10.3389/fimmu.2017.01807

Computational Pipeline for the PGV-001 Neoantigen Vaccine Trial
Cited by: 48
Author(s): Alex Rubinsteyn, Julia Kodysh, Isaac Hodes, Sebastien Mondet, Bülent Arman Aksoy, John P. Finnigan, Nina Bhardwaj, Jeff Hammerbacher
Software Mentions: 2
Published: over 8 years ago

10.1002/cti2.1175

Partial absence of PD‐1 expression by tumor‐infiltrating EBV‐specific CD8⁺ T cells in EBV‐driven lymphoepithelioma‐like carcinoma
Cited by: 7
Author(s): Yannick Simoni, Étienne Becht, Shamin Li, Chiew Yee Loh, Joe Yeong, Tony Kiat Hon Lim, Angela Takano, Daniel S.W. Tan, Evan W. Newell
Software Mentions: 2
Published: over 6 years ago

10.3390/ijms22073585

Gene Expression Analysis of Induced Plum pox virus (Sharka) Resistance in Peach (Prunus persica) by Almond (P. dulcis) Grafting
Cited by: 5
Author(s): M. Rubio, Pedro J. Martínez-García, Azam Nikbakht Dehkordi, Ángela S. Prudencio, E. Gómez, Bernardo Rodamilans, F. Dicenta, Juan Antonio Garcı́a, Pedro Martínez‐Gómez
Software Mentions: 2
Published: over 5 years ago

10.1186/s40170-020-00233-6

Protein synthesis inhibitors stimulate MondoA transcriptional activity by driving an accumulation of glucose 6-phosphate
Cited by: 8
Author(s): Blake R. Wilde, Mohan R. Kaadige, Katrin P. Guillen, Andrew Butterfield, Bryan E. Welm, Donald E. Ayer
Software Mentions: 2
Published: over 5 years ago

10.1038/s41597-019-0256-6

Transcriptomic profile of cystic fibrosis airway epithelial cells undergoing repair
Cited by: 17
Author(s): Alice Zoso, Aderonke Sofoluwe, Marc Bacchetta, Marc Chanson
Software Mentions: 2
Published: over 6 years ago

10.3389/fimmu.2020.00453

Tissue-Specific Factors Differentially Regulate the Expression of Antigen-Processing Enzymes During Dendritic Cell Ontogeny
Cited by: 9
Author(s): Karim Mahiddine, Chervin Hassel, Claire Murat, Maeva Girard, Sylvie Guerder
Software Mentions: 2
Published: over 6 years ago

10.3390/cancers13061472

Persistent Inflammatory Stimulation Drives the Conversion of MSCs to Inflammatory CAFs That Promote Pro-Metastatic Characteristics in Breast Cancer Cells
Cited by: 17
Author(s): Linor Rubinstein-Achiasaf, Dina Morein, Hagar Ben-Yaakov, Yulia Liubomirski, Tsipi Meshel, Eti Elbaz, Orly Dorot, Edward Pichinuk, Michael Gershovits, Miguel Weil, Adit Ben‐Baruch
Software Mentions: 2
Published: over 5 years ago

10.3389/fimmu.2019.00816

Comparative Transcriptomic Analysis Identifies a Range of Immunologically Related Functional Elaborations of Lymph Node Associated Lymphatic and Blood Endothelial Cells
Cited by: 34
Author(s): Stella J. Berendam, Alexander F. Koeppel, Nicole R. Godfrey, Sherin J. Rouhani, Amber N. Woods, Anthony B. Rodriguez, J. David Peske, Kara L. Cummings, Stephen D. Turner, Víctor H. Engelhard
Software Mentions: 2
Published: over 7 years ago

10.1038/s41375-021-01146-z

Menin is necessary for long term maintenance of meningioma-1 driven leukemia
Cited by: 8
Author(s): Clara Libbrecht, Hongbo Xie, Molly C. Kingsley, Jessica N. Haladyna, Simone S. Riedel, Fatemeh Alikarami, Alexandra Lenard, Gerard M. McGeehan, Patricia Ernst, Kathrin M. Bernt
Software Mentions: 2
Published: over 5 years ago

10.3390/cancers11020190

Intratumoural Heterogeneity Underlies Distinct Therapy Responses and Treatment Resistance in Glioblastoma
Cited by: 36
Author(s): Seçkin Akgül, Ann‐Marie Patch, Rochelle C.J. D’Souza, Pamela Mukhopadhyay, Kátia Nones, Sarah Kempe, Stephen H. Kazakoff, Rosalind L. Jeffree, Brett W. Stringer, John V. Pearson, Nicola Waddell, Bryan W. Day
Software Mentions: 2
Published: over 7 years ago

10.1186/s13054-018-2242-3

Identification of a transcriptome profile associated with improvement of organ function in septic shock patients after early supportive therapy
Cited by: 14
Author(s): Matteo Barcella, Bernardo Bollen Pinto, Daniele Braga, Francesca D’Avila, Federico Tagliaferri, Marie-Angélique Cazalis, Guillaume Monneret, Antoine Herpain, Karim Bendjelid, Cristina Barlassina
Software Mentions: 2
Published: over 7 years ago

10.3390/ijms22031450

A Molecular Signature Determines the Prognostic and Therapeutic Subtype of Non-Muscle-Invasive Bladder Cancer Responsive to Intravesical Bacillus Calmette-Guérin Therapy
Cited by: 5
Author(s): Seon‐Kyu Kim, Seonghwan Park, Yeong Uk Kim, Young Joon Byun, Xuan‐Mei Piao, Pildu Jeong, Kyeong Ja Kim, Hee Youn Lee, Sung Pil Seo, Ho Won Kang, Dong-Won Kim, Yong‐June Kim, Sang Cheol Lee, Sung‐Kwon Moon, You‐Jin Jeon, Wun-Jae Kim, Seok Joong Yun
Software Mentions: 2
Published: over 5 years ago

10.1038/s42003-021-01944-2

Deletion of LBR N-terminal domains recapitulates Pelger-Huet anomaly phenotypes in mouse without disrupting X chromosome inactivation
Cited by: 4
Author(s): Alexander N. Young, Emerald Perlas, Nerea Ruiz-Blanes, Andreas Hierholzer, Nicola Pomella, Belén Martı́n-Martı́n, Alessandra Liverziani, Joanna W. Jachowicz, Thomas Giannakouŕos, Andrea Cerase
Software Mentions: 2
Published: over 5 years ago

10.3389/fgene.2020.606285

Identification of Key Tissue-Specific, Biological Processes by Integrating Enhancer Information in Maize Gene Regulatory Networks
Cited by: 7
Author(s): Maud Fagny, Marieke L. Kuijjer, Maike Stam, Johann Joets, Olivier Turc, Julien Rozière, Stéphanie Pateyron, Anthony Venon, Clémentine Vitte
Software Mentions: 2
Published: over 5 years ago

10.3389/fgene.2021.657330

Transcriptional Profiling of Porcine HCC Xenografts Provides Insights Into Tumor Cell Microenvironment Signaling
Cited by: 3
Author(s): Shovik S. Patel, Amitha Sandur, Mohammed El-Kebir, Ron C. Gaba, Lawrence B. Schook, Kyle M. Schachtschneider
Software Mentions: 2
Published: about 5 years ago

10.1186/s40163-020-00116-7

A systematic review on spatial crime forecasting
Cited by: 39
Author(s): Ourania Kounadi, Alina Ristea, Adelson de Araujo, Michael Leitner
Software Mentions: 2
Published: about 6 years ago

10.1038/s41597-020-00581-4

Cultivar-specific transcriptome and pan-transcriptome reconstruction of tetraploid potato
Cited by: 23
Author(s): Marko Petek, Maja Zagorščak, Živa Ramšak, Sheri Sanders, Špela Tomaž, Elizabeth Tseng, Mohamed Zouine, Anna Coll, Kristina Gruden
Software Mentions: 2
Published: almost 6 years ago

10.3389/fvets.2020.00615

Synthetic Alkaloid Treatment Influences the Intestinal Epithelium and Mesenteric Adipose Transcriptome in Holstein Steers
Cited by: 4
Author(s): Kyle J McLean, R.L. Baldwin, Congjun Li, J. L. Klotz, J. L. Edwards, K. R. McLeod
Software Mentions: 2
Published: almost 6 years ago

10.3390/cancers11030402

Identification of Targetable Lesions in Anaplastic Thyroid Cancer by Genome Profiling
Cited by: 29
Author(s): Naveen Ravi, Minjun Yang, Sigurdur Gretarsson, Caroline Jansson, Nektaria Mylona, Saskia Sydow, Eleanor Luise Woodward, Lars Ekblad, Johan Wennerberg, Kajsa Paulsson
Software Mentions: 2
Published: over 7 years ago

10.3390/cancers13092045

Targeting Cancer Stem Cells with Differentiation Agents as an Alternative to Genotoxic Chemotherapy for the Treatment of Malignant Testicular Germ Cell Tumors
Cited by: 5
Author(s): Amanda R. Loehr, Timothy M. Pierpont, Eric Gelsleichter, Anabella Maria D Galang, Irma Fernández, Elizabeth S. Moore, Matthew Z Guo, Andrew D. Miller, Robert S. Weiss
Software Mentions: 2
Published: about 5 years ago

10.3389/fgene.2019.00500

Identification of Breast Cancer Stem Cell Related Genes Using Functional Cellular Assays Combined With Single-Cell RNA Sequencing in MDA-MB-231 Cells
Cited by: 25
Author(s): Emma Jonasson, Salim Ghannoum, Emma Persson, Jan Ch Karlsson, Thomas Kroneis, Erik Larsson, Göran Landberg, Anders Ståhlberg
Software Mentions: 2
Published: about 7 years ago

10.1007/s10142-017-0555-y

Transcriptome profile of the human placenta
Cited by: 27
Author(s): Marta Majewska, Aleksandra Lipka, Łukasz Paukszto, J Jastrzebski, Kamil Myszczyński, Marek Gowkielewicz, Marcin Jóźwik, Mariusz Majewski
Software Mentions: 2
Published: over 9 years ago

10.1523/ENEURO.0495-18.2019

A Neuron-Optimized CRISPR/dCas9 Activation System for Robust and Specific Gene Regulation
Cited by: 80
Author(s): Katherine E. Savell, Svitlana V. Bach, Morgan E. Zipperly, Jasmin S. Revanna, Nicholas A. Goska, Jennifer J. Tuscher, Corey G. Duke, Faraz Sultan, Julia N. Burke, Derek M. Williams, Lara Ianov, Jeremy J. Day
Software Mentions: 2
Published: over 7 years ago

10.3389/fgene.2019.00710

Transcriptome Analysis Reveals Differential Expression of Genes Regulating Hepatic Triglyceride Metabolism in Pekin Ducks During Dietary Threonine Deficiency
Cited by: 9
Author(s): Yong Jiang, Ming Xie, Wenlei Fan, Jiajia Xue, Zhengkui Zhou, Jing Tang, Chen Guo-hong, Shuisheng Hou
Software Mentions: 2
Published: almost 7 years ago

10.3390/cancers11020208

ORAI1 and ORAI3 in Breast Cancer Molecular Subtypes and the Identification of ORAI3 as a Hypoxia Sensitive Gene and a Regulator of Hypoxia Responses
Cited by: 42
Author(s): Iman Azimi, Michael J. G. Milevskiy, Silke B. Chalmers, Kunsala T. D. S. Yapa, Mélanie Robitaille, Christopher Henry, Gregory J. Baillie, Erik W. Thompson, Sarah J. Roberts‐Thomson, Gregory R. Monteith
Software Mentions: 2
Published: over 7 years ago

10.1172/jci.insight.138734

HPV transcript expression affects cervical cancer response to chemoradiation
Cited by: 10
Author(s): Fiona Ruiz, Matthew Inkman, Ramachandran Rashmi, Naoshad Muhammad, Nishanth Gabriel, Christopher A. Miller, Michael D. McLellan, Michael A. Goldstein, Stephanie Markovina, Perry W. Grigsby, Jin Zhang, Julie K. Schwarz
Software Mentions: 2
Published: almost 5 years ago

10.1186/s12974-017-0915-5

MHC class II expression and potential antigen-presenting cells in the retina during experimental autoimmune uveitis
Cited by: 42
Author(s): Deborah A. Lipski, Rémi Dewispelaere, Vincent Foucart, Laure Caspers, Matthieu Defrance, Catherine Bruyns, François Willermain
Software Mentions: 2
Published: about 9 years ago

10.1534/g3.116.036194

Age and Diet Affect Genetically Separable Secondary Injuries that Cause Acute Mortality Following Traumatic Brain Injury in <i>Drosophila</i>
Cited by: 32
Author(s): Rebeccah J. Katzenberger, Barry Ganetzky, David A. Wassarman
Software Mentions: 2
Published: over 9 years ago

10.3390/ijms21165605

Murine Long Noncoding RNA Morrbid Contributes in the Regulation of NRAS Splicing in Hepatocytes In Vitro
Cited by: 6
Author(s): Anna S. Fefilova, Pavel Melnikov, Tatiana Prikazchikova, Tatiana O. Abakumova, Ilya I. Kurochkin, Pavel Mazin, Rustam H. Ziganshin, Olga V. Sergeeva, Timofei S. Zatsepin
Software Mentions: 2
Published: almost 6 years ago

10.1038/srep16512

Dynamic changes in host gene expression associated with H5N8 avian influenza virus infection in mice
Cited by: 37
Author(s): Su Jin Park, Mukesh Kumar, Hyeok Il Kwon, Rak Kyun Seong, Kyudong Han, Jae Min Song, Chul-Joong Kim, Young Ki Choi, Ok Sarah Shin
Software Mentions: 2
Published: over 10 years ago

10.1038/srep16894

Resequencing of the common marmoset genome improves genome assemblies and gene-coding sequence analysis
Cited by: 31
Author(s): Kengo Sato, Yoshio Kuroki, Wakako Kumita, Asao Fujiyama, Atsushi Toyoda, Jun Kawai, Atsushi Iriki, Erika Sasaki, Hideyuki Okano, Yasubumi Sakakibara
Software Mentions: 2
Published: over 10 years ago

10.3389/fgene.2018.00379

SUMO-Targeted Ubiquitin Ligases (STUbLs) Reduce the Toxicity and Abnormal Transcriptional Activity Associated With a Mutant, Aggregation-Prone Fragment of Huntingtin
Cited by: 7
Author(s): Kentaro Ohkuni, Nagesh Pasupala, Jennifer L Peek, Grace Lauren Holloway, Gloria D. Sclar, Reuben Levy-Myers, Richard E. Baker, Munira A. Basrai, Oliver Kerscher
Software Mentions: 2
Published: almost 8 years ago

10.1534/g3.118.200300

Toward Identifying Subnetworks from FBF Binding Landscapes in <i>Caenorhabditis</i> Spermatogenic or Oogenic Germlines
Cited by: 15
Author(s): Douglas F. Porter, A. Krishna Prasad, Brian H Carrick, Peggy Kroll-Connor, Marvin Wickens, Judith Kimble
Software Mentions: 2
Published: over 7 years ago

10.3390/ijms21165633

The Chloroplast RNA Binding Protein CP31A Has a Preference for mRNAs Encoding the Subunits of the Chloroplast NAD(P)H Dehydrogenase Complex and Is Required for Their Accumulation
Cited by: 5
Author(s): Benjamin Lenzen, Thilo Rühle, Marie-Kristin Lehniger, Ayako Okuzaki, Mathias Labs, Jose M. Muiño, Uwe Ohler, Dario Leister, Christian Schmitz‐Linneweber
Software Mentions: 2
Published: almost 6 years ago

10.3389/fgene.2020.552490

Plant miRNAs Reduce Cancer Cell Proliferation by Targeting MALAT1 and NEAT1: A Beneficial Cross-Kingdom Interaction
Cited by: 11
Author(s): Flaviana Marzano, Mariano Francesco Caratozzolo, Arianna Consiglio, Flavio Licciulli, Sabino Liuni, Elisabetta Sbisà, Domenica D’Elia, Apollonia Tullo, Domenico Catalano
Software Mentions: 2
Published: almost 6 years ago

10.3389/fgene.2020.535622

The FpPPR1 Gene Encodes a Pentatricopeptide Repeat Protein That Is Essential for Asexual Development, Sporulation, and Pathogenesis in Fusarium pseudograminearum
Cited by: 2
Author(s): Limin Wang, Shunpei Xie, Yinshan Zhang, Ruijiao Kang, Mengjuan Zhang, Min Wang, Haiyang Li, Linlin Chen, Hongxia Yuan, Shengli Ding, Liang Shen, Honglian Li
Software Mentions: 2
Published: over 5 years ago

10.3390/cancers12061603

A Novel JAK1 Mutant Breast Implant-Associated Anaplastic Large Cell Lymphoma Patient-Derived Xenograft Fostering Pre-Clinical Discoveries
Cited by: 11
Author(s): Danilo Fiore, Luca Vincenzo Cappelli, Paul Zumbo, Jude M. Phillip, Zhaoqi Liu, Shuhua Cheng, Liron Yoffe, Paola Ghione, Federica Maggio, Ahmet Doğan, Inna Khodos, Elisa de Stanchina, Joseph Casano, Clarisse Kayembe, Wayne Tam, Doron Betel, Robin Foà, Leandro Cerchietti, Raúl Rabadán, Steven M. Horwitz, David M. Weinstock, Giorgio Inghirami
Software Mentions: 2
Published: about 6 years ago

10.1097/HS9.0000000000000522

Performances of Targeted RNA Sequencing for the Analysis of Fusion Transcripts, Gene Mutation, and Expression in Hematological Malignancies
Cited by: 2
Author(s): Sandrine Hayette, Béatrice Grange, Maxime Vallée, Claire Bardel, Sarah Huet, Isabelle Mosnier, Kaddour Chabane, Thomas Simonet, Marie Balsat, Maël Heiblig, Isabelle Tigaud, Franck E. Nicolini, Sylvain Mareschal, Gilles Salles, Pierre Sujobert
Software Mentions: 2
Published: over 5 years ago

10.3389/fgene.2019.00643

Depletion of Hemoglobin Transcripts and Long-Read Sequencing Improves the Transcriptome Annotation of the Polar Bear (Ursus maritimus)
Cited by: 20
Author(s): Ashley Byrne, Megan A. Supple, Roger Volden, Kristin L. Laidre, Beth Shapiro, Christopher Vollmers
Software Mentions: 2
Published: about 7 years ago

10.1186/s12974-016-0644-1

Transcriptome sequencing reveals that LPS-triggered transcriptional responses in established microglia BV2 cell lines are poorly representative of primary microglia
Cited by: 91
Author(s): Amitabh Das, Sun Hwa Kim, Sarder Arifuzzaman, Tae-Ho Yoon, Jin Choul Chai, Young Seek Lee, Kyoung Sun Park, Kyoung Hwa Jung, Young Gyu Chai
Software Mentions: 2
Published: about 10 years ago

10.1534/g3.119.400083

A Reference Genome Sequence for the European Silver Fir (<i>Abies alba</i> Mill.): A Community-Generated Genomic Resource
Cited by: 48
Author(s): Elena Mosca, Fernando Cruz, Jèssica Gómez-Garrido, Luca Bianco, Christian Rellstab, Sabine Brodbeck, Katalin Csilléry, Bruno Fady, Matthias Fladung, Barbara Fussi, Dušan Gömöry, Santiago C. González‐Martínez, Delphine Grivet, Marta Gut, Jon Kehlet Hansen, Katrin Heer, Zeki Kaya, Konstantin V. Krutovsky, Birgit Kersten, Sascha Liepelt, Lars Opgenoorth, Christoph Sperisen, Kristian K. Ullrich, G. G. Vendramin, Marjana Westergren, Birgit Ziegenhagen, Tyler Alioto, Félix Gugerli, Berthold Heinze, Mária Höhn, Michela Troggio, David B. Neale
Software Mentions: 2
Published: about 7 years ago

10.1534/g3.119.400330

A Non-Dicer RNase III and Four Other Novel Factors Required for RNAi-Mediated Transposon Suppression in the Human Pathogenic Yeast <i>Cryptococcus neoformans</i>
Cited by: 15
Author(s): Jordan E. Burke, Adam D. Longhurst, Prashanthi Natarajan, Beiduo Rao, S. John Liu, Jade Sales-Lee, Yasaman Mortensen, James J. Moresco, Jolene K. Diedrich, John R. Yates, Hiten Madhani
Software Mentions: 2
Published: about 7 years ago

10.1534/g3.119.400201

Molecular Traits of Long Non-protein Coding RNAs from Diverse Plant Species Show Little Evidence of Phylogenetic Relationships
Cited by: 12
Author(s): Caitlin M. A. Simopoulos, Elizabeth A. Weretilnyk, G. Brian Golding
Software Mentions: 2
Published: almost 7 years ago

10.3390/ijms21165831

BrassicaEDB: A Gene Expression Database for Brassica Crops
Cited by: 37
Author(s): Haoyu Chao, Li Tian, Chaoyu Luo, Hualei Huang, Yingfei Ruan, Xiaodong Li, Yue Niu, Yonghai Fan, Wei Sun, Kai Zhang, Jiana Li, Cunmin Qu, Kun Lü
Software Mentions: 2
Published: almost 6 years ago

10.3390/ijms21176424

Antibiotic Treatment Prior to Injury Improves Post-Traumatic Osteoarthritis Outcomes in Mice
Cited by: 16
Author(s): Melanie E. Mendez, Deepa K. Murugesh, Aimy Sebastian, Nicholas R. Hum, Summer A. McCloy, Edward A. Kuhn, Blaine A. Christiansen, Gabriela G. Loots
Software Mentions: 2
Published: almost 6 years ago

10.1534/g3.119.400357

Utilization of Tissue Ploidy Level Variation in <i>de Novo</i> Transcriptome Assembly of <i>Pinus sylvestris</i>
Cited by: 13
Author(s): Darío I. Ojeda, Tiina M. Mattila, Tom Ruttink, Sonja Kujala, Katri Kärkkäinen, Jukka‐Pekka Verta, Tanja Pyhäjärvi
Software Mentions: 2
Published: almost 7 years ago

10.1038/s42003-020-01543-7

Systemic viral spreading and defective host responses are associated with fatal Lassa fever in macaques
Cited by: 17
Author(s): Nicolas Baillet, Stéphanie Reynard, Émeline Perthame, Jimmy Hortion, Alexandra Journeaux, Mathieu Mateo, Xavier Carnec, Justine Schaeffer, Caroline Picard, Laura Barrot, Stéphane Barron, Audrey Vallvé, Aurélie Duthey, Frédéric Jacquot, Cathy Boehringer, Grégory Jouvion, Natalia Pietrosemoli, Rachel Legendre, Marie‐Agnès Dillies, Richard Allan, Catherine Legras-Lachuer, Caroline Carbonnelle, Hervé Raoul, Sylvain Baize
Software Mentions: 2
Published: over 5 years ago

10.3390/cancers13051067

Dive into Single, Seek Out Multiple: Probing Cancer Metastases via Single-Cell Sequencing and Imaging Techniques
Cited by: 3
Author(s): Shang Su, Xiaohong Li
Software Mentions: 2
Published: over 5 years ago

10.3390/ijms22137164

Transcriptional Modulation of the Hippo Signaling Pathway by Drugs Used to Treat Bipolar Disorder and Schizophrenia
Cited by: 9
Author(s): Bruna Panizzutti, Chiara C. Bortolasci, Briana Spolding, Srisaiyini Kidnapillai, Timothy Connor, Mark F. Richardson, Trang T. T. Truong, Zoe Liu, Gerwyn Morris, Laura J. Gray, Jee Hyun Kim, Olivia Dean, Michael Berk, Ken Walder
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pgen.1008676

Germ cell-intrinsic effects of sex chromosomes on early oocyte differentiation in mice
Cited by: 17
Author(s): Norio Hamada, Nobuhiko Hamazaki, So Shimamoto, Orie Hikabe, Go Nagamatsu, Yuki Takada, Kiyoko Kato, Kozaburo Hayashi
Software Mentions: 2
Published: over 6 years ago

10.3389/fgene.2020.00474

Bulked Segregant RNA-Seq Reveals Distinct Expression Profiling in Chinese Wheat Cultivar Jimai 23 Responding to Powdery Mildew
Cited by: 10
Author(s): Tong Zhu, Liru Wu, Huagang He, Jiancheng Song, Mengshu Jia, Liancheng Liu, Xiaolu Wang, Ran Han, Liping Niu, Wei Du, Xu Zhang, Wenrui Wang, Liang Xiao, Haosheng Li, Jing Liu, Hongxing Xu, Cheng Liu, Pengtao Ma
Software Mentions: 2
Published: about 6 years ago

10.1371/journal.pgen.1006552

SBDS-Deficient Cells Have an Altered Homeostatic Equilibrium due to Translational Inefficiency Which Explains their Reduced Fitness and Provides a Logical Framework for Intervention
Cited by: 31
Author(s): Piera Calamita, Annarita Miluzio, Andrew F. Russo, Elisa Pesce, Sara Ricciardi, Farhat L. Khanim, Cristina Cheroni, Roberta Alfieri, Marilena Mancino, Chiara Gorrini, Grazisa Rossetti, Ilaria Peluso, Massimiliano Pagani, Diego L. Medina, Johanna M. Rommens, Stefano Biffo
Software Mentions: 2
Published: over 9 years ago

10.3389/fgene.2020.562855

Whole Transcriptome Analysis Identifies the Taxonomic Status of a New Chinese Native Cattle Breed and Reveals Genes Related to Body Size
Cited by: 2
Author(s): Xiaodong Zheng, Jin Cheng, Wenjuan Qin, Nyamsuren Balsai, Xuan-Jian Shang, Mengting Zhang, Hongquan Chen
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pgen.1008581

Makorin 1 controls embryonic patterning by alleviating Bruno1-mediated repression of oskar translation
Cited by: 11
Author(s): Annabelle Dold, Hong Han, Niankun Liu, Andrea Hildebrandt, Mirko Brüggemann, Cornelia Rücklé, Heike Hänel, Anke Busch, Petra Beli, Kathi Zarnack, Julian König, Jean‐Yves Roignant, Paul Lasko
Software Mentions: 2
Published: over 6 years ago

10.1534/g3.119.400923

Sex Chromosome Evolution in Muscid Flies
Cited by: 12
Author(s): Richard P. Meisel, Pia U. Olafson, Kiran Adhikari, Felix D. Guerrero, Kranti Konganti, Joshua B. Benoit
Software Mentions: 2
Published: over 6 years ago

10.1534/g3.119.401025

Reduced Function of the Glutathione S-Transferase S1 Suppresses Behavioral Hyperexcitability in<i>Drosophila</i>Expressing Mutant Voltage-Gated Sodium Channels
Cited by: 1
Author(s): Hung-Lin Chen, Junko Kasuya, Patrick Lansdon, Garrett A. Kaas, Hanxi Tang, Maggie Sodders, Toshihiro Kitamoto
Software Mentions: 2
Published: over 6 years ago

10.3389/fgene.2019.00150

Assessment of a Highly Multiplexed RNA Sequencing Platform and Comparison to Existing High-Throughput Gene Expression Profiling Techniques
Cited by: 4
Author(s): Eric Reed, Elizabeth Moses, Xiaohui Xiao, Gang Liu, Joshua D. Campbell, Catalina Perdomo, Stefano Monti
Software Mentions: 2
Published: over 7 years ago

10.1093/gigascience/giaa037

The gene-rich genome of the scallop Pecten maximus
Cited by: 46
Author(s): Nathan J. Kenny, Shane McCarthy, Olga Dudchenko, Katherine James, Emma Betteridge, Craig Corton, Jale Dolucan, Daniel Mead, Karen Oliver, Arina D. Omer, Sarah Pelan, Yan Ryan, Ying Sims, Jason Skelton, Michelle Smith, James Torrance, David Weisz, Anil Wipat, E Aiden, Kerstin Howe, Suzanne T. Williams
Software Mentions: 2
Published: about 6 years ago

10.1038/s41598-019-50298-7

CD138 plasma cells may predict brain metastasis recurrence following resection and stereotactic radiosurgery
Cited by: 3
Author(s): M. Soike, Jennifer Logue, Shadi Qasem, Ryan T. Hughes, E. McTyre, Jing Su, Pierre L. Triozzi, Maurizio Bendandi, Hui-Wen Lo, Tamjeed Ahmed, Stacey S. O’Neill, Waldemar Debinski, Boris Pasche, Kounosuke Watabe, Lance D. Miller, Michael D. Chan, Jimmy Ruiz
Software Mentions: 2
Published: almost 7 years ago

10.26508/lsa.201900533

Distinct signals and immune cells drive liver pathology and glomerulonephritis in ABIN1[D485N] mice
Cited by: 14
Author(s): Sambit K. Nanda, Tsvetana Petrova, Francesco Marchesi, Marek Gierliński, M Razsolkov, Katherine L. Lee, Stephen W. Wright, Vikram Rao, Philip Cohen, J. Simon C. Arthur
Software Mentions: 2
Published: over 6 years ago

10.3389/fgene.2021.676935

Genome and Transcriptome Sequencing of Populus × sibirica Identified Sex-Associated Allele-Specific Expression of the CLC Gene
Cited by: 1
Author(s): Elena N. Pushkova, George S. Krasnov, Valentina A. Lakunina, Roman O. Novakovskiy, Liubov V. Povkhova, Ekaterina M. Dvorianinova, А. Д. Бениаминов, Maria S. Fedorova, Anastasiya V. Snezhkina, Anna V. Kudryavtseva, Alexey A. Dmitriev, Nataliya V. Melnikova
Software Mentions: 2
Published: almost 5 years ago

10.1172/jci.insight.149381

GADD45A is a protective modifier of neurogenic skeletal muscle atrophy
Cited by: 11
Author(s): Jeffrey T. Ehmsen, Riki Kawaguchi, Damlanur Kaval, Anna E. Johnson, Daniel Nachun, Giovanni Coppola, Ahmet Höke
Software Mentions: 2
Published: about 5 years ago

10.1371/journal.pgen.1007842

RNA-on-X 1 and 2 in Drosophila melanogaster fulfill separate functions in dosage compensation
Cited by: 20
Author(s): Maria Kim, Marie-Line Faucillion, Jonas Larsson
Software Mentions: 2
Published: over 7 years ago

10.3389/fgene.2021.651298

Draft Genome Assembly and Transcriptome Dataset for European Turnip (Brassica rapa L. ssp. rapifera), ECD4 Carrying Clubroot Resistance
Cited by: 4
Author(s): Sin Gi Park, Eonji Noh, Su Ryun Choi, Boram Choi, In Gang Shin, Seung il Yoo, Dong Jin Lee, Shuaifei Ji, Hae Suk Kim, Yoon Jung Hwang, Jung Sun Kim, Jacqueline Batley, Yong Pyo Lim, David Edwards, Chang Pyo Hong
Software Mentions: 2
Published: about 5 years ago

10.1155/2019/9526725

Characterization and Validation of an “Acute Aerobic Exercise Load” as a Tool to Assess Antioxidative and Anti-inflammatory Nutrition in Healthy Subjects Using a Statistically Integrated Approach in a Comprehensive Clinical Trial
Cited by: 1
Author(s): Youjin Kim, Sungkyoung Choi, Sung Young Lee, Saejong Park, Ji Yeon Kim, Taesung Park, Oran Kwon
Software Mentions: 2
Published: almost 7 years ago

10.1371/journal.pgen.1008091

Expression estimation and eQTL mapping for HLA genes with a personalized pipeline
Cited by: 57
Author(s): Vitor R. C. Aguiar, Jônatas César, Olivier Delaneau, Emmanouil T. Dermitzakis, Diogo Meyer
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-019-51470-9

Transcriptome profiling of mouse samples using nanopore sequencing of cDNA and RNA molecules
Cited by: 77
Author(s): Camille Sessegolo, Corinne Cruaud, Corinne Da Silva, Audric Cologne, Marion Dubarry, Thomas Derrien, Vincent Lacroix, Jean‐Marc Aury
Software Mentions: 2
Published: almost 7 years ago

10.1093/g3journal/jkaa021

Transcriptome analysis implicates secondary metabolite production, redox reactions, and programmed cell death during allorecognition inCryphonectria parasitica
Cited by: 2
Author(s): Anatoly Belov, Thomas E. Witte, David P. Overy, Myron L. Smith
Software Mentions: 2
Published: over 5 years ago

10.1093/g3journal/jkaa046

Roles for RNA export factor, <i>Nxt1</i>, in ensuring muscle integrity and normal RNA expression in <i>Drosophila</i>
Cited by: 3
Author(s): Kevin van der Graaf, Katia Jindrich, Robert Mitchell, Helen White-Cooper
Software Mentions: 2
Published: over 5 years ago

10.3390/ijms21186584

Transcriptome of the Aedes aegypti Mosquito in Response to Human Complement Proteins
Cited by: 4
Author(s): Gloria I. Giraldo-Calderón, Arley Calle-Tobón, Paula Rozo-López, Tonya M. Colpitts, Yoonseong Park, Guillermo Rúa‐Uribe, Berlin Londoño-Rentería
Software Mentions: 2
Published: almost 6 years ago

10.1093/gigascience/giy131

Efficient and accurate detection of splice junctions from RNA-seq with Portcullis
Cited by: 87
Author(s): Daniel Mapleson, Luca Venturini, Gemy Kaithakottil, David Swarbreck
Software Mentions: 2
Published: over 7 years ago

10.1093/g3journal/jkab218

The amino acid substitution affects cellular response to mistranslation
Cited by: 8
Author(s): Matthew D. Berg, Yi Zhu, Bianca Y. Ruiz, Raphaël Loll-Krippleber, Joshua Isaacson, Bryan-Joseph San Luis, Julie Genereaux, Charles Boone, Judit Villén, Grant W. Brown, Christopher J. Brandl
Software Mentions: 2
Published: about 5 years ago

10.3389/fgene.2021.714152

Pri smORF Peptides Are Wide Mediators of Ecdysone Signaling, Contributing to Shape Spatiotemporal Responses
Cited by: 2
Author(s): Azza Dib, Jennifer Zanet, Alexandra Mancheno-Ferris, Mélanie Gallois, Damien Markus, Philippe Valenti, Simon Marques-Prieto, Serge Plaza, Yuji Kageyama, Yuji Kageyama, Hélène Chanut-Delalande, François Payre
Software Mentions: 2
Published: almost 5 years ago

10.1172/jci.insight.151005

NR4A family members regulate T cell tolerance to preserve immune homeostasis and suppress autoimmunity
Cited by: 13
Author(s): Ryosuke Hiwa, Hailyn V. Nielsen, James L. Mueller, Ravi Mandla, Julie Zikherman
Software Mentions: 2
Published: almost 5 years ago

10.3390/ijms21197386

Genome-Wide Development and Validation of Cost-Effective KASP Marker Assays for Genetic Dissection of Heat Stress Tolerance in Maize
Cited by: 16
Author(s): A. B. Jagtap, Yogesh Vikal, Gurmukh S. Johal
Software Mentions: 2
Published: almost 6 years ago

10.1038/s41598-019-51838-x

Transcriptome analysis reveals microvascular endothelial cell-dependent pericyte differentiation
Cited by: 18
Author(s): Maarten M. Brandt, Christian G.M. van Dijk, Ranganath Maringanti, Ihsan Chrifi, Rafael Kramann, Marianne C. Verhaar, Dirk J. Duncker, Michal Mokrý, Caroline Cheng
Software Mentions: 2
Published: over 6 years ago

10.1002/cam4.3122

Identification of the key genes associated with chemotherapy sensitivity in ovarian cancer patients
Cited by: 4
Author(s): Hui Zheng, Meiqin Zhang, Shuang Ma, Wenting Yang, Shuanshuan Xie, Yanchun Wang, Yixuan Liu, Jinyan Kai, Qian Ma, Renquan Lu, Lin Guo
Software Mentions: 2
Published: about 6 years ago

10.3390/genes8080206

Viral Infection Identifies Micropeptides Differentially Regulated in smORF-Containing lncRNAs
Cited by: 40
Author(s): Brandon S. Razooky, Benedikt Obermayer, Joshua Biggs O'May, Alexander Tarakhovsky
Software Mentions: 2
Published: almost 9 years ago

10.1038/s41598-019-51911-5

Differentiation of Induced Pluripotent Stem Cells towards Mesenchymal Stromal Cells is Hampered by Culture in 3D Hydrogels
Cited by: 20
Author(s): Roman Goetzke, Hans Keijdener, Julia Franzen, Alina Ostrowska, Selina Nüchtern, Petra Mela, Wolfgang Wagner
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-019-52374-4

Gene expression profile analysis of ileum transcriptomes in pigs fed Gelsemium elegans plants
Cited by: 1
Author(s): Chong-Yin Huang, Kun Yang, Junsheng Cao, Yujuan Li, Ziyuan Wang, Hui Yu, Zhi-Liang Sun, Xiaofeng Zheng, Zhao‐Ying Liu
Software Mentions: 2
Published: over 6 years ago

10.3390/ijms22136663

Expression Profile of New Marker Genes Involved in Differentiation of Canine Adipose-Derived Stem Cells into Osteoblasts
Cited by: 2
Author(s): Maurycy Jankowski, Mariusz Kaczmarek, Grzegorz Wąsiatycz, Claudia Dompe, Paul Mozdziak, J. M. Jaśkowski, Hanna Piotrowska‐Kempisty, Bartosz Kempisty
Software Mentions: 2
Published: about 5 years ago

10.3390/genes9030123

Delimiting Coalescence Genes (C-Genes) in Phylogenomic Data Sets
Cited by: 29
Author(s): Mark S. Springer, John Gatesy
Software Mentions: 2
Published: over 8 years ago

10.3390/genes9030142

Integration of lncRNA and mRNA Transcriptome Analyses Reveals Genes and Pathways Potentially Involved in Calf Intestinal Growth and Development during the Early Weeks of Life
Cited by: 22
Author(s): Eveline M. Ibeagha‐Awemu, Duy Ngoc, Pier-Luc Dudemaine, Bridget E. Fomenky, Nathalie Bissonnette
Software Mentions: 2
Published: over 8 years ago

10.3389/fgene.2019.00230

Systems Biology Reveals NR2F6 and TGFB1 as Key Regulators of Feed Efficiency in Beef Cattle
Cited by: 22
Author(s): Pâmela Almeida Alexandre, Marina Naval-Sánchez, Laércio R. Porto-Neto, José Bento Sterman Ferraz, Antônio Reverter, Heidge Fukumasu
Software Mentions: 2
Published: over 7 years ago

10.3389/fgene.2019.00889

Best Foot Forward: Nanopore Long Reads, Hybrid Meta-Assembly, and Haplotig Purging Optimizes the First Genome Assembly for the Southern Hemisphere Blacklip Abalone (Haliotis rubra)
Cited by: 17
Author(s): Han Ming Gan, Mun Hua Tan, Christopher M. Austin, Craig D. H. Sherman, Yen Ting Wong, Jan M. Strugnell, Mark Gervis, Luke McPherson, Adam D. Miller
Software Mentions: 2
Published: almost 7 years ago

10.1172/jci.insight.149149

Endothelium-protective, histone-neutralizing properties of the polyanionic agent defibrotide
Cited by: 20
Author(s): Hui Shi, Alex A. Gandhi, Stephanie A. Smith, Qiuyu Wang, Diane Chiang, Srilakshmi Yalavarthi, Ramadan A. Ali, Chao Liu, Gautam Sule, Pei‐Suen Tsou, Yu Zuo, Yogendra Kanthi, Evan A. Farkash, Jiandie D. Lin, James H. Morrissey, Jason S. Knight
Software Mentions: 2
Published: almost 5 years ago

10.3390/genes10010054

Genomes of Three Closely Related Caribbean Amazons Provide Insight for Species History and Conservation
Cited by: 8
Author(s): Sofia M. Kolchanova, Sergei Kliver, Aleksei S. Komissarov, Pavel Dobrinin, Gaik Tamazian, Kirill Grigorev, Walter Wolfsberger, Audrey J. Majeske, Jafet Vélez-Valentín, Ricardo Valentín de la Rosa, Joanne R Paul-Murphy, David Sánchez-Migallón Guzmán, Michael H. Court, Juan L. Rodríguez-Flores, Juan Carlos Martínez‐Cruzado, Tarás K. Oleksyk
Software Mentions: 2
Published: over 7 years ago

10.1038/s41598-019-52257-8

Global transcriptome analysis of rat hypothalamic arcuate nucleus demonstrates reversal of hypothalamic gliosis following surgically and diet induced weight loss
Cited by: 7
Author(s): Pernille Barkholt, Kristoffer Rigbolt, Mechthilde Falkenhahn, Thomas Hübschle, Uwe Schwahn, María L. Fernández-Cachón, Thorsten Schmidt, Stefan Theis, Henrik H. Hansen, Anders Hay‐Schmidt, Philip J. Pedersen, Niels Vrang, Jacob Jelsing
Software Mentions: 2
Published: over 6 years ago

10.1186/s13148-020-00892-8

Ten-eleven translocation methyl-cytosine dioxygenase 2 deficiency exacerbates renal ischemia-reperfusion injury
Cited by: 5
Author(s): Yan Huang, Li Tan, Yuqi Liu, Ning Huang, Jing Cang, Hao Wang
Software Mentions: 2
Published: about 6 years ago

10.3390/genes10030196

Cohesin-Mediated Genome Architecture Does Not Define DNA Replication Timing Domains
Cited by: 17
Author(s): Phoebe Oldach, Conrad A. Nieduszynski
Software Mentions: 2
Published: over 7 years ago

10.3390/genes10060406

Transcriptome Changes of Skeletal Muscle RNA-Seq Speculates the Mechanism of Postprandial Hyperglycemia in Diabetic Goto-Kakizaki Rats During the Early Stage of T2D
Cited by: 7
Author(s): Wenlu Zhang, Yuhuan Meng, Shuang Fu, Xingsong Li, Zixi Chen, Lizhen Huang, Hongli Du
Software Mentions: 2
Published: about 7 years ago

10.1038/s41598-019-52577-9

Developmental transcriptomes of the sea star, Patiria miniata, illuminate how gene expression changes with evolutionary distance
Cited by: 12
Author(s): Tsvia Gildor, Gregory A. Cary, Maya Lalzar, Veronica F. Hinman, Smadar Ben-Tabou de-Leon
Software Mentions: 2
Published: over 6 years ago

10.1371/journal.pgen.1008272

Effector gene reshuffling involves dispensable mini-chromosomes in the wheat blast fungus
Cited by: 91
Author(s): Zhao Peng, Ely Oliveira-Garcia, Guifang Lin, Ying Hu, Matthew J. Dalby, Pierre Migeon, Haibao Tang, Mark L. Farman, David E. Cook, Frank F. White, Barbara Valent, Sanzhen Liu
Software Mentions: 2
Published: almost 7 years ago

10.3390/ijms21217814

Investigation of the Impact from IL-2, IL-7, and IL-15 on the Growth and Signaling of Activated CD4+ T Cells
Cited by: 23
Author(s): Canaan Coppola, Brooks Hopkins, Steven Huhn, Zhimei Du, Zuyi Huang, William J. Kelly
Software Mentions: 2
Published: over 5 years ago

10.1038/s41598-019-53391-z

A human expression system based on HEK293 for the stable production of recombinant erythropoietin
Cited by: 32
Author(s): Christine Lin Chin, Justin B. Goh, Harini Srinivasan, Kaiwen Ivy Liu, Gowher Ali, Raghuvaran Shanmugam, Hsueh Lee Lim, Matthew S F Choo, Wen Qin Tang, Andy Hee-Meng Tan, Terry Nguyen-Khuong, Meng How Tan, Say Kong Ng
Software Mentions: 2
Published: over 6 years ago

10.1038/s41598-019-53268-1

Elemental Zn and its Binding Protein Zinc-α2-Glycoprotein are Elevated in HPV-Positive Oropharyngeal Squamous Cell Carcinoma
Cited by: 8
Author(s): Kate Poropatich, Tatjana Paunesku, Alia Zander, Brian Wray, Matthew J. Schipma, Prarthana Dalal, Mark Agulnik, Si Chen, Barry Lai, Olga Antipova, Evan Maxey, Koshonna Brown, Michael Beau Wanzer, Demirkan Gursel, Hanli Fan, Alfred Rademaker, Gayle E. Woloschak, Bharat B. Mittal
Software Mentions: 2
Published: over 6 years ago

10.1038/s41438-020-0314-4

Genome-wide analysis of expression quantitative trait loci (eQTLs) reveals the regulatory architecture of gene expression variation in the storage roots of sweet potato
Cited by: 34
Author(s): Lei Zhang, Yan Yu, Tianye Shi, Meng Kou, Jian Sun, Tao Xu, Qiang Li, Shaoyuan Wu, Qinghe Cao, Wenqian Hou, Zongyun Li
Software Mentions: 2
Published: about 6 years ago

10.1038/s41438-021-00619-7

DNA methylation affects photoperiodic tuberization in potato (Solanum tuberosum L.) by mediating the expression of genes related to the photoperiod and GA pathways
Cited by: 13
Author(s): Yanjun Ai, Shenglin Jing, Zhengnan Cheng, Botao Song, Conghua Xie, Jun Liu, Jun Zhou
Software Mentions: 2
Published: almost 5 years ago

10.3390/genes11010103

The velvet Regulator VosA Governs Survival and Secondary Metabolism of Sexual Spores in Aspergillus nidulans
Cited by: 13
Author(s): Min-Ju Kim, Mi-Kyung Lee, Huy Quang Pham, Myeong Ju Gu, Bohan Zhu, Sung-Hun Son, Dongyup Hahn, Jae‐Ho Shin, Jae‐Hyuk Yu, Hee-Soo Park, Kap-Hoon Han
Software Mentions: 2
Published: over 6 years ago

10.3390/ijms21217966

Differential Defense Responses of Upland and Lowland Switchgrass Cultivars to a Cereal Aphid Pest
Cited by: 5
Author(s): Lise Pingault, Nathan A. Palmer, Kyle G. Koch, Tiffany Heng-Moss, Jeffrey D. Bradshaw, Javier Seravalli, Paul Twigg, Joe Louis, Gautam Sarath
Software Mentions: 2
Published: over 5 years ago