/s13071-017-2326-y

Differential gene expression in Anopheles stephensi following infection with drug-resistant Plasmodium yoelii
Cited by: 4
Author(s): Jingru Zhang, Jiacheng Huang, Feng Zhu, Jian Zhang
Software Mentions: 3
Published: about 9 years ago

10.1186/s13071-015-0939-6

Preliminary expression profile of cytokines in brain tissue of BALB/c mice with Angiostrongylus cantonensis infection
Cited by: 20
Author(s): Liping Yu, Xiaoying Wu, Jie Wei, Qi Liao, Liang Xu, Siqi Luo, Xiaofeng Zeng, Yi Zhao, Ziquan Lv, Zhongdao Wu
Software Mentions: 3
Published: over 11 years ago

10.1186/s13071-020-04476-6

Major SCP/TAPS protein expansion in Lucilia cuprina is associated with novel tandem array organisation and domain architecture
Cited by: 1
Author(s): Yair D J Prawer, Andreas J. Stroehlein, Neil D. Young, Shilpa Kapoor, Ross S. Hall, Razi Ghazali, Philip Batterham, Robin B. Gasser, Trent Perry, Clare A. Anstead
Software Mentions: 3
Published: almost 6 years ago

10.7717/peerj.1527

Genome-wide identification of hypoxia-induced enhancer regions
Cited by: 8
Author(s): Nick Kamps-Hughes, Jessica L. Preston, Melissa A Randel, Eric A. Johnson
Software Mentions: 3
Published: over 10 years ago

10.7717/peerj.201

Characterization of RNA in exosomes secreted by human breast cancer cell lines using next-generation sequencing
Cited by: 173
Author(s): Piroon Jenjaroenpun, Yuliya Kremenska, Vrundha M. Nair, Maksym Kremenskoy, Baby Joseph, Igor V. Kurochkin
Software Mentions: 3
Published: almost 13 years ago

10.7717/peerj.11919

The whole-genome and expression profile analysis of <i>WRKY</i> and <i>RGAs</i> in <i>Dactylis glomerata</i> showed that <i>DG6C02319.1</i> and Dg<i>WRKYs</i> may cooperate in the immunity against rust
Cited by: 4
Author(s): Juncai Ren, Jialing Hu, Ailing Zhang, Shuping Ren, Tingting Jing, Xiaoshan Wang, Min Sun, Linkai Huang, Bing Zeng
Software Mentions: 3
Published: about 5 years ago

10.7717/peerj.8947

Transcriptomic changes across the life cycle of <i>Trypanosoma cruzi II</i>
Cited by: 8
Author(s): Lissa Cruz-Saavedra, Gustavo Adolfo Vallejo, Felipe Guhl, Juan David Ramírez
Software Mentions: 3
Published: over 6 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: over 12 years ago

10.7717/peerj.8144

Navigating oxygen deprivation: liver transcriptomic responses of the red eared slider turtle to environmental anoxia
Cited by: 10
Author(s): Kyle K. Biggar, Jing Zhang, Kenneth B. Storey
Software Mentions: 3
Published: almost 7 years ago

10.7717/peerj.2829

Hydrogel scaffolds promote neural gene expression and structural reorganization in human astrocyte cultures
Cited by: 12
Author(s): V. Bleu Knight, Elba E. Serrano
Software Mentions: 3
Published: over 9 years ago

10.1002/prp2.386

Rifampin modulation of xeno- and endobiotic conjugating enzyme mRNA expression and associated microRNAs in human hepatocytes
Cited by: 16
Author(s): Brandon T. Gufford, Jason Robarge, Michael T. Eadon, Hongyu Gao, Hai Lin, Yunlong Liu, Zeruesenay Desta, Todd C. Skaar
Software Mentions: 3
Published: over 8 years ago

10.14814/phy2.13534

Human hair follicle transcriptome profiling: a minimally invasive tool to assess molecular adaptations upon low‐volume, high‐intensity interval training
Cited by: 7
Author(s): Jing Zhang, Sarah J. Wallace, Maria Y. Shiu, Ingrid Smith, Shawn G. Rhind, Valérie S. Langlois
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pone.0074256

Gene Regulatory Networks Elucidating Huanglongbing Disease Mechanisms
Cited by: 90
Author(s): Federico Martinelli, Russell L. Reagan, Sandra L. Uratsu, My L. Phu, Ute Albrecht, Wenwei Zhao, Cristina E. Davis, Kim D. Bowman, Abhaya M. Dandekar
Software Mentions: 3
Published: almost 13 years ago

10.1371/journal.pone.0207715

Distinct genes and pathways associated with transcriptome differences in early cardiac development between fast- and slow-growing broilers
Cited by: 9
Author(s): J. Zhang, Carl J. Schmidt, Susan J. Lamont
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.pone.0081925

Gene Expression, Single Nucleotide Variant and Fusion Transcript Discovery in Archival Material from Breast Tumors
Cited by: 51
Author(s): Nadine Norton, Zhifu Sun, Yan W. Asmann, Daniel J. Serie, Brian M. Necela, Aditya Bhagwate, Jin Jen, Bruce W. Eckloff, Krishna R. Kalari, Kevin J. Thompson, Jennifer M. Carr, Jennifer M. Kachergus, Xochiquetzal J. Geiger, Edith A. Perez, E. Aubrey Thompson
Software Mentions: 3
Published: almost 13 years ago

10.1371/journal.pone.0138782

Transcriptome Profiling of Pediatric Core Binding Factor AML
Cited by: 13
Author(s): Chih Hao Hsu, Cu Nguyen, Chunhua Yan, Rhonda E. Ries, Qing Rong Chen, Ying Hu, Fabiana Ostronoff, Derek L. Stirewalt, George A. Komatsoulis, Shawn Levy, Daoud Meerzaman, Soheil Meshinchi
Software Mentions: 3
Published: almost 11 years ago

10.1371/journal.pone.0239627

Swimming under elevated hydrostatic pressure increases glycolytic activity in gas gland cells of the European eel
Cited by: 5
Author(s): Gabriel Schneebauer, Constantin Lindemann, Victoria Drechsel, Lasse Marohn, Klaus Wysujack, Elena Santidrian, Ron P. Dirks, Reinhold Hanel, Bernd Pelster
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0133751

Smooth Muscle Cell Genome Browser: Enabling the Identification of Novel Serum Response Factor Target Genes
Cited by: 43
Author(s): Moon Young Lee, Chanjae Park, Robyn M. Berent, Paul J. Park, Robert Fuchs, Syn Hannah, Chin Albert, Jared Townsend, Craig C. Benson, Doug Redelman, Tong Shen, Sang-Youel Park, Joseph M. Miano, Kenton M. Sanders, Seungil Ro
Software Mentions: 3
Published: about 11 years ago

10.1371/journal.pone.0070053

Full Transcriptome Analysis of Early Dorsoventral Patterning in Zebrafish
Cited by: 11
Author(s): Erika Fodor, Áron Zsigmond, Balázs Horváth, J. Molnár, István Nagy, Gábor Tóth, Stephen W. Wilson, Máté Varga
Software Mentions: 3
Published: about 13 years ago

10.1371/journal.pone.0194036

Allele-specific DNA methylation of disease susceptibility genes in Japanese patients with inflammatory bowel disease
Cited by: 11
Author(s): Hirofumi Chiba, Yoichi Kakuta, Yoshitaka Kinouchi, Yosuke Kawai, Kazuhiro Watanabe, Munenori Nagao, Takeo Naito, Motoyuki Onodera, Rintaro Moroi, Masatake Kuroha, Yoshitake Kanazawa, Tsutomu Kimura, Hisashi Shiga, Katsuya Endo, Kenichi Negoro, Masao Nagasaki, Michiaki Unno, Tooru Shimosegawa
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0147147

Systematic Identification and Characterization of Long Non-Coding RNAs in the Silkworm, Bombyx mori
Cited by: 94
Author(s): Yuqian Wu, Tingcai Cheng, Chun Li, Duolian Liu, Quan Zhang, Rodney Long, Ping Zhao, Qingyou Xia
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0136653

RNA-Seq Analysis of Differential Splice Junction Usage and Intron Retentions by DEXSeq
Cited by: 42
Author(s): Yafang Li, Xiayu Rao, William Mattox, Christopher I. Amos, Bin Liu
Software Mentions: 3
Published: about 11 years ago

10.1371/journal.pone.0206055

Transcriptome profiling of transgenic potato plants provides insights into variability caused by plant transformation
Cited by: 9
Author(s): Dae Kwan Ko, Satya Swathi Nadakuduti, David S. Douches, C. Robin Buell
Software Mentions: 3
Published: almost 8 years ago

10.1371/journal.pone.0184115

Transcriptome analysis of the pectoral muscles of local chickens and commercial broilers using Ribo-Zero ribonucleic acid sequencing
Cited by: 12
Author(s): Yanhua Zhang, Donghua Li, Ruili Han, Yanbin Wang, Guoxi Li, Xiaojun Liu, Yadong Tian, Xiangtao Kang, Zhuanjian Li
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pone.0111407

Whole Transcriptome Profiling of Maize during Early Somatic Embryogenesis Reveals Altered Expression of Stress Factors and Embryogenesis-Related Genes
Cited by: 82
Author(s): Stella Salvo, Candice N. Hirsch, C. Robin Buell, Shawn M. Kaeppler, Heidi F. Kaeppler
Software Mentions: 3
Published: almost 12 years ago

10.1371/journal.pone.0155378

CTCF and CohesinSA-1 Mark Active Promoters and Boundaries of Repressive Chromatin Domains in Primary Human Erythroid Cells
Cited by: 7
Author(s): Laurie A. Steiner, Vincent P. Schulz, Yelena Makismova, Kimberly Lezon-Geyda, Patrick G. Gallagher
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0199021

Transcriptomic response to GABA-producing Lactobacillus plantarum CGMCC 1.2437T induced by L-MSG
Cited by: 28
Author(s): Kejin Zhuang, Yujun Jiang, Xiaohan Feng, Li Li, Fangfang Dang, Wei Zhang, Chaoxin Man
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0158621

Comparative Digital Gene Expression Analysis of the Arabidopsis Response to Volatiles Emitted by Bacillus amyloliquefaciens
Cited by: 26
Author(s): Haiting Hao, Xia Zhao, Qianhan Shang, Yun Wang, Zhihong Guo, Yubao Zhang, Ruo–Yu Wang
Software Mentions: 3
Published: about 10 years ago

10.1371/journal.pone.0181761

The integrated analysis of RNA-seq and microRNA-seq depicts miRNA-mRNA networks involved in Japanese flounder (Paralichthys olivaceus) albinism
Cited by: 12
Author(s): Na Wang, Ruoqing Wang, Renkai Wang, Yongsheng Tian, Changwei Shao, Xiaodong Jia, Songlin Chen
Software Mentions: 3
Published: about 9 years ago

10.1371/journal.pone.0120020

Assessing Associations between the AURKA-HMMR-TPX2-TUBG1 Functional Module and Breast Cancer Risk in BRCA1/2 Mutation Carriers
Cited by: 34
Author(s): Ignacio Blanco, Karoline Kuchenbaecker, Daniel Cuadras, Xianshu Wang, Daniel Barrowdale, Gorka Ruíz de Garibay, Pablo Librado, Alejandro Sánchez-Gracia, Julio Rozas, Núria Bonifaci, Lesley McGuffog, V. Shane Pankratz, Abul B.M.M.K. Islam, Francesca Mateo, Antoni Berenguer, Audrey Petit, Isabel Catalá, Joan Brunet, Lídia Feliubadaló, Eva Tornero, Javier Benı́tez, Ana Osorio, Teresa Ramón, Cajal Teresa, Heli Nevanlinna, Kristiina Aittomäki, Banu K. Arun, Amanda E. Toland, Beth Y. Karlan, Christine Walsh, Jenny Lester, Mark H. Greene, L. Phuong, Robert L. Nussbaum, Irene L. Andrulis, Susan M. Domchek, Katherine L. Nathanson, Timothy R. Rebbeck, Rósa B. Barkardóttir, Anna Jakubowska, Jan Lubiński, Katarzyna Durda, Katarzyna Jaworska–Bieniek, Kathleen Claes, Tom Van Maerken, Orland Dı́ez, Thomas V.O. Hansen, Lars Jønson, Anne–Marie Gerdes, Bent Ejlertsen, Miguel de la Hoya, Trinidad Caldés, Alison M. Dunning, Clare Oliver, Elena Fineberg, Margaret Cook, Susan Peock, Emma McCann, Alex Murray, Chris Jacobs, Gabriella Pichert, Fiona Lalloo, Carol Chu, Huw Dorkins, Joan Paterson, Kai Ren Ong, Manuel R. Teixeira, Thais Bonfim Teixeira, Frans B.L. Hogervorst, Annemarie H. van der Hout, Caroline Seynaeve, Rob B. van der Luijt, Marjolijn J. L. Ligtenberg, Peter Devilee, Juul T. Wijnen, Matti A. Rookus, Hanne Meijers-Heijboer, Marinus J. Blok, Ans M.W. van den Ouweland, Cora M. Aalfs, Gustavo C. Rodriguez, Kelly‐Anne Phillips, Marion Piedmonte, Stacy Nerenstone, Victoria Bae‐Jump, David M. O’Malley, Elena Ratner, Rita K. Schmutzler, Barbara Wappenschmidt, Kerstin Rhiem, Christoph Engel, Alfons Meindl, Nina Ditsch, Norbert Arnold, Hansjoerg Plendl, Dieter Niederacher, Christian Sutter, Shan Wang-Gohrke, Doris Steinemann, Sabine Preisler-Adams, Karin Kast, Raymonda Varon-Mateeva, Andrea Gehrig, Anders Bojesen, Inge Søkilde Pedersen, Lone Sunde, Uffe Birk Jensen, Mads Thomassen, Torben A. Kruse, Lenka Foretová, Paolo Peterlongo, Loris Bernard, Bernard Peissel, Giulietta Scuvera, Siranoush Manoukian, Paolo Radice, Laura Ottini, Marco Montagna, Simona Agata, Christine M. Maugard, Jacques Simard, Penny Soucy, Andreas Berger, A. Fink-Retter, Christian F. Singer, Christine Rappaport, Daphne Geschwantler-Kaulich, Muy Kheng Tea, Georg Pfeiler, Esther M. John, Alexander Miron, Susan L. Neuhausen, Mary Beth Terry, Wendy K. Chung, Mary B. Daly, David E. Goldgar, Ramūnas Janavičius, Cecilia M. Dorfling, Elizabeth J. van Rensburg, Florentia Fostira, Irene Konstantopoulou, Judy E. Garber, Andrew K. Godwin, Edith Olàh, Steven A. Narod, Gad Rennert, Shani Shimon Paluch, Yael Laitman, Eitan Friedman, Annelie Liljegren, Johanna Rantala, Marie Stenmark-Askmalm, Niklas Loman, Evgeny N. Imyanitov, Ute Hamann, Amanda B. Spurdle, Sue Healey, Jeffrey N. Weitzel, Josef Herzog, David A. Margileth, Chiara Gorrini, Manel Esteller, Antonio Gómez, Sergi Sayols, Enrique Vidal, Holger Heyn, Dominique Stoppa‐Lyonnet, Mélanie Léone, Laure Barjhoux, Marion Fassy-Colcombet, Antoine de Pauw, Christine Lasset, Sandra Fert Ferrer, Laurent Castéra, Pascaline Berthet, François Cornélis, Yves Jean Bignon, Francesca Damiola, Sylvie Mazoyer, Olga M. Sinilnikova, Christopher A. Maxwell, Joseph Vijai, Mark E. Robson, Noah D. Kauff, Marina Corines, Danylko Villano, Julie M. Cunningham, Adam F. Lee, Noralane M. Lindor, Conxi Lázaro, Douglas F. Easton, Kenneth Offit, Georgia Chenevix-Trench, Fergus J. Couch, Antonis C. Antoniou, Miguel Ángel Pujana
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pone.0018493

Massive-Scale RNA-Seq Analysis of Non Ribosomal Transcriptome in Human Trisomy 21
Cited by: 62
Author(s): Valerio Costa, Claudia Angelini, Luciana D’Apice, Margherita Mutarelli, Amelia Casamassimi, Linda Sommese, Maria Gallo, Marianna Aprile, Roberta Esposito, Luigi Leone, Aldo Donizetti, Stefania Crispi, Monica Rienzo, Berardo Sarubbi, Raffaele Calabrò, Marco Picardi, Paola Salvatore, Teresa Infante, Piergiuseppe De Berardinis, Claudio Napoli, Alfredo Ciccodicola
Software Mentions: 3
Published: over 15 years ago

10.1371/journal.pone.0187966

RNA-seq reveals transcriptome changes in goats following myostatin gene knockout
Cited by: 24
Author(s): Lamei Wang, Bei Cai, Shiwei Zhou, Haijing Zhu, Qu Liu, Xiaolong Wang
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pone.0251732

Phlpp1 is induced by estrogen in osteoclasts and its loss in Ctsk-expressing cells does not protect against ovariectomy-induced bone loss
Cited by: 2
Author(s): Marcelline K. Hanson, Ismael Y. Karkache, David H. H. Molstad, Andrew Norton, Kim C. Mansky, Elizabeth W. Bradley
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0121961

SNP Identification from RNA Sequencing and Linkage Map Construction of Rubber Tree for Anchoring the Draft Genome
Cited by: 34
Author(s): Jeremy R. Shearman, Duangjai Sangsrakru, Nukoon Jomchai, Panthita Ruang-areerate, Chutima Sonthirod, Chaiwat Naktang, Kanikar Theerawattanasuk, Somvong Tragoonrung, Sithichoke Tangphatsornruang
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pone.0189476

Transcriptomic analysis of chicken Myozenin 3 regulation reveals its potential role in cell proliferation
Cited by: 12
Author(s): Maosen Ye, Fei Ye, Liutao He, Bin Luo, Feng Yang, Can Cui, Xiaoling Zhao, Huadong Yin, Diyan Li, Hengyong Xu, Yan Wang, Qing Zhu
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pone.0124003

ALDB: A Domestic-Animal Long Noncoding RNA Database
Cited by: 73
Author(s): Aimin Li, Junying Zhang, Zhongyin Zhou, Lei Wang, Yujuan Liu, Yajun Liu
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pone.0122396

Integration of Transcriptome and Whole Genomic Resequencing Data to Identify Key Genes Affecting Swine Fat Deposition
Cited by: 19
Author(s): Kai Xing, Feng Zhu, Lichao Zhai, Huijie Liu, Yuan Wang, Zhijun Wang, Shaokang Chen, Zhuocheng Hou, Chuduan Wang
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pone.0234628

A lncRNA-miRNA-mRNA network for human primed, naive and extended pluripotent stem cells
Cited by: 7
Author(s): Zheng-lai Ma, Yanni Li, Yingying Zhang, Jiaxin Chen, Tao Tan, Yong Fan
Software Mentions: 3
Published: over 6 years ago

10.1371/journal.pone.0165395

TCGA Expedition: A Data Acquisition and Management System for TCGA Data
Cited by: 56
Author(s): Uma Chandran, Olga Medvedeva, M. Michael Barmada, Philip D. Blood, Anish Chakka, Soumya Luthra, Antonio M. Ferreira, Kim F. Wong, Adrian V. Lee, Zhihui Zhang, Robert Budden, James R. Scott, Annerose Berndt, Jeremy M. Berg, Rebecca S. Jacobson
Software Mentions: 3
Published: almost 10 years ago

10.1371/journal.pone.0155061

Comparative Analysis of Transcriptomes among Bombyx mori Strains and Sexes Reveals the Genes Regulating Melanic Morph and the Related Phenotypes
Cited by: 3
Author(s): Songzhen He, Xiaoling Tong, Kunpeng Lu, Yaru Lu, Jiangwen Luo, Wenhao Yang, Min Chen, Minjin Han, Hai Hu, Cheng Lü, Fangyin Dai
Software Mentions: 3
Published: over 10 years ago

10.1371/journal.pone.0221938

De novo transcriptome profile of coccolithophorid alga Emiliania huxleyi CCMP371 at different calcium concentrations with proteome analysis
Cited by: 11
Author(s): Onyou Nam, Jong-Moon Park, Hookeun Lee, EonSeon Jin
Software Mentions: 3
Published: about 7 years ago

10.3390/cancers13184645

Quinacrine Induces Nucleolar Stress in Treatment-Refractory Ovarian Cancer Cell Lines
Cited by: 6
Author(s): Derek B. Oien, Upasana Ray, Christopher L. Pathoulas, Ling Jin, Prabhu Thirusangu, Deok‐Beom Jung, Joseph E. Kumka, Yu Xiao, Sayantani Sarkar Bhattacharya, Dennis Montoya, Jeremy Chien, Viji Shridhar
Software Mentions: 3
Published: about 5 years ago

10.3390/cancers12102766

Targeted Inhibition of the NUP98-NSD1 Fusion Oncogene in Acute Myeloid Leukemia
Cited by: 27
Author(s): Sagarajit Mohanty, Nidhi Jyotsana, Amit Sharma, Arnold Kloos, Razif Gabdoulline, Basem Othman, Courteney K. Lai, Renate Schottmann, Madhvi Mandhania, Johannes Schmoellerl, Florian Grebien, Euan Ramsay, Anitha Thomas, Hans‐Peter Vornlocher, Arnold Ganser, Felicitas Thol, Michael Heuser
Software Mentions: 3
Published: almost 6 years ago

10.3390/cancers12030764

Global DNA Hypomethylation in Epithelial Ovarian Cancer: Passive Demethylation and Association with Genomic Instability
Cited by: 41
Author(s): Wa Zhang, David Klinkebiel, Carter J. Barger, Sanjit Pandey, Chittibabu Guda, Austin Miller, Stacey N. Akers, Kunle Odunsi, Adam R. Karpf
Software Mentions: 3
Published: over 6 years ago

10.1016/j.cell.2016.05.029

Dynamic Axonal Translation in Developing and Mature Visual Circuits
Cited by: 345
Author(s): Toshiaki Shigeoka, Hosung Jung, Jane Jung, Benita Turner-Bridger, Jiyeon Ohk, Julie Qiaojin Lin, Paul S. Amieux, Christine E. Holt
Software Mentions: 3
Published: over 10 years ago

10.1186/s13578-019-0308-9

Zika virus antagonizes interferon response in patients and disrupts RIG-I–MAVS interaction through its CARD-TM domains
Cited by: 34
Author(s): Yiwen Hu, Xinhuai Dong, Zhenjian He, Yun Wu, Shihao Zhang, Jiajie Lin, Yi Yang, Jiahui Chen, Shu An, Yingxian Yin, Zhiyong Shen, Gucheng Zeng, Han Tian, Junchao Cai, Hongyu Guan, Jueheng Wu, Mengfeng Li, Xun Zhu
Software Mentions: 3
Published: over 7 years ago

10.1038/s42003-019-0461-z

C/EBPβ-LIP induces cancer-type metabolic reprogramming by regulating the let-7/LIN28B circuit in mice
Cited by: 11
Author(s): Tobias Ackermann, Götz Hartleben, Christine Müller, Guido Mastrobuoni, Marco Groth, Britt A. Sterken, Mohamad Amr Zaini, Sameh A. Youssef, Hidde R. Zuidhof, Sara Russo Krauss, Gertrud Kortman, Gerald de Haan, Alain de Bruin, Zhao Qi Wang, Matthias Platzer, Stefan Kempa, Cornelis F. Calkhoven
Software Mentions: 3
Published: over 7 years ago

10.1038/s42003-021-02412-7

From the first touch to biofilm establishment by the human pathogen Candida glabrata: a genome-wide to nanoscale view
Cited by: 7
Author(s): Mafalda Cavalheiro, Diana Pereira, Cécile Formosa-Dague, Carolina Leitão, Pedro Pais, Easter Ndlovu, Romeu Viana, Andreia I. Pimenta, Rui Santos, Azusa Takahashi‐Nakaguchi, Michiyo Okamoto, Mihaela Ola, Hiroji Chibana, Arsénio M. Fialho, Geraldine Butler, Étienne Dague, Miguel C. Teixeira
Software Mentions: 3
Published: about 5 years ago

10.1038/s42003-018-0089-4

De novo genome assembly of Oryza granulata reveals rapid genome expansion and adaptive evolution
Cited by: 19
Author(s): Zhigang Wu, Dongming Fang, Rui Yang, Fei Gao, Xingyu An, Xiaoxuan Zhuo, Yafei Li, Chuandeng Yi, Tao Zhang, Chengzhi Liang, Peng Cui, Zhukuan Cheng, Qiong Luo
Software Mentions: 3
Published: about 8 years ago

10.1038/s42003-020-01143-5

Host-parasite tissue adhesion by a secreted type of β-1,4-glucanase in the parasitic plant Phtheirospermum japonicum
Cited by: 26
Author(s): Ken-ichi Kurotani, Takanori Wakatake, Yasunori Ichihashi, Koji Okayasu, Yu Sawai, Satoshi Ogawa, Songkui Cui, Takamasa Suzuki, Ken Shirasu, Michitaka Notaguchi
Software Mentions: 3
Published: about 6 years ago

10.1038/s42003-020-0775-x

Trypanosomatid parasite dynamically changes the transcriptome during infection and modifies honey bee physiology
Cited by: 24
Author(s): Qiushi Liu, Jing Lei, Alistair C. Darby, Tatsuhiko Kadowaki
Software Mentions: 3
Published: over 6 years ago

10.1016/j.csbj.2021.04.068

Refinement of bamboo genome annotations through integrative analyses of transcriptomic and epigenomic data
Cited by: 3
Author(s): Xuelian Ma, Hansheng Zhao, Hengyu Yan, Minghao Sheng, Yaxin Cao, Kebin Yang, Hao Xu, Wenying Xu, Zhimin Gao, Zhen Su
Software Mentions: 3
Published: over 5 years ago

10.2174/1389202911314030004

Review: Alternative Splicing (AS) of Genes As An Approach for Generating Protein Complexity
Cited by: 75
Author(s): Bishakha Roy, Larisa M. Haupt, Lyn R. Griffiths
Software Mentions: 3
Published: over 13 years ago

10.1093/dnares/dst017

DDBJ Read Annotation Pipeline: A Cloud Computing-Based Pipeline for High-Throughput Analysis of Next-Generation Sequencing Data
Cited by: 69
Author(s): Hideki Nagasaki, Takako Mochizuki, Yuichi Kodama, Satoshi Saruhashi, Shota Morizaki, Hideaki Sugawara, Hajime Ohyanagi, Nori Kurata, Kousaku Okubo, Toshihisa Takagi, Eli Kaminuma, Yasukazu Nakamura
Software Mentions: 3
Published: over 13 years ago

10.1016/j.dib.2019.104893

Dataset on the formation of Thioredoxin interacting protein (Txnip) containing redox sensitive high molecular weight nucleoprotein complexes
Cited by: 1
Author(s): Cristiane Lumi Hirata, Shinji Ito, Hiroshi Masutani
Software Mentions: 3
Published: over 6 years ago

10.1016/j.dib.2019.104587

Estradiol and genistein effects on the sea bass (Dicentrarchus labrax) scales: Transcriptome dataset
Cited by: 4
Author(s): Patrícia I. S. Pinto, André R. Andrade, Michael A. S. Thorne, M. Dulce Estêvão, Adelino V.M. Canário, Deborah M. Power
Software Mentions: 3
Published: almost 7 years ago

10.1016/j.dib.2020.106096

A collection of transcriptomic and proteomic datasets from sesame in response to salt stress
Cited by: 5
Author(s): Yujuan Zhang, Donghua Li, Rong Zhou, Aili Liu, Linhai Wang, Yanxin Zhang, Huihui Gong, Xiurong Zhang, Jun You
Software Mentions: 3
Published: almost 6 years ago

10.1093/database/bay003

TISSUES 2.0: an integrative web resource on mammalian tissue expression
Cited by: 110
Author(s): Oana Palasca, Alberto Santos, Christian Stolte, Jan Gorodkin, Lars Juhl Jensen
Software Mentions: 3
Published: over 8 years ago

10.1016/j.devcel.2016.02.013

Neural Progenitors Adopt Specific Identities by Directly Repressing All Alternative Progenitor Transcriptional Programs
Cited by: 75
Author(s): Eva Kutějová, Noriaki Sasai, Ankita Shah, Mina Gouti, James Briscoe
Software Mentions: 3
Published: over 10 years ago

10.1242/dev.152413

Unraveling transcriptome dynamics in human spermatogenesis
Cited by: 107
Author(s): Sabrina Z. Jan, Tinke L. Vormer, Aldo Jongejan, Michael D. Röling, Sherman J. Silber, Dirk G. de Rooij, Geert Hamer, Sjoerd Repping, Ans M.M. van Pelt
Software Mentions: 3
Published: over 9 years ago

10.1007/s00125-017-4500-3

Systems biology of the IMIDIA biobank from organ donors and pancreatectomised patients defines a novel transcriptomic signature of islets from individuals with type 2 diabetes
Cited by: 121
Author(s): Michele Solimena, Anke M. Schulte, Lorella Marselli, Florian Ehehalt, Daniela Richter, Manuela Kleeberg, Hassan Mziaut, Klaus-Peter Knoch, Julia Parnis, Marco Bugliani, Afshan Siddiq, Anne Jörns, Frédéric Burdet, Robin Liechti, Mara Suleiman, Daniel Margerie, Farooq Syed, Marius Distler, Robert Grützmann, Enrico Petretto, Aida Moreno‐Moral, Carolin Wegbrod, Anke Sönmez, Katja Pfriem, Anne Friedrich, Jörn Meinel, Claes B. Wollheim, Gustavo Baretton, Raphaël Scharfmann, Everson Nogoceke, Ezio Bonifacio, Dorothée Sturm, Birgit Meyer‐Puttlitz, Ugo Boggi, Hans‐Detlev Saeger, Franco Filipponi, Mathias Lesche, Paolo Meda, Andreas Dahl, Leonore Wigger, Ioannis Xénarios, Mario Falchi, Bernard Thorens, Jürgen Weitz, Krister Bokvist, Sigurd Lenzen, Guy A. Rutter, Philippe Froguel, Manon von Bülow, Mark Ibberson, Piero Marchetti
Software Mentions: 3
Published: almost 9 years ago

10.1186/1746-1596-9-142

NF-κB signaling and vesicle transport are correlated with the reactivation of the memory trace of morphine dependence
Cited by: 9
Author(s): Junyi Ye, Zhaoyang Yang, Candong Li, Meimei Cai, Daizhan Zhou, Qin Zhang, Wei Y, Ting Wang, Yun Liu
Software Mentions: 3
Published: about 12 years ago

10.1242/dmm.030536

Comprehensive analysis of gene expression patterns in Friedreich's ataxia fibroblasts by RNA sequencing reveals altered levels of protein synthesis factors and solute carriers
Cited by: 34
Author(s): Marek Napierala, Yanjie Li, Yue Lu, Kevin Lin, Lauren Hauser, David R. Lynch, Марек Напиерала
Software Mentions: 3
Published: almost 9 years ago

10.1016/j.ebiom.2014.10.003

An Endotoxin Tolerance Signature Predicts Sepsis and Organ Dysfunction at Initial Clinical Presentation
Cited by: 110
Author(s): Olga M. Pena, David G. Hancock, Ngan H. Lyle, Adam Linder, James A. Russell, Jianguo Xia, Christopher D. Fjell, John H. Boyd, Robert E. W. Hancock
Software Mentions: 3
Published: almost 12 years ago

10.15252/embj.201798783

Lmo2 expression defines tumor cell identity during T‐cell leukemogenesis
Cited by: 31
Author(s): Idoia García-Ramírez, Sanil Bhatia, Guillermo Rodríguez-Hernández, Inés González-Herrero, Carolin Walter, Sara González de Tena-Dávila, Salma Parvin, Oskar A. Haas, Wilhelm Woessmann, Martin Stanulla, Martin Schrappe, Martin Dugas, Yasodha Natkunam, Alberto Órfão, Verónica Domínguez, B. Pintado, Óscar Blanco, Diego Alonso-López, Javier De Las Rivas, Alberto Martín-Lorenzo, Rafael Jiménez, Francisco Javier García Criado, María Begoña García Cenador, Izidore S. Lossos, Carolina Vicente-Dueñas, Arndt Borkhardt, Julia Hauer, Isidro Sánchez-Garcı́a
Software Mentions: 3
Published: over 8 years ago

10.15252/embj.2019102147

<scp>SLC</scp> 1A3 contributes to L‐asparaginase resistance in solid tumors
Cited by: 40
Author(s): Jianhui Sun, Remco Nagel, Esther A. Zaal, Alejandro P. Ugalde, Ruiqi Han, Natalie Proost, Ji Ying Song, Abhijeet Pataskar, Artur M Burylo, Haigen Fu, Gerrit J. Poelarends, Marieke van de Ven, Olaf van Tellingen, Celia R. Berkers, Reuven Agami
Software Mentions: 3
Published: about 7 years ago

10.15252/emmm.201708552

Comprehensive evaluation of coding region point mutations in microsatellite‐unstable colorectal cancer
Cited by: 9
Author(s): Johanna Kondelin, Kari Salokas, Lilli Saarinen, Kristian Ovaska, Heli Rauanheimo, Roosa‐Maria Plaketti, Jiri Hamberg, Xiaonan Liu, Leena Yadav, Alexandra E. Gylfe, Tatiana Cajuso, Ulrika A. Hänninen, Kimmo Palin, Heikki Ristolainen, Riku Katainen, Eevi Kaasinen, Tomas Tanskanen, Mervi Aavikko, Minna Taipale, Jussi Taipale, Laura Renkonen–Sinisalo, Anna Lepistö, Selja Koskensalo, Jan Böhm, Jukka–Pekka Mecklin∥, Halit Ongen, Emmanouil T. Dermitzakis, Outi Kilpivaara, Pia Vahteristo, Mikko Turunen, Sampsa Hautaniemi, Sari Tuupanen, Auli Karhu, Niko Välimäki, Markku Varjosalo, Esa Pitkänen, Lauri A. Aaltonen
Software Mentions: 3
Published: about 8 years ago

10.15252/emmm.201607006

Transcriptional response to hepatitis C virus infection and interferon‐alpha treatment in the human liver
Cited by: 48
Author(s): Tujana Boldanova, Aleksei Suslov, Markus H. Heim, Anamaria Necşulea
Software Mentions: 3
Published: over 9 years ago

10.15252/embr.201949602

Coordinated control of adiposity and growth by anti‐anabolic kinase ERK7
Cited by: 6
Author(s): Kiran Hasygar, Onur Deniz, Ying Liu, Josef Gullmets, Riikka Hynynen, Hanna Ruhanen, Krista Kokki, Reijo Käkelä, Ville Hietakangas
Software Mentions: 3
Published: over 5 years ago

10.3389/fphys.2018.01755

The Use of Targeted Next Generation Sequencing to Explore Candidate Regulators of TGF-β1’s Impact on Kidney Cells
Cited by: 7
Author(s): Bo Wang, Guanyu Ji, Haroon Naeem, Junwen Wang, Phillip Kantharidis, David Powell, Sharon D. Ricardo
Software Mentions: 3
Published: almost 8 years ago

10.3389/fphys.2020.612036

Impact of Ringer’s Solution Challenge Stress to Immunostimulatory Experiment, Insights From Japanese Flounder
Cited by: 1
Author(s): Jinxiang Liu, Zan Li, Yujue Wang, Quanqi Zhang
Software Mentions: 3
Published: almost 6 years ago

10.3389/fphys.2020.617492

Mitochondrial Calcium Uniporter Deficiency in Zebrafish Causes Cardiomyopathy With Arrhythmia
Cited by: 13
Author(s): Adam D. Langenbacher, Hirohito Shimizu, Welkin Hsu, Yali Zhao, Alexandria Borges, Carla M. Koehler, Jau-Nian Chen
Software Mentions: 3
Published: over 5 years ago

10.3389/fpls.2016.01255

Photosynthate Regulation of the Root System Architecture Mediated by the Heterotrimeric G Protein Complex in Arabidopsis
Cited by: 28
Author(s): Yashwanti Mudgil, Abhijit Karve, Paulo José Pereira Lima Teixeira, Kun Jiang, Meral Tunc‐Ozdemir, Alan M. Jones
Software Mentions: 3
Published: about 10 years ago

10.3389/fpls.2015.01247

Genome-Wide Analysis of the AP2/ERF Superfamily Genes and their Responses to Abiotic Stress in Medicago truncatula
Cited by: 84
Author(s): Yongjun Shu, Ying Liu, Jun Zhang, Lili Song, Changhong Guo
Software Mentions: 3
Published: over 10 years ago

10.3389/fpls.2021.686121

Extracellular Fragmented Self-DNA Is Involved in Plant Responses to Biotic Stress
Cited by: 10
Author(s): Francesca Barbero, Michela Guglielmotto, Monirul Islam, Massimo E. Maffei
Software Mentions: 3
Published: about 5 years ago

10.3389/fpls.2018.01486

WRKY Transcription Factors Associated With NPR1-Mediated Acquired Resistance in Barley Are Potential Resources to Improve Wheat Resistance to Puccinia triticina
Cited by: 26
Author(s): Jing Gao, Weishuai Bi, Huanpeng Li, Jiaojiao Wu, Xiaoyan Yu, Daqun Liu, Xiaodong Wang
Software Mentions: 3
Published: almost 8 years ago

10.3389/fpls.2014.00594

Annotation of a hybrid partial genome of the coffee rust (Hemileia vastatrix) contributes to the gene repertoire catalog of the Pucciniales
Cited by: 33
Author(s): Marco Cristancho, David Octavio Botero-Rozo, William J. Giraldo, Javier F. Tabima, Diego Mauricio Riaño-Pachón, Carolina Escobar, Yomara Rozo, Luis Fernando Rivera, Andrés Durán, Silvia Restrepo, Tamar Eilam, Y. Anikster, Álvaro Gaitán
Software Mentions: 3
Published: almost 12 years ago

10.3389/fpls.2019.01333

AppleMDO: A Multi-Dimensional Omics Database for Apple Co-Expression Networks and Chromatin States
Cited by: 34
Author(s): Lingling Da, Yue Liu, Jiaotong Yang, Tian Tian, Jiajie She, Xuelian Ma, Wenying Xu, Zhen Su
Software Mentions: 3
Published: almost 7 years ago