77 Works

Data from: Genome reannotation of the lizard Anolis carolinensis based on 14 adult and embryonic deep transcriptomes

Walter L. Eckalbar, Elizabeth D. Hutchins, Glenn J. Markov, April N. Allen, Jason J. Corneveaux, Kerstin Lindblad-Toh, Federica Di Palma, Matthew J. Huentelman, Kenro Kusumi & Jessica Alföldi
Background: The green anole lizard, Anolis carolinensis, is a key species for both laboratory and field-based studies of evolutionary genetics, development, neurobiology, physiology, behavior, and ecology. As the first non-avian reptilian genome sequenced, A. carolinesis is also a prime reptilian model for comparison with other vertebrate genomes. The public databases of Ensembl and NCBI have provided a first generation gene annotation of the anole genome that relies primarily on sequence conservation with related species. A...

Data from: Genome-Wide Analyses Suggest Mechanisms Involving Early B-Cell Development in Canine IgA Deficiency

Mia Olsson, Katarina Tengvall, Marcel Frankowiack, Marcin Kierczak, Kerstin Bergvall, Erik Axelsson, Linda Tintle, Eliane Marti, Petra Roosje, Tosso Leeb, Åke Hedhammar, Lennart Hammarström & Kerstin Lindblad-Toh
Immunoglobulin A deficiency (IgAD) is the most common primary immune deficiency disorder in both humans and dogs, characterized by recurrent mucosal tract infections and a predisposition for allergic and other immune mediated diseases. In several dog breeds, low IgA levels have been observed at a high frequency and with a clinical resemblance to human IgAD. In this study, we used genome-wide association studies (GWAS) to identify genomic regions associated with low IgA levels in dogs...

Data from: Loggerhead sea turtle embryos (Caretta caretta) regulate expression of stress-response and developmental genes when exposed to a biologically realistic heat stress

Blair P. Bentley, Brian J. Haas, Jamie N. Tedeschi & Oliver Berry
Oviparous reptile embryos are expected to breach their critical thermal maxima if temperatures reach those predicted under current climate change models due to the lack the maternal buffering processes and parental care. Heat shock proteins (HSPs) are integral in the molecular response to thermal stress, and their expression is heritable, but the roles of other candidate families such as the heat shock factors (HSFs) have not been determined in reptiles. Here we subject embryonic sea...

Data from: Polygenic adaptation on height is overestimated due to uncorrected stratification in genome-wide association studies

Mashaal Sohail, Robert M. Maier, Andrea Ganna, Alex Bloemendal, Alicia R. Martin, Michael C. Turchin, Charleston W. K. Chang, Joel Hirschhorn, Mark J. Daly, Nick Patterson, Benjamin Neale, Iain Mathieson, David Reich & Shamil R. Sunyaev
Genetic predictions of height differ among human populations and these differences have been interpreted as evidence of polygenic adaptation. These differences were first detected using SNPs genome-wide significantly associated with height, and shown to grow stronger when large numbers of sub-significant SNPs were included, leading to excitement about the prospect of analyzing large fractions of the genome to detect polygenic adaptation for multiple traits. Previous studies of height have been based on SNP effect size...

Structural insights into dpCoA-RNA decapping by NudC

Wei Zhou, Zeyuan Guan, Fen Zhao, Yage Ye, Fang Yang, Ping Yin & Delin Zhang
Various kinds of cap structures, such as m7G, triphosphate groups, NAD and dpCoA, protect the 5′ terminus of RNA. The cap structures bond covalently to RNA and affect its stability, translation, and transport. The removal of the caps is mainly executed by Nudix hydrolase family proteins, including Dcp2, RppH and NudC. Numerous efforts have been made to elucidate the mechanism underlying the removal of m7G, triphosphate group, and NAD caps. In contrast, few studies related...

Additional file 1 of Elucidating the diversity of malignant mesenchymal states in glioblastoma by integrative analysis

Rony Chanoch-Myers, Adi Wider, Mario L. Suva & Itay Tirosh
Additional file 1: Table S1. MES signatures from published studies. Table S2. Cohorts details. Table S3. Functional MES signatures. Table S4. Top-scoring genes from PCA analysis.

Additional file 5 of Population structure discovery in meta-analyzed microbial communities and inflammatory bowel disease using MMUPHin

Siyuan Ma, Dmitry Shungin, Himel Mallick, Melanie Schirmer, Long H. Nguyen, Raivo Kolde, Eric Franzosa, Hera Vlamakis, Ramnik Xavier & Curtis Huttenhower
Additional file 5: Supplemental Table 3. Detailed specification for omnibus and per-feature differential abundance testing models.

Additional file 8 of Population structure discovery in meta-analyzed microbial communities and inflammatory bowel disease using MMUPHin

Siyuan Ma, Dmitry Shungin, Himel Mallick, Melanie Schirmer, Long H. Nguyen, Raivo Kolde, Eric Franzosa, Hera Vlamakis, Ramnik Xavier & Curtis Huttenhower
Additional file 8: Supplemental Table 6. Per-study and meta-analytically aggregated effect sizes of tests on the interaction between disease/treatment and sample type/disease on per-feature abundances.

Additional file 5 of STAT3/miR-130b-3p/MBNL1 feedback loop regulated by mTORC1 signaling promotes angiogenesis and tumor growth

Hongwu Li, Ping Liu, Dapeng Li, Zixi Wang, Zhao Ding, Meng Zhou, Xu Chen, Manli Miao, Junli Ding, Wei Lin, Yehai Liu & Xiaojun Zha
Additional file 5: Supplementary Table 9. List of the downregulated differentially expressed genes from DEGs in angiofibroma(AF) of TSC patients vs. normal skin. All genes were identified with FDR-adjusted p-value < 0.05 and absolute value of log2(FC) > 1.

Data from: Covalent disruptor of YAP-TEAD association suppresses defective Hippo signaling

Mengyang Fan, Wenchao Lu, Jianwei Che, Nicholas Kwiatkowski, Yang Gao, Hyuk-Soo Seo, Scott Ficarro, Prafulla Gokhale, Yao Liu, Ezekiel Geffken, Jimit Lakhani, Kijun Song, Miljan Kuljanin, Wenzhi Ji, Jie Jiang, Zhixiang He, Jason Tse, Andrew Boghossian, Matthew Rees, Melissa Ronan, Jennifer Roth, Joseph Mancias, Jarrod Marto, Sirano Dhe-Paganon, Tinghu Zhang … & Nathanael Gray
The transcription factor TEAD, together with its coactivator YAP/TAZ, is a key transcriptional modulator of the Hippo pathway. Activation of TEAD transcription by YAP has been implicated in a number of malignancies, and this complex represents a promising target for drug discovery. Here, we employed covalent fragment screening approach followed by structure-based design to develop an irreversible TEAD inhibitor MYF-03-69. Using a range of in vitro and cell-based assays we demonstrated that through a covalent...

sj-xlsx-3-npx-10.1177_1934578X221143637 - Supplemental material for Exploring the Potential Mechanism of Danshen in the Treatment of Concurrent Ischemic Heart Disease and Depression Using Network Pharmacology, Molecular Docking, and Molecular Dynamics Simulation

Zhiyao Liu, Hailiang Huang, Ying Yu, Yuqi Jia, Xiaowen Dang, Yajie Wang & Lei Huang
Supplemental material, sj-xlsx-3-npx-10.1177_1934578X221143637 for Exploring the Potential Mechanism of Danshen in the Treatment of Concurrent Ischemic Heart Disease and Depression Using Network Pharmacology, Molecular Docking, and Molecular Dynamics Simulation by Zhiyao Liu, Hailiang Huang, Ying Yu, Yuqi Jia, Xiaowen Dang, Yajie Wang and Lei Huang in Natural Product Communications

sj-xlsx-3-npx-10.1177_1934578X221143637 - Supplemental material for Exploring the Potential Mechanism of Danshen in the Treatment of Concurrent Ischemic Heart Disease and Depression Using Network Pharmacology, Molecular Docking, and Molecular Dynamics Simulation

Zhiyao Liu, Hailiang Huang, Ying Yu, Yuqi Jia, Xiaowen Dang, Yajie Wang & Lei Huang
Supplemental material, sj-xlsx-3-npx-10.1177_1934578X221143637 for Exploring the Potential Mechanism of Danshen in the Treatment of Concurrent Ischemic Heart Disease and Depression Using Network Pharmacology, Molecular Docking, and Molecular Dynamics Simulation by Zhiyao Liu, Hailiang Huang, Ying Yu, Yuqi Jia, Xiaowen Dang, Yajie Wang and Lei Huang in Natural Product Communications

sj-xlsx-7-npx-10.1177_1934578X221143637 - Supplemental material for Exploring the Potential Mechanism of Danshen in the Treatment of Concurrent Ischemic Heart Disease and Depression Using Network Pharmacology, Molecular Docking, and Molecular Dynamics Simulation

Zhiyao Liu, Hailiang Huang, Ying Yu, Yuqi Jia, Xiaowen Dang, Yajie Wang & Lei Huang
Supplemental material, sj-xlsx-7-npx-10.1177_1934578X221143637 for Exploring the Potential Mechanism of Danshen in the Treatment of Concurrent Ischemic Heart Disease and Depression Using Network Pharmacology, Molecular Docking, and Molecular Dynamics Simulation by Zhiyao Liu, Hailiang Huang, Ying Yu, Yuqi Jia, Xiaowen Dang, Yajie Wang and Lei Huang in Natural Product Communications

Data from: The shepherds' tale: a genome-wide study across 9 dog breeds implicates two loci in the regulation of fructosamine serum concentration in Belgian shepherds

Simon K. G. Forsberg, Marcin Kierczak, Ingrid Ljungvall, Anne-Christine Merveille, Vassiliki Gouni, Maria Wiberg, Jakob Lundgren Willesen, Sofia Hanås, Anne-Sophie Lequarré, Louise Mejer Sørensen, Laurent Tiret, Kathleen McEntee, Eija Seppälä, Jørgen Koch, Géraldine Battaille, Hannes Lohi, Merete Fredholm, Valerie Chetboul, Jens Häggström, Örjan Carlborg, Kerstin Lindblad-Toh & Katja Höglund
Diabetes mellitus is a serious health problem in both dogs and humans. Certain dog breeds show high prevalence of the disease, whereas other breeds are at low risk. Fructosamine and glycated hemoglobin (HbA1c) are two major biomarkers of glycaemia where serum concentrations reflect glucose turnover over the past few weeks to months. In this study, we searched for genetic factors influencing variation in serum fructosamine concentration in healthy dogs using data from nine dog breeds....

Data from: Accounting for experimental noise reveals that mRNA levels, amplified by post-transcriptional processes, largely determine steady-state protein levels in yeast

Gábor Csárdi, Alexander Franks, David S. Choi, Edoardo M. Airoldi & David Allan Drummond
Cells respond to their environment by modulating protein levels through mRNA transcription and post-transcriptional control. Modest observed correlations between global steady-state mRNA and protein measurements have been interpreted as evidence that mRNA levels determine roughly 40% of the variation in protein levels, indicating dominant post-transcriptional effects. However, the techniques underlying these conclusions, such as correlation and regression, yield biased results when data are noisy, missing systematically, and collinear---properties of mRNA and protein measurements---which motivated us...

Source code for StrVCTVRE: a supervised learning method to predict the pathogenicity of human genome structural variants

Andrew Sharo, Zhiqiang Hu, Shamil Sunyaev & Steven Brenner
Whole genome sequencing resolves many clinical cases where standard diagnostic methods have failed. However, at least half of these cases remain unresolved after whole genome sequencing. Structural variants (SVs; genomic variants larger than 50 base pairs) of uncertain significance are the genetic cause of a portion of these unresolved cases. As sequencing methods using long or linked reads become more accessible and SV detection algorithms improve, clinicians and researchers are gaining access to thousands of...

Updates to data versions and analytic methods influence the reproducibility of results from epigenome-wide association studies

Alexandre A. Lussier, Yiwen Zhu, Brooke J. Smith, Andrew J. Simpkin, Andrew D.A.C. Smith, Matthew J. Suderman, Esther Walton, Kerry J. Ressler & Erin C. Dunn
Biomedical research has grown increasingly cooperative through the sharing of consortia-level epigenetic data. Since consortia preprocess data prior to distribution, new processing pipelines can lead to different versions of the same dataset. Similarly, analytic frameworks evolve to incorporate cutting-edge methods and best practices. However, it remains unknown how different data and analytic versions alter the results of epigenome-wide analyses, which could influence the replicability of epigenetic associations. Thus, we assessed the impact of these changes...

Exosomal microRNA-150-5p from bone marrow mesenchymal stromal cells mitigates cerebral ischemia/reperfusion injury via targeting toll-like receptor 5

Xue Li, Ting Bi & Shuo Yang
MicroRNA (miR)-150-5p has been investigated in many studies, while the role of exosomal miR-150-5p from bone arrow mesenchymal stromal cells (BMSCs) on cerebral ischemia/reperfusion (I/R) injury is not fully explored. This research aims to probe the effects of exosomal miR-150-5p from BMSCs on cerebral I/R injury via regulating B-cell translocation gene 2 (TLR5). Bone marrow mesenchymal stem cell-derived exosomes (BMSCs-Exo) were isolated and identified. The middle cerebral artery occlusion (MCAO) rat model was established and...

Exosomal microRNA-150-5p from bone marrow mesenchymal stromal cells mitigates cerebral ischemia/reperfusion injury via targeting toll-like receptor 5

Shuo Yang, Xue Li & Ting Bi
MicroRNA (miR)-150-5p has been investigated in many studies, while the role of exosomal miR-150-5p from bone marrow mesenchymal stromal cells (BMSCs) on cerebral ischemia/reperfusion (I/R) injury is not fully explored. This research aims to probe the effects of exosomal miR-150-5p from BMSCs on cerebral I/R injury via regulating B-cell translocation gene 2 (TLR5). BMSCs were cultured and transfected with miR-150-5p mimic, then exosomes from BMSCs were extracted. The middle cerebral artery occlusion (MCAO) rat model...

Evaluating the influences of confounding variables on benchmark dose using a case study in the field of ionizing radiation

Nadine Adam, Ngoc Q. Vuong, Hailey Adams, Byron Kuo, Afshin Beheshti, Carole Yauk, Ruth Wilkins & Vinita Chauhan
A vast amount of data regarding the effects of radiation stressors on transcriptional changes has been produced over the past few decades. These data have shown remarkable consistency across platforms and experimental design, enabling increased understanding of early molecular effects of radiation exposure. However, the value of transcriptomic data in the context of risk assessment is not clear and represents a gap that is worthy of further consideration. Recently, benchmark dose (BMD) modeling has shown...

Additional file 3 of STAT3/miR-130b-3p/MBNL1 feedback loop regulated by mTORC1 signaling promotes angiogenesis and tumor growth

Hongwu Li, Ping Liu, Dapeng Li, Zixi Wang, Zhao Ding, Meng Zhou, Xu Chen, Manli Miao, Junli Ding, Wei Lin, Yehai Liu & Xiaojun Zha
Additional file 3: Supplementary Table S7. List of the predict target genes of miR-130b-3p from prediction softwares TargetScan, RNA22, PicTar, miRDB and miRWalk.

Additional file 4 of Population structure discovery in meta-analyzed microbial communities and inflammatory bowel disease using MMUPHin

Siyuan Ma, Dmitry Shungin, Himel Mallick, Melanie Schirmer, Long H. Nguyen, Raivo Kolde, Eric Franzosa, Hera Vlamakis, Ramnik Xavier & Curtis Huttenhower
Additional file 4: Supplemental Table 2. Full set of varying simulation parameters evaluated for MMUPHin validation.

Additional file 7 of Population structure discovery in meta-analyzed microbial communities and inflammatory bowel disease using MMUPHin

Siyuan Ma, Dmitry Shungin, Himel Mallick, Melanie Schirmer, Long H. Nguyen, Raivo Kolde, Eric Franzosa, Hera Vlamakis, Ramnik Xavier & Curtis Huttenhower
Additional file 7: Supplemental Table 5. Per-study and meta-analytically aggregated effect sizes of tests on per-feature abundance associated with disease phenotypic severity.

sj-xlsx-4-npx-10.1177_1934578X221143637 - Supplemental material for Exploring the Potential Mechanism of Danshen in the Treatment of Concurrent Ischemic Heart Disease and Depression Using Network Pharmacology, Molecular Docking, and Molecular Dynamics Simulation

Zhiyao Liu, Hailiang Huang, Ying Yu, Yuqi Jia, Xiaowen Dang, Yajie Wang & Lei Huang
Supplemental material, sj-xlsx-4-npx-10.1177_1934578X221143637 for Exploring the Potential Mechanism of Danshen in the Treatment of Concurrent Ischemic Heart Disease and Depression Using Network Pharmacology, Molecular Docking, and Molecular Dynamics Simulation by Zhiyao Liu, Hailiang Huang, Ying Yu, Yuqi Jia, Xiaowen Dang, Yajie Wang and Lei Huang in Natural Product Communications

sj-xlsx-5-npx-10.1177_1934578X221143637 - Supplemental material for Exploring the Potential Mechanism of Danshen in the Treatment of Concurrent Ischemic Heart Disease and Depression Using Network Pharmacology, Molecular Docking, and Molecular Dynamics Simulation

Zhiyao Liu, Hailiang Huang, Ying Yu, Yuqi Jia, Xiaowen Dang, Yajie Wang & Lei Huang
Supplemental material, sj-xlsx-5-npx-10.1177_1934578X221143637 for Exploring the Potential Mechanism of Danshen in the Treatment of Concurrent Ischemic Heart Disease and Depression Using Network Pharmacology, Molecular Docking, and Molecular Dynamics Simulation by Zhiyao Liu, Hailiang Huang, Ying Yu, Yuqi Jia, Xiaowen Dang, Yajie Wang and Lei Huang in Natural Product Communications

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