10.1371/journal.pone.0234748

Identification of functionally connected multi-omic biomarkers for Alzheimer’s disease using modularity-constrained Lasso
Cited by: 5
Author(s): Linhui Xie, Pradeep Varathan, Kwangsik Nho, Andrew J. Saykin, Paul Salama, Jingwen Yan
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0209626

Integrative multiomics study for validation of mechanisms in radiation-induced ischemic heart disease in Mayak workers
Cited by: 10
Author(s): Anna Papież, Omid Azimzadeh, Tamara V. Azizova, М. Б. Мосеева, Nataša Anastasov, Jan Smida, Soile Tapio, Joanna Polańska
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0197459

Bone formation transcripts dominate the differential gene expression profile in an equine osteoporotic condition associated with pulmonary silicosis
Cited by: 1
Author(s): Regina Zavodovskaya, Susan M. Stover, Brian G Murphy, Scott A. Katzman, Blythe Durbin‐Johnson, Monica Britton, Carrie J. Finno
Software Mentions: 1
Published: about 8 years ago

10.1371/journal.pone.0200417

Downregulation of splicing regulator RBFOX1 compromises visual depth perception
Cited by: 12
Author(s): Lin Gu, Dean Bok, Fei Yu, Joseph Caprioli, Natik Piri
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0203543

Plausibility of the zebrafish embryos/larvae as an alternative animal model for autism: A comparison study of transcriptome changes
Cited by: 15
Author(s): Sang‐Woo Lee, Hang-Suk Chun, Jieon Lee, Han-Jin Park, Ki-Tae Kim, Cheol-Hee Kim, Seokjoo Yoon, Woo‐Keun Kim
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0141298

Evidence of Extensive Alternative Splicing in Post Mortem Human Brain HTT Transcription by mRNA Sequencing
Cited by: 17
Author(s): Adam Labadorf, Richard H. Myers
Software Mentions: 1
Published: over 10 years ago

10.1002/advs.202004303

Copper Promotes Tumorigenesis by Activating the PDK1‐AKT Oncogenic Pathway in a Copper Transporter 1 Dependent Manner
Cited by: 54
Author(s): Jianping Guo, Ji Cheng, Nana Zheng, Xiaomei Zhang, Xiaoming Dai, Linli Zhang, C. Hu, Xueji Wu, Qiwei Jiang, Depei Wu, Hitoshi Okada, Pier Paolo Pandolfi
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.pone.0175393

Identification of human short introns
Cited by: 13
Author(s): Emmanuel L. Abebrese, Sadia Ali, Zachary R. Arnold, Victoria M. Andrews, Katharine Fairlie Armstrong, Lindsay H. Burns, Hannah R. Crowder, R. Thomas Day, Daniel G. Hsu, Katherine Jarrell, Grace Lee, Yi Luo, Daphine Mugayo, Zain Raza, Kyle Friend
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0182238

Minimum variance rooting of phylogenetic trees and implications for species tree reconstruction
Cited by: 60
Author(s): Uyen Mai, Erfan Sayyari, Siavash Mirarab
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0219280

Loss of function mutation of Eftud2, the gene responsible for mandibulofacial dysostosis with microcephaly (MFDM), leads to pre-implantation arrest in mouse
Cited by: 20
Author(s): Marie‐Claude Beauchamp, Anissa Djedid, Kevin Daupin, Kayla Clokie, Shruti Kumar, Jacek Majewski, Loydie A. Jerome-Majewska
Software Mentions: 1
Published: about 7 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: almost 6 years ago

10.1371/journal.pone.0219938

An important role of podoplanin in hair follicle growth
Cited by: 9
Author(s): Sun Young Yoon, Lothar C. Dieterich, Carlotta Tacconi, Marko Sesartić, Yuliang He, Lorenz M. Brunner, Oh Sang Kwon, Michael Detmar
Software Mentions: 1
Published: almost 7 years ago

10.1371/journal.pone.0238117

Temporal transcriptome analysis suggest modulation of multiple pathways and gene network involved in cell-cell interaction during early phase of high altitude exposure
Cited by: 6
Author(s): Priya Gaur, Supriya Saini, Koushik Ray, Nadira Kushubakova, Almaz Akunov, Abdirashit Maripov, Akpay Sarybaev, Shashi Bala Singh, Bhuvnesh Kumar, Praveen Vats
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0241851

Grant application outcomes for biomedical researchers who participated in the National Research Mentoring Network’s Grant Writing Coaching Programs
Cited by: 18
Author(s): Anne Marie Weber-Main, Richard McGee, Kristin Eide Boman, Japera Hemming, Meldra Hall, Thaddeus Unold, Eileen M. Harwood, Laurie E. Risner, Ann D. Smith, Kimberly Lawson, Jeffrey A. Engler, Clifford J. Steer, Dedra Buchwald, Harlan P. Jones, Spero M. Manson, Elizabeth Ofili, Nancy B. Schwartz, Jamboor K. Vishwanatha, Kolawole S. Okuyemi
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0164962

Discriminative Prediction of A-To-I RNA Editing Events from DNA Sequence
Cited by: 4
Author(s): Jiangming Sun, Yang De Marinis, Peter Osmark, Pratibha Singh, Annika Bagge, B. Valtat, Petter Vikman, Peter Sartipy, Hindrik Mulder
Software Mentions: 1
Published: over 9 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

10.1186/s12864-015-1267-0

Splicing landscape of the eight collaborative cross founder strains
Cited by: 7
Author(s): Christina Zheng, Beth Wilmot, Nicole A.R. Walter, Denesa Oberbeck, Sunita Kawane, Robert P. Searles, Shannon K. McWeeney, Robert Hitzemann
Software Mentions: 1
Published: over 11 years ago

10.1371/journal.pone.0242884

MEF2 transcription factors differentially contribute to retinal ganglion cell loss after optic nerve injury
Cited by: 6
Author(s): Xin Xia, Caroline Yu, Minjuan Bian, Catalina Sun, Bogdan Tanasă, Kun-Che Chang, Dawn M. Bruffett, Hrishikesh Thakur, Shweta Shah, Cara Knasel, Evan G. Cameron, Michael S. Kapiloff, Jeffrey L. Goldberg
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0033967

High Throughput Multiple Locus Variable Number of Tandem Repeat Analysis (MLVA) of Staphylococcus aureus from Human, Animal and Food Sources
Cited by: 39
Author(s): Daniel Sobral, Štefan Schwarz, Dominique Bergonier, Anne Brisabois, Andrea T. Feßler, Florence Gilbert, Kristina Kadlec, B. Lebeau, Fabienne Loisy-Hamon, Michaël Treilles, Christine Pourcel, Gilles Vergnaud
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pone.0211244

Myc-induced nuclear antigen constrains a latent intestinal epithelial cell-intrinsic anthelmintic pathway
Cited by: 5
Author(s): M.R.A. Pillai, Belgacem Mihi, Kenji Ishiwata, Kiminori Nakamura, Naoya Sakuragi, David Finkelstein, Maureen A. McGargill, Toshinori Nakayama, Tokiyoshi Ayabe, Mathew L. Coleman, Mark Bix
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0148164

Expression of mRNA Encoding Mcu and Other Mitochondrial Calcium Regulatory Genes Depends on Cell Type, Neuronal Subtype, and Ca2+ Signaling
Cited by: 25
Author(s): Nóra M. Márkus, Philip Hasel, Jing Qiu, Karen Bell, Samuel Heron, Peter C. Kind, Owen Dando, T. Ian Simpson, Giles E. Hardingham
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0239275

The R2R3-MYB gene family in banana (Musa acuminata): Genome-wide identification, classification and expression patterns
Cited by: 33
Author(s): Boas Pucker, Ashutosh Pandey, Bernd Weißhaar, Ralf Stracke
Software Mentions: 1
Published: almost 6 years ago

10.1371/journal.pone.0157758

Characterisation of CDKL5 Transcript Isoforms in Human and Mouse
Cited by: 47
Author(s): Ralph D. Hector, Owen Dando, Nicoletta Landsberger, Charlotte Kilstrup‐Nielsen, Peter C. Kind, Mark E.S. Bailey, Stuart Cobb
Software Mentions: 1
Published: about 10 years ago

10.7554/eLife.28652

Host proteostasis modulates influenza evolution
Cited by: 30
Author(s): Angela M Phillips, Luna O Gonzalez, Emmanuel E Nekongo, Anna I. Ponomarenko, Sean M. McHugh, Vincent Butty, Stuart S. Levine, Yu‐Shan Lin, Leonid A. Mirny, Matthew D. Shoulders
Software Mentions: 1
Published: almost 9 years ago

10.1186/s12864-016-3262-5

Sequence-specific bias correction for RNA-seq data using recurrent neural networks
Cited by: 13
Author(s): Yao-Zhong Zhang, Rui Yamaguchi, Seiya Imoto, Satoru Miyano
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pone.0149229

Major Transcriptome Changes Accompany the Growth of Pseudomonas aeruginosa in Blood from Patients with Severe Thermal Injuries
Cited by: 30
Author(s): Cassandra Kruczek, Kameswara Rao Kottapalli, Sharmila Dissanaike, Nyaradzo Dzvova, John Griswold, Jane A. Colmer-Hamood, Abdul N. Hamood
Software Mentions: 1
Published: over 10 years ago

10.1371/journal.pone.0186888

TrpA1 activation in peripheral sensory neurons underlies the ionic basis of pain hypersensitivity in response to vinca alkaloids
Cited by: 19
Author(s): Nina Boiko, Geraldo Medrano, Elizabeth Montano, Nan Jiang, Claire Williams, Ngonidzashe B Madungwe, Jean C. Bopassa, Charles C. Kim, Jay Z. Parrish, Kenneth M. Hargreaves, James D. Stockand, Benjamin A. Eaton
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0089459

MARIS: Method for Analyzing RNA following Intracellular Sorting
Cited by: 88
Author(s): Siniša Hrvatin, Francis Deng, Barry O'Donnell, David K. Gifford, Douglas A. Melton
Software Mentions: 1
Published: over 12 years ago

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

10.1371/journal.pone.0036566

Classification of HIV-1 Sequences Using Profile Hidden Markov Models
Cited by: 7
Author(s): Sanjiv K. Dwivedi, Supratim Sengupta
Software Mentions: 1
Published: about 14 years ago

10.1371/journal.pone.0201756

Identification of genomic regions associated with agronomic and biofortification traits in DH populations of rice
Cited by: 46
Author(s): B. P. Mallikarjuna Swamy, Gwen Iris L. Descalsota, Chau Thanh Nha, Amery Amparado, Mary Ann Inabangan-Asilo, Christine Manito, Frances Tesoro, Russell Reinke
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12864-019-5845-4

Characterization of the bovine salivary gland transcriptome associated with Mycobacterium avium subsp. paratuberculosis experimental challenge
Cited by: 9
Author(s): S. Mallikarjunappa, Mounir Adnane, Paul Cormican, Niel A. Karrow, Kieran G. Meade
Software Mentions: 1
Published: about 7 years ago

10.1371/journal.pone.0211709

Modeling financial interval time series
Cited by: 1
Author(s): Lin Liang, Li Hsien Sun
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0221008

Genetic variation for root architectural traits in response to phosphorus deficiency in mungbean at the seedling stage
Cited by: 29
Author(s): V. R. Reddy, Muraleedhar S. Aski, Gyan P. Mishra, Harsh Kumar Dikshit, Akanksha Singh, Renu Pandey, Madan Pal Singh, Gayacharan, Vinita Ramtekey, Priti, Neha Rai, Ramakrishnan M. Nair
Software Mentions: 1
Published: about 6 years ago

10.1186/s12864-021-07733-9

Characterization of nucleic acids from extracellular vesicle-enriched human sweat
Cited by: 17
Author(s): Geneviève Bart, Daniel Fischer, Anatoly Samoylenko, Artem Zhyvolozhnyi, Pavlo Stehantsev, Ilkka Miinalainen, Mika Kaakinen, Tuomas Nurmi, Prateek Singh, Susanna Kosamo, Lauri Rannaste, Sirja Viitala, Jussi Hiltunen, Seppo Vainio
Software Mentions: 1
Published: about 5 years ago

10.1371/journal.pone.0207503

Distinct vascular genomic response of proton and gamma radiation—A pilot investigation
Cited by: 3
Author(s): Emanuela Ricciotti, Dimitra Sarantopoulou, Gregory R. Grant, Jenine K. Sanzari, Gabriel Krigsfeld, Amber J. Kiliti, Ann R. Kennedy, Tilo Großer
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0192170

Induction of epigenetic variation in Arabidopsis by over-expression of DNA METHYLTRANSFERASE1 (MET1)
Cited by: 14
Author(s): Samuel George Philip Brocklehurst, Michael R. Watson, Ian Carr, Suzan Out, Iris Heidmann, Peter Meyer
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0122602

Binary Gene Expression Patterning of the Molt Cycle: The Case of Chitin Metabolism
Cited by: 23
Author(s): Shai Abehsera, Lilah Glazer, Jenny Tynyakov, Inbar Plaschkes, Vered Chalifa‐Caspi, Isam Khalaila, Eliahu D. Aflalo, Amir Sagi
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0232081

Engineering a 3D in vitro model of human skeletal muscle at the single fiber scale
Cited by: 15
Author(s): Anna Urciuolo, Elena Serena, Rusha Ghua, Susi Zatti, Monica Giomo, Nicolò Mattei, Massimo Vetralla, Giulia Selmin, Camilla Luni, Nicola Vitulo, Giorgio Valle, Libero Vitiello, Nicola Elvassore
Software Mentions: 1
Published: about 6 years ago

10.1371/journal.pone.0187773

Lung epithelial response to cigarette smoke and modulation by the nicotinic alpha 7 receptor
Cited by: 18
Author(s): Lorise C. Gahring, Elizabeth J. Myers, Diane M. Dunn, Robert B. Weiss, Scott W. Rogers
Software Mentions: 1
Published: over 8 years ago

10.1371/journal.pone.0125414

The Expansion of Thymopoiesis in Neonatal Mice Is Dependent on Expression of High Mobility Group A 2 Protein (Hmga2)
Cited by: 5
Author(s): Beata Berent-Maoz, Encarnación Montecino-Rodriguez, Michael P. Fice, David Casero, Christopher S. Seet, William E. Lowry, Kenneth Dorshkind
Software Mentions: 1
Published: about 11 years ago

10.1371/journal.pone.0200477

SAP97 regulates behavior and expression of schizophrenia risk enriched gene sets in mouse hippocampus
Cited by: 14
Author(s): Preetika Gupta, Ogul E. Uner, Soumyashant Nayak, Gregory R. Grant, Robert G. Kalb
Software Mentions: 1
Published: almost 8 years ago

10.3390/cancers13071546

Pulsed-Focused Ultrasound Slows B16 Melanoma and 4T1 Breast Tumor Growth through Differential Tumor Microenvironmental Changes
Cited by: 5
Author(s): Gadi Cohen, Parwathy Chandran, Rebecca M. Lorsung, Ömer Aydın, Lauren E. Tomlinson, Robert Rosenblatt, Scott R. Burks, Joseph A. Frank
Software Mentions: 1
Published: over 5 years ago

10.3390/cancers12071719

Dysregulation of MITF Leads to Transformation in MC1R-Defective Melanocytes
Cited by: 5
Author(s): Timothy J. Lavelle, Tine Norman Alver, Karen‐Marie Heintz, Patrik Wernhoff, Vegard Nygaard, Sigve Nakken, Geir Frode Øy, Sigurd Leinæs Bøe, Alfonso Urbanucci, Eivind Hovig
Software Mentions: 1
Published: about 6 years ago

10.3390/cancers13092250

IGF2 Mediates Resistance to Isoform-Selective-Inhibitors of the PI3K in HPV Positive Head and Neck Cancer
Cited by: 6
Author(s): Mai Badarni, Manu Prasad, Artemiy Golden, Baisali Bhattacharya, Liron Levin, Ksenia M. Yegodayev, Orr Dimitstein, Ben‐Zion Joshua, Limor Cohen, Ekaterina Khrameeva, Dexin Kong, Angel Porgador, Alex Braiman, Jennifer R. Grandis, Barak Rotblat, Moshe Elkabets
Software Mentions: 1
Published: about 5 years ago

10.1186/s12864-018-5341-2

Kinetics of the chromosome 14 microRNA cluster ortholog and its potential role during placental development in the pregnant mare
Cited by: 21
Author(s): Pouya Dini, Peter Daels, Shavahn C. Loux, A. Esteller-Vico, Mariano Carossino, Kirsten E. Scoggin, Barry A. Ball
Software Mentions: 1
Published: over 7 years ago

10.3390/cancers12030620

RNA Immune Signatures from Pan-Cancer Analysis Are Prognostic for High-Grade Serous Ovarian Cancer and Other Female Cancers
Cited by: 12
Author(s): Wendell Jones, Chad M. Michener, Charles V. Biscotti, Elena Ioana Braicu, Jalid Sehouli, Mahrukh K. Ganapathi, Ram Ganapathi
Software Mentions: 1
Published: over 6 years ago

10.1002/advs.202100805

A 3D Fiber‐Hydrogel Based Non‐Viral Gene Delivery Platform Reveals that microRNAs Promote Axon Regeneration and Enhance Functional Recovery Following Spinal Cord Injury
Cited by: 33
Author(s): Na Zhang, Junquan Lin, Vincent Po Hen Lin, Ulla Milbreta, Jiah Shin Chin, Elaine Guo Yan Chew, Michelle Mulan Lian, Jia Nee Foo, Kunyu Zhang, Wutian Wu, Sing Yian Chew
Software Mentions: 1
Published: about 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: about 10 years ago

10.1038/s41419-021-03880-9

Effects of short-chain fatty acids in inhibiting HDAC and activating p38 MAPK are critical for promoting B10 cell generation and function
Cited by: 36
Author(s): Zhang‐Qi Feng, Yi Qiu, Yilian Huang, Hang Zou, Cheng Xiao, Qingru Niu, Aoxiang Luo, Jianbo Sun
Software Mentions: 1
Published: about 5 years ago

10.1038/cddis.2017.197

All-trans retinoic acid and arsenic trioxide fail to derepress the monocytic differentiation driver Irf8 in acute promyelocytic leukemia cells
Cited by: 14
Author(s): Xiang-Zhen Liu, Juan Chen, Shanhe Yu, Yan Li, Hong Guo, Jian-Min Dai, Wu Zhang, Jiang Zhu
Software Mentions: 1
Published: about 9 years ago

10.1038/s41419-021-03539-5

Epigenetic regulation of p62/SQSTM1 overcomes the radioresistance of head and neck cancer cells via autophagy-dependent senescence induction
Cited by: 21
Author(s): Myungjin Lee, Hae Yun Nam, Hee-Bum Kang, Won Hyeok Lee, Geunhee Lee, Gi‐Jun Sung, Myung Woul Han, Kyung–Ja Cho, Eun‐Ju Chang, Kyung‐Chul Choi, Seong Who Kim, Sang Yoon Kim
Software Mentions: 1
Published: over 5 years ago

10.1038/s41419-019-1858-9

Deletion of OSBPL2 in auditory cells increases cholesterol biosynthesis and drives reactive oxygen species production by inhibiting AMPK activity
Cited by: 21
Author(s): Hongshun Wang, Changsong Lin, Jun Yao, Hairong Shi, Cui Zhang, Qinjun Wei, Yajie Lu, Zhibin Chen, Guangqian Xing, Xin Cao
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41419-021-04146-0

The long non-coding RNA HOTAIRM1 promotes tumor aggressiveness and radiotherapy resistance in glioblastoma
Cited by: 18
Author(s): Ulvi Ahmadov, Daniel Picard, Jasmin Bartl, Manuela Silginer, Marija Trajkovic‐Arsic, Nan Qin, Lena Blümel, Marietta Wolter, Jonathan Lim, David Pauck, Alina M Winkelkotte, Marlen Melcher, Maike Langini, Viktoria Marquardt, Felix Sander, Anja Stefanski, Sascha Steltgens, Christina Hassiepen, Anna Kaufhold, Frank Meyer, Annette Seibt, Lara Kleinesudeik, Anika Hain, Carsten Münk, Christiane B. Knobbe-Thomsen, Alexander Schramm, Ute Fischer, Gabriel Leprivier, Kai Stühler, Simone Fulda, Jens T. Siveke, Felix Distelmaier, Arndt Borkhardt, Michael Weller, Guido Reifenberger, Marc Remke
Software Mentions: 1
Published: almost 5 years ago

10.1038/cddis.2016.188

MDM2 facilitates adipocyte differentiation through CRTC-mediated activation of STAT3
Cited by: 26
Author(s): Philip Hallenborg, Majken Siersbæk, Iñigo Barrio-Hernandez, Ronni Nielsen, Karsten Kristiansen, Susanne Mandrup, Lars Grøntved, Blagoy Blagoev
Software Mentions: 1
Published: about 10 years ago

10.1038/s41419-020-02754-w

The longevity-associated variant of BPIFB4 improves a CXCR4-mediated striatum–microglia crosstalk preventing disease progression in a mouse model of Huntington’s disease
Cited by: 14
Author(s): Alba Di Pardo, Elena Ciaglia, Monica Cattaneo, Anna Maciąg, Francesco Montella, Valentina Lopardo, Anna Ferrario, Francesco Villa, Michele Madonna, Enrico Amico, Albino Carrizzo, Antonio L. Damato, Giuseppe Pepe, Federico Marracino, Alberto Auricchio, Carmine Vecchione, Vittorio Maglione, Annibale Alessandro Puca
Software Mentions: 1
Published: almost 6 years ago

10.1038/s41419-020-2536-7

The HMGB1-RAGE axis modulates the growth of autophagy-deficient hepatic tumors
Cited by: 14
Author(s): Bilon Khambu, Honghai Hong, Sheng Liu, Gang Liu, Xiaoyun Chen, Zheng Dong, Jun Wan, Xiao Ming Yin
Software Mentions: 1
Published: about 6 years ago

10.1038/s41419-020-2257-y

Lipid desaturation-associated endoplasmic reticulum stress regulates MYCN gene expression in hepatocellular carcinoma cells
Cited by: 30
Author(s): Xian‐Yang Qin, Ting Su, Wenkui Yu, Soichi Kojima
Software Mentions: 1
Published: over 6 years ago

10.1038/s41419-019-1946-x

The stem cell-associated transcription co-factor, ZNF521, interacts with GLI1 and GLI2 and enhances the activity of the Sonic hedgehog pathway
Cited by: 15
Author(s): Stefania Scicchitano, Marco Giordano, Valeria Lucchino, Ylenia Montalcini, Emanuela Chiarella, Annamaria Aloisio, Bruna Codispoti, Pietro Zoppoli, Valentina Melocchi, Fabrizio Bianchi, Enrico De Smaele, Maria Mesuraca, Giovanni Morrone
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41419-018-0796-2

CCL5-deficiency enhances intratumoral infiltration of CD8+ T cells in colorectal cancer
Cited by: 48
Author(s): Shengbo Zhang, Ming Zhong, Chao Wang, Yanjie Xu, Wei‐Qiang Gao, Yan Zhang
Software Mentions: 1
Published: almost 8 years ago

10.1038/s41419-019-1799-3

Mitofusin 1 is required for female fertility and to maintain ovarian follicular reserve
Cited by: 60
Author(s): Man Zhang, Muhammed Burak Bener, Zongliang Jiang, Tianren Wang, Ecem Esencan, Richard T. Scott, Tamás L. Horváth, Emre Seli
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41419-018-0769-5

High-throughput analysis of the RNA-induced silencing complex in myotonic dystrophy type 1 patients identifies the dysregulation of miR-29c and its target ASB2
Cited by: 16
Author(s): M Cappella, Alessandra Perfetti, Beatrice Cardinali, José Manuel García-Manteiga, Matteo Carrara, Claudia Provenzano, Paola Fuschi, Rosanna Cardani, Laura Valentina Renna, Giovanni Meola, Germana Falcone, Fabio Martelli
Software Mentions: 1
Published: about 8 years ago

10.1038/s41419-019-1477-5

The lncRNA TP73-AS1 is linked to aggressiveness in glioblastoma and promotes temozolomide resistance in glioblastoma cancer stem cells
Cited by: 112
Author(s): Gal Mazor, Liron Levin, Daniel Picard, Ulvi Ahmadov, Helena Carén, Arndt Borkhardt, Guido Reifenberger, Gabriel Leprivier, Marc Remke, Barak Rotblat
Software Mentions: 1
Published: over 7 years ago

10.1038/s41420-021-00607-9

Whole exome and transcriptome sequencing reveal clonal evolution and exhibit immune-related features in metastatic colorectal tumors
Cited by: 8
Author(s): Chunxue Li, Juan Xu, Xiangfeng Wang, Chao Zhang, Zicheng Yu, Jiucheng Liu, Zaixian Tai, Ziwen Luo, Xin Yi, Zhaoyang Zhong
Software Mentions: 1
Published: almost 5 years ago

10.1038/s41420-020-0246-7

TFEB-mediated lysosomal biogenesis and lysosomal drug sequestration confer resistance to MEK inhibition in pancreatic cancer
Cited by: 27
Author(s): Ben Zhao, Laura Dierichs, Jiangning Gu, Marija Trajkovic‐Arsic, Ralf A. Hilger, Konstantinos Savvatakis, Silvia Vega-Rubín-de-Celis, Sven-Thorsten Liffers, Samuel Peña-Llopis, Diana Behrens, Stephan A. Hahn, Jens T. Siveke, Smiths Lueong
Software Mentions: 1
Published: over 6 years ago

10.1038/s41421-018-0059-5

Maintenance of human haematopoietic stem and progenitor cells in vitro using a chemical cocktail
Cited by: 12
Author(s): Mengmeng Jiang, Haide Chen, Shih‐Wei Lai, Renying Wang, Yunfei Qiu, Fang Ye, Lijiang Fei, Huiyu Sun, Yang Xu, Xinyi Jiang, Ziyu Zhou, Tingyue Zhang, Yanwei Li, Jin Xie, Qun Fang, Robert Peter Gale, Xiaoping Han, He Huang, Guoji Guo
Software Mentions: 1
Published: over 7 years ago

10.1038/s41421-019-0131-9

Concurrent activation of growth factor and nutrient arms of mTORC1 induces oxidative liver injury
Cited by: 11
Author(s): Chun‐Seok Cho, Allison H. Kowalsky, Sim Namkoong, Sung-Rye Park, Shuangcheng Wu, Boyoung Kim, Amanda James, Bondong Gu, Ian A. Semple, M.A. Tohamy, Sumeet Solanki, Uhn‐Soo Cho, Joel K. Greenson, Yatrik M. Shah, Myung-Jin Kim, Jun Hee Lee
Software Mentions: 1
Published: over 6 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: almost 5 years ago

10.1016/j.chom.2018.07.011

High-Definition Analysis of Host Protein Stability during Human Cytomegalovirus Infection Reveals Antiviral Factors and Viral Evasion Mechanisms
Cited by: 79
Author(s): Katie Nightingale, Kai‐Min Lin, Benjamin J. Ravenhill, Colin Davies, Luis Nobre, Ceri Alan Fielding, Eva Růčková, Alice Fletcher-Etherington, Lior Soday, Hester Nichols, Daniel Sugrue, Edward Chung Yern Wang, Pablo Moreno-Ger, Yagnesh Umrania, Edward L. Huttlin, Robin Antrobus, Andrew J. Davison, Gavin W. G. Wilkinson, Richard J. Stanton, Peter Tomašec, Michael P. Weekes
Software Mentions: 1
Published: almost 8 years ago

10.1111/cmi.13156

Blind killing of both male and female Drosophila embryos by a natural variant of the endosymbiotic bacterium Spiroplasma poulsonii
Cited by: 8
Author(s): Florent Masson, Sandra P. Calderon-Copete, Fanny Schüpfer, Aurélien Vigneron, Samuel Rommelaere, Mario Gonzalo Garcia-Arraez, Juan C. Paredes, Bruno Lemaître
Software Mentions: 1
Published: over 6 years ago

10.1016/j.celrep.2021.108890

The effect of spike mutations on SARS-CoV-2 neutralization
Cited by: 180
Author(s): Chloe Rees-Spear, Luke Muir, Sarah A. Griffith, Judith Heaney, Yoann Aldon, Jonne L. Snitselaar, Peter Thomas, Carl Graham, Jeffrey Seow, Nayung Lee, Annachiara Rosa, Chloë Roustan, Catherine Houlihan, Rogier W. Sanders, Ravindra Gupta, Peter Cherepanov, Hans J. Stauss, Eleni Nastouli, Katie J. Doores, Marit J. van Gils, Laura E McCoy
Software Mentions: 1
Published: over 5 years ago

10.1016/j.celrep.2021.109464

Spliceosomal component PRP-40 is a central regulator of microexon splicing
Cited by: 13
Author(s): Bikash Choudhary, Olivia Marx, Adam Norris
Software Mentions: 1
Published: almost 5 years ago

10.1016/j.celrep.2021.109044

Modeling cell-specific dynamics and regulation of the common gamma chain cytokines
Cited by: 8
Author(s): Ali M. Farhat, Adam C. Weiner, Cori Posner, Zoe S Kim, Brian T Orcutt-Jahns, Scott M. Carlson, Aaron S. Meyer
Software Mentions: 1
Published: over 5 years ago

10.7554/eLife.09207

SPOP mutation leads to genomic instability in prostate cancer
Cited by: 142
Author(s): Gunther Boysen, Christopher E. Barbieri, Davide Prandi, Mirjam Blattner, Sung-Suk Chae, Arun Dahija, Srilakshmi Nataraj, Dennis Huang, Clarisse Marotz, Limei Xu, Julie Huang, Paola Lecca, Sagar Chhangawala, Liu D, Pengbo Zhou, Andrea Sboner, Johann S. de Bono, Francesca Demichelis, Yariv Houvras, Mark A. Rubin
Software Mentions: 1
Published: almost 11 years ago

10.1016/j.celrep.2018.07.091

Regulated Capture of Vκ Gene Topologically Associating Domains by Transcription Factories
Cited by: 13
Author(s): Sophiya Karki, Domenick E. Kennedy, Kaitlin C. McLean, Adrian T. Grzybowski, Mark Maienschein‐Cline, Shiladitya Banerjee, Heping Xu, Elizabeth M. Davis, Malay Mandal, Christine M. Labno, Sarah E. Powers, Michelle M. Le Beau, Aaron R. Dinner, Harinder Singh, Alexander J. Ruthenburg, Marcus R. Clark
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12864-019-6122-2

The effects of a globin blocker on the resolution of 3’mRNA sequencing data in porcine blood
Cited by: 4
Author(s): Kyu-Sang Lim, Qian Dong, Pamela Renate Moll, Jana Vitkovska, Gregor Wiktorin, Stephanie Bannister, Dalia Daujotytė, Christopher K. Tuggle, Joan K. Lunney, Graham Plastow, Jack C. M. Dekkers
Software Mentions: 1
Published: over 6 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: almost 5 years ago

10.1016/j.celrep.2019.07.043

Nicotinamide Riboside Augments the Aged Human Skeletal Muscle NAD+ Metabolome and Induces Transcriptomic and Anti-inflammatory Signatures
Cited by: 226
Author(s): Yasir Elhassan, Katarína Kľučková, Rachel Fletcher, Mark S. Schmidt, Antje Garten, Craig Doig, David Cartwright, Lucy Oakey, Claire V. Burley, Ned Jenkinson, Martin Wilson, Samuel J. E. Lucas, İldem Akerman, Alex P. Seabright, Yu‐Chiang Lai, Daniel A. Tennant, Peter Nightingale, Gareth A. Wallis, K. Manolopoulos, Charles Brenner, Andrew Philp, Gareth G. Lavery
Software Mentions: 1
Published: almost 7 years ago

10.1186/s12864-021-07784-y

Transcriptomic coordination at hepatic steatosis indicates robust immune cell engagement prior to inflammation
Cited by: 3
Author(s): Youwen Zhang, Ioulia Chatzistamou, Hippokratis Kiaris
Software Mentions: 1
Published: about 5 years ago

10.1007/s10577-021-09658-1

Genome-wide mapping of histone modifications during axenic growth in two species of Leptosphaeria maculans showing contrasting genomic organization
Cited by: 13
Author(s): Jessica L. Soyer, Colin Clairet, Nicolas Lapalu, Thierry Rouxel, Eva H. Stukenbrock, Isabelle Fudal
Software Mentions: 1
Published: about 5 years ago

10.1111/cen.14109

Primary adrenal insufficiency: New genetic causes and their long‐term consequences
Cited by: 45
Author(s): Federica Buonocore, John C. Achermann
Software Mentions: 1
Published: over 6 years ago

10.1186/s13148-018-0598-5

Histone deacetylase inhibitors exert anti-tumor effects on human adherent and stem-like glioma cells
Cited by: 45
Author(s): Halina Waś, Sylwia Król, Dante Rotili, Antonello Mai, Bartosz Wojtaś, Bożena Kamińska, Marta Maleszewska
Software Mentions: 1
Published: over 7 years ago

10.1186/s12864-017-4414-y

Computational approach to discriminate human and mouse sequences in patient-derived tumour xenografts
Cited by: 51
Author(s): Maurizio Callari, Ankita Batra, R N Batra, Stephen‐John Sammut, Wendy Greenwood, Harry Clifford, Colin Hercus, Suet Feung Chin, Alejandra Bruna, Oscar M. Rueda, Carlos Caldas
Software Mentions: 1
Published: over 8 years ago

10.1186/s12864-020-07304-4

Comparative evaluation for the globin gene depletion methods for mRNA sequencing using the whole blood-derived total RNAs
Cited by: 9
Author(s): Jin Sung Jang, Brianna Berg, Eileen L. Holicky, Bruce W. Eckloff, Mark M. Mutawe, Minerva M. Carrasquillo, Nilüfer Ertekin-Taner, Julie M. Cuninngham
Software Mentions: 1
Published: over 5 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: over 19 years ago

10.1186/s13148-021-01023-7

BRG1 knockdown inhibits proliferation through multiple cellular pathways in prostate cancer
Cited by: 11
Author(s): Katherine A. Giles, Cathryn M. Gould, Joanna Achinger-Kawecka, Scott G. Page, Georgia R. Kafer, Samuel Rogers, Phuc-Loi Luu, Anthony J. Cesare, Susan J. Clark, Phillippa C. Taberlay
Software Mentions: 1
Published: over 5 years ago

10.1186/s13148-015-0087-z

Epigenetic reprogramming of melanoma cells by vitamin C treatment
Cited by: 69
Author(s): Christopher B. Gustafson, Chao Yang, Kevin M. Dickson, Hongwei Shao, Derek Van Booven, J. William Harbour, Zhao Jun Liu, Gaofeng Wang
Software Mentions: 1
Published: about 11 years ago

10.1186/s12864-017-4335-9

Biclustering of transcriptome sequencing data reveals human tissue-specific circular RNAs
Cited by: 8
Author(s): Yuchen Liu, Yu-Jung Chiu, Jiànróng Lǐ, Chuan-Hu Sun, Chun-Chi Liu, Hsien-Da Huang
Software Mentions: 1
Published: over 8 years ago

10.1007/s00062-017-0639-z

Iatrogenic Vessel Dissection in Endovascular Treatment of Acute Ischemic Stroke
Cited by: 34
Author(s): Barbara Goeggel Simonetti, Justine Hulliger, Etienne Mathier, Simon Jung, Urs Fischer, Hakan Sarıkaya, Johannes Slotboom, Gerhard Schroth, Pasquale Mordasini, Jan Gralla, Marcel Arnold
Software Mentions: 1
Published: over 8 years ago

10.1002/cti2.1314

RNA sequencing identifies global transcriptional changes in peripheral CD4⁺ cells during active oesophagitis and following epicutaneous immunotherapy in eosinophilic oesophagitis
Cited by: 0
Author(s): Melanie A. Ruffner, Zhe Zhang, Kelly Maurer, Amanda B. Muir, Antonella Cianferoni, Kathleen E. Sullivan, Jonathan M. Spergel
Software Mentions: 1
Published: over 5 years ago

10.1177/1759091415593066

Combined HDAC1 and HDAC2 Depletion Promotes Retinal Ganglion Cell Survival After Injury Through Reduction of p53 Target Gene Expression
Cited by: 42
Author(s): Frédéric Lebrun-Julien, Ueli Suter
Software Mentions: 1
Published: about 11 years ago

10.1186/s12864-017-4241-1

ExUTR: a novel pipeline for large-scale prediction of 3′-UTR sequences from NGS data
Cited by: 31
Author(s): Zixia Huang, Emma C. Teeling
Software Mentions: 1
Published: over 8 years ago

10.1038/s42003-019-0685-y

Draft genome assembly and transcriptome data of the icefish Chionodraco myersi reveal the key role of mitochondria for a life without hemoglobin at subzero temperatures
Cited by: 22
Author(s): Luca Bargelloni, Massimiliano Babbucci, Serena Ferraresso, Chiara Papetti, Nicola Vitulo, R. Carraro, Marianna Pauletto, Gianfranco Santovito, Magnus Lucassen, Felix Christopher Mark, Lorenzo Zane, Tomaso Patarnello
Software Mentions: 1
Published: over 6 years ago

10.1038/s42003-020-01246-z

Omental macrophages secrete chemokine ligands that promote ovarian cancer colonization of the omentum via CCR1
Cited by: 47
Author(s): Venkatesh Krishnan, Supreeti Tallapragada, Bruce T. Schaar, Kalika Kamat, Anita M. Chanana, Yue Zhang, Sonia A. Patel, Vinita Parkash, Carrie W. Rinker‐Schaeffer, Ann K. Folkins, Erinn B. Rankin, Oliver Dorigo
Software Mentions: 1
Published: almost 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: almost 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: about 7 years ago

10.1186/s12864-020-07018-7

Expression of mitochondrial protein genes encoded by nuclear and mitochondrial genomes correlate with energy metabolism in dairy cattle
Cited by: 14
Author(s): Jigme Dorji, Christy J. Vander Jagt, Josie B. Garner, L. C. Marett, Brett Mason, Coralie M. Reich, Ruidong Xiang, Emily L. Clark, Benjamin G. Cocks, Amanda J. Chamberlain, Iona M. MacLeod, Hans D. Daetwyler
Software Mentions: 1
Published: over 5 years ago

10.1038/s42003-020-01573-1

The spatial RNA integrity number assay for in situ evaluation of transcriptome quality
Cited by: 8
Author(s): Linda Kvastad, Konstantin Carlberg, Ludvig Larsson, Eva Gracia Villacampa, Alexander Stuckey, Linnea Stenbeck, Annelie Mollbrink, Margherita Zamboni, Jens P Magnusson, Elisa Basmaci, Alia Shamikh, Gabriela Prochazka, A Schaupp, Åke Borg, Lars Fugger, Monica Nistér, Joakim Lundeberg
Software Mentions: 1
Published: over 5 years ago

10.1186/s12864-018-4909-1

Whole-transcriptome changes in gene expression accompany aging of sensory neurons in Aplysia californica
Cited by: 16
Author(s): Justin B. Greer, Michael C. Schmale, Lynne A. Fieber
Software Mentions: 1
Published: almost 8 years ago

10.1038/s42003-020-0928-y

BMPR2 promotes fatty acid oxidation and protects white adipocytes from cell death in mice
Cited by: 13
Author(s): Shuwen Qian, Jiabao Pan, Yan Su, Yan Tang, Yina Wang, Ying Zou, Yi Zhao, Hong Ma, Youyou Zhang, Yang Liu, Liang Guo, Qi‐Qun Tang
Software Mentions: 1
Published: about 6 years ago