10.7554/eLife.59303

One-shot analysis of translated mammalian lncRNAs with AHARIBO
Cited by: 13
Author(s): L. Minati, Claudia Firrito, Alessia Del Piano, Alberto Peretti, Simone Sidoli, Daniele Peroni, Romina Belli, Francesco Gandolfi, Alessandro Romanel, Paola Bernabò, Jacopo Zasso, Alessandro Quattrone, Graziano Guella, Fabio Lauria, Gabriella Viero, Massimiliano Clamer
Software Mentions: 1
Published: over 5 years ago

10.7554/eLife.13374

Metabolic reprogramming during neuronal differentiation from aerobic glycolysis to neuronal oxidative phosphorylation
Cited by: 404
Author(s): Xinde Zheng, Leah Boyer, Mingji Jin, Jérôme Mertens, Yongsung Kim, Li Ma, Michael W. Hamm, Fred H. Gage, Tony Hunter
Software Mentions: 1
Published: over 10 years ago

10.7554/eLife.65482

Scaled, high fidelity electrophysiological, morphological, and transcriptomic cell characterization
Cited by: 27
Author(s): Brian R. Lee, Agata Budzillo, Kristen Hadley, Jeremy A. Miller, Tim Jarsky, Katherine Baker, DiJon Hill, Lisa Kim, Rusty Mann, Lindsay Ng, Aaron Oldre, Ram Rajanbabu, Jessica Trinh, Sara Vargas, Thomas Braun, Rachel Dalley, Nathan W. Gouwens, Brian Kalmbach, Tae Kyung Kim, Kimberly A. Smith, Gilberto Soler-Llavina, Staci A. Sorensen, Bosiljka Tasic, Jonathan T. Ting, Ed Lein, Hongkui Zeng, Gabe J. Murphy, Jim Berg
Software Mentions: 1
Published: about 5 years ago

10.1093/bioinformatics/btaa779

Shark: fishing relevant reads in an RNA-Seq sample
Cited by: 7
Author(s): Luca Denti, Yuri Pirola, Marco Previtali, Tamara Ceccato, Gianluca Della Vedova, Raffaella Rizzi, Paola Bonizzoni
Software Mentions: 1
Published: about 6 years ago

10.7554/eLife.47702

The alternative regenerative strategy of bearded dragon unveils the key processes underlying vertebrate tooth renewal
Cited by: 22
Author(s): Lotta Salomies, Julia Eymann, Imran Khan, Nicolas Di-Poı̈
Software Mentions: 1
Published: about 7 years ago

10.7554/eLife.47098

Evidence for DNA-mediated nuclear compartmentalization distinct from phase separation
Cited by: 204
Author(s): David McSwiggen, Anders S. Hansen, Sheila S Teves, Hervé Marie-Nelly, Yvonne Hao, Alec Heckert, Dinesh Vyas, Claire Dugast-Darzacq, Robert Tjian, Xavier Darzacq
Software Mentions: 1
Published: over 7 years ago

10.7554/eLife.59166

Metabolic but not transcriptional regulation by PKM2 is important for natural killer cell responses
Cited by: 17
Author(s): Jessica Walls, Jeffrey Subleski, Erika M. Palmieri, Marieli Gonzalez-Cotto, Clair M. Gardiner, Daniel W. McVicar, David K. Finlay
Software Mentions: 1
Published: about 6 years ago

10.7554/eLife.49117

The endonuclease Cue2 cleaves mRNAs at stalled ribosomes during No Go Decay
Cited by: 132
Author(s): Karole N. D’Orazio, Colin Chih-Chien Wu, Niladri K. Sinha, Raphaël Loll-Krippleber, Grant W. Brown, Rachel Green
Software Mentions: 1
Published: over 7 years ago

10.7554/eLife.53404

YAP regulates cell size and growth dynamics via non-cell autonomous mediators
Cited by: 28
Author(s): Douaa Mugahid, Marian Kalocsay, Xili Liu, Jonathan Scott Gruver, Leonid Peshkin, Marc W. Kirschner
Software Mentions: 1
Published: over 6 years ago

10.7554/eLife.45418

Neural crest-specific deletion of Rbfox2 in mice leads to craniofacial abnormalities including cleft palate
Cited by: 20
Author(s): Dasan Mary Cibi, Masum M. Mia, Shamini Guna Shekeran, Lim Sze Yun, Reddemma Sandireddy, Priyanka Gupta, Monalisa Hota, Li Sun, Sujoy Ghosh, Manvendra K. Singh
Software Mentions: 1
Published: about 7 years ago

10.7554/eLife.22906

Position- and Hippo signaling-dependent plasticity during lineage segregation in the early mouse embryo
Cited by: 114
Author(s): Eszter Pósfai, Sophie Petropoulos, Flávia Regina Oliveira de Barros, John P. Schell, Igor Jurišica, Rickard Sandberg, Fredrik Lanner, Janet Rossant
Software Mentions: 1
Published: over 9 years ago

10.3390/ijms21144849

Dual Leucine Zipper Kinase Is Constitutively Active in the Adult Mouse Brain and Has Both Stress-Induced and Homeostatic Functions
Cited by: 7
Author(s): Sunil Goodwani, Celia G. Fernandez, Paul Acton, Virginie Buggia-Prévot, Morgan McReynolds, Jiacheng Ma, Cheng Hu, Mary E. Hamby, Yongying Jiang, Le Kang, Michael Soth, Philip Jones, William J. Ray
Software Mentions: 1
Published: about 6 years ago

10.3390/ijms21155420

DNA Methyltransferase 1 (DNMT1) Acts on Neurodegeneration by Modulating Proteostasis-Relevant Intracellular Processes
Cited by: 12
Author(s): Cathrin Bayer, Georg Pitschelatow, Nina Hannemann, Jenice Linde, Julia Reichard, Daniel Pensold, Geraldine Zimmer-Bensch
Software Mentions: 1
Published: about 6 years ago

10.3390/ijms21176096

DEAD-Box Helicase 4 (Ddx4)+ Stem Cells Sustain Tumor Progression in Non-Serous Ovarian Cancers
Cited by: 2
Author(s): Stella D’Oronzo, Erica Silvestris, Domenica Lovero, Paola Cafforio, Loren Duda, Gennaro Cormio, Angelo Paradiso, Raffaele Palmirotta, Franco Silvestris
Software Mentions: 1
Published: about 6 years ago

10.3390/ijms21176314

Targeting Adaptive IRE1α Signaling and PLK2 in Multiple Myeloma: Possible Anti-Tumor Mechanisms of KIRA8 and Nilotinib
Cited by: 7
Author(s): Yusuke Yamashita, Shuhei Morita, Hiroki Hosoi, Hirotsugu Kobata, Shohei Kishimoto, Tatsuya Ishibashi, Hiroyuki Mishima, Akira Kinoshita, Bradley J. Backes, Koh-ichiro Yoshiura, Feroz R. Papa, Takashi Sawada, Shinobu Tamura
Software Mentions: 1
Published: about 6 years ago

10.3390/ijms21197079

Alternative Splicing Regulation of an Alzheimer’s Risk Variant in CLU
Cited by: 10
Author(s): Seonggyun Han, Kwangsik Nho, Younghee Lee
Software Mentions: 1
Published: almost 6 years ago

10.3390/ijms21207466

The BDNF rs6265 Polymorphism is a Modifier of Cardiomyocyte Contractility and Dilated Cardiomyopathy
Cited by: 5
Author(s): F Raucci, Anand Prakash Singh, Jonathan H. Soslow, Larry W. Markham, Lin Zhong, Wejdan Aljafar, Natasja Lessiohadi, Cassandra P. Awgulewitsch, Prachi Umbarkar, Qinkun Zhang, Presley L. Cannon, Maciej S. Buchowski, Joseph T. Roland, Erica J. Carrier, W. Bryan Burnette, Antonis K. Hatzopoulos, Hind Lal, Cristi L. Galindo
Software Mentions: 1
Published: almost 6 years ago

10.3390/ijms21218322

LINC00973 Induces Proliferation Arrest of Drug-Treated Cancer Cells by Preventing p21 Degradation
Cited by: 4
Author(s): Dmitry S. Karpov, Pavel Spirin, Andrei O. Zheltukhin, Vera V. Tutyaeva, Olga L. Zinovieva, E. N. Grineva, Vera A. Matrosova, George S. Krasnov, Anastasiya V. Snezhkina, Anna V. Kudryavtseva, Vladimir Prassolov, T. D. Mashkova, Н. А. Лисицын
Software Mentions: 1
Published: almost 6 years ago

10.3390/ijms21228785

Human Thymic CD10+ PD-1+ Intraepithelial Lymphocyte Precursors Acquire Interleukin-15 Responsiveness at the CD1a– CD95+ CD28– CCR7– Developmental Stage
Cited by: 7
Author(s): Lore Billiet, Glenn Goetgeluk, Sarah Bonte, Stijn De Munter, Laurenz De Cock, Melissa Pille, Joline Ingels, Hanne Jansen, Karin Weening, Filip Van Nieuwerburgh, Tessa Kerre, Tom Taghon, Georges Leclercq, Bart Vandekerckhove
Software Mentions: 1
Published: almost 6 years ago

10.3390/ijms22094504

HERV-Derived Ervpb1 Is Conserved in Simiiformes, Exhibiting Expression in Hematopoietic Cell Lineages Including Macrophages
Cited by: 1
Author(s): Ayumi Matsuzawa, Jiyoung Lee, So Nakagawa, Johbu Itoh, Mahoko Takahashi Ueda, Satomi Mitsuhashi, Yuta Kochi, Tomoko Kaneko-Ishino, Fumitoshi Ishino
Software Mentions: 1
Published: over 5 years ago

10.3390/ijms22094750

Targeting Mitochondrial Metabolism in Clear Cell Carcinoma of the Ovaries
Cited by: 7
Author(s): Xiaonan Zhang, Mihir Shetty, Valentino Clemente, Stig Linder, Martina Bazzaro
Software Mentions: 1
Published: over 5 years ago

10.3390/ijms22094791

Identification of Novel Fusion Transcripts in High Grade Serous Ovarian Cancer
Cited by: 3
Author(s): A.M. Newtson, Henry Reyes Pineda, Eric J. Devor, Michael J. Goodheart, Jesús González Bosquet
Software Mentions: 1
Published: over 5 years ago

10.3390/ijms22105290

Calvaria Bone Transcriptome in Mouse Models of Osteogenesis Imperfecta
Cited by: 6
Author(s): Pierre Moffatt, Iris Boraschi-Diaz, Juliana Marulanda, Ghalib Bardai, Frank Rauch
Software Mentions: 1
Published: over 5 years ago

10.3390/ijms22115741

Molecular Insights into the Role of Cysteine-Rich Peptides in Induced Resistance to Fusarium oxysporum Infection in Tomato Based on Transcriptome Profiling
Cited by: 7
Author(s): Marina P. Slezina, Е. А. Истомина, Tatyana V. Korostyleva, Alexey S. Kovtun, Artem S. Kasianov, Alexey A. Konopkin, Л. А. Щербакова
Software Mentions: 1
Published: over 5 years ago

10.3390/ijms22126478

Differential Regulation of Gonadotropins as Revealed by Transcriptomes of Distinct LH and FSH Cells of Fish Pituitary
Cited by: 15
Author(s): Lian Hollander-Cohen, Matan Golan, Berta Levavi‐Sivan
Software Mentions: 1
Published: over 5 years ago

10.3390/ijms22136872

Sympathetic Denervation Alters the Inflammatory Response of Resident Muscularis Macrophages upon Surgical Trauma and Ameliorates Postoperative Ileus in Mice
Cited by: 9
Author(s): Shilpashree Mallesh, Reiner Schneider, Bianca Schneiker, Mariola Lysson, Patrik Efferz, Eaton Lin, Wouter J. de Jonge, Sven Wehner
Software Mentions: 1
Published: about 5 years ago

10.3390/ijms22137002

Sex-Based Differences in Cardiac Gene Expression and Function in BDNF Val66Met Mice
Cited by: 1
Author(s): Marcus Negron, Jeffrey Kristensen, Van Thuan Nguyen, Lauren E Gansereit, F Raucci, Julia L Chariker, Aaron Heck, Imamulhaq Brula, Gabrielle Kitchen, Cassandra P. Awgulewitsch, Lin Zhong, Eric C. Rouchka, Simran Banga, Cristi L. Galindo
Software Mentions: 1
Published: about 5 years ago

10.3390/ijms22158083

Effects of Dihydrotanshinone I on Proliferation and Invasiveness of Paclitaxel-Resistant Anaplastic Thyroid Cancer Cells
Cited by: 5
Author(s): Lorenzo Allegri, Francesca Capriglione, Valentina Maggisano, Giuseppe Damante, Federica Baldan
Software Mentions: 1
Published: about 5 years ago

10.3390/ijms22158322

Efficient Generation of Neural Stem Cells from Embryonic Stem Cells Using a Three-Dimensional Differentiation System
Cited by: 5
Author(s): Sang Hoon Yoon, Mi-Rae Bae, Hyeonwoo La, Hyuk Song, Kwonho Hong, Jeong Tae
Software Mentions: 1
Published: about 5 years ago

10.3390/ijms22168359

TRPM2 Oxidation Activates Two Distinct Potassium Channels in Melanoma Cells through Intracellular Calcium Increase
Cited by: 28
Author(s): Loretta Ferrera, Raffaella Barbieri, Cristiana Picco, Paolo Zuccolini, Alessia Remigante, Sara Bertelli, Maria Rita Fumagalli, Giovanni Zifarelli, Caterina A. M. La Porta, Paola Gavazzo, Michael Pusch
Software Mentions: 1
Published: about 5 years ago

10.3390/ijms22168385

LINC01133 Inhibits Invasion and Promotes Proliferation in an Endometriosis Epithelial Cell Line
Cited by: 2
Author(s): Iveta Yotova, Quanah J. Hudson, Florian M. Pauler, Katharina Proestling, Isabella Haslinger, Lorenz Kuessel, Alexandra Perricos, H Husslein, René Wenzl
Software Mentions: 1
Published: about 5 years ago

10.3390/ijms22179618

Pathogenic Effects of Mineralocorticoid Pathway Activation in Retinal Pigment Epithelium
Cited by: 9
Author(s): Jérémie Canonica, Min Zhao, Tatiana Favez, Emmanuelle Gélizé, Laurent Jonet, Laura Kowalczuk, Justine Guégan, Damien Le Menuet, Say Viengchareun, Marc Lombès, Eric Pussard, Yvan Arsenijévic, Francine Béhar-Cohen
Software Mentions: 1
Published: about 5 years ago

10.3390/ijms22189865

Alternative Splicing Regulation of Low-Frequency Genetic Variants in Exon 2 of TREM2 in Alzheimer’s Disease by Splicing-Based Aggregation
Cited by: 10
Author(s): Seonggyun Han, Yirang Na, Insong Koh, Kwangsik Nho, Younghee Lee
Software Mentions: 1
Published: about 5 years ago

10.2196/10875

Electronic Systems for Patients to Report and Manage Side Effects of Cancer Treatment: Systematic Review
Cited by: 110
Author(s): Lorraine Warrington, Kate Absolom, Mark Conner, Ian Kellar, Beverly Clayton, Michael Ayres, Galina Velikova
Software Mentions: 1
Published: over 7 years ago

10.2196/14953

The Potential for the Internet and Telehealth in Caregiver Support. Comment on “Using Technology to Facilitate Fidelity Assessments: The Tele-STAR Caregiver Intervention”
Cited by: 0
Author(s): Kohei Kajiwara, Jun Kako, Hiromitsu Noto, Yasufumi Oosono, Masamitsu Kobayashi
Software Mentions: 1
Published: over 5 years ago

10.2196/13415

Web-Based Interventions to Improve Mental Health in Home Caregivers of People With Dementia: Meta-Analysis
Cited by: 49
Author(s): Yinan Zhao, Hui Feng, Mingyue Hu, Hongxing Hu, Hui Li, Hongting Ning, Huijing Chen, Lulu Liao, Linlin Peng
Software Mentions: 1
Published: over 7 years ago

10.2196/13599

Using Technology to Facilitate Fidelity Assessments: The Tele-STAR Caregiver Intervention
Cited by: 9
Author(s): Allison Lindauer, Glenise McKenzie, David LaFazia, Loriann McNeill, Katherine Mincks, Natasha Spoden, Marcella Myers, Nora Mattek, Linda Teri
Software Mentions: 1
Published: over 7 years ago

10.2196/jmir.7564

Web-Based Interventions to Improve Mental Health, General Caregiving Outcomes, and General Health for Informal Caregivers of Adults With Chronic Conditions Living in the Community: Rapid Evidence Review
Cited by: 100
Author(s): Jenny Ploeg, Maureen Markle‐Reid, Ruta Valaitis, Carrie McAiney, Wendy Duggleby, Amy Bartholomew, Diana Sherifali
Software Mentions: 1
Published: about 9 years ago

10.2196/jmir.4025

Web-Based STAR E-Learning Course Increases Empathy and Understanding in Dementia Caregivers: Results from a Randomized Controlled Trial in the Netherlands and the United Kingdom
Cited by: 124
Author(s): Bart Hattink, Franka Meiland, Henriëtte van der Roest, Peter Kevern, Francesca Abiuso, Johan Bengtsson, Angele Giuliano, Annalise Duca, Jennifer Sanders, Fern Basnett, Chris Nugent, Paul Kingston, Rose-Marie Dröes
Software Mentions: 1
Published: almost 11 years ago

10.21307/jofnem-2019-052

Genome Announcement: The Draft Genomes of Two Radopholus similis populations from Costa Rica
Cited by: 5
Author(s): Catherine L. Wram, Cedar Hesse, Sulochana K. Wasala, Dana K. Howe, Amy B. Peetz, Dee R. Denver, Danny A. Humphreys-Pereira, Inga A. Zasada
Software Mentions: 1
Published: over 7 years ago

10.1186/s12984-020-00790-3

A comprehensive scheme for the objective upper body assessments of subjects with cerebellar ataxia
Cited by: 11
Author(s): Ha Manh Tran, Khoa D. Nguyen, Pubudu N. Pathirana, Malcolm Horne, Laura Power, David J. Szmulewicz
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12974-020-01842-0

Stress-induced NLRP3 inflammasome activation negatively regulates fear memory in mice
Cited by: 56
Author(s): Yuan Dong, Shuoshuo Li, Yiming Lu, Xiaoheng Li, Yuhe Liao, Zhixin Peng, Yunfeng Li, Lin Hou, Zengqiang Yuan, Jinbo Cheng
Software Mentions: 1
Published: about 6 years ago

10.1186/s13059-014-0451-x

Cfp1 is required for gene expression-dependent H3K4 trimethylation and H3K9 acetylation in embryonic stem cells
Cited by: 44
Author(s): Thomas Clouaire, Shaun Webb, Adrian Bird
Software Mentions: 1
Published: about 12 years ago

10.1186/s13024-019-0311-y

Human Interleukin-34 facilitates microglia-like cell differentiation and persistent HIV-1 infection in humanized mice
Cited by: 46
Author(s): Saumi Mathews, Amanda Branch Woods, Ikumi Katano, Edward Makarov, Midhun Ben Thomas, Howard E. Gendelman, Larisa Y. Poluektova, Mamoru Ito, Santhi Gorantla
Software Mentions: 1
Published: over 7 years ago

10.1186/s13059-015-0608-2

Transcript and protein expression decoupling reveals RNA binding proteins and miRNAs as potential modulators of human aging
Cited by: 66
Author(s): Yuning Wei, Hai Hu, Gangcai Xie, Ning Fu, Zhibin Ning, Rong Zeng, Philipp Khaitovich
Software Mentions: 1
Published: over 11 years ago

10.15252/emmm.202012063

Trans‐generational epigenetic regulation associated with the amelioration of Duchenne Muscular Dystrophy
Cited by: 8
Author(s): Julie Martone, Michela Lisi, Francesco Castagnetti, Alessandro Rosa, V. Di Carlo, Enrique Blanco, Adriano Setti, Davide Mariani, Alessio Colantoni, Tiziana Santini, Lucia Perone, Luciano Di Croce, Irene Bozzoni
Software Mentions: 1
Published: about 6 years ago

10.1186/1471-2164-7-286

Novel subtractive transcription-based amplification of mRNA (STAR) method and its application in search of rare and differentially expressed genes in AD brains
Cited by: 9
Author(s): Qing Yan Liu, Roy Sooknanan, Lawrence T. Malek, Maria Ribecco-Lutkiewicz, Joy X Lei, Hui Shen, Bolesław Lach, P. Roy Walker, Joel Martin, Marianna Sikorska
Software Mentions: 1
Published: almost 20 years ago

10.1093/molbev/msw139

Reverse Transcription Errors and RNA–DNA Differences at Short Tandem Repeats
Cited by: 13
Author(s): Arkarachai Fungtammasan, Marta Tomaszkiewicz, Rebeca Campos-Sánchez, Kristin A. Eckert, Michael DeGiorgio, Kateryna D. Makova
Software Mentions: 1
Published: about 10 years ago

10.1186/s13059-015-0692-3

Single-cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells
Cited by: 218
Author(s): Kyu‐Tae Kim, Hye Won Lee, Hae‐Ock Lee, Sang Cheol Kim, Yun Jee Seo, Wingyan Chung, Hye Hyeon Eum, Do‐Hyun Nam, Junhyong Kim, Kyeung Min Joo, Woong-Yang Park
Software Mentions: 1
Published: over 11 years ago

10.3389/fmicb.2019.03124

Genomics Evolutionary History and Diagnostics of the Alternaria alternata Species Group Including Apple and Asian Pear Pathotypes
Cited by: 32
Author(s): Andrew D. Armitage, Helen M. Cockerton, S. Sreenivasaprasad, J. W. Woodhall, Charles R. Lane, Richard J. Harrison, John P. Clarkson
Software Mentions: 1
Published: over 6 years ago

10.18632/oncotarget.26673

The X-linked tumor suppressor TSPX downregulates cancer-drivers/oncogenes in prostate cancer in a C-terminal acidic domain dependent manner
Cited by: 5
Author(s): Tatsuo Kido, Yunmin Li, Yuichiro Tanaka, Rajvir Dahiya, Yun‐Fai Chris Lau
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0122420

High Resolution Mapping of Enhancer-Promoter Interactions
Cited by: 3
Author(s): Christopher Reeder, Michael Closser, Huay Mei Poh, Kuljeet Singh Sandhu, Hynek Wichterle, David K. Gifford
Software Mentions: 1
Published: over 11 years ago

10.15252/embj.2020106449

Yeast translation elongation factor eEF3 promotes late stages of tRNA translocation
Cited by: 16
Author(s): Namit Ranjan, Agnieszka A. Pochopien, Colin Chih-Chien Wu, Bertrand Beckert, Sophie Blanchet, Rachel Green, Marina V. Rodnina, Daniel N. Wilson
Software Mentions: 1
Published: over 5 years ago

10.3389/fcimb.2019.00097

Macrophages Infected by a Pathogen and a Non-pathogen Spotted Fever Group Rickettsia Reveal Differential Reprogramming Signatures Early in Infection
Cited by: 22
Author(s): Pedro Curto, Sean P. Riley, Isaura Simões, Juan José Martínez
Software Mentions: 1
Published: over 7 years ago

10.1186/s13024-021-00468-x

SETD7-mediated monomethylation is enriched on soluble Tau in Alzheimer’s disease
Cited by: 3
Author(s): Maria Bichmann, Nuria Prat Oriol, Ebru Ercan-Herbst, David C. Schöndorf, Borja Gomez Ramos, Vera Schwärzler, Marie A. Neu, Annabelle Schlüter, Xue Wang, Lina Jin, Chenqi Hu, Yu Tian, Janina S. Ried, Per Haberkant, Laura Gasparini, Dagmar E. Ehrnhoefer
Software Mentions: 1
Published: about 5 years ago

10.3389/fonc.2020.611467

Identification of STRBP as a Novel JAK2 Fusion Partner Gene in a Young Adult With Philadelphia Chromosome-Like B-Lymphoblastic Leukemia
Cited by: 4
Author(s): Xinyue Zhang, Haiping Dai, Zheng Li, Jia Yin, Xingping Lang, Chen Yang, Sheng Xiao, Mingqing Zhu, Dandan Liu, Hong Liu, Hongjie Shen, Depei Wu, Xiaowen Tang
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0219267

Schlafen 3 knockout mice display gender-specific differences in weight gain, food efficiency, and expression of markers of intestinal epithelial differentiation, metabolism, and immune cell function
Cited by: 15
Author(s): Emilie E. Vomhof-DeKrey, Jun Lee, Jack Lansing, Calvin Brown, Diane C. Darland, Marc D. Basson
Software Mentions: 1
Published: about 7 years ago

10.1186/s13059-016-0873-8

Long non-coding RNAs display higher natural expression variation than protein-coding genes in healthy humans
Cited by: 120
Author(s): Aleksandra E. Kornienko, Christoph P. Dotter, Philipp M. Guenzl, Heinz Gisslinger, Bettina Gisslinger, Ciara Cleary, Róbert Královics, Florian M. Pauler, Denise P. Barlow
Software Mentions: 1
Published: over 10 years ago

10.1186/s12864-017-3992-z

Identification of SNPs associated with muscle yield and quality traits using allelic-imbalance analyses of pooled RNA-Seq samples in rainbow trout
Cited by: 28
Author(s): Rafet Al-Tobasei, Ali R. Ali, Timothy D. Leeds, Sixin Liu, Yniv Palti, Brett Kenney, Mohamed Salem
Software Mentions: 1
Published: about 9 years ago

10.1186/s13059-016-0917-0

The real cost of sequencing: scaling computation to keep pace with data generation
Cited by: 259
Author(s): Paul Muir, Shantao Li, Shaoke Lou, Daifeng Wang, Daniel Spakowicz, Jing Zhang, George M. Weinstock, Farren J. Isaacs, Joel Rozowsky, Mark Gerstein
Software Mentions: 1
Published: over 10 years ago

10.15252/embj.201798357

Cancer cells copy migratory behavior and exchange signaling networks via extracellular vesicles
Cited by: 56
Author(s): Sander Christiaan Steenbeek, Thang V. Pham, Joep de Ligt, Anoek Zomer, Jaco C. Knol, Sander R. Piersma, Tim Schelfhorst, Rick Huisjes, Raymond M. Schiffelers, Edwin Cuppen, Connie R. Jiménez, Jacco van Rheenen
Software Mentions: 1
Published: over 8 years ago

10.3389/fonc.2020.632187

A-to-I RNA Editing in Cancer: From Evaluating the Editing Level to Exploring the Editing Effects
Cited by: 14
Author(s): Heming Wang, Sinuo Chen, Jiayi Wei, Guangqi Song, Yicheng Zhao
Software Mentions: 1
Published: over 5 years ago

10.1186/s13059-016-0956-6

A transcriptome-based global map of signaling pathways in the ovarian cancer microenvironment associated with clinical outcome
Cited by: 81
Author(s): Silke Reinartz, Florian Finkernagel, Till Adhikary, Verena Rohnalter, Tim Schumann, Yvonne Schober, Wolfgang Andreas Nockher, Andrea Nist, Thorsten Stiewe, Julia M. Jansen, Uwe Wagner, Sabine Müller‐Brüsselbach, Rolf Müller
Software Mentions: 1
Published: over 10 years ago

10.1186/s13059-016-0984-2

Comprehensive analysis of promoter-proximal RNA polymerase II pausing across mammalian cell types
Cited by: 66
Author(s): Daniel S. Day, Bing Zhang, Sean Stevens, Francesco Ferrari, Erica Larschan, Peter J. Park, William T. Pu
Software Mentions: 1
Published: over 10 years ago

10.1038/s41598-020-67742-8

Network of clinically-relevant lncRNAs-mRNAs associated with prognosis of hepatocellular carcinoma patients
Cited by: 10
Author(s): Li Min Lim, Yu Jin, Henry Yang, Alexander Yaw Fui Chung, Brian K. P. Goh, Pierce Kah‐Hoe Chow, Chung Yip Chan, William K. Blanks, Peng Chung Cheow, Ser Yee Lee, Tony Kiat-Hon Lim, Samuel S. Chong, London Lucien Peng Jin Ooi, Caroline Lee
Software Mentions: 1
Published: about 6 years ago

10.7554/eLife.49158

Neuronal TORC1 modulates longevity via AMPK and cell nonautonomous regulation of mitochondrial dynamics in C. elegans
Cited by: 65
Author(s): Yue Zhang, Anne Lanjuin, Suvagata Roy Chowdhury, Meeta Mistry, Carlos Giovanni Silva-García, Heather J. Weir, Chia-Lin Lee, Caroline C. Escoubas, Emina Tabakovic, William Mair
Software Mentions: 1
Published: about 7 years ago

10.1038/s41598-020-68431-2

Alternative splicing of flowering time gene FT is associated with halving of time to flowering in coconut
Cited by: 10
Author(s): Wei Xia, Rui Liu, Jun Zhang, Annaliese S. Mason, Zhiying Li, Shufang Gong, Yazhu Zhong, Yajing Dou, Xuan Sun, Hang Fan, Yong Xiao
Software Mentions: 1
Published: about 6 years ago

10.1186/s13059-016-1079-9

Extensive RNA editing and splicing increase immune self-representation diversity in medullary thymic epithelial cells
Cited by: 52
Author(s): Miri Danan-Gotthold, C. Guyon, Matthieu Giraud, Erez Y. Levanon, Jakub Abramson
Software Mentions: 1
Published: almost 10 years ago

10.1186/s12967-018-1495-6

Limited utility of tissue micro-arrays in detecting intra-tumoral heterogeneity in stem cell characteristics and tumor progression markers in breast cancer
Cited by: 14
Author(s): Pascale Kündig, Charlotte Giesen, Hartland W. Jackson, Bernd Bodenmiller, Bärbel Papassotirolopus, Sandra N. Freiberger, Catharine Aquino, Lennart Opitz, Zsuzsanna Varga
Software Mentions: 1
Published: over 8 years ago

10.7554/eLife.60259

Caenorhabditis elegans methionine/S-adenosylmethionine cycle activity is sensed and adjusted by a nuclear hormone receptor
Cited by: 33
Author(s): Gabrielle E. Giese, Melissa Walker, Olga Ponomarova, Hefei Zhang, Xuhang Li, Gregory Minevich, Albertha J.M. Walhout
Software Mentions: 1
Published: almost 6 years ago

10.1186/s12864-020-6670-5

Hybrid transcriptome sequencing approach improved assembly and gene annotation in Cynara cardunculus (L.)
Cited by: 12
Author(s): G. Puglia, Andrey D. Prjibelski, Domenico Vitale, Elena Bushmanova, Karl Schmid, S.A. Raccuia
Software Mentions: 1
Published: about 6 years ago

10.1002/cjp2.158

<i>NTRK</i> fusions in osteosarcoma are rare and non‐functional events
Cited by: 15
Author(s): Baptiste Ameline, Karim H. Saba, Michal Kováč, Linda Magnusson, Olaf Witt, Stefan Bielack, Michaela Nathrath, Karolin Hansén Nord, Daniel Baumhoer
Software Mentions: 1
Published: over 6 years ago

10.1186/s12864-019-5533-4

A high-throughput SNP discovery strategy for RNA-seq data
Cited by: 40
Author(s): Yun Zhao, Ke Wang, Wenli Wang, Tingting Yin, Weiqi Dong, Changjie Xu
Software Mentions: 1
Published: over 7 years ago

10.3389/fcell.2020.00477

Regulation of Neurogenesis by FGF Signaling and Neurogenin in the Invertebrate Chordate Ciona
Cited by: 16
Author(s): Kwantae Kim, Susanne Gibboney, Florian Razy-Krajka, Elijah K. Lowe, Wei Wang, Alberto Stolfi
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0212193

Whole blood human transcriptome and virome analysis of ME/CFS patients experiencing post-exertional malaise following cardiopulmonary exercise testing
Cited by: 20
Author(s): Jérôme Bouquet, Tony Li, Jennifer L. Gardy, Xiaoying Kang, Staci R. Stevens, Jared Stevens, Mark VanNess, Christopher R. Snell, James E. Potts, Ruth R. Miller, Muhammad Morshed, Mark McCabe, Shoshana Parker, Miguel Uyaguari, Patrick Tang, Theodore S. Steiner, Wee‐Shian Chan, Astrid-Marie De Souza, André Mattman, David M. Patrick, Charles Y. Chiu
Software Mentions: 1
Published: over 7 years ago

10.1186/s13059-017-1270-7

Population and allelic variation of A-to-I RNA editing in human transcriptomes
Cited by: 40
Author(s): Eddie Park, Jianqiang Guo, Shihao Shen, Levon Demirdjian, Ying Wu, Lan Lin, Yi Xing
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0030020

Prognostic Significance and Gene Expression Profiles of p53 Mutations in Microsatellite-Stable Stage III Colorectal Adenocarcinomas
Cited by: 28
Author(s): Venkat R. Katkoori, Chandrakumar Shanmugam, Xiaoqian Jia, Swaroop P. Vitta, Meenakshi Sthanam, Tom Callens, Ludwine Messiaen, Dongquan Chen, Bin Zhang, Harvey L. Bumpers, Temesgen Samuel, Upender Manne
Software Mentions: 1
Published: over 14 years ago

10.1016/j.ebiom.2021.103243

Increased apolipoprotein-B:A1 ratio predicts cardiometabolic risk in patients with juvenile onset SLE
Cited by: 20
Author(s): George Robinson, Kirsty E. Waddington, Leda Coelewij, Junjie Peng, Meena Naja, Chris Wincup, Anna Radziszewska, Hannah Peckham, David Isenberg, Yiannis Ioannou, Coziana Ciurtin, Inés Pineda-Torra, Elizabeth C. Jury
Software Mentions: 1
Published: over 5 years ago

10.1016/j.ebiom.2019.11.048

A multistage sequencing strategy pinpoints novel candidate alleles for Emery-Dreifuss muscular dystrophy and supports gene misregulation as its pathomechanism
Cited by: 24
Author(s): Peter Meinke, Alastair Kerr, Rafal Czapiewski, Jose I. de las Heras, Charles R Dixon, Elizabeth Harris, Heike Kölbel, Francesco Muntoni, Ulrike Schara, Volker Straub, Benedikt Schöser, Manfred Wehnert, Eric C. Schirmer
Software Mentions: 1
Published: over 6 years ago

10.7554/eLife.42424

Different genetic mechanisms mediate spontaneous versus UVR-induced malignant melanoma
Cited by: 19
Author(s): Blake Ferguson, Herlina Y. Handoko, Pamela Mukhopadhyay, Arash Chitsazan, Lois Balmer, Grant Morahan, Graeme J. Walker
Software Mentions: 1
Published: over 7 years ago

10.1242/dmm.039545

Active receptor tyrosine kinases, but not Brachyury, are sufficient to trigger chordoma in zebrafish
Cited by: 11
Author(s): Gianluca D’Agati, Elena M. Cabello, Karl Frontzek, Elisabeth J. Rushing, Robin W. Klemm, Mark D. Robinson, Richard M. White, Christian Mosimann, Alexa Burger
Software Mentions: 1
Published: over 7 years ago

10.1242/dmm.040782

Targeted knockout of GABA receptor gamma 2 subunit provokes transient light-induced reflex seizures in zebrafish larvae
Cited by: 24
Author(s): Meijiang Liao, Uday Praful Kundap, Richard Rosch, Dominic R. W. Burrows, Martin P. Meyer, Bouchra Ouled Amar Bencheikh, Patrick Cossette, Éric Samarut
Software Mentions: 1
Published: over 7 years ago

10.1242/dmm.026104

From integrative genomics to systems genetics in the rat to link genotypes to phenotypes
Cited by: 25
Author(s): Aida Moreno‐Moral, Enrico Petretto
Software Mentions: 1
Published: almost 10 years ago

10.1186/s13059-017-1330-z

The influence of microRNAs and poly(A) tail length on endogenous mRNA–protein complexes
Cited by: 42
Author(s): Olivia S. Rissland, Alexander O. Subtelny, Miranda Wang, Andrew Lugowski, Beth Nicholson, John Laver, Sachdev S. Sidhu, Craig Smibert, Howard D. Lipshitz, David P. Bartel
Software Mentions: 1
Published: almost 9 years ago

10.1186/s13059-017-1339-3

Intron retention enhances gene regulatory complexity in vertebrates
Cited by: 74
Author(s): Ulf Schmitz, Natalia Pinello, Fangzhi Jia, Sultan Alasmari, William Ritchie, Maria-Cristina Keightley, S. Shini, Graham J. Lieschke, Justin Wong, John E.J. Rasko
Software Mentions: 1
Published: almost 9 years ago

10.18632/oncotarget.26797

Clinical validation of the tempus xT next-generation targeted oncology sequencing assay
Cited by: 101
Author(s): Nike Beaubier, Robert Tell, Denise Lau, Jerod Parsons, Stephen J. Bush, Jason Perera, Shelly Sorrells, Timothy Baker, Alan L. Chang, Jackson Michuda, Catherine Iguartua, Shelley M. MacNeil, Kaanan P. Shah, Philip Ellis, Kimberly Yeatts, Brett Mahon, Timothy J. Taxter, Martin Bontrager, Aly A. Khan, Robert Huether, Eric Lefkofsky, Kevin P. White
Software Mentions: 1
Published: over 7 years ago

10.7554/eLife.37527

Species-specific maturation profiles of human, chimpanzee and bonobo neural cells
Cited by: 84
Author(s): Maria C. Marchetto, Branka Hrvoj-Mihić, Bilal E. Kerman, Diana Yu, Krishna C. Vadodaria, Sara B. Linker, Iñigo Narvaiza, Renata Santos, Ahmet M. Denli, Ana Cristina Mendes, Ruth Oefner, Jonathan Cook, Lauren McHenry, Jaeson Michael Grasmick, Kelly J. Heard, Callie Fredlender, Lynne Randolph‐Moore, Rijul S. Kshirsagar, Rea Xenitopoulos, Grace Chou, Nasun Hah, Alysson R. Muotri, Krishnan Padmanabhan, Katerina Semendeferi, Fred H. Gage
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-020-68944-w

A G-quadruplex-binding compound shows potent activity in human gemcitabine-resistant pancreatic cancer cells
Cited by: 15
Author(s): Ahmed A. Ahmed, Chiara Marchetti, Stephan A. Ohnmacht, Stephen Neidle
Software Mentions: 1
Published: about 6 years ago

10.1186/s13059-018-1389-1

An obesity-associated gut microbiome reprograms the intestinal epigenome and leads to altered colonic gene expression
Cited by: 98
Author(s): Yufeng Qin, John D. Roberts, Sara A. Grimm, Fred B. Lih, Leesa J. Deterding, Ruifang Li, Kaliopi Chrysovergis, Paul A. Wade
Software Mentions: 1
Published: over 8 years ago

10.1242/dmm.030056

Generation of a double binary transgenic zebrafish model to study myeloid gene regulation in response to oncogene activation in melanocytes
Cited by: 12
Author(s): Amy Kenyon, Daria Gavriouchkina, Jernej Zorman, Vanessa Chong, Giorgio Napolitani, Vincenzo Cerundolo, Tatjana Sauka‐Spengler
Software Mentions: 1
Published: over 8 years ago

10.7554/eLife.54298

Targeting mir128-3p alleviates myocardial insulin resistance and prevents ischemia-induced heart failure
Cited by: 13
Author(s): Andrea Ruiz‐Velasco, Min Zi, Susanne Hille, Tayyiba Azam, Namrita Kaur, Juwei Jiang, Binh Nguyen, Karolina Sekeres, Pablo Binder, Lucy Collins, Fay Pu, Han Xiao, Kaomei Guan, Norbert Frey, Elizabeth J. Cartwright, Oliver Müller, Xin Wang, Wei Liu
Software Mentions: 1
Published: over 6 years ago

10.1242/dmm.038513

Mandibular dysmorphology due to abnormal embryonic osteogenesis in FGFR2-related craniosynostosis mice
Cited by: 19
Author(s): Susan M. Motch Perrine, Meng Wu, Nicholas B. Stephens, Divya Kriti, Harm van Bakel, Ethylin Wang Jabs, Joan T. Richtsmeier
Software Mentions: 1
Published: over 7 years ago

10.1242/dmm.040105

Characterization of the human GnRH neuron developmental transcriptome using a <i>GNRH1</i>-TdTomato reporter line in human pluripotent stem cells
Cited by: 17
Author(s): Carina Lund, Venkatram Yellapragada, Sanna Vuoristo, Diego Balboa, Sara Trova, Cécile Allet, Nazli Eskici, Kristiina Pulli, Paolo Giacobini, Timo Tuuri, Taneli Raivio
Software Mentions: 1
Published: over 6 years ago

10.1186/s13059-018-1421-5

SQUID: transcriptomic structural variation detection from RNA-seq
Cited by: 24
Author(s): Cong Ma, Mingfu Shao, Carl Kingsford
Software Mentions: 1
Published: over 8 years ago

10.1242/dmm.038083

Modelling the MYC-driven normal-to-tumour switch in breast cancer
Cited by: 13
Author(s): Corey Lourenco, Manpreet Kalkat, Kathleen E. Houlahan, Jason De Melo, Joseph Longo, Susan J. Done, Paul C. Boutros, Linda Z. Penn
Software Mentions: 1
Published: about 7 years ago

10.1007/s12035-019-01822-3

Endothelial Cell-Specific Transcriptome Reveals Signature of Chronic Stress Related to Worse Outcome After Mild Transient Brain Ischemia in Mice
Cited by: 4
Author(s): Stephanie Wegner, Ria Uhlemann, Valérie Boujon, Burcu Ersoy, Matthias Endres, Golo Kronenberg, Karen Gertz
Software Mentions: 1
Published: almost 7 years ago

10.1186/s13059-018-1446-9

SINC-seq: correlation of transient gene expressions between nucleus and cytoplasm reflects single-cell physiology
Cited by: 43
Author(s): Mahmoud N. Abdelmoez, Kei Iida, Yusuke Oguchi, Hidekazu Nishikii, Ryuji Yokokawa, Hidetoshi Kotera, Shunsuke Uemura, Juan G. Santiago, Hirofumi Shintaku
Software Mentions: 1
Published: over 8 years ago

10.1186/s12967-020-02371-3

Decidual CD8+T cells exhibit both residency and tolerance signatures modulated by decidual stromal cells
Cited by: 18
Author(s): Lu Liu, Xixi Huang, Chunfang Xu, Chunqin Chen, Weijie Zhao, Da‐Jin Li, Liping Li, Li Wang, Meirong Du
Software Mentions: 1
Published: over 6 years ago

10.3791/51714

Averaging of Viral Envelope Glycoprotein Spikes from Electron Cryotomography Reconstructions using Jsubtomo
Cited by: 16
Author(s): Juha T. Huiskonen, Marie-Laure Parsy, Sai Li, David Bitto, Max Renner, Thomas A. Bowden
Software Mentions: 1
Published: almost 12 years ago

10.1186/s12967-021-02844-z

Expression and regulatory roles of lncRNAs in G-CIMP-low vs G-CIMP-high Glioma: an in-silico analysis
Cited by: 4
Author(s): Indrani Datta, Houtan Noushmehr, Chaya Brodie, Laila Poisson
Software Mentions: 1
Published: over 5 years ago