10.1038/s41598-020-69451-8

Intrinsic transcriptomic sex differences in human endothelial cells at birth and in adults are associated with coronary artery disease targets
Cited by: 31
Author(s): Robin Hartman, Daniek Kapteijn, Saskia Haitjema, Mireille N. Bekker, Michal Mokrý, Gérard Pasterkamp, Mete Civelek, Hester M. den Ruijter
Software Mentions: 6
Published: about 6 years ago

10.1080/22221751.2020.1799723

Dysregulation in Akt/mTOR/HIF-1 signaling identified by proteo-transcriptomics of SARS-CoV-2 infected cells
Cited by: 203
Author(s): Sofia Appelberg, Soham Gupta, Sara Svensson Akusjärvi, Anoop T. Ambikan, Flora Mikaeloff, Elisa Saccon, Ákos Végvári, Rui Benfeitas, Maike Sperk, Marie Ståhlberg, Shuba Krishnan, Kamal Singh, Josef Penninger, Alì Mirazimi, Ujjwal Neogi
Software Mentions: 6
Published: over 6 years ago

10.1038/s41598-020-63355-3

Limits in the detection of m6A changes using MeRIP/m6A-seq
Cited by: 120
Author(s): Alexa B. R. McIntyre, Nandan S. Gokhale, Leandro Cerchietti, Samie R. Jaffrey, Stacy M. Horner, Christopher E. Mason
Software Mentions: 6
Published: over 6 years ago

10.3390/cells10040921

Sex-Biased lncRNA Signature in Fetal Growth Restriction (FGR)
Cited by: 2
Author(s): Aleksandra Lipka, J Jastrzebski, Łukasz Paukszto, Karol G Makowczenko, Elżbieta Łopieńska–Biernat, Marek Gowkielewicz, Ewa Lepiarczyk, Marta Wiszpolska, Mariusz Majewski, Marta Majewska
Software Mentions: 6
Published: over 5 years ago

10.1038/s41598-020-66224-1

Genomic deregulation of PRMT5 supports growth and stress tolerance in chronic lymphocytic leukemia
Cited by: 5
Author(s): Ann-Kathrin Schnormeier, Claudia Pommerenke, Maren Kaufmann, Hans Drexler, Max Koeppel
Software Mentions: 6
Published: about 6 years ago

10.1186/s12864-020-6748-0

Draft genome sequences of Hirudo medicinalis and salivary transcriptome of three closely related medicinal leeches
Cited by: 19
Author(s): Vladislav V. Babenko, Oleg V. Podgorny, Valentin A. Manuvera, Artem S. Kasianov, Alexander I. Manolov, Ekaterina N. Grafskaia, Dmitriy A. Shirokov, Alexey S. Kurdyumov, D. V. Vinogradov, Anastasia S. Nikitina, Sergey I. Kovalchuk, Nikolay Anikanov, Ivan Butenko, Olga Pobeguts, Daria Matyushkina, Daria V. Rakitina, Elena S. Kostryukova, Victor G. Zgoda, I. P. Baskova, В. М. Трухан, Mikhail S. Gelfand, Vadim M. Govorun, Helgi B. Schiöth, В. Н. Лазарев
Software Mentions: 6
Published: over 6 years ago

10.1186/s12915-018-0615-3

Mitochondrial unfolded protein response transcription factor ATFS-1 promotes longevity in a long-lived mitochondrial mutant through activation of stress response pathways
Cited by: 79
Author(s): Ziyun Wu, Megan M. Senchuk, Dylan J. Dues, Benjamin K. Johnson, Jason Cooper, Leira Lew, Emily Machiela, Claire E. Schaar, Heather DeJonge, T. Keith Blackwell, Jeremy M. Van Raamsdonk
Software Mentions: 6
Published: over 7 years ago

10.1186/s12920-021-01003-z

Repeat to gene expression ratios in leukemic blast cells can stratify risk prediction in acute myeloid leukemia
Cited by: 5
Author(s): Megumi Onishi-Seebacher, Galina Erikson, Zoe Sawitzki, Devon P. Ryan, Gabriele Greve, Michael Lübbert, Thomas Jenuwein
Software Mentions: 6
Published: about 5 years ago

10.3390/biomedicines9091120

Neural Precursor Cells Expanded Inside the 3D Micro-Scaffold Nichoid Present Different Non-Coding RNAs Profiles and Transcript Isoforms Expression: Possible Epigenetic Modulation by 3D Growth
Cited by: 3
Author(s): Letizia Messa, Bianca Barzaghini, Federica Rey, Cecilia Pandini, Gian Vincenzo Zuccotti, Cristina Cereda, Stephana Carelli, Manuela Teresa Raimondi
Software Mentions: 6
Published: almost 5 years ago

10.1038/s41598-021-98414-w

Integrated genomics point to immune vulnerabilities in pleural mesothelioma
Cited by: 7
Author(s): Anca Năstase, Amit Kumar Mandal, Shir Kiong Lu, Hima Anbunathan, Deborah Morris-Rosendahl, Yu Zhi Zhang, Xiaoming Sun, Spyridon Gennatas, Robert C. Rintoul, Matthew Edwards, Alex Bowman, Tatyana Chernova, T. Benepal, Eric Lim, Alison Taylor, Andrew G. Nicholson, Sanjay Popat, Anne E. Willis, Marion MacFarlane, Mark Lathrop, Anne M. Bowcock, Miriam F. Moffatt, William Cookson
Software Mentions: 6
Published: almost 5 years ago

10.12688/f1000research.8964.1

RiboProfiling: a Bioconductor package for standard Ribo-seq pipeline processing
Cited by: 58
Author(s): Alexandra Popa, Kévin Lebrigand, Agnès Paquet, Nicolas Nottet, Karine Robbe-Sermesant, Rainer Waldmann, Pascal Barbry
Software Mentions: 6
Published: about 10 years ago

10.1186/s12864-021-07974-8

SCReadCounts: estimation of cell-level SNVs expression from scRNA-seq data
Cited by: 8
Author(s): N M Prashant, Nawaf Alomran, Yu Chen, Hongyu Liu, Pavlos Bousounis, Mercedeh Movassagh, Nathan Edwards, Anélia Horvath
Software Mentions: 6
Published: almost 5 years ago

10.1038/s41598-017-17407-w

Activity-Dependent Regulation of Alternative Cleavage and Polyadenylation During Hippocampal Long-Term Potentiation
Cited by: 37
Author(s): Mariana Fontes, Ayşegül Güvenek, Riki Kawaguchi, Dinghai Zheng, Alden Huang, Victoria M. Ho, Patrick B. Chen, Xiaochuan Liu, Thomas J. O’Dell, Giovanni Coppola, Bin Tian, Kelsey C. Martin
Software Mentions: 6
Published: over 8 years ago

10.1038/s41598-019-50119-x

Tissue-specific mouse mRNA isoform networks
Cited by: 12
Author(s): Gaurav Kandoi, Julie A. Dickerson
Software Mentions: 6
Published: almost 7 years ago

10.1038/s41392-020-00437-8

CREBBP/EP300 mutations promoted tumor progression in diffuse large B-cell lymphoma through altering tumor-associated macrophage polarization via FBXW7-NOTCH-CCL2/CSF1 axis
Cited by: 72
Author(s): Yan‐Jiun Huang, Kedan Cai, Pengpeng Xu, Li Wang, Chuanxin Huang, Ying Fang, Shu Cheng, Xiao Jian Sun, Feng Liu, Jinyan Huang, Mengmeng Ji, Wei‐Li Zhao
Software Mentions: 6
Published: over 5 years ago

10.1016/j.stem.2019.07.009

Distinct Molecular Trajectories Converge to Induce Naive Pluripotency
Cited by: 27
Author(s): Hannah Stuart, Giuliano Giuseppe Stirparo, Tim Lohoff, Lawrence E. Bates, Masaki Kinoshita, Chee Lim, Elsa Joana Sousa, Katsiaryna Maskalenka, Aliaksandra Radzisheuskaya, Andrew A. Malcolm, Mariana R. P. Alves, Rebecca L. Lloyd, Sonia Nestorowa, Peter Humphreys, William Mansfield, Wolf Reik, Paul Bertone, Jennifer Nichols, Berthold Göttgens, José C.R. Silva
Software Mentions: 6
Published: almost 7 years ago

10.1038/s41598-019-50864-z

Circular RNA differential expression in blood cell populations and exploration of circRNA deregulation in pediatric acute lymphoblastic leukemia
Cited by: 62
Author(s): Enrico Gaffo, Elena Boldrin, Anna Dal Molin, Silvia Bresolin, Annagiulia Bonizzato, Luca Trentin, Chiara Frasson, Klaus‐Michael Debatin, Lueder Hinrich Meyer, Geertruy te Kronnie, Stefania Bortoluzzi
Software Mentions: 6
Published: almost 7 years ago

10.1016/j.stem.2021.04.031

Naive stem cell blastocyst model captures human embryo lineage segregation
Cited by: 139
Author(s): Akira Yanagida, Daniel Spindlow, Jennifer Nichols, Anish Dattani, Austin Smith, Ge Guo
Software Mentions: 6
Published: about 5 years ago

10.3390/cells8080921

Genes Controlled by DNA Methylation Are Involved in Wilms Tumor Progression
Cited by: 12
Author(s): João Victor da Silva Guerra, Bruna Maria de Sá Pereira, Jéssica Gonçalves Vieira da Cruz, Nicole de Miranda Scherer, Carolina Furtado, Rafaela Montalvão de Azevedo, Paulo Sérgio Lopes de Oliveira, Paulo Faria, Mariana Boroni, Beatriz de Camargo, Mariana Maschietto
Software Mentions: 6
Published: about 7 years ago

10.3390/cells8091004

Characterizing Human Cell Types and Tissue Origin Using the Benford Law
Cited by: 6
Author(s): Sne Morag, Mali Salmon‐Divon
Software Mentions: 6
Published: almost 7 years ago

10.1371/journal.pgen.1008804

Activation of cryptic splicing in bovine WDR19 is associated with reduced semen quality and male fertility
Cited by: 24
Author(s): Maya Hiltpold, Guanglin Niu, Naveen Kumar Kadri, Danang Crysnanto, Zih-Hua Fang, Mirjam Spengeler, F. Schmitz‐Hsu, Christian Fuerst, Hermann Schwarzenbacher, Franz R. Seefried, Frauke Seehusen, Ulrich Witschi, Angelika Schnieke, R. Fries, Heinrich Bollwein, Krzysztof Flisikowski, Hubert Pausch
Software Mentions: 6
Published: over 6 years ago

10.1038/s41422-020-00455-9

Discriminating mild from critical COVID-19 by innate and adaptive immune single-cell profiling of bronchoalveolar lavages
Cited by: 203
Author(s): Els Wauters, Pierre Van Mol, Abhishek D. Garg, S.L. Jansen, Yannick Van Herck, Lore Vanderbeke, Ayse Bassez, Bram Boeckx, Bert Malengier‐Devlies, Anna Timmerman, Thomas Van Brussel, Tina Van Buyten, Rogier Schepers, Elisabeth Heylen, Dieter Dauwe, Christophe Dooms, Jan Gunst, Greet Hermans, Philippe Meersseman, Dries Testelmans, Jonas Yserbyt, Sabine Tejpar, Walter De Wever, Patrick Matthys, Maria Bosisio, Michaël P Casaer, Frederik De Smet, Paul De Munter, Stéphanie Humblet-Baron, Adrian Liston, Natalie Lorent, Kim Martinod, Paul Proost, Jeroen Raes, Karin Thevissen, Robin Vos, Birgit Weynand, Carine Wouters, Johan Neyts, Joost Wauters, Junbin Qian, Diether Lambrechts
Software Mentions: 6
Published: over 5 years ago

10.1186/s12915-018-0547-y

Species comparison of liver proteomes reveals links to naked mole-rat longevity and human aging
Cited by: 52
Author(s): Ivonne Heinze, Martin Bens, Enrico Calzia, Susanne Holtze, Oleksandr Dakhovnik, Arne Sahm, Joanna Kirkpatrick, Karol Szafranski, Natalie Romanov, Sai Nagender Sama, Kerstin Hölzer, Stephan Singer, Maria A. Ermolaeva, Matthias Platzer, Thomas B. Hildebrandt, Alessandro Ori
Software Mentions: 6
Published: about 8 years ago

10.1186/s12864-018-4738-2

Functional signaling and gene regulatory networks between the oocyte and the surrounding cumulus cells
Cited by: 43
Author(s): Fernando H. Biase, Katelyn M. Kimble
Software Mentions: 6
Published: over 8 years ago

10.1186/s13046-021-02034-1

Immuno-genomic classification of colorectal cancer organoids reveals cancer cells with intrinsic immunogenic properties associated with patient survival
Cited by: 14
Author(s): Eun Jeong Cho, Minsuh Kim, Daum Jo, Jihye Kim, Ji-Hye Oh, Hee Chul Chung, Sun-Hye Lee, Deokhoon Kim, Sung Chun, Jihun Kim, Hyeonjin Lee, Tae Won Kim, Chang Sik Yu, Chang‐Keun Sung, Se Jin Jang
Software Mentions: 6
Published: about 5 years ago

10.1016/j.xcrm.2021.100267

Cabozantinib and dasatinib synergize to induce tumor regression in non-clear cell renal cell carcinoma
Cited by: 2
Author(s): Hui Wen Lue, Daniel S. Derrick, Soumya Rao, Ahna Van Gaest, Larry C. Cheng, Jennifer Podolak, Samantha Lawson, Changhui Xue, Devin Garg, Ralph E. White, Christopher W. Ryan, Justin M. Drake, Anna Ritz, Laura M. Heiser, George V. Thomas
Software Mentions: 6
Published: over 5 years ago

10.1186/s12915-018-0608-2

Migration through a small pore disrupts inactive chromatin organization in neutrophil-like cells
Cited by: 35
Author(s): Elsie C. Jacobson, Jo K. Perry, David S. Long, Ada L. Olins, Bryon E. Wright, Mark H. Vickers, Justin M. O’Sullivan
Software Mentions: 6
Published: over 7 years ago

10.1016/j.stem.2020.11.005

Capture of Mouse and Human Stem Cells with Features of Formative Pluripotency
Cited by: 125
Author(s): Masaki Kinoshita, M. Barber, William Mansfield, Yingzhi Cui, Daniel Spindlow, Giuliano Giuseppe Stirparo, Sabine Dietmann, Jennifer Nichols, Austin Smith
Software Mentions: 6
Published: over 5 years ago

10.1016/j.celrep.2019.11.026

Splice-Junction-Based Mapping of Alternative Isoforms in the Human Proteome
Cited by: 53
Author(s): Edward Lau, Yu Han, Damon R. Williams, Cody T Thomas, Rajani Shrestha, Joseph C. Wu, Maggie Lam
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.ppat.1009567

ATRX limits the accessibility of histone H3-occupied HSV genomes during lytic infection
Cited by: 7
Author(s): Joseph M Cabral, Camille H. Cushman, Catherine Sodroski, David M. Knipe
Software Mentions: 6
Published: over 5 years ago

10.1186/s12864-017-4386-y

Global accumulation of circRNAs during aging in Caenorhabditis elegans
Cited by: 127
Author(s): Mariela Cortés-López, Matthew Gruner, Daphne A. Cooper, Hannah N. Gruner, Alexandru-Ioan Voda, Alexander M. van der Linden, Pedro Miura
Software Mentions: 6
Published: over 8 years ago

10.1084/jem.20192275

<i>NCKAP1L</i> defects lead to a novel syndrome combining immunodeficiency, lymphoproliferation, and hyperinflammation
Cited by: 44
Author(s): Carla Castro, Michelle Rosenzwajg, Raphaël Carapito, Mohammad Shahrooei, Martina Konantz, Amjad Khan, Zhichao Miao, Miriam Groß, Thibaud Tranchant, Mirjana Radosavljevic, Nicodème Paul, Tristan Stemmelen, Fabien Pitoiset, Aurélie Hirschler, Benoît Nespola, Anne Molitor, Véronique Rolli, Angélique Pichot, Laura Faletti, Bruno Rinaldi, Sylvie Friant, Mark Mednikov, Hatice Karaüzüm, M. Javad Aman, Christine Carapito, Claudia Lengerke, Vahid Ziaee, Wafaa Eyaid, Stephan Ehl, Fayhan Alroqi, Nima Parvaneh, Seiamak Bahram
Software Mentions: 6
Published: about 6 years ago

10.1084/jem.20192386

Transcription cofactor GRIP1 differentially affects myeloid cell–driven neuroinflammation and response to IFN-β therapy
Cited by: 4
Author(s): Sanda Mimouna, David A. Rollins, Gayathri Shibu, Bowranigan Tharmalingam, Dinesh K Deochand, Xi Chen, David J. Oliver, Yurii Chinenov, Inez Rogatsky
Software Mentions: 6
Published: almost 6 years ago

10.1371/journal.ppat.1007852

The landscape of transcription initiation across latent and lytic KSHV genomes
Cited by: 11
Author(s): Xiang Ye, Yang Zhao, John Karijolich
Software Mentions: 6
Published: about 7 years ago

10.1186/s12915-021-01002-7

A cell-to-patient machine learning transfer approach uncovers novel basal-like breast cancer prognostic markers amongst alternative splice variants
Cited by: 12
Author(s): Jean-Philippe Villemin, Claudio Lorenzi, Marie-Sarah Cabrillac, Andrew Oldfield, William Ritchie, Reini F. Luco
Software Mentions: 6
Published: over 5 years ago

10.26508/lsa.201800175

A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs
Cited by: 16
Author(s): Charlotte Soneson, Michael I. Love, Rob Patro, Shobbir Hussain, Dheeraj Malhotra, Mark D. Robinson
Software Mentions: 6
Published: over 7 years ago

10.3389/fpls.2021.683681

Insertion of Badnaviral DNA in the Late Blight Resistance Gene (R1a) of Brinjal Eggplant (Solanum melongena)
Cited by: 9
Author(s): Saad Serfraz, Vikas Sharma, Florian Maumus, Xavier Aubriot, Andrew D. W. Geering, Pierre‐Yves Teycheney
Software Mentions: 6
Published: about 5 years ago

10.1186/s12864-015-2346-y

CANEapp: a user-friendly application for automated next generation transcriptomic data analysis
Cited by: 12
Author(s): Dmitry Velmeshev, Patrick Lally, Marco Magistri, Mohammad Ali Faghihi
Software Mentions: 6
Published: over 10 years ago

10.1371/journal.pgen.1007552

High-resolution transcriptional dissection of in vivo Atoh1-mediated hair cell conversion in mature cochleae identifies Isl1 as a co-reprogramming factor
Cited by: 56
Author(s): Tetsuji Yamashita, Fei Zheng, David Finkelstein, Zoe Kellard, Caroline Robert, Celeste Rosencrance, Ken Sugino, John Easton, Charles Gawad, Jian Zuo
Software Mentions: 6
Published: about 8 years ago

10.20892/j.issn.2095-3941.2020.0073

Single-cell RNA-seq reveals the immune escape and drug resistance mechanisms of mantle cell lymphoma
Cited by: 23
Author(s): Liang Wang, Steven Mo, Xin Li, Yuanyuan He, Jing Yang
Software Mentions: 6
Published: over 6 years ago

10.15252/msb.202110253

Model‐guided development of an evolutionarily stable yeast chassis
Cited by: 5
Author(s): Filipa Pereira, Helena Lopes, Paulo Maia, Britta Meyer, Justyna Nocon, Paula Jouhten, D. Konstantinidis, Eleni Kafkia, Miguel Rocha, Peter Kötter, Isabel Rocha, Kiran R. Patil
Software Mentions: 6
Published: about 5 years ago

10.1186/s12870-019-2222-z

Transcriptomic and metabolomic analyses provide insight into the volatile compounds of citrus leaves and flowers
Cited by: 15
Author(s): Haipeng Zhang, Mengjun Chen, Wen Huang, Zhenhua Wang, Jiajing Chen, Fang Liu, Hongyan Zhang, Zongzhou Xie, Dong Jiang, Yunjiang Cheng, Juan Xu
Software Mentions: 6
Published: over 6 years ago

10.1186/s12915-021-00996-4

Reorganization of the 3D chromatin architecture of rice genomes during heat stress
Cited by: 39
Author(s): Zhe Liang, Qian Zhang, Changmian Ji, Guihua Hu, Pingxian Zhang, Yifan Wang, Liwen Yang, Xiaofeng Gu
Software Mentions: 5
Published: over 5 years ago

10.1186/s12870-020-02702-y

Alternative splicing profiling provides insights into the molecular mechanisms of peanut peg development
Cited by: 3
Author(s): Xiaobo Zhao, Chunjuan Li, Hao Zhang, Yan Cheng, Quanxi Sun, Juan Wang, Cuiling Yuan, Shiguang Shan
Software Mentions: 5
Published: almost 6 years ago

10.1242/jcs.232223

Tox4 modulates cell fate reprogramming
Cited by: 12
Author(s): Lotte Vanheer, Juan Song, Natalie De Geest, Adrian Janiszewski, Irene Talón, Caterina Provenzano, Taeho Oh, Joel Chappell, Vincent Pasque
Software Mentions: 5
Published: over 7 years ago

10.3389/fcell.2020.00639

DNA Methyltransferase 1 (DNMT1) Function Is Implicated in the Age-Related Loss of Cortical Interneurons
Cited by: 14
Author(s): Anne M. Hahn, Daniel Pensold, Cathrin Bayer, Jessica Tittelmeier, Lourdes González-Bermúdez, Lisa Marx-Blümel, Jenice Linde, Jonas Groß, Gabriela Salinas-Riester, Thomas Lingner, Julia von Maltzahn, Marc Spehr, Tomas Pieler, Anja Urbach, Geraldine Zimmer-Bensch
Software Mentions: 5
Published: about 6 years ago

10.26508/lsa.202000709

Myeloid transformation by <i>MLL</i>-<i>ENL</i> depends strictly on C/EBP
Cited by: 4
Author(s): Radosław Wesołowski, Elisabeth Kowenz‐Leutz, Karin Zimmermann, Dorothea Dörr, Maria Hofstätter, Robert K. Slany, Alexander Mildner, Achim Leutz
Software Mentions: 5
Published: almost 6 years ago

10.1186/s12864-017-4031-9

unitas: the universal tool for annotation of small RNAs
Cited by: 83
Author(s): Daniel Gebert, Charlotte Hewel, David Rosenkranz
Software Mentions: 5
Published: almost 9 years ago

10.1016/j.molcel.2018.09.033

Exon Junction Complex Shapes the Transcriptome by Repressing Recursive Splicing
Cited by: 73
Author(s): Lorea Blázquez, Warren Emmett, Rupert Faraway, Jose Mario Bello Pineda, Simon Bajew, André Gohr, Nejc Haberman, Christopher R. Sibley, Robert K. Bradley, Manuel Irimia, Jernej Ule
Software Mentions: 5
Published: almost 8 years ago

10.1186/s40478-017-0414-z

Serum microRNA miR-501-3p as a potential biomarker related to the progression of Alzheimer’s disease
Cited by: 118
Author(s): Norikazu Hara, Masataka Kikuchi, Akinori Miyashita, Hiroyuki Hatsuta, Yuko Saito, Kensaku Kasuga, Shigeo Murayama, Takeshi Ikeuchi, Ryozo Kuwano
Software Mentions: 5
Published: over 9 years ago

10.1186/s12864-017-4007-9

Equine skeletal muscle adaptations to exercise and training: evidence of differential regulation of autophagosomal and mitochondrial components
Cited by: 28
Author(s): Kenneth Bryan, Beatrice A. McGivney, Gabriella Farries, Paul A. McGettigan, C. L. McGivney, K. F. Gough, David E. MacHugh, Lisa Katz, Emmeline W. Hill
Software Mentions: 5
Published: about 9 years ago

10.1016/j.cell.2021.03.062

Splice site m6A methylation prevents binding of U2AF35 to inhibit RNA splicing
Cited by: 88
Author(s): Mateusz Mendel, Kamila Delaney, Radha Raman Pandey, Kuan-Ming Chen, Joanna M. Wenda, Cathrine Broberg Vågbø, Florian Steiner, David Homolka, Ramesh S. Pillai
Software Mentions: 5
Published: about 5 years ago

10.1016/j.molcel.2019.11.021

Histone H2AK119 Mono-Ubiquitination Is Essential for Polycomb-Mediated Transcriptional Repression
Cited by: 208
Author(s): Simone Tamburri, Elisa Lavarone, Daniel Fernández-Pérez, E. J. Conway, Marika Zanotti, Daria Manganaro, Diego Pasini
Software Mentions: 5
Published: over 6 years ago

10.1186/s12859-019-2728-2

UTAP: User-friendly Transcriptome Analysis Pipeline
Cited by: 88
Author(s): Refael Kohen, Jonathan Barlev, Gil Hornung, Gil Stelzer, Ester Feldmesser, Kiril Kogan, Marilyn Safran, Dena Leshkowitz
Software Mentions: 5
Published: over 7 years ago

10.1186/s12864-019-5496-5

OMICfpp: a fuzzy approach for paired RNA-Seq counts
Cited by: 1
Author(s): Alberto Berral-González, Ángela L. Riffo‐Campos, Guillermo Ayala
Software Mentions: 5
Published: over 7 years ago

10.1186/s13073-021-00952-5

Distinct transcriptional programs stratify ovarian cancer cell lines into the five major histological subtypes
Cited by: 39
Author(s): Bethany Barnes, Louisa Nelson, Anthony Tighe, George J. Burghel, I‐Hsuan Lin, Sudha Desai, Joanne C. McGrail, Robert D. Morgan, Stephen S. Taylor
Software Mentions: 5
Published: almost 5 years ago

10.18632/aging.101341

Central role of the p53 pathway in the noncoding-RNA response to oxidative stress
Cited by: 45
Author(s): Paola Fuschi, Matteo Carrara, Christine Voellenkle, José Manuel García-Manteiga, Paolo Righini, Biagina Maimone, Elena Sangalli, Francesco Villa, Claudia Specchia, Mario Picozza, Giovanni Nano, Carlo Gaetano, Gaia Spinetti, Annibale Alessandro Puca, Alessandra Magenta, Fabio Martelli
Software Mentions: 5
Published: over 8 years ago

10.1186/s12864-021-07937-z

The genome of the extremophile Artemia provides insight into strategies to cope with extreme environments
Cited by: 13
Author(s): Stephanie De Vos, Stéphane Rombauts, Louis Coussement, Wannes Dermauw, Marnik Vuylsteke, Patrick Sorgeloos, James S. Clegg, Ziro Nambu, Filip Van Nieuwerburgh, Parisa Norouzitallab, Thomas Van Leeuwen, Tim De Meyer, Gilbert Van Stappen, Yves Van de Peer, Peter Bossier
Software Mentions: 5
Published: almost 5 years ago

10.1186/s13073-020-00783-w

The murine Microenvironment Cell Population counter method to estimate abundance of tissue-infiltrating immune and stromal cell populations in murine samples using gene expression
Cited by: 50
Author(s): Florent Petitprez, Sacha Lévy, Chengming Sun, Maxime Meylan, Christophe Linhard, Étienne Becht, Nabila Elarouci, David Tavel, Lubka T. Roumenina, Mira Ayadi, Catheriné Sautès-Fridman, Aurélien de Reyniès
Software Mentions: 5
Published: almost 6 years ago

10.1186/s12864-017-3673-y

Male fertility status is associated with DNA methylation signatures in sperm and transcriptomic profiles of bovine preimplantation embryos
Cited by: 95
Author(s): Jenna Kropp Schmidt, José A. Carrillo, Hadjer Namous, Daniels Alyssa, Sana M. Salih, Jiuzhou Song, Hasan Khatib
Software Mentions: 5
Published: over 9 years ago

10.1186/s13073-021-00924-9

The host transcriptional response to Candidemia is dominated by neutrophil activation and heme biosynthesis and supports novel diagnostic approaches
Cited by: 8
Author(s): Julie M. Steinbrink, Rachel A. Myers, Kaiyuan Hua, Melissa D. Johnson, Jessica Seidelman, Ephraim L. Tsalik, Ricardo Henao, Geoffrey S. Ginsburg, Christopher W. Woods, Barbara D. Alexander, Micah T. McClain
Software Mentions: 5
Published: about 5 years ago

10.1186/s13073-017-0432-2

Type 2 diabetes and obesity induce similar transcriptional reprogramming in human myocytes
Cited by: 33
Author(s): Leif Väremo, Tora Ida Henriksen, Camilla Schéele, Christa Broholm, Maria Pedersen, Mathias Uhlén, Bente Klarlund Pedersen, Jens Nielsen
Software Mentions: 5
Published: about 9 years ago

10.1186/s13073-020-00747-0

Strain-resolved microbiome sequencing reveals mobile elements that drive bacterial competition on a clinical timescale
Cited by: 37
Author(s): Soumaya Zlitni, Alex Bishara, Eli L. Moss, Е. И. Ткаченко, Joyce B. Kang, Rebecca Culver, Tessa M. Andermann, Ziming Weng, Christina M. Wood, Christine Handy, Hanlee P. Ji, Serafim Batzoglou, Ami S. Bhatt
Software Mentions: 5
Published: about 6 years ago

10.1186/s13041-021-00835-1

Altered hippocampal transcriptome dynamics following sleep deprivation
Cited by: 14
Author(s): Marie E. Gaine, Ethan Bahl, Snehajyoti Chatterjee, Jacob J. Michaelson, Ted Abel, Lisa C. Lyons
Software Mentions: 5
Published: about 5 years ago

10.1186/s13059-021-02494-w

Differential regulation of mRNA fate by the human Ccr4-Not complex is driven by coding sequence composition and mRNA localization
Cited by: 12
Author(s): Sarah L. Gillen, Chiara Giacomelli, Kelly Hodge, Sara Zanivan, Martin Bushell, Ania Wilczynska
Software Mentions: 5
Published: almost 5 years ago

10.1186/s13073-016-0348-2

Epigenomic and metabolic responses of hypothalamic POMC neurons to gestational nicotine exposure in adult offspring
Cited by: 9
Author(s): José P. Silva, Guerline Lambert, Derek Van Booven, Claes Wahlestedt
Software Mentions: 5
Published: almost 10 years ago

10.1186/s13578-020-00399-y

Alternative splicing signatures in preimplantation embryo development
Cited by: 12
Author(s): Geng Tian, Jing Li, Ji Wu
Software Mentions: 5
Published: over 6 years ago

10.1172/JCI91363

The U2AF1S34F mutation induces lineage-specific splicing alterations in myelodysplastic syndromes
Cited by: 70
Author(s): Bon Ham Yip, Violetta Steeples, Emmanouela Repapi, Richard N. Armstrong, Miriam Llorian, S. Roy, Jacqueline Shaw, Hamid Dolatshad, Stephen Taylor, Amit Verma, Matthias Bartenstein, Paresh Vyas, Nicholas C. P. Cross, Luca Malcovati, Mario Cazzola, Eva Hellström‐Lindberg, Seishi Ogawa, Christopher W.J. Smith, Andrea Pellagatti, Jacqueline Boultwood
Software Mentions: 5
Published: over 9 years ago

10.3390/cancers12113208

Impact of Genetic Ancestry on Prognostic Biomarkers in Uveal Melanoma
Cited by: 2
Author(s): Daniel A. Rodriguez, Margarita Dorantes Sánchez, Christina L. Decatur, Zélia M. Corrêa, Eden R. Martin, J. William Harbour
Software Mentions: 5
Published: almost 6 years ago

10.1016/j.cell.2016.09.006

Inheritable Silencing of Endogenous Genes by Hit-and-Run Targeted Epigenetic Editing
Cited by: 349
Author(s): Angelo Amabile, Alessandro Migliara, Paola Capasso, Mauro Biffi, Davide Cittaro, Luigi Naldini, Angelo Lombardo
Software Mentions: 5
Published: almost 10 years ago

10.1186/s12864-020-06911-5

Wild mice with different social network sizes vary in brain gene expression
Cited by: 2
Author(s): Patrícia C. Lopes, Barbara König
Software Mentions: 5
Published: about 6 years ago

10.1186/s13059-021-02505-w

Mapping and modeling the genomic basis of differential RNA isoform expression at single-cell resolution with LR-Split-seq
Cited by: 23
Author(s): Elisabeth Rebboah, Fairlie Reese, Katherine Williams, Gabriela Balderrama-Gutierrez, Cassandra McGill, Diane Trout, Isaryhia Rodriguez, Heidi Yahan Liang, B Wold, A Mortazavi
Software Mentions: 5
Published: almost 5 years ago

10.1186/s13059-021-02397-w

A trans locus causes a ribosomopathy in hypertrophic hearts that affects mRNA translation in a protein length-dependent fashion
Cited by: 4
Author(s): Franziska Witte, Jorge Ruiz-Orera, Camilla Ciolli Mattioli, Susanne Blachut, Eleonora Adami, Jana Felicitas Schulz, Valentin Schneider-Lunitz, Oliver Hummel, Giannino Patone, Michael Mücke, Jan Šilhavý, Matthias Heinig, Leonardo Bottolo, Daniel Sanchı́s, Martin Vingron, Marina Chekulaeva, Michal Pravenec, Norbert Hübner, Sebastiaan van Heesch
Software Mentions: 5
Published: about 5 years ago

10.1186/s12864-021-07849-y

Genome-wide identification and characterization of caffeoyl-coenzyme A O-methyltransferase genes related to the Fusarium head blight response in wheat
Cited by: 7
Author(s): Guang Yang, Wenqiu Pan, Ruoyu Zhang, Yan Pan, Qifan Guo, Weining Song, Wenbin Zheng, Xiaojun Nie
Software Mentions: 5
Published: about 5 years ago

10.1186/s13059-021-02446-4

Retrotransposons as pathogenicity factors of the plant pathogenic fungus Botrytis cinerea
Cited by: 20
Author(s): Antoine Porquier, Constance Tisserant, F. Salinas, Carla Glassl, Lucas E. Wange, Wolfgang Enard, Andreas Hauser, Matthias Hahn, Arne Weiberg
Software Mentions: 5
Published: about 5 years ago

10.1186/s13059-021-02334-x

The impact of cell type and context-dependent regulatory variants on human immune traits
Cited by: 27
Author(s): Zepeng Mu, Wei Wei, Benjamin Jung Fair, Jinlin Miao, Ping Zhu, Yang Li
Software Mentions: 5
Published: over 5 years ago

10.1002/advs.202001402

TRADES: Targeted RNA Demethylation by SunTag System
Cited by: 25
Author(s): Jing Mo, Zonggui Chen, Shanshan Qin, Shu Li, Chuangang Liu, Lu Zhang, Ruoxi Ran, Ying Kong, Fang Wang, Song-Mei Liu, Yu Zhou, Xiaolian Zhang, Xiaocheng Weng, Xiang Zhou
Software Mentions: 5
Published: about 6 years ago

10.1186/s13059-021-02348-5

Genetic and environmental modulation of transposition shapes the evolutionary potential of Arabidopsis thaliana
Cited by: 65
Author(s): Pierre Baduel, Basile Leduque, Amandine Ignace, Isabelle Gy, José Pedro Gil, Olivier Loudet, Vincent Colot, Leandro Quadrana
Software Mentions: 5
Published: over 5 years ago

10.1093/molbev/msz099

Return to the Sea, Get Huge, Beat Cancer: An Analysis of Cetacean Genomes Including an Assembly for the Humpback Whale (Megaptera novaeangliae)
Cited by: 72
Author(s): Marc Tollis, Jooke Robbins, Andrew E. Webb, Lukas F. K. Kuderna, Aleah F. Caulin, Jacinda D Garcia, Martine Bérubé, Nader Pourmand, Tomàs Marquès-Bonet, Mary J. O’Connell, Per Palsbøll, Carlo C. Maley
Software Mentions: 5
Published: over 7 years ago

10.1016/j.ajhg.2021.04.024

Bi-allelic loss-of-function variants in BCAS3 cause a syndromic neurodevelopmental disorder
Cited by: 6
Author(s): Holger Hengel, Shabab B. Hannan, Sarah Dyack, Sara MacKay, Ulrich Schatz, Martin Fleger, Andreas Kurringer, Ghassan Balousha, Zaïd Ghanim, Fowzan S. Alkuraya, Hamad Alzaidan, Hessa S. Alsaif, Tadahiro Mitani, Sevcan Tuğ Bozdoğan, Davut Pehlivan, James R. Lupski, Joseph J Gleeson, Mohammadreza Dehghani, Mohammad Yahya Vahidi Mehrjardi, Elliott H. Sherr, Kendall C. Parks, Emanuela Argilli, Amber Begtrup, Hamid Galehdari, Osama Balousha, Gholamreza Shariati, Neda Mazaheri, Reza Azizi Malamiri, Alistair T. Pagnamenta, Helen Kingston, Siddharth Banka, Adam Jackson, Mathew Osmond, Angelika Rieß, Tobias B. Haack, Thomas Nägele, Stefanie Schuster, Stefan Hauser, Jakob Admard, Nicolas Casadei, Ana Velić, Boris Maček, Stephan Ossowski, Henry Houlden, Reza Maroofian, Lüdger Schöls
Software Mentions: 5
Published: about 5 years ago

10.1186/s13059-021-02296-0

2passtools: two-pass alignment using machine-learning-filtered splice junctions increases the accuracy of intron detection in long-read RNA sequencing
Cited by: 12
Author(s): Matthew T Parker, Katarzyna Knop, Geoffrey J. Barton, Gordon G. Simpson
Software Mentions: 5
Published: over 5 years ago

10.1186/s13059-021-02298-y

SRSF3 and SRSF7 modulate 3′UTR length through suppression or activation of proximal polyadenylation sites and regulation of CFIm levels
Cited by: 26
Author(s): Oliver D. Schwich, Nicole Blümel, Mario Keller, Marius Wegener, Samarth Thonta Setty, Melinda Elaine Brunstein, Ina Poser, Igor Ruiz de los Mozos, Beatrix Suess, Christian Münch, François McNicoll, Kathi Zarnack, Michaela Müller-McNicoll
Software Mentions: 5
Published: over 5 years ago

10.1186/s13195-020-00716-0

Prognosis prediction model for conversion from mild cognitive impairment to Alzheimer’s disease created by integrative analysis of multi-omics data
Cited by: 27
Author(s): Daichi Shigemizu, Shintaro Akiyama, Sayuri Higaki, Toshiyuki Sugimoto, Takashi Sakurai, Keith A. Boroevich, Alok Sharma, Tatsuhiko Tsunoda, Takahiro Ochiya, Shumpei Niida, Kouichi Ozaki
Software Mentions: 5
Published: almost 6 years ago

10.1186/s13059-021-02263-9

Optimized RNA-targeting CRISPR/Cas13d technology outperforms shRNA in identifying functional circRNAs
Cited by: 62
Author(s): Yang Zhang, Tuan M. Nguyen, Xiao‐Ou Zhang, Limei Wang, Tin Phan, John G. Clohessy, Pier Paolo Pandolfi
Software Mentions: 5
Published: over 5 years ago

10.1186/s13059-021-02464-2

Systematic functional interrogation of human pseudogenes using CRISPRi
Cited by: 11
Author(s): Ming Sun, Yunfei Wang, Caishang Zheng, Yanjun Wei, Jiakai Hou, Peng Zhang, Wei He, Xiangdong Lv, Yao Ding, Han Liang, Chung-Chau Hon, Xi Chen, Xu Han, Yiwen Chen
Software Mentions: 5
Published: almost 5 years ago

10.1242/bio.040683

Fgf3 is crucial for the generation of monoaminergic cerebrospinal fluid contacting cells in zebrafish
Cited by: 4
Author(s): Isabel Reuter, Jana Jäckels, Susanne Kneitz, Jochen Kuper, Klaus–Peter Lesch, Christina Lillesaar
Software Mentions: 5
Published: over 7 years ago

10.1186/s12864-016-3118-z

Web-based bioinformatics workflows for end-to-end RNA-seq data computation and analysis in agricultural animal species
Cited by: 10
Author(s): Weizhong Li, René Richter, Yunsup Jung, Quanyin Zhu, Robert W. Li
Software Mentions: 5
Published: almost 10 years ago

10.3390/cancers12061487

Only Hematopoietic Stem and Progenitor Cells from Cord Blood Are Susceptible to Malignant Transformation by MLL-AF4 Translocations
Cited by: 12
Author(s): Kathy-Ann Secker, Lukas Bruns, Hildegard Keppeler, Johan Jeong, Thomas Hentrich, Julia M. Schulze‐Hentrich, Barbara Mankel, Falko Fend, Dominik Schneidawind, Corina Schneidawind
Software Mentions: 5
Published: about 6 years ago

10.1186/s12864-020-07107-7

Development and comparison of RNA-sequencing pipelines for more accurate SNP identification: practical example of functional SNP detection associated with feed efficiency in Nellore beef cattle
Cited by: 13
Author(s): Stephanie Lam, J. Zeidan, F. Miglior, Aroa Suárez-Vega, Isabel Gómez-Redondo, Pablo Augusto de Souza Fonseca, Leluo Guan, Sinéad M. Waters, Ángela Cánovas
Software Mentions: 5
Published: almost 6 years ago

10.1186/s12864-016-2745-8

An optimized protocol for generation and analysis of Ion Proton sequencing reads for RNA-Seq
Cited by: 17
Author(s): Yongxian Yuan, Huaiqian Xu, Rufina Leung
Software Mentions: 5
Published: about 10 years ago

10.1186/s12864-017-3810-7

The Cyprinodon variegatus genome reveals gene expression changes underlying differences in skull morphology among closely related species
Cited by: 27
Author(s): Ezra Lencer, Wesley C. Warren, Richard G. Harrison, Amy R. McCune
Software Mentions: 5
Published: about 9 years ago

10.1186/s12859-019-2947-6

Yanagi: Fast and interpretable segment-based alternative splicing and gene expression analysis
Cited by: 3
Author(s): Mohamed K. Gunady, Stephen M. Mount, Héctor Corrada Bravo
Software Mentions: 5
Published: about 7 years ago

10.1186/s13059-020-02129-6

sn-spMF: matrix factorization informs tissue-specific genetic regulation of gene expression
Cited by: 16
Author(s): Yuan He, Surya B. Chhetri, Marios Arvanitis, Kaushik Srinivasan, François Aguet, Kristin Ardlie, Alvaro N. Barbeira, Rodrigo Bonazzola, Hae Kyung Im, Christopher D. Brown, Alexis Battle
Software Mentions: 5
Published: almost 6 years ago

10.1186/s12864-020-6495-2

Whole-genome sequencing of wild Siberian musk deer (Moschus moschiferus) provides insights into its genetic features
Cited by: 8
Author(s): Yang Li, Menggen Dalai, Rongguo Su, Weili Lin, Myagmarsuren Erdenedalai, Batkhuu Luvsantseren, Chimedragchaa Chimedtseren, Zhen Wang, Surong Hasi
Software Mentions: 5
Published: over 6 years ago

10.3390/cancers12010037

Molecular Signature of Subtypes of Non-Small-Cell Lung Cancer by Large-Scale Transcriptional Profiling: Identification of Key Modules and Genes by Weighted Gene Co-Expression Network Analysis (WGCNA)
Cited by: 158
Author(s): Magdalena Niemira, François Collin, Anna Szałkowska, Agnieszka Bielska, Karolina Chwiałkowska, Joanna Reszeć, Jacek Nikliński, Mirosław Kwaśniewski, Adam Krętowski
Software Mentions: 5
Published: over 6 years ago

10.1002/advs.202004973

In Vivo Induction of Regulatory T Cells Via CTLA‐4 Signaling Peptide to Control Autoimmune Encephalomyelitis and Prevent Disease Relapse
Cited by: 13
Author(s): Gil Ran Kim, Won-Ju Kim, Su-Ho Lim, Hong-Gyun Lee, Ja Hyun Koo, Kyung Ho Nam, Sung Min Kim, Sung Dong Park, Je-Min Choi
Software Mentions: 5
Published: over 5 years ago

10.1186/s13068-020-01838-1

Genome-scale metabolic modeling underscores the potential of Cutaneotrichosporon oleaginosus ATCC 20509 as a cell factory for biofuel production
Cited by: 16
Author(s): Nhung Pham, Maarten J.M.F. Reijnders, María Suárez-Diez, Bart Nijsse, Jan Springer, Gerrit Eggink, Peter J. Schaap
Software Mentions: 5
Published: over 5 years ago

10.1186/s13059-021-02460-6

Functional genomics atlas of synovial fibroblasts defining rheumatoid arthritis heritability
Cited by: 23
Author(s): Xin Ge, Mojca Frank-Bertoncelj, Kerstin Klein, Amanda McGovern, Tadeja Kuret, Miranda Houtman, Blaž Burja, Raphael Micheroli, Chenfu Shi, Miriam Marks, Andrew Filer, Christopher D. Buckley, Gisela Orozco, Oliver Distler, Andrew P. Morris, Paul Martin, Stephen Eyre, Caroline Ospelt
Software Mentions: 5
Published: almost 5 years ago

10.1093/molbev/msaa110

Selection following Gene Duplication Shapes Recent Genome Evolution in the Pea Aphid Acyrthosiphon pisum
Cited by: 10
Author(s): Rosa Fernández, Marina Marcet‐Houben, Fabrice Legeai, Gautier Richard, Stéphanie Robin, Valentin Wucher, Cinta Pegueroles, Toni Gabaldón, Denis Tagu
Software Mentions: 5
Published: over 6 years ago

10.1172/JCI133187

Mesenchymal niche remodeling impairs hematopoiesis via stanniocalcin 1 in acute myeloid leukemia
Cited by: 45
Author(s): Alexander Waclawiczek, Ashley Hamilton, Kevin Rouault-Pierre, Ander Abarrategi, Manuel Garcia-Albornoz, Farideh Miraki-Moud, Nourdine Bah, John G. Gribben, Jude Fitzgibbon, David Taussig, Dominique Bonnet
Software Mentions: 5
Published: over 6 years ago