cran: STAR | Projects | Ecosyste.ms: Papers

10.1038/s41598-021-97258-8

Novel interferon-sensitive genes unveiled by correlation-driven gene selection and systems biology
Cited by: 3
Author(s): Cristina Cheroni, Lara Manganaro, Lorena Donnici, Valeria Bevilacqua, Raoul J. P. Bonnal, Riccardo Rossi, Raffaele De Francesco
Software Mentions: 5
Published: about 5 years ago

10.7554/eLife.52004

Single cell transcriptional signatures of the human placenta in term and preterm parturition
Cited by: 173
Author(s): Roger Piqué-Regi, Roberto Romero, Adi L. Tarca, Edward Sendler, Yi Xu, Valeria Garcia‐Flores, Yaozhu Leng, Francesca Luca, Sonia S. Hassan, Nardhy Gomez-López
Software Mentions: 5
Published: almost 7 years ago

10.3389/fimmu.2021.645446

Antiretroviral Treatment-Induced Decrease in Immune Activation Contributes to Reduced Susceptibility to Tuberculosis in HIV-1/Mtb Co-infected Persons
Cited by: 4
Author(s): Katalin A. Wilkinson, Deborah Schneider-Luftman, Rachel Lai, Christopher Barrington, Nishtha Jhilmeet, David M. Lowe, Gavin Kelly, Robert J. Wilkinson
Software Mentions: 5
Published: over 5 years ago

10.12688/wellcomeopenres.14735.2

Mapping targets for small nucleolar RNAs in yeast
Cited by: 16
Author(s): Tatiana Dudnakova, Hywel Dunn-Davies, Rosie Peters, David Tollervey
Software Mentions: 5
Published: almost 8 years ago

10.7554/eLife.49424

Single-cell transcriptomes and whole-brain projections of serotonin neurons in the mouse dorsal and median raphe nuclei
Cited by: 164
Author(s): Jing Ren, Alina Isakova, Drew Friedmann, Jiawei Zeng, Sophie M. Grutzner, Albert Pun, Grace Zhao, Sai Saroja Kolluru, Ruiyu Wang, Rui Lin, Pengcheng Li, Anan Li, Jennifer L. Raymond, Qi Luo, Minmin Luo, Stephen R. Quake, Liqun Luo
Software Mentions: 5
Published: almost 7 years ago

10.1371/journal.pgen.1007559

Transcriptome analysis of adult Caenorhabditis elegans cells reveals tissue-specific gene and isoform expression
Cited by: 141
Author(s): Rachel Kaletsky, Victoria Yao, April Williams, Alexi Runnels, Alicja Tadych, Shaoqiang Zhou, Olga G. Troyanskaya, Coleen T. Murphy
Software Mentions: 5
Published: about 8 years ago

10.1371/journal.pgen.1007268

Activation of DAF-16/FOXO by reactive oxygen species contributes to longevity in long-lived mitochondrial mutants in Caenorhabditis elegans
Cited by: 106
Author(s): Megan M. Senchuk, Dylan J. Dues, Claire E. Schaar, Benjamin K. Johnson, Zachary Madaj, Megan J. Bowman, Mary E. Winn, Jeremy M. Van Raamsdonk
Software Mentions: 5
Published: over 8 years ago

10.7554/eLife.62850

Individual differences in honey bee behavior enabled by plasticity in brain gene regulatory networks
Cited by: 24
Author(s): Beryl M. Jones, Vikyath D. Rao, Tim Gernat, Tobias Jagla, Amy Cash Ahmed, Rubin Be, Troy J. Comi, Shounak Bhogale, Syed Sameed Husain, Charles Blatti, Martin Middendorf, Saurabh Sinha, Sriram Chandrasekaran, Gene E. Robinson
Software Mentions: 5
Published: almost 6 years ago

10.3389/fcell.2021.669354

Transcriptomic Signature of Human Embryonic Thyroid Reveals Transition From Differentiation to Functional Maturation
Cited by: 7
Author(s): Geert Dom, Petr Dmitriev, Marie-Alexandra Lambot, Guy Van Vliet, Daniel Glinoer, Frédérick Libert, Anne Lefort, Jacques Emile Dumont, Carine Maenhaut
Software Mentions: 5
Published: over 5 years ago

10.1186/s13293-018-0205-7

Tissue-specific pathways and networks underlying sexual dimorphism in non-alcoholic fatty liver disease
Cited by: 55
Author(s): Zeyneb Kurt, Rio Barrere‐Cain, Jonnby LaGuardia, Margarete Mehrabian, Calvin Pan, Simon T. Hui, Frode Norheim, Zhiqiang Zhou, Yehudit Hasin, Aldons J. Lusis, Xia Yang
Software Mentions: 5
Published: almost 8 years ago

10.1371/journal.ppat.1007050

Isolation of a natural DNA virus of Drosophila melanogaster, and characterisation of host resistance and immune responses
Cited by: 48
Author(s): William H. Palmer, Nathan Medd, Philippa M. Beard, Darren J. Obbard
Software Mentions: 5
Published: over 8 years ago

10.1371/journal.pgen.1007661

Balancing selection on a recessive lethal deletion with pleiotropic effects on two neighboring genes in the porcine genome
Cited by: 29
Author(s): Martijn F.L. Derks, Marcos S. Lopes, Mirte Bosse, Ole Madsen, Bert Dibbits, B. Harlizius, M.A.M. Groenen, Hendrik Jan Megens
Software Mentions: 5
Published: about 8 years ago

10.3390/genes12071058

Exposure to Fine Particulate Matter Air Pollution Alters mRNA and miRNA Expression in Bone Marrow-Derived Endothelial Progenitor Cells from Mice
Cited by: 4
Author(s): Xiaohong Li, Petra Haberzettl, Daniel J. Conklin, Aruni Bhatnagar, Eric C. Rouchka, Mei Zhang, Timothy E. O’Toole
Software Mentions: 5
Published: over 5 years ago

10.1186/s13058-019-1230-0

Elacestrant (RAD1901) exhibits anti-tumor activity in multiple ER+ breast cancer models resistant to CDK4/6 inhibitors
Cited by: 44
Author(s): Hemang Patel, Nianjun Tao, Kyung Min Lee, Mariela Huerta, Heike Arlt, Tara Mullarkey, Steven Troy, Carlos L. Arteaga, Teeru Bihani
Software Mentions: 5
Published: almost 7 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: almost 6 years ago

10.3389/fimmu.2019.01863

Molecular Characterization of Human Lymph Node Stromal Cells During the Earliest Phases of Rheumatoid Arthritis
Cited by: 13
Author(s): Emmanuel Karouzakis, J Hähnlein, Cristoforo Grasso, Johanna F. Semmelink, Paul P. Tak, Daniëlle M. Gerlag, Caroline Ospelt, Lisa G. M. van Baarsen
Software Mentions: 5
Published: about 7 years ago

10.7717/peerj.11237

NGScloud2: optimized bioinformatic analysis using Amazon Web Services
Cited by: 4
Author(s): Fernando Mora‐Márquez, José Luis Vázquez-Poletti, Unai López de Heredia
Software Mentions: 5
Published: over 5 years ago

10.3389/fimmu.2020.550769

HDAC3 Mediates the Inflammatory Response and LPS Tolerance in Human Monocytes and Macrophages
Cited by: 26
Author(s): Mohammed Ghiboub, Jing Zhao, Andrew Y. Li Yim, Ronald Schilderink, Caroline Verseijden, Patricia H. P. van Hamersveld, José Duarte, Theodorus B. M. Hakvoort, Iris Admiraal, Nicola Harker, David F. Tough, Peter Henneman, Menno P.J. de Winther, Wouter J. de Jonge
Software Mentions: 5
Published: about 6 years ago

10.1038/s41598-020-70131-w

Transcriptomic profile of adverse neurodevelopmental outcomes after neonatal encephalopathy
Cited by: 6
Author(s): Paolo Montaldo, Aubrey J. Cunnington, Vânia Oliveira, Ravi Swamy, Prathik Bandya, Stuti Pant, Peter J Lally, Phoebe Ivain, Josephine Mendoza, Gaurav Atreja, Padmesh Vadakepat, Mythili Baburaj, Monica Sebastian, Indiramma Yasashwi, Chinnathambi Kamalarathnam, Rema Chandramohan, Mangalabharathi Sundaram, Kumutha Kumaraswami, Shobha Kumar, Naveen Benakappa, Swati Manerkar, Jayashree Mondhkar, Vinayagam Prakash, Mohammed Sajjid, Arasar Seeralar, Ismat Jahan, Sadeka Choudhury Moni, Mohammod Shahidullah, Radhika Sujatha, M Chandrasekaran, Siddarth Ramji, Seetha Shankaran, Myrsini Kaforou, Jethro Herberg, Sudhin Thayyil
Software Mentions: 5
Published: about 6 years ago

10.1155/2018/2439527

RNA-seq Reveals the Overexpression of IGSF9 in Endometrial Cancer
Cited by: 11
Author(s): Zonggao Shi, Chunyan Li, Laura Tarwater, Jun Li, Yang Li, William Kaliney, Darshan S. Chandrashekar, M. Sharon Stack
Software Mentions: 5
Published: almost 9 years ago

10.3390/genes12030385

Maternal Vitamin and Mineral Supplementation and Rate of Maternal Weight Gain Affects Placental Expression of Energy Metabolism and Transport-Related Genes
Cited by: 25
Author(s): Wellison J. S. Diniz, Lawrence P. Reynolds, P. P. Borowicz, Alison K Ward, Kevin K. Sedivec, Kacie L McCarthy, Cierrah J Kassetas, Friederike Baumgaertner, James D Kirsch, Sheri T. Dorsam, Tammi L Neville, J Chris Forcherio, Ronald Scott, J. S. Caton, Carl R Dahlen
Software Mentions: 5
Published: over 5 years ago

10.3389/fimmu.2019.01629

Sonic Hedgehog Is a Determinant of γδ T-Cell Differentiation in the Thymus
Cited by: 12
Author(s): Konstantinos Mengrelis, Ching‐In Lau, Jasmine Rowell, Anisha Solanki, S. Norris, Scott R. Ross, M. Ono, Susan V. Outram, Tessa Crompton
Software Mentions: 5
Published: about 7 years ago

10.1016/j.isci.2021.102847

High glucose macrophage exosomes enhance atherosclerosis by driving cellular proliferation & hematopoiesis
Cited by: 25
Author(s): Laura Bouchareychas, Phat Duong, Tuan Anh Phu, Eric Alsop, Bessie Meechoovet, Rebecca Reiman, M. Ng, Ryō Yamamoto, Hiromitsu Nakauchi, Warren J. Gasper, Kendall Van Keuren‐Jensen, Robert L. Raffaı̈
Software Mentions: 5
Published: about 5 years ago

10.3390/ijms21186488

Lipid Stores and Lipid Metabolism Associated Gene Expression in Porcine and Bovine Parthenogenetic Embryos Revealed by Fluorescent Staining and RNA-seq
Cited by: 16
Author(s): Arkadiusz Kajdasz, Ewelina Warzych, Natalia Derebecka, Zofia E. Madeja, D. Lechniak, Joanna Wesoły, Piotr Pawlak
Software Mentions: 5
Published: about 6 years ago

10.1002/pld3.220

Identification of nodulation‐related genes in Medicago truncatula using genome‐wide association studies and co‐expression networks
Cited by: 4
Author(s): Jean Michel Michno, Junqi Liu, Joseph Jeffers, Robert M. Stupar, Chad L. Myers
Software Mentions: 5
Published: over 6 years ago

10.1038/s42003-018-0122-7

Genomic analysis of Sparus aurata reveals the evolutionary dynamics of sex-biased genes in a sequential hermaphrodite fish
Cited by: 44
Author(s): Marianna Pauletto, Tereza Manousaki, Serena Ferraresso, Massimiliano Babbucci, Alexandros Tsakogiannis, Bruno Louro, Nicola Vitulo, Viet Ha Quoc, R. Carraro, Daniela Bertotto, Rafaella Franch, Francesco Maroso, Muhammad Aslam, Anna K. Sonesson, Barbara Simionati, G Malacrida, Alessandro Cestaro, Stefano Caberlotto, Elena Sarropoulou, C. C. Mylonas, Deborah M. Power, Tomaso Patarnello, Adelino V.M. Canário, Costas S. Tsigenopoulos, Luca Bargelloni
Software Mentions: 5
Published: about 8 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

10.1038/s41598-020-60065-8

Functional omics analyses reveal only minor effects of microRNAs on human somatic stem cell differentiation
Cited by: 7
Author(s): Jessica Schira‐Heinen, A. Czapla, Marion Hendricks, Andreas Kloetgen, Wasco Wruck, James Adjaye, Gesine Kögler, Hans Müller, Kai Stühler, Hans‐Ingo Trompeter
Software Mentions: 5
Published: over 6 years ago

10.1038/s41598-020-60638-7

Aberrant expression of PAR bZIP transcription factors is associated with epileptogenesis, focus on hepatic leukemia factor
Cited by: 7
Author(s): Lukáš Rambousek, Tilo Gschwind, Carlos Lafourcade, Jean-Charles Paterna, Linda Dib, Jean‐Marc Fritschy, Adriano Fontana
Software Mentions: 5
Published: over 6 years ago

10.1534/g3.120.401622

Alternative Splicing During the Chlamydomonas reinhardtii Cell Cycle
Cited by: 10
Author(s): Manishi Pandey, Gary D. Stormo, Susan K. Dutcher
Software Mentions: 5
Published: about 6 years ago

10.3390/ijms22052738

Identification of Overexpressed Genes in Malignant Pleural Mesothelioma
Cited by: 11
Author(s): Federica Morani, Luisa Bisceglia, Giulia Rosini, Luciano Mutti, Ombretta Melaiu, Stefano Landi, Federica Gemignani
Software Mentions: 5
Published: over 5 years ago

10.1038/s42003-020-01181-z

Transcriptomic and proteomic signatures of stemness and differentiation in the colon crypt
Cited by: 27
Author(s): Amber N. Habowski, Jessica L. Flesher, Jennifer Bates, Chia‐Feng Tsai, Kendall J. Martin, Rui Zhao, Anand K. Ganesan, Robert A. Edwards, Tujin Shi, H. Steven Wiley, Yongsheng Shi, Klemens J. Hertel, Marian L. Waterman
Software Mentions: 5
Published: about 6 years ago

10.1371/journal.pgen.1005305

Identification of Chemical Inhibitors of β-Catenin-Driven Liver Tumorigenesis in Zebrafish
Cited by: 62
Author(s): Kimberley Evason, Macrina T. Francisco, Vladislava Juric, Sanjeev Balakrishnan, Maria del Pilar Lopez Pazmino, John D. Gordan, Sanjay Kakar, Jan M. Spitsbergen, Andrei Goga, Didier Y. R. Stainier
Software Mentions: 5
Published: over 11 years ago

10.3390/genes12010048

Probably Correct: Rescuing Repeats with Short and Long Reads
Cited by: 3
Author(s): Monika Čechová
Software Mentions: 5
Published: almost 6 years ago

10.3390/genes11040415

Gene Expression Profiling of Corpus luteum Reveals Important Insights about Early Pregnancy in Domestic Sheep
Cited by: 14
Author(s): Kisun Pokharel, Jaana Peippo, Melak Weldenegodguad, Mervi Honkatukia, Menghua Li, Juha Kantanen
Software Mentions: 5
Published: over 6 years ago

10.1186/s13567-021-00972-4

Transcriptomic analysis of equine chorioallantois reveals immune networks and molecular mechanisms involved in nocardioform placentitis
Cited by: 8
Author(s): Hesham A. Ali, Shavahn C. Loux, Laura Kennedy, Kirsten E. Scoggin, Pouya Dini, Carleigh E. Fedorka, Theodore S. Kalbfleisch, A. Esteller-Vico, David W. Horohov, Erdal Erol, Craig N. Carter, Jon J. Smith, Barry A. Ball
Software Mentions: 5
Published: over 5 years ago

10.1093/bib/bbaa339

FR-Match: robust matching of cell type clusters from single cell RNA sequencing data using the Friedman–Rafsky non-parametric test
Cited by: 9
Author(s): Yun Zhang, Brian D. Aevermann, Trygve E. Bakken, Jeremy A. Miller, Rebecca D. Hodge, Ed Lein, Richard H. Scheuermann
Software Mentions: 5
Published: almost 6 years ago

10.1186/s12974-019-1500-x

Contribution of LTi and TH17 cells to B cell aggregate formation in the central nervous system in a mouse model of multiple sclerosis
Cited by: 18
Author(s): Verena Schropp, Jörn Rohde, Damiano M. Rovituso, Samir Jabari, Richa Bharti, Stefanie Küerten
Software Mentions: 5
Published: over 7 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: almost 8 years ago

10.3390/pharmaceutics13081105

Evaluation of an Intravitreal Rho-Associated Kinase Inhibitor Depot Formulation in a Rat Model of Diabetic Retinopathy
Cited by: 2
Author(s): Cécile Lebon, Heike Neubauer, Marianne Berdugo, Kimberley Delaunay, Elke Markert, Kolja Becker, Katja S. Baum-Kroker, J. Prestle, Holger Fuchs, Remko A. Bakker, Francine Behar‐Cohen
Software Mentions: 5
Published: about 5 years ago

10.1371/journal.pgen.1007793

Synthetic STARR-seq reveals how DNA shape and sequence modulate transcriptional output and noise
Cited by: 26
Author(s): Stefanie Schöne, Melissa Bothe, Edda Einfeldt, Marina Borschiwer, Philipp Benner, Martin Vingron, Morgane Thomas‐Chollier, Sebastiaan H. Meijsing
Software Mentions: 5
Published: almost 8 years ago

10.1002/ctm2.246

Circulating tumor cell characterization of lung cancer brain metastases in the cerebrospinal fluid through single‐cell transcriptome analysis
Cited by: 33
Author(s): Haoyu Ruan, Yihang Zhou, Jie Shen, Yue Zhai, Ying Xu, Linyu Pi, Run Huang, Kun Chen, Xiangyu Li, Wendong Ma, Zhiyuan Wu, Xuan Deng, Xiaozhu Wang, Chao Zhang, Ming Guan
Software Mentions: 5
Published: almost 6 years ago

10.1038/s42003-020-1001-6

Mutually suppressive roles of KMT2A and KDM5C in behaviour, neuronal structure, and histone H3K4 methylation
Cited by: 25
Author(s): Christina N Vallianatos, Brynne Raines, Robert S. Porter, Katherine M Bonefas, Michael C. Wu, Patricia M. Garay, Katie M. Collette, Young Ah Seo, Yali Dou, Catherine E. Keegan, Natalie C. Tronson, Shigeki Iwase
Software Mentions: 5
Published: over 6 years ago

10.1038/s41598-017-14595-3

UClncR: Ultrafast and comprehensive long non-coding RNA detection from RNA-seq
Cited by: 27
Author(s): Zhifu Sun, Asha Nair, Xianfeng Chen, Naresh Prodduturi, Junwen Wang, Jean Pierre A. Kocher
Software Mentions: 5
Published: almost 9 years ago

10.3390/ijms22179228

SARS-CoV-2 Impairs Dendritic Cells and Regulates DC-SIGN Gene Expression in Tissues
Cited by: 13
Author(s): Guoshuai Cai, Mulong Du, Yohan Bossé, Helmut Albrecht, Fei Qin, Xizhi Luo, X Michelle Androulakis, Chao Cheng, Mitzi Nagarkatti, Mitzi Nagarkatti, David C. Christiani, Michael L. Whitfield, Christopher I. Amos, Feifei Xiao
Software Mentions: 5
Published: about 5 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: over 6 years ago

10.1038/s41598-017-14942-4

Genome-wide profiling of nardilysin target genes reveals its role in epigenetic regulation and cell cycle progression
Cited by: 6
Author(s): Yusuke Morita, Mikiko Ohno, Kiyoto Nishi, Yutaka Hiraoka, Sayaka Saijo, Shintaro Matsuda, Toru Kita, Takeshi Kimura, Eiichiro Nishi
Software Mentions: 5
Published: almost 9 years ago

10.1186/s13148-021-01018-4

Novel DNA methylation signatures of tobacco smoking with trans-ethnic effects
Cited by: 44
Author(s): Colette Christiansen, Juan Castillo-Fernandez, Arce Domingo‐Relloso, Wei Zhao, Julia S. El-Sayed Moustafa, Pei-Chien Tsai, Jane Maddock, Karin Haack, Shelley A. Cole, Sharon L.R. Kardia, Mariam Molokhia, Matthew Suderman, Chris Power, Caroline L Relton, Andrew Wong, Diana Kuh, Alissa Goodman, Kerrin S. Small, Jennifer A. Smith, María Téllez-Plaza, Ana Navas-Acién, George B. Ploubidis, Rebecca Hardy, Jordana T. Bell
Software Mentions: 5
Published: over 5 years ago

10.1038/s41598-017-11807-8

Genomic and transcriptomic analysis of the toluene degrading black yeast Cladophialophora immunda
Cited by: 36
Author(s): Barbara Blasi, Hakim Tafer, Christina Kustor, Caroline Poyntner, Ksenija Lopandić, Katja Sterflinger
Software Mentions: 5
Published: about 9 years ago

10.1038/s41598-017-14451-4

Expression and regulation of long noncoding RNAs during the osteogenic differentiation of periodontal ligament stem cells in the inflammatory microenvironment
Cited by: 13
Author(s): Qingbin Zhang, Li Chen, Shiman Cui, Yan Li, Qi Zhao, Weimin Cao, Shixiang Lai, Sanjun Yin, Zhixiang Zuo
Software Mentions: 5
Published: almost 9 years ago

10.1534/g3.119.401006

The Developmental Transcriptome of Aedes albopictus, a Major Worldwide Human Disease Vector
Cited by: 25
Author(s): Stephanie Gamez, Igor Antoshechkin, Stelia C. Méndez‐Sánchez, Omar S. Akbari
Software Mentions: 5
Published: over 6 years ago

10.1186/s13148-016-0234-1

Amnion as a surrogate tissue reporter of the effects of maternal preeclampsia on the fetus
Cited by: 8
Author(s): Masako Suzuki, Ryo Maekawa, Nicole E. Patterson, David M. Reynolds, Brent Calder, Sandra E. Reznik, Hye Heo, Francine Einstein, John M. Greally
Software Mentions: 5
Published: over 10 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

10.1186/s13148-020-00879-5

G9a regulates tumorigenicity and stemness through genome-wide DNA methylation reprogramming in non-small cell lung cancer
Cited by: 25
Author(s): Rajendra P. Pangeni, Lu Yang, Keqiang Zhang, Jinhui Wang, Wendong Li, Chao Guo, Xinwei Yun, Ting Sun, Jami Wang, Dan J. Raz
Software Mentions: 5
Published: over 6 years ago

10.1534/g3.119.400770

Experimental DNA Demethylation Associates with Changes in Growth and Gene Expression of Oak Tree Seedlings
Cited by: 10
Author(s): Luke Browne, Alayna Mead, Courtney Horn, Kevin W. Chang, Zeynep A Celikkol, Claudia L. Henriquez, Feiyang Ma, Eric Beraut, Rachel S. Meyer, Victoria L. Sork
Software Mentions: 5
Published: over 6 years ago

10.1534/g3.118.200852

Tissue-Specific Transcriptome Analysis Reveals Candidate Genes for Terpenoid and Phenylpropanoid Metabolism in the Medicinal Plant Ferula assafoetida
Cited by: 21
Author(s): Hajar Amini, Mohammad Reza Naghavi, Tong Shen, Yanhong Wang, Jaber Nasiri, Ikhlas A. Khan, Oliver Fiehn, Philipp Zerbe, Julin Maloof
Software Mentions: 5
Published: over 7 years ago

10.1038/s41598-017-11036-z

SRSF1 suppresses selection of intron-distal 5′ splice site of DOK7 intron 4 to generate functional full-length Dok-7 protein
Cited by: 3
Author(s): Khalid Ahsan, Akio Matsubara, Mohammad Alinoor Rahman, Jun‐ichi Takeda, Mohammad Nazim, Bisei Ohkawara, Mikako Ito, Kinji Ohno
Software Mentions: 5
Published: about 9 years ago

10.3390/biom11020291

Determination of Genotoxicity Attributed to Diesel Exhaust Particles in Normal Human Embryonic Lung Cell (WI-38) Line
Cited by: 4
Author(s): Joong Won Lee, Hee Jae Lee, Young Joo Lee, Yong Beom Lim, Woo Jong Sim, Ji Hye Jang, Hye Ryeon Heo, Hyunwoo Lim, Ji Won Jung, Jin Sik Kim
Software Mentions: 5
Published: over 5 years ago

10.3390/ijms221910297

Circular RNAs Repertoire and Expression Profile during Brassica rapa Pollen Development
Cited by: 10
Author(s): Saeid Babaei, Mohan B. Singh, Prem L. Bhalla
Software Mentions: 5
Published: about 5 years ago

10.1007/s10142-018-0639-3

Hotspots in the genomic architecture of field drought responses in wheat as breeding targets
Cited by: 38
Author(s): Sergio Gálvez, Rosa Mérida-García, C. Camino, Philippa Borrill, Michaël Abrouk, Ricardo H. Ramírez-González, Sezgi Biyiklioglu, Francisco Amil-Ruíz, Gabriel Dorado, Hikmet Budak, Victoria González-Dugo, Pablo J. Zarco‐Tejada, R. Appels, Cristóbal Uauy, Pilar Hernández
Software Mentions: 5
Published: almost 8 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

10.1534/g3.120.401345

Reference Genome for the Highly Transformable Setaria viridis ME034V
Cited by: 30
Author(s): Peter Thielen, Amanda L. Pendleton, Robert A. Player, Kenneth V. Bowden, Thomas J. Lawton, Jennifer H. Wisecaver
Software Mentions: 5
Published: about 6 years ago

10.1371/journal.pgen.1007233

RNF8 and SCML2 cooperate to regulate ubiquitination and H3K27 acetylation for escape gene activation on the sex chromosomes
Cited by: 43
Author(s): Shannel R. Adams, So Maezawa, Kris G. Alavattam, Hironori Abe, Akihiko Sakashita, Megan Shroder, Tyler J. Broering, Julie Sroga Rios, Michael A. Thomas, Xinhua Lin, Carolyn M. Price, Artem Barski, Paul R. Andreassen, Satoshi H. Namekawa
Software Mentions: 5
Published: over 8 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: over 5 years ago

10.18632/oncotarget.26929

Deregulated expression of NKL homeobox genes in T-cell lymphomas
Cited by: 10
Author(s): Stefan Nagel, Claudia Pommerenke, Roderick A.F. MacLeod, Corinna Meyer, Maren Kaufmann, Silke Fähnrich, Hans Drexler
Software Mentions: 5
Published: over 7 years ago

10.1371/journal.pgen.1008261

Restricted and non-essential redundancy of RNAi and piRNA pathways in mouse oocytes
Cited by: 26
Author(s): Eliška Táborská, Josef Pasulka, Radek Malı́k, Filip Horvat, Irena Jenickova, Zoe Jelić Matošević, Petr Svoboda
Software Mentions: 5
Published: almost 7 years ago

10.3390/ijms22115858

Calreticulin Deficiency Disturbs Ribosome Biogenesis and Results in Retardation in Embryonic Kidney Development
Cited by: 4
Author(s): Nazli Serin, Gry H. Dihazi, Asima Tayyeb, Christof Lenz, Gerhard A. Müller, Michael Zeisberg, Hassan Dihazi
Software Mentions: 5
Published: over 5 years ago

10.7554/eLife.67714

The cryptic gonadotropin-releasing hormone neuronal system of human basal ganglia
Cited by: 13
Author(s): Katalin Skrapits, Miklós Sárvári, Imre Farkas, Balázs Göcz, Szabolcs Takács, Éva Rumpler, Viktória Váczi, Csaba Vastagh, Gergely Rácz, András Matolcsy, Norbert Solymosi, Szilárd Póliska, Blanka Tóth, Ferenc Erdélyi, Gábor Szabó, Michael D. Culler, Cécile Allet, Ludovica Cotellessa, Vincent Prévot, Paolo Giacobini, Erik Hrabovszky
Software Mentions: 5
Published: over 5 years ago

10.3389/fimmu.2020.575488

Integrated Analysis of Transcriptome and Secretome From Umbilical Cord Mesenchymal Stromal Cells Reveal New Mechanisms for the Modulation of Inflammation and Immune Activation
Cited by: 18
Author(s): Mónica Cruz-Barrera, Nathalia Flórez-Zapata, Nicolás Lemus-Diaz, Carlos O. Medina, Cristian Camilo Galindo, Lorena-Xiomara González-Acero, Luz Correa, Bernardo Camacho, Jens Gruber, Gustavo Salguero
Software Mentions: 5
Published: about 6 years ago

10.18632/oncotarget.25329

Genome-wide multi-omics profiling of the 8p11-p12 amplicon in breast carcinoma
Cited by: 13
Author(s): Toshima Z. Parris, Elisabeth Werner Rönnerman, Hanna Engqvist, Jana Biermann, Katarina Truvé, Szilárd Nemes, Eva Forssell-Aronsson, Giovanni Solinas, Anikó Kovács, Per Karlsson, Khalil Helou
Software Mentions: 5
Published: over 8 years ago

10.1038/s41598-021-93297-3

Zfp57 inactivation illustrates the role of ICR methylation in imprinted gene expression during neural differentiation of mouse ESCs
Cited by: 7
Author(s): Basilia Acurzio, Ankit Verma, Alessia Polito, Carlo Giaccari, Francesco Cecere, Salvatore Fioriniello, Floriana Della Ragione, Annalisa Fico, Flavia Cerrato, Claudia Angelini, Robert Feil, Andrea Riccio
Software Mentions: 5
Published: over 5 years ago

10.3390/genes11050504

Pitfalls in Single Clone CRISPR-Cas9 Mutagenesis to Fine-Map Regulatory Intervals
Cited by: 5
Author(s): Ruoyu Tian, Yidan Pan, Thomas H A Etheridge, Harshavardhan Deshmukh, Dalia Gulick, Greg Gibson, Gang Bao, Ciaran M. Lee
Software Mentions: 5
Published: over 6 years ago

10.18632/oncotarget.13062

Genomic profiling is predictive of response to cisplatin treatment but not to PI3K inhibition in bladder cancer patient-derived xenografts
Cited by: 29
Author(s): Lei Wei, Sreenivasulu Chintala, Eric Ciamporcero, Swathi Ramakrishnan, May Elbanna, Jianmin Wang, Qiang Hu, Sean T. Glenn, Mitsuko Murakami, Lu Liu, Eduardo Cortes Gomez, Yuchen Sun, Jacob Conroy, Kiersten Marie Miles, Malathi Kullappan, Sudha Ramaiah, Anand Anbarasu, Anna Woloszynska‐Read, Candace S. Johnson, Jeffrey M. Conroy, Song Liu, Carl Morrison, Роберто Пили
Software Mentions: 5
Published: almost 10 years ago

10.18632/oncotarget.14091

The role of miR-17-92 in the miRegulatory landscape of Ewing sarcoma
Cited by: 13
Author(s): Raphaela Schwentner, David Herrero-Martín, Maximilian Kauer, Cornelia Mutz, Anna M. Katschnig, Grzegorz Sienski, Javier Alonso, Dave N.T. Aryee, Heinrich Kovar
Software Mentions: 5
Published: almost 10 years ago

10.1371/journal.pntd.0009587

Transcriptomic analysis and molecular docking reveal genes involved in the response of Aedes aegypti larvae to an essential oil extracted from Eucalyptus
Cited by: 9
Author(s): Ivana Sierra, José Manuel Latorre-Estivalis, Lucila Traverso, Paula Valeria Gonzalez, Ariel A Aptekmann, Alejandro D. Nadra, Héctor Mario Masuh, Sheila Ons
Software Mentions: 5
Published: about 5 years ago

10.1038/s41598-020-59808-4

Meta-analysis of honey bee neurogenomic response links Deformed wing virus type A to precocious behavioral maturation
Cited by: 29
Author(s): Ian M. Traniello, Syed Bukhari, Jessica L. Kevill, Amy Cash Ahmed, Adam R. Hamilton, Nicholas L. Naeger, Declan C. Schroeder, Gene E. Robinson
Software Mentions: 5
Published: over 6 years ago

10.1038/s41598-019-51379-3

Tissue- and Species-Specific Patterns of RNA metabolism in Post-Mortem Mammalian Retina and Retinal Pigment Epithelium
Cited by: 9
Author(s): Les Kallestad, Seth Blackshaw, Ahmad M. Khalil, Krzysztof Palczewski
Software Mentions: 5
Published: almost 7 years ago

10.1371/journal.pgen.1008687

Conserved nuclear hormone receptors controlling a novel plastic trait target fast-evolving genes expressed in a single cell
Cited by: 35
Author(s): Bogdan Sieriebriennikov, Shuai Sun, James W. Lightfoot, Hanh Witte, Eduardo Moreno, Christian Rödelsperger, Ralf J. Sommer
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.ppat.1009674

Tissue-specific transcriptional profiling of plasmacytoid dendritic cells reveals a hyperactivated state in chronic SIV infection
Cited by: 5
Author(s): Michelle Y.H. Lee, Amit A. Upadhyay, Hasse Walum, Chi N. Chan, Reem A. Dawoud, Christine Grech, Justin Harper, Kirti A. Karunakaran, Sydney A. Nelson, Ernestine Mahar, Kyndal Goss, Diane G. Carnathan, Barbara Cervasi, Kiran Gill, Gregory K. Tharp, Elizabeth R. Wonderlich, Vijayakumar Velu, Simon M. Barratt‐Boyes, Mirko Paiardini, Guido Silvestri, Jacob D. Estes, Steven E. Bosinger
Software Mentions: 5
Published: over 5 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: about 10 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/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

10.1093/gigascience/giab067

Association of female reproductive tract microbiota with egg production in layer chickens
Cited by: 5
Author(s): Yuan Su, Shilin Tian, Diyan Li, Wei Zhu, Tao Wang, Suchismita Mishra, Ranlei Wei, Zhongxian Xu, Mengnan He, Xiaoling Zhao, Huadong Yin, Xiaolan Fan, Bo Zeng, Mingyao Yang, Deying Yang, Qingyong Ni, Yan Li, Mingwang Zhang, Qing Zhu, Mingzhou Li
Software Mentions: 5
Published: about 5 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: about 9 years ago

10.1371/journal.pbio.3000704

Single-cell mapping reveals new markers and functions of lymphatic endothelial cells in lymph nodes
Cited by: 83
Author(s): Noriki Fujimoto, Yuliang He, Marco D’Addio, Carlotta Tacconi, Michael Detmar, Lothar C. Dieterich
Software Mentions: 5
Published: over 6 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: over 5 years ago

10.1093/gigascience/giaa088

A haplotype-resolved, de novo genome assembly for the wood tiger moth (Arctia plantaginis) through trio binning
Cited by: 16
Author(s): Eugenie C Yen, Shane McCarthy, Juan A. Galarza, Tomas N Generalovic, Sarah Pelan, Petr Nguyen, Joana I. Meier, Ian A. Warren, Johanna Mappes, Richard Durbin, Chris D. Jiggins
Software Mentions: 5
Published: about 6 years ago

10.1093/gigascience/giaa112

A molecular map of lung neuroendocrine neoplasms
Cited by: 15
Author(s): Aurélie Gabriel, Emilie Mathian, Lise Mangiante, Catherine Voegele, Vincent Cahais, Akram Ghantous, James McKay, Nicolas Alcala, Lynnette Fernández-Cuesta, Matthieu Foll
Software Mentions: 5
Published: almost 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

10.1093/gigascience/giy132

Comprehensive evaluation of RNA-seq analysis pipelines in diploid and polyploid species
Cited by: 21
Author(s): Miriam Payá‐Milans, James W. Olmstead, Gerardo H. Nunez, Timothy A. Rinehart, Margaret Staton
Software Mentions: 5
Published: almost 8 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: almost 9 years ago

10.1371/journal.pcbi.1004105

Transcriptome Sequencing Reveals Potential Mechanism of Cryptic 3’ Splice Site Selection in SF3B1-mutated Cancers
Cited by: 173
Author(s): Christopher DeBoever, Emanuela M. Ghia, Peter J. Shepard, Laura Z. Rassenti, Christian Barrett, Kristen Jepsen, Catriona Jamieson, Dennis A. Carson, Thomas J. Kipps, Kelly A. Frazer
Software Mentions: 5
Published: over 11 years ago

10.1093/gigascience/giy086

Whole genome and transcriptome maps of the entirely black native Korean chicken breed Yeonsan Ogye
Cited by: 17
Author(s): Jang il Sohn, Kyoungwoo Nam, Hyosun Hong, Jun Mo Kim, Dajeong Lim, Kyung Tai Lee, Yoon Jung, Chang Yeon Cho, Namshin Kim, Han Ha Chai, Jin Wu Nam
Software Mentions: 5
Published: over 8 years ago

10.1371/journal.pcbi.1008195

VALERIE: Visual-based inspection of alternative splicing events at single-cell resolution
Cited by: 9
Author(s): Wei Wen, Adam J. Mead, Supat Thongjuea
Software Mentions: 5
Published: about 6 years ago

10.1371/journal.pgen.1006017

Comparative Genomic Analysis of Drechmeria coniospora Reveals Core and Specific Genetic Requirements for Fungal Endoparasitism of Nematodes
Cited by: 42
Author(s): Kévin Lebrigand, Le He, Nishant Thakur, Marie-Jeanne Arguel, Jolanta Polanowska, Bernard Henrissat, Éric Record, Ghislaine Magdelenat, Valérie Barbe, Sylvain Raffaele, Pascal Barbry, Jonathan J. Ewbank
Software Mentions: 5
Published: over 10 years ago

10.1186/s13059-019-1922-x

DENDRO: genetic heterogeneity profiling and subclone detection by single-cell RNA sequencing
Cited by: 31
Author(s): Zilu Zhou, Baocheng Xu, Andy J. Minn, Nancy R. Zhang
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pgen.1008770

Multiple mechanisms regulate H3 acetylation of enhancers in response to thyroid hormone
Cited by: 19
Author(s): Stine M. Præstholm, Majken Siersbæk, Ronni Nielsen, Xuguang Zhu, Anthony N. Hollenberg, Sheue-yann Cheng, Lars Grøntved
Software Mentions: 5
Published: over 6 years ago

10.1186/s13059-019-1860-7

CRUP: a comprehensive framework to predict condition-specific regulatory units
Cited by: 26
Author(s): Anna Ramisch, Verena Heinrich, Laura V. Glaser, Alisa Fuchs, Xinyi Yang, Philipp Benner, Robert Schöpflin, Na Li, Sarah Kinkley, Anja Römer-Hillmann, John Longinotto, Steffen Heyne, Beate Czepukojc, Sonja M. Kessler, Alexandra K. Kiemer, Cristina Cadenas, Laura Arrigoni, Nina Gasparoni, Thomas Manke, Thomas Pap, J. Andrew Pospisilik, Jan G. Hengstler, Jörn Walter, Sebastiaan H. Meijsing, Ho‐Ryun Chung, Martin Vingron
Software Mentions: 5
Published: almost 7 years ago

10.1186/s13059-020-01960-1

Hemispheric asymmetry in the human brain and in Parkinson’s disease is linked to divergent epigenetic patterns in neurons
Cited by: 35
Author(s): Peipei Li, Elizabeth Ensink, Sean Lang, Lee Marshall, Meghan Schilthuis, Jared Lamp, Irving E. Vega, Viviane Labrie
Software Mentions: 5
Published: over 6 years ago

10.1186/s13059-019-1878-x

Evaluation of commonly used analysis strategies for epigenome- and transcriptome-wide association studies through replication of large-scale population studies
Cited by: 24
Author(s): Jeroen van Rooij, Pooja R. Mandaviya, Annique Claringbould, Janine F. Felix, Jenny van Dongen, Rick Jansen, Lude Franke, Peter A.C. ’t Hoen, B.T. Heijmans, Joyce B. J. van Meurs
Software Mentions: 5
Published: almost 7 years ago

Projects: cran: STAR

Science Score: 100/100

Bonuses:

Papers Mentioning STAR 5,759