10.1186/s12915-020-00785-5

A tissue level atlas of the healthy human virome
Cited by: 47
Author(s): Ryuichi Kumata, Jumpei Ito, Keiichi Takahashi, Tadaki Suzuki, Kei Sato
Software Mentions: 2
Published: about 6 years ago

10.1186/s12915-020-00796-2

Mutation of amphioxus Pdx and Cdx demonstrates conserved roles for ParaHox genes in gut, anus and tail patterning
Cited by: 13
Author(s): Yunxin Zhong, Carlos Herrera-Úbeda, Jordi García-Fernández, Guang Li, Peter W.H. Holland
Software Mentions: 2
Published: about 6 years ago

10.1186/s42490-021-00049-5

3D-printed microplate inserts for long term high-resolution imaging of live brain organoids
Cited by: 26
Author(s): Mariana Oksdath Mansilla, Camilo Salazar-Hernandez, Sally L. Perrin, Kaitlin G. Scheer, Gökhan Cildir, John Toubia, Kristýna Šediváková, Melinda N Tea, Sakthi Lenin, Elise Ponthier, Erica C. F. Yeo, Vinay Tergaonkar, Santosh Poonnoose, Rebecca J. Ormsby, Stuart M. Pitson, Michael P. Brown, Lisa M. Ebert, Guillermo A. Gómez
Software Mentions: 2
Published: over 5 years ago

10.1186/s12885-020-07134-3

Transcriptomic insight into salinomycin mechanisms in breast cancer cell lines: synergistic effects with dasatinib and induction of estrogen receptor β
Cited by: 8
Author(s): Vanessa Bellat, Alice Verchère, Sally A. Ashe, Benedict Law
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12885-021-08641-7

Inhibition of STAT3 enhances sensitivity to tamoxifen in tamoxifen-resistant breast cancer cells
Cited by: 12
Author(s): Seo Yun Moon, Heejin Lee, Seoree Kim, Ji Hyung Hong, Sang Hoon Chun, Hee Yeon Lee, Keunsoo Kang, Ho Shik Kim, Hye Sung Won, Yoon Ho Ko
Software Mentions: 2
Published: almost 5 years ago

10.1186/s12885-021-08798-1

Stemness-related LncRNA pair signature for predicting therapy response in gastric cancer
Cited by: 14
Author(s): Quan Jiang, Hao Chen, Zhaoqing Tang, Jie Sun, Yuanyuan Ruan, Fenglin Liu, Yihong Sun
Software Mentions: 2
Published: almost 5 years ago

10.1186/s12885-019-5657-6

Developing a real-time electronic symptom monitoring system for patients after discharge following cancer-related surgery
Cited by: 41
Author(s): Kerry Avery, Hollie Richards, Amanda Portal, Trudy Reed, Ruth Harding, Caroline Robert, Leon Bamforth, Kate Absolom, Elaine O’Connell Francischetto, Galina Velikova, Jane M Blazeby
Software Mentions: 2
Published: about 7 years ago

10.1186/s12885-020-07448-2

Distinctive roles of syntaxin binding protein 4 and its action target, TP63, in lung squamous cell carcinoma: a theranostic study for the precision medicine
Cited by: 8
Author(s): Bilguun Erkhem-Ochir, Kyoichi Kaira, Reika Kawabata‐Iwakawa, Susumu Rokudai, Kimihiro Shimizu, Takehiko Yokobori, Tetsunari Oyama, Ken Shirabe, Masahiko Nishiyama
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12885-016-2837-5

MiR-9 is overexpressed in spontaneous canine osteosarcoma and promotes a metastatic phenotype including invasion and migration in osteoblasts and osteosarcoma cell lines
Cited by: 29
Author(s): Joelle M. Fenger, Ryan D. Roberts, O. Hans Iwenofu, Misty D. Bear, Xiaoli Zhang, Jason I. Couto, Jaime F. Modiano, William C. Kisseberth, Cheryl A. London
Software Mentions: 2
Published: almost 10 years ago

10.1186/s12885-017-3825-0

Chemotherapy weakly contributes to predicted neoantigen expression in ovarian cancer
Cited by: 32
Author(s): Timothy J. O’Donnell, Elizabeth L. Christie, Arun Ahuja, Jacqueline Buros, Bülent Arman Aksoy, David D.L. Bowtell, Alexandra Snyder, Jeff Hammerbacher
Software Mentions: 2
Published: over 8 years ago

10.1186/s12885-021-08131-w

Synonymous mutations that regulate translation speed might play a non-negligible role in liver cancer development
Cited by: 18
Author(s): Qun Li, Jian Li, Chunpeng Yu, Shuai Chang, Lingling Xie, Song Wang
Software Mentions: 2
Published: over 5 years ago

10.1186/s12861-019-0200-1

YWHA (14-3-3) protein isoforms and their interactions with CDC25B phosphatase in mouse oogenesis and oocyte maturation
Cited by: 21
Author(s): Alaa Eisa, Santanu De, Ariana C. Detwiler, Eva Gilker, Alexander C. Ignatious, Srinivasan Vijayaraghavan, Douglas Kline
Software Mentions: 2
Published: over 6 years ago

10.1186/s12902-021-00775-w

The role of FDX1 in granulosa cell of Polycystic ovary syndrome (PCOS)
Cited by: 20
Author(s): Zhi Wang, Hui Dong, Yang Li, Ping Cheng Yi, Qing Wang, Dongmei Huang
Software Mentions: 2
Published: about 5 years ago

10.1186/s12862-015-0423-0

Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants
Cited by: 304
Author(s): Stephen A. Smith, Michael J. Moore, Joseph W. Brown, Ya Yang
Software Mentions: 2
Published: almost 11 years ago

10.1186/s12862-020-1580-3

The evolutionary arms race between transposable elements and piRNAs in Drosophila melanogaster
Cited by: 31
Author(s): Shiqi Luo, Hong Zhang, Yuange Duan, Xuesong Yao, Andrew G. Clark, Jian Lü
Software Mentions: 2
Published: over 6 years ago

10.1186/1471-2148-14-67

An empirical evaluation of two-stage species tree inference strategies using a multilocus dataset from North American pines
Cited by: 23
Author(s): Michael DeGiorgio, John Syring, Andrew J. Eckert, Aaron Liston, Richard Cronn, David B. Neale, Noah A. Rosenberg
Software Mentions: 2
Published: over 12 years ago

10.1186/s12876-020-01356-2

Human translatability of the GAN diet-induced obese mouse model of non-alcoholic steatohepatitis
Cited by: 40
Author(s): Henrik H. Hansen, Helene M Ægidius, Denise Oró, Simon S. Evers, Sara Heebøll, Peter Lykke Eriksen, Karsten Thomsen, Anja Bengtsson, Sanne Skovgård Veidal, Michel Feigh, Malte P. Suppli, Filip K. Knop, Henning Grønbæk, Diego A. Miranda, James L. Trevaskis, Niels Vrang, Jacob Jelsing, Kristoffer Rigbolt
Software Mentions: 2
Published: about 6 years ago

10.1186/s12863-015-0249-1

Understanding rice adaptation to varying agro-ecosystems: trait interactions and quantitative trait loci
Cited by: 43
Author(s): Shalabh Dixit, Alexandre Grondin, Cheng‐Ruei Lee, Amelia Henry, Thomas Mitchell-Olds, Arvind Kumar
Software Mentions: 2
Published: almost 11 years ago

10.1186/s12863-021-00976-1

Transcriptome signature of miRNA-26b KO mouse model suggests novel targets
Cited by: 3
Author(s): Emiel P. C. van der Vorst, Mario Pepe, Linsey J. F. Peters, Markus Haberbosch, Yvonne Jansen, Ronald Naumann, Georgios T. Stathopoulos, Kiril Bidzhekov
Software Mentions: 2
Published: about 5 years ago

10.1186/s12864-019-6379-5

Exploring the changing landscape of cell-to-cell variation after CTCF knockdown via single cell RNA-seq
Cited by: 11
Author(s): Wei Wang, Gang Ren, Ni Hong, Wenfei Jin
Software Mentions: 2
Published: over 6 years ago

10.1186/s12864-021-07553-x

Rapid genetic adaptation to recently colonized environments is driven by genes underlying life history traits
Cited by: 8
Author(s): Xiaoshen Yin, Alexander S. Martinez, Marı́a S. Sepúlveda, Mark R. Christie
Software Mentions: 2
Published: about 5 years ago

10.1186/s12864-021-07597-z

Genomic analysis of novel Yarrowia-like yeast symbionts associated with the carrion-feeding burying beetle Nicrophorus vespilloides
Cited by: 3
Author(s): Karina Brinkrolf, Shantanu Shukla, Sven Griep, Oliver Rupp, Philipp Heise, Alexander Goesmann, David G. Heckel, Heiko Vogel, Andreas Vilcinskas
Software Mentions: 2
Published: about 5 years ago

10.1186/s12864-018-4475-6

Novel read density distribution score shows possible aligner artefacts, when mapping a single chromosome
Cited by: 6
Author(s): Fedor Naumenko, Irina Abnizova, Nathan Beka, Mikhail A. Genaev, Yuriy L. Orlov
Software Mentions: 2
Published: over 8 years ago

10.1186/s12864-018-5012-3

Transcriptome dynamics associated with resistance and susceptibility against fusarium head blight in four wheat genotypes
Cited by: 68
Author(s): Youlian Pan, Ziying Liu, Hélène Rocheleau, François Fauteux, Yunli Wang, Curt McCartney, Thérèse Ouellet
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12864-021-07947-x

A single chromosome strain of S. cerevisiae exhibits diminished ethanol metabolism and tolerance
Cited by: 1
Author(s): Tyler W. Doughty, Rong Yu, Lucy Fang I. Chao, Zhongjun Qin, Verena Siewers, Jens Nielsen
Software Mentions: 2
Published: almost 5 years ago

10.1186/s12864-020-07088-7

Proteotranscriptomics assisted gene annotation and spatial proteomics of Bombyx mori BmN4 cell line
Cited by: 7
Author(s): Michael Levin, Marion Scheibe, Falk Butter
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12864-019-6369-7

Transcriptome-wide association study identifies putative elicitors/suppressor of Puccinia graminis f. sp. tritici that modulate barley rpg4-mediated stem rust resistance
Cited by: 5
Author(s): Roshan Sharma Poudel, Jonathan Richards, Subidhya Shrestha, Shyam Solanki, Robert Brueggeman
Software Mentions: 2
Published: over 6 years ago

10.1186/s12864-021-07433-4

SARS-CoV-2 early infection signature identified potential key infection mechanisms and drug targets
Cited by: 18
Author(s): Yue Li, Ashley Duche, Michael R. Sayer, Don Roosan, Farid G. Khalafalla, Rennolds S. Ostrom, Jennifer Totonchy, Moom R. Roosan
Software Mentions: 2
Published: over 5 years ago

10.1186/1471-2164-15-620

The transcriptional landscape of mouse beta cells compared to human beta cells reveals notable species differences in long non-coding RNA and protein-coding gene expression
Cited by: 236
Author(s): Chris Benner, Talitha van der Meulen, Elena Cacéres, Kristof Tigyi, Cynthia J. Donaldson, Mark O. Huising
Software Mentions: 2
Published: almost 12 years ago

10.1186/s12864-016-2698-y

Enhanced whole exome sequencing by higher DNA insert lengths
Cited by: 7
Author(s): Claudia Pommerenke, Robert Geffers, Boyke Bunk, Sabin Bhuju, Sonja Eberth, Hans G. Drexler, Hilmar Quentmeier
Software Mentions: 2
Published: about 10 years ago

10.1186/s12864-018-4585-1

Cross-site comparison of ribosomal depletion kits for Illumina RNAseq library construction
Cited by: 41
Author(s): Zachary T. Herbert, Jamie P. Kershner, Vincent Butty, Jyothi Thimmapuram, Sulbha Choudhari, Yuriy O. Alekseyev, Jun Fan, Jessica W. Podnar, Edward R. Wilcox, Jenny Gipson, Allison F. Gillaspy, Kristen Jepsen, Sandra Splinter BonDurant, Krystalynne Morris, Maura Berkeley, Ashley LeClerc, Stephen D. Simpson, Gary Sommerville, Leslie Grimmett, Marie Adams, Stuart S. Levine
Software Mentions: 2
Published: over 8 years ago

10.1186/s12864-020-06963-7

SOX10-regulated promoter use defines isoform-specific gene expression in Schwann cells
Cited by: 11
Author(s): Elizabeth A. Fogarty, Jacob O. Kitzman, Anthony Antonellis
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12864-021-07538-w

Unique adaptations in neonatal hepatic transcriptome, nutrient signaling, and one-carbon metabolism in response to feeding ethyl cellulose rumen-protected methionine during late-gestation in Holstein cows
Cited by: 9
Author(s): Valentino Palombo, Abdulrahman S. Alharthi, Fernanda Batistel, C. Parys, Jessie Guyader, Erminio Trevisi, Mariasilvia D’Andrea, Juan J. Loor
Software Mentions: 2
Published: about 5 years ago

10.1186/s12864-018-4497-0

RNA secondary structure profiling in zebrafish reveals unique regulatory features
Cited by: 9
Author(s): Kriti Kaushik, Ambily Sivadas, Shamsudheen Karuthedath Vellarikkal, Ankit Verma, Rijith Jayarajan, Satyaprakash Pandey, Tavpritesh Sethi, Souvik Maiti, Vinod Scaria, Sridhar Sivasubbu
Software Mentions: 2
Published: over 8 years ago

10.1186/s12864-019-6222-z

Effects of parental genetic divergence on gene expression patterns in interspecific hybrids of Camellia
Cited by: 11
Author(s): Min Zhang, Yi‐Wei Tang, Ji Qi, Xin-Kai Liu, Di Yan, Nai-Sheng Zhong, Nai-Qi Tao, Ji-Yin Gao, Yuguo Wang, Zhigang Song, Jinshui Yang, Wenju Zhang
Software Mentions: 2
Published: over 6 years ago

10.1186/s12864-019-6256-2

Comparative genomics applied to Mucor species with different lifestyles
Cited by: 21
Author(s): Annie Lebreton, Erwan Corre, Jean‐Luc Jany, Loraine Brillet-Guéguen, Carlos Pèrez-Arques, Victoriano Garre, Misharl Monsoor, Robert Debuchy, Christophe Le Meur, Emmanuel Coton, Georges Barbier, Laurence Meslet‐Cladière
Software Mentions: 2
Published: over 6 years ago

10.1186/s12864-017-3986-x

Nutrient supply affects the mRNA expression profile of the porcine skeletal muscle
Cited by: 17
Author(s): Tainã Figueiredo Cardoso, Raquel Quintanilla, J. Tibau, Marta Gil, Emilio Mármol-Sánchez, Olga González‐Rodríguez, Rayner González-Prendes, Marcel Amills
Software Mentions: 2
Published: almost 9 years ago

10.1186/s12864-019-6342-5

Evolution of cis- and trans-regulatory divergence in the chicken genome between two contrasting breeds analyzed using three tissue types at one-day-old
Cited by: 11
Author(s): Qiong Wang, Yaxiong Jia, Yuan Wang, Zhihua Jiang, Xiang Zhou, Zebin Zhang, Changsheng Nie, Junying Li, Ning Yang, Lujiang Qu
Software Mentions: 2
Published: over 6 years ago

10.1186/s12864-015-1887-4

Transcriptome sequencing and analysis of major genes involved in calcium signaling pathways in pear plants (Pyrus calleryana Decne.)
Cited by: 19
Author(s): Yuanyuan Xu, Yong Li, Jing Lin, Zhonghua Wang, Qiyun Yang, Chang YouHong
Software Mentions: 2
Published: almost 11 years ago

10.1186/s12864-017-3581-1

Variant discovery in the sheep milk transcriptome using RNA sequencing
Cited by: 34
Author(s): Aroa Suárez-Vega, Beatriz Gutiérrez-Gil, Christophe Klopp, Gwenola Tosser‐Klopp, Juan José Arranz
Software Mentions: 2
Published: over 9 years ago

10.1186/s12864-021-07832-7

Embryonic thermal manipulation impacts the postnatal transcriptome response of heat-challenged Japanese quails
Cited by: 4
Author(s): Anaïs Vitorino Carvalho, Christelle Hennequet-Antier, Aurélien Brionne, Sabine Crochet, Justine Jimenez, Nathalie Couroussé, Anne Collin, Vincent Coustham
Software Mentions: 2
Published: about 5 years ago

10.1186/s12864-021-08032-z

Multi-tiered analyses of honey bees that resist or succumb to parasitic mites and viruses
Cited by: 6
Author(s): Daniel Weaver, Brandi L. Cantarel, Christine G. Elsik, Dawn L. Boncristiani, Jay Evans
Software Mentions: 2
Published: almost 5 years ago

10.1186/s12864-018-4619-8

The performance of coalescent-based species tree estimation methods under models of missing data
Cited by: 63
Author(s): Michael Nute, Jed Chou, Erin K. Molloy, Tandy Warnow
Software Mentions: 2
Published: about 8 years ago

10.1186/s12864-018-4486-3

FuSpot: a web-based tool for visual evaluation of fusion candidates
Cited by: 1
Author(s): Jackson A. Killian, Taha M. Topiwala, Alex R. Pelletier, David Frankhouser, Pearlly S. Yan, Ralf Bundschuh
Software Mentions: 2
Published: over 8 years ago

10.1186/s12864-019-5608-2

Purification of high-quality RNA from a small number of fluorescence activated cell sorted zebrafish cells for RNA sequencing purposes
Cited by: 4
Author(s): Siebe Loontiens, Lisa Depestel, Suzanne Vanhauwaert, Givani Dewyn, Charlotte Gistelinck, Karen Verboom, Wouter Van Loocke, Filip Matthijssens, Andy Willaert, Jo Vandesompele, Franki Speleman, Kaat Durinck
Software Mentions: 2
Published: over 7 years ago

10.1186/s12864-018-4719-5

Transcriptional profiling of swine mammary gland during the transition from colostrogenesis to lactogenesis using RNA sequencing
Cited by: 29
Author(s): Valentino Palombo, Juan J. Loor, Mariasilvia D’Andrea, Mario Vailati-Riboni, Khuram Shahzad, Uffe Krogh, Peter Kappel Theil
Software Mentions: 2
Published: about 8 years ago

10.1186/s12864-020-6587-z

RNA-Seq and secondary metabolite analyses reveal a putative defence-transcriptome in Norway spruce (Picea abies) against needle bladder rust (Chrysomyxa rhododendri) infection
Cited by: 13
Author(s): Carlos Trujillo-Moya, Andrea Ganthaler, Wolfgang Stöggl, Ilse Kranner, Silvio Schüler, Reinhard Ertl, Sarah Schlosser, Jan-Peter George, Stefan Mayr
Software Mentions: 2
Published: about 6 years ago

10.1186/s12864-015-1876-7

Comparison of stranded and non-stranded RNA-seq transcriptome profiling and investigation of gene overlap
Cited by: 77
Author(s): Shanrong Zhao, Ying Zhang, William Gordon, Jie Quan, Hualin Simon Xi, Sarah Du, David von Schack, Baohong Zhang
Software Mentions: 2
Published: almost 11 years ago

10.1186/s12864-020-07301-7

RNA sequencing identifies transcriptional changes in the rabbit larynx in response to low humidity challenge
Cited by: 8
Author(s): Taylor W Bailey, Andrea Pires dos Santos, Naíla Cannes do Nascimento, Shaojun Xie, Jyothi Thimmapuram, M. Preeti Sivasankar, Abigail Cox
Software Mentions: 2
Published: over 5 years ago

10.1186/s12864-020-6673-2

Comparison of RNA isolation methods on RNA-Seq: implications for differential expression and meta-analyses
Cited by: 30
Author(s): Amanda N. Scholes, Jeffrey A. Lewis
Software Mentions: 2
Published: over 6 years ago

10.1186/s12864-020-6657-2

An improved de novo genome assembly of the common marmoset genome yields improved contiguity and increased mapping rates of sequence data
Cited by: 8
Author(s): Vasanthan Jayakumar, Hiromi Ishii, Misato Seki, Wakako Kumita, Takashi Inoue, Sumitaka Hase, Kengo Sato, Hideyuki Okano, Erika Sasaki, Yasubumi Sakakibara
Software Mentions: 2
Published: over 6 years ago

10.1186/s12864-020-6484-5

Assessment of branch point prediction tools to predict physiological branch points and their alteration by variants
Cited by: 28
Author(s): Raphaël Leman, Hélène Tubeuf, Sabine Raad, Isabelle Tournier, Céline Derambure, Raphaël Lanos, Pascaline Gaildrat, G Castelain, Julie Hauchard, Audrey Killian, Stéphanie Baert‐Desurmont, Angélina Legros, Nicolas Goardon, Céline Quesnelle, Agathe Ricou, Laurent Castéra, Dominique Vaur, Gérald Le Gac, Chandran Ka, Yann Fichou, Françoise Bonnet‐Dorion, Nicolas Sévenet, Marine Guillaud‐Bataille, Nadia Boutry‐Kryza, Inès Schultz, Virginie Caux‐Moncoutier, Maria Rossing, Logan C. Walker, Amanda B. Spurdle, Claude Houdayer, Alexandra Martins, Sophie Krieger
Software Mentions: 2
Published: over 6 years ago

10.1186/s12864-018-4962-9

Dietary supplementation with olive mill wastewaters induces modifications on chicken jejunum epithelial cell transcriptome and modulates jejunum morphology
Cited by: 18
Author(s): Marcella Sabino, Katia Cappelli, Stefano Capomaccio, Luisa Pascucci, Ilaria Biasato, Andrea Verini-Supplizi, Andrea Valiani, Massimo Trabalza‐Marinucci
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12864-019-5817-8

Genome description of Phlebia radiata 79 with comparative genomics analysis on lignocellulose decomposition machinery of phlebioid fungi
Cited by: 16
Author(s): Mari Mäkinen, Jaana Kuuskeri, Pia Laine, Olli‐Pekka Smolander, Andriy Kovalchuk, Zhen Zeng, Fred O. Asiegbu, Lars Paulín, Petri Auvinen, Taina Lundell
Software Mentions: 2
Published: about 7 years ago

10.1186/s12864-018-5327-0

A high-fat diet alters genome-wide DNA methylation and gene expression in SM/J mice
Cited by: 31
Author(s): Madeline Rose Keleher, Syeda Nuzhat Fatima Zaidi, Lauren Hicks, Shyam Shah, Xiaoyun Xing, Daofeng Li, Ting Wang, James M. Cheverud
Software Mentions: 2
Published: over 7 years ago

10.1186/s12864-018-4591-3

MicroRNA expression profiles of bovine monocyte-derived macrophages infected in vitro with two strains of Streptococcus agalactiae
Cited by: 22
Author(s): Anna Lewandowska-Sabat, Silje Camilla Furre Hansen, T. R. Solberg, Olav Østerås, B. Heringstad, Preben Boysen, I. Olsaker
Software Mentions: 2
Published: over 8 years ago

10.1186/s12864-016-3161-9

Impact of RNA degradation on fusion detection by RNA-seq
Cited by: 34
Author(s): Jaime Davila, Numrah Fadra, Xiaoke Wang, Amber McDonald, Asha Nair, Barbara R. Crusan, Xia Wu, Joseph H. Blommel, Jin Jen, Kandelaria M. Rumilla, Robert B. Jenkins, Umut Aypar, Eric W. Klee, Benjamin R. Kipp, Kevin C. Halling
Software Mentions: 2
Published: over 9 years ago

10.1186/s12864-020-07120-w

Comparative transcriptome analysis reveals that PCK1 is a potential gene affecting IMF deposition in buffalo
Cited by: 21
Author(s): Jieping Huang, Feng Xue, Ruirui Zhu, Duo Guo, Yutong Wei, Xiaodan Cao, Yun Ma, Deshun Shi
Software Mentions: 2
Published: over 5 years ago

10.1186/s12864-017-4354-6

Deciphering the genetic regulation of peripheral blood transcriptome in pigs through expression genome-wide association study and allele-specific expression analysis
Cited by: 20
Author(s): Tatiana Maroilley, Gaëtan Lemonnier, Jérôme Lecardonnel, Diane Esquerré, Yuliaxis Ramayo-Caldas, Marie‐José Mercat, Claire Rogel‐Gaillard, Jordi Estellé
Software Mentions: 2
Published: over 8 years ago

10.1186/s12864-020-6584-2

Sirt2-associated transcriptome modifications in cisplatin-induced neuronal injury
Cited by: 4
Author(s): Xin Zhao, Wei Du, Manchao Zhang, Zainab Atiq, Fang Xia
Software Mentions: 2
Published: over 6 years ago

10.1186/s12864-019-6292-y

Efficient depletion of ribosomal RNA for RNA sequencing in planarians
Cited by: 22
Author(s): Iana V Kim, E. J. Ross, Sascha Dietrich, Kristina Döring, Alejandro Sánchez Alvarado, Claus-D. Kuhn
Software Mentions: 2
Published: over 6 years ago

10.1186/s12864-020-06952-w

A tentacle for every occasion: comparing the hunting tentacles and sweeper tentacles, used for territorial competition, in the coral Galaxea fascicularis
Cited by: 12
Author(s): Oshra Yosef, Yotam Popovits, Assaf Malik, Maya Ofek-Lalzer, Tali Mass, Daniel Sher
Software Mentions: 2
Published: almost 6 years ago

10.1186/s12864-019-5676-3

Comprehensive kinome NGS targeted expression profiling by KING-REX
Cited by: 1
Author(s): Giovanni Carapezza, Carlo Cusi, Ettore Rizzo, Laura Raddrizzani, Sebastiano Di Bella, Alessio Somaschini, Antonella Leone, Rosita Lupi, Margherita Mutarelli, Vincenzo Nigro, Diego di Bernardo, Paolo Magni, Antonella Isacchi, Roberta Bosotti
Software Mentions: 2
Published: about 7 years ago

10.1186/s12864-020-06854-x

Maternal dietary resistant starch does not improve piglet’s gut and liver metabolism when challenged with a high fat diet
Cited by: 2
Author(s): Martine Schroyen, Julie Leblois, Julie Uerlings, Bing Li, Ester Arévalo Sureda, Sébastien Massart, José Wavreille, Jérôme Bindelle, Nadia Everaert
Software Mentions: 2
Published: about 6 years ago

10.1186/s12864-020-07344-w

Correction for both common and rare cell types in blood is important to identify genes that correlate with age
Cited by: 5
Author(s): Damiano Pellegrino-Coppola, Annique Claringbould, Maartje Stutvoet, Dorret I. Boomsma, M. Arfan Ikram, P. Eline Slagboom, Harm-Jan Westra, Lude Franke
Software Mentions: 2
Published: over 5 years ago

10.1186/s12864-018-4911-7

Analysis of Brachypodium miRNA targets: evidence for diverse control during stress and conservation in bioenergy crops
Cited by: 18
Author(s): Karl R. Franke, Skye Schmidt, Sunhee Park, Dong‐Hoon Jeong, Monica Accerbi, Pamela J. Green
Software Mentions: 2
Published: almost 8 years ago

10.1186/s12864-020-6462-y

Transcriptome-wide map of m6A circRNAs identified in a rat model of hypoxia mediated pulmonary hypertension
Cited by: 48
Author(s): Hua Su, Guowen Wang, Lingfang Wu, Xiaochun Ma, Kejing Ying, Ruifeng Zhang
Software Mentions: 2
Published: over 6 years ago

10.1002/cam4.3122

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

10.1002/cam4.3325

Virome assembly and annotation in brain tissue based on next‐generation sequencing
Cited by: 6
Author(s): Zihao Yuan, Xiaohua Ye, Lisha Zhu, Ningyan Zhang, Zhiqiang An, W. Jim Zheng
Software Mentions: 2
Published: almost 6 years ago

10.1186/s40170-020-00233-6

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

10.1186/s40170-020-00235-4

In vivo assessment of glutamine anaplerosis into the TCA cycle in human pre-malignant and malignant clonal plasma cells
Cited by: 14
Author(s): Wilson I. Gonsalves, Jin Sung Jang, Erik Jessen, Taro Hitosugi, Laura A. Evans, Dragan Jevremović, Xuan-Mai Pettersson, Alexander Graham Bush, Jaimee Gransee, Emilie Anderson, Santosh Kumar, K. Sreekumaran Nair
Software Mentions: 2
Published: over 5 years ago

10.26502/fccm.92920215

Transcriptional Regulation of Structural and Functional Adaptations in a Developing Adulthood Myocardium
Cited by: 2
Author(s): Sini Sunny, Anil K. Challa, Aijun Qiao, Arun Jyothidasan, Prasanna Krishnamurthy, Muralidharan Thoddi Ramamurthy, David K. Crossman, Steven M. Pogwizd, Senthilkumar Cinghu, Namakkal S. Rajasekaran
Software Mentions: 2
Published: over 5 years ago

10.1186/s12933-018-0713-0

Adverse effects of Hif1a mutation and maternal diabetes on the offspring heart
Cited by: 22
Author(s): Radka Čerychová, Romana Bohuslavová, F Papoušek, David Sedmera, Pavel Abaffy, Vladimı́r Beneš, František Kolář, Gabriela Pavlínková
Software Mentions: 2
Published: about 8 years ago

10.1038/s41375-019-0403-2

RUNX proteins desensitize multiple myeloma to lenalidomide via protecting IKZFs from degradation
Cited by: 32
Author(s): Nan Zhou, Álvaro Gutiérrez-Uzquiza, Zheng Xiang, Renxu Chang, Dan T. Vogl, Alfred L. Garfall, Luca Bernabei, Anita Saraf, Laurence Florens, Michael P. Washburn, Anuradha Illendula, John H. Bushweller, Luca Busino
Software Mentions: 2
Published: over 7 years ago

10.1038/s41375-018-0184-z

Genetic predisposition to B-cell acute lymphoblastic leukemia at 14q11.2 is mediated by a CEBPE promoter polymorphism
Cited by: 18
Author(s): James B. Studd, Minjun Yang, Zhenhua Li, Jayaram Vijayakrishnan, Yi Lü, Allen Eng Juh Yeoh, Kajsa Paulsson, Richard S. Houlston
Software Mentions: 2
Published: about 8 years ago

10.1038/s41375-019-0546-1

Cryptic genomic lesions in adverse-risk acute myeloid leukemia identified by integrated whole genome and transcriptome sequencing
Cited by: 12
Author(s): Jaeseung C. Kim, Philip C. Zuzarte, Tracy Murphy, Michelle Chan-Seng-Yue, Andrew Brown, Paul M. Krzyzanowski, Adam C. Smith, Faiyaz Notta, Mark D. Minden, John Douglas Mcpherson
Software Mentions: 2
Published: almost 7 years ago

10.1038/leu.2016.149

Cryptic splicing events in the iron transporter ABCB7 and other key target genes in SF3B1-mutant myelodysplastic syndromes
Cited by: 97
Author(s): Hamid Dolatshad, Andrea Pellagatti, Fabio G. Liberante, Miriam Llorian, Emmanouela Repapi, Violetta Steeples, S. Roy, L Scifo, Richard N. Armstrong, Jacqueline Shaw, Bon Ham Yip, Sally Killick, Rajko Kušec, Stephen Taylor, Ken I. Mills, Kienan I. Savage, Christopher W.J. Smith, Jacqueline Boultwood
Software Mentions: 2
Published: about 10 years ago

10.1038/s41375-021-01146-z

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

10.1038/s41375-020-0771-7

Investigating the role of the innate immune response in relapse or blast crisis in chronic myeloid leukemia
Cited by: 7
Author(s): Weiqi Huang, Bin Liu, Elizabeth A. Eklund
Software Mentions: 2
Published: over 6 years ago

10.3390/life11080846

Establishment of an Intradermal Ear Injection Model of IL-17A and IL-36γ as a Tool to Investigate the Psoriatic Cytokine Network
Cited by: 1
Author(s): David Kluwig, Sebastian Huth, Ali T. Abdallah, Carolina M. Pfaff, Katharina Fietkau, Laura Huth, Yvonne Marquardt, Jens Malte Baron, Bernhard Lüscher
Software Mentions: 2
Published: almost 5 years ago

10.26508/lsa.201900523

Functional annotation of noncoding mutations in cancer
Cited by: 2
Author(s): Husen M. Umer, Karolina Smolińska, Jan Komorowski, Claes Wadelius
Software Mentions: 2
Published: almost 5 years ago

10.26508/lsa.201800233

m⁶A-mRNA methylation regulates cardiac gene expression and cellular growth
Cited by: 91
Author(s): Vivien Kmietczyk, Eva Riechert, Laura Kalinski, Etienne Boileau, Ellen Malovrh, Brandon Malone, Agnieszka Górska, Christoph Hofmann, Eshita Varma, Lonny Jürgensen, Verena Kamuf-Schenk, Janine Altmüller, Rewati Tappu, Martin Busch, Patrick Most, Hugo A. Katus, Christoph Dieterich, Mirko Völkers
Software Mentions: 2
Published: over 7 years ago

10.26508/lsa.202000640

EBV renders B cells susceptible to HIV-1 in humanized mice
Cited by: 21
Author(s): Donal McHugh, Renier Myburgh, Nicole Caduff, Michael Spohn, Yik Lim Kok, Christian W. Keller, Anita Murer, Bithi Chatterjee, Julia Rühl, Christine Engelmann, Obinna Chijioke, Isaak Quast, Mohaned Shilaih, Victoria P Strouvelle, Katja Neumann, Thomas Menter, Stephan Dirnhofer, Janice K. P. Lam, Kwai Fung Hui, Simon Bredl, Erika Schlaepfer, Silvia Sorce, Andrea Zbinden, Riccarda Capaul, Jan D. Lünemann, Adriano Aguzzi, Aks Chiang, Werner Kempf, Alexandra Trkola, Karin J. Metzner, Markus G. Manz, Adam Grundhoff, Roberto F. Speck, Christian Münz
Software Mentions: 2
Published: about 6 years ago

10.26508/lsa.201800024

CHRAC/ACF contribute to the repressive ground state of chromatin
Cited by: 24
Author(s): Alessandro Scacchetti, Laura Brueckner, Dhawal Jain, Tamás Schauer, Xu Zhang, Frank Schnorrer, Bas van Steensel, Tobias Straub, Peter B. Becker
Software Mentions: 2
Published: over 8 years ago

10.26508/lsa.202000808

The chromatin landscape of primary synovial sarcoma organoids is linked to specific epigenetic mechanisms and dependencies
Cited by: 18
Author(s): Gaylor Boulay, Luisa Cironi, Sara P. Garcia, Shruthi Rengarajan, Yu-Hang Xing, Lukuo Lee, Mary E. Awad, Beverly Naigles, Sowmya Iyer, Liliane C. Broye, Tuğba Keskin, Alexandra Cauderay, Carlo Fusco, Igor Letovanec, Ivan Chebib, Petur Nielsen, Stéphane Tercier, Stéphane Cherix, Tu Nguyen-Ngoc, Gregory M. Coté, Edwin Choy, Paolo Provero, Mario L. Suvà, Miguel N. Rivera, Ivan Stamenkovic, Nicolò Riggi
Software Mentions: 2
Published: over 5 years ago

10.26508/lsa.201800018

Small RNA-Seq reveals novel miRNAs shaping the transcriptomic identity of rat brain structures
Cited by: 6
Author(s): Anaïs Soula, Mélissa Valere, María-José López-González, Vicky Ury-Thiery, Alexis Groppi, Marc Landry, Macha Nikolski, Alexandre Favereaux
Software Mentions: 2
Published: almost 8 years ago

10.26508/lsa.201800197

A role for MED14 and UVH6 in heterochromatin transcription upon destabilization of silencing
Cited by: 13
Author(s): Pierre Bourguet, Stève de Bossoreille, Leticia López-González, Marie-Noëlle Pouch-Pélissier, Ángeles Gómez-Zambrano, Anthony Devert, Thierry Pélissier, Romain Pogorelcnik, Isabelle Vaillant, Olivier Mathieu
Software Mentions: 2
Published: over 7 years ago

10.26508/lsa.201900623

Nup93 regulates breast tumor growth by modulating cell proliferation and actin cytoskeleton remodeling
Cited by: 31
Author(s): Simone Bersini, Nikki K. Lytle, Roberta Schulte, Ling Huang, Geoffrey M. Wahl, Martin W. Hetzer
Software Mentions: 2
Published: over 6 years ago

10.26508/lsa.201900533

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

10.1186/s12936-021-03839-3

Early whole blood transcriptional responses to radiation-attenuated Plasmodium falciparum sporozoite vaccination in malaria naïve and malaria pre-exposed adult volunteers
Cited by: 5
Author(s): Fergal J. Duffy, Ying Du, Jason Carnes, Judith E. Epstein, Stephen L. Hoffman, Salim Abdulla, Said Jongo, Maxmillian Mpina, Claudia Daubenberger, John D. Aitchison, Ken Stuart
Software Mentions: 2
Published: about 5 years ago

10.3390/md18080386

De novo Transcriptome of the Non-saxitoxin Producing Alexandrium tamutum Reveals New Insights on Harmful Dinoflagellates
Cited by: 19
Author(s): Giorgio Maria Vingiani, Dārta Štālberga, Pasquale De Luca, Adrianna Ianora, Danièle De Luca, Chiara Lauritano
Software Mentions: 2
Published: almost 6 years ago

10.1097/MD.0000000000022964

Long non-coding RNAs expression profile and functional analysis of acute ischemic stroke
Cited by: 7
Author(s): Jia Li, Miao Hao, Ben Yang, Tianji Shi, Yingyu Zhang, Jun Feng, Jiajun Chen
Software Mentions: 2
Published: over 5 years ago

10.1016/j.metabol.2019.153947

AKR1D1 is a novel regulator of metabolic phenotype in human hepatocytes and is dysregulated in non-alcoholic fatty liver disease
Cited by: 44
Author(s): Νικόλαος Νικολάου, Laura Gathercole, Lea Marchand, Sara Althari, Niall Dempster, Charlotte Green, Martijn van de Bunt, Catriona McNeil, Anastasia Arvaniti, Beverly Hughes, Bruno Sgromo, Richard Gillies, Hanns‐Ulrich Marschall, T.M. Penning, John D. Ryan, Wiebke Arlt, Leanne Hodson, Jeremy Tomlinson
Software Mentions: 2
Published: almost 7 years ago

10.1111/1751-7915.12713

Transcriptional response of<i>Escherichia coli</i>to ammonia and glucose fluctuations
Cited by: 39
Author(s): Joana Danica Simen, Michael Löffler, Günter Jäger, Karin Schäferhoff, Andreas Freund, Jakob Matthes, Jan Müller, Ralf Takors, RecogNice-Team
Software Mentions: 2
Published: about 9 years ago

10.15698/mic2019.03.672

Simultaneous profiling of sexually transmitted bacterial pathogens, microbiome, and concordant host response in cervical samples using whole transcriptome sequencing analysis
Cited by: 7
Author(s): Catherine M. O’Connell, Hayden Brochu, Jenna Girardi, Erin Harrell, Aiden Jones, Toni Darville, Arlene C. Seña, Xinxia Peng
Software Mentions: 2
Published: over 7 years ago

10.1186/s40168-017-0317-z

Optimization and validation of sample preparation for metagenomic sequencing of viruses in clinical samples
Cited by: 41
Author(s): Dagmara W. Lewandowska, Osvaldo Zagordi, Fabienne-Desirée Geissberger, Verena Kufner, Stefan Schmutz, Jürg Böni, Karin J. Metzner, Alexandra Trkola, Michael Huber
Software Mentions: 2
Published: almost 9 years ago

10.1186/s40168-020-00952-4

Modulating gut microbiota in a mouse model of Graves’ orbitopathy and its impact on induced disease
Cited by: 29
Author(s): Sajad Moshkelgosha, Hedda Luise Verhasselt, Giulia Masetti, Danila Covelli, Filippo Biscarini, Mareike Horstmann, Anke Daser, Astrid M. Westendorf, Christoph Jesenek, Svenja Philipp, Salvador Díaz‐Cano, J. Paul Banga, Daryn R. Michael, Sue Plummer, Julian R. Marchesi, Anja Eckstein, Marian Ludgate, Utta Berchner‐Pfannschmidt
Software Mentions: 2
Published: over 5 years ago

10.3390/mi11030322

Selective Retrieval of Individual Cells from Microfluidic Arrays Combining Dielectrophoretic Force and Directed Hydrodynamic Flow
Cited by: 11
Author(s): Pierre-Emmanuel Marie Thiriet, Jörn Pezoldt, Gabriele Gambardella, Kevin Keim, Bart Deplancke, Carlotta Guiducci
Software Mentions: 2
Published: over 6 years ago

10.3390/microorganisms9081670

Coordinated Diel Gene Expression of Cyanobacteria and Their Microbiome
Cited by: 7
Author(s): Kai Wang, Xiaozhen Mou
Software Mentions: 2
Published: almost 5 years ago

10.3390/microorganisms9071463

Use of Oxidative Stress Responses to Determine the Efficacy of Inactivation Treatments on Cryptosporidium Oocysts
Cited by: 3
Author(s): Tefera Tadesse, Kristoffer Relling Tysnes, Lucy J. Robertson
Software Mentions: 2
Published: about 5 years ago