Results 41 to 50 of about 71,340 (293)

SRTsim: spatial pattern preserving simulations for spatially resolved transcriptomics

Genome Biology, 2023
AbstractSpatially resolved transcriptomics (SRT)-specific computational methods are often developed, tested, validated, and evaluated in silico using simulated data. Unfortunately, existing simulated SRT data are often poorly documented, hard to reproduce, or unrealistic.
Zhu, Jiaqiang, Shang, Lulu, Zhou, Xiang
openaire   +3 more sources

Transferrin receptor 1‐mediated iron uptake supports thermogenic activation in human cervical‐derived adipocytes

FEBS Letters, EarlyView.
In this study, we found that human cervical‐derived adipocytes maintain intracellular iron level by regulating the expression of iron transport‐related proteins during adrenergic stimulation. Melanotransferrin is predicted to interact with transferrin receptor 1 based on in silico analysis.
Rahaf Alrifai, Mizuki Seo, Gyath Karadsheh, Fachrur Rizal Mahendra, Máté Á Demény, Ferenc Győry, János András Mótyán, László Fésüs, Endre Kristóf, Rini Arianti   +9 more
wiley   +1 more source

Molecular processes underlying synergistic linuron mineralization in a triple-species bacterial consortium biofilm revealed by differential transcriptomics [PDF]

, 2018
The proteobacteria Variovorax sp. WDL1, Comamonas testosteroni WDL7, and Hyphomicrobium sulfonivorans WDL6 compose a triple-species consortium that synergistically degrades and grows on the phenylurea herbicide linuron.
Anders, Aziz, Beliaev, Bers, Bleichrodt, Boon, Breugelmans, Breugelmans, Cerqueda-Garcia, Colwell, Dealtry, Dejonghe, Dwyer, Foster, Frias-Lopez, Garbeva, Garcia, Gonzalez-Torres, Hansen, Horemans, Horemans, Horemans, Horemans, Horinouchi, Ilut, Kanehisa, Kell, Kimes, Krol, Love, MacLean, Maeyer, Nadell, Palama, Perez, Reasoner, Rickard, Rosenthal, Russell, Sabag-Daigle, Sambrook, Shimoyama, Subramoni, Suzuki, Tai, Teramoto, Ward, Wenter, West, Wu, Zerbino, Zgur-Bertok, Zhou   +52 more
core   +2 more sources

Diversity and complexity in neural organoids

FEBS Letters, EarlyView.
Neural organoid research aims to expand genetic diversity on one side and increase tissue complexity on the other. Chimeroids integrate multiple donor genomes within single organoids. Self‐organising multi‐identity organoids, exogenous cell seeding, or enforced assembly of region‐specific organoids contribute to tissue complexity.
Ilaria Chiaradia, Madeline A. Lancaster
wiley   +1 more source

Detection of differentially expressed genes in spatial transcriptomics data by spatial analysis of spatial transcriptomics: A novel method based on spatial statistics

Frontiers in Neuroscience, 2022
BackgroundSpatial transcriptomics (STs) simultaneously obtains the location and amount of gene expression within a tissue section. However, current methods like FindMarkers calculated the differentially expressed genes (DEGs) based on the classical ...
Zhihua Qiu, Zhihua Qiu, Shaojun Li, Ming Luo, Shuanggen Zhu, Zhijian Wang, Yongjun Jiang   +6 more
doaj   +1 more source

Transcriptional network analysis of PTEN‐protein‐deficient prostate tumors reveals robust stromal reprogramming and signs of senescent paracrine communication

Molecular Oncology, EarlyView.
Combining PTEN protein assessment and transcriptomic profiling of prostate tumors, we uncovered a network enriched in senescence and extracellular matrix (ECM) programs associated with PTEN loss and conserved in a mouse model. We show that PTEN‐deficient cells trigger paracrine remodeling of the surrounding stroma and this information could help ...
Ivana Rondon‐Lorefice, Jose I. Lopez, Aitziber Ugalde‐Olano, Maite Zufiaurre, Ianire Astobiza, Natalia Martin‐Martin, Laura Bozal‐Basterra, Saioa Garcia‐Longarte, Amaia Zabala‐Letona, Sofia Rey, Aida Santos‐Martin, Miguel Unda, Ana Loizaga‐Iriarte, Mariona Graupera, Paolo Nuciforo, Arkaitz Carracedo, Isabel Mendizabal   +16 more
wiley   +1 more source

Multiomics modeling of the immunome, transcriptome, microbiome, proteome and metabolome adaptations during human pregnancy. [PDF]

, 2019
MotivationMultiple biological clocks govern a healthy pregnancy. These biological mechanisms produce immunologic, metabolomic, proteomic, genomic and microbiomic adaptations during the course of pregnancy.
Agard, Bruno, Aghaeepour, Nima, Ando, Kazuo, Angst, Martin S, Callahan, Benjamin, Contrepois, Kévin, Culos, Anthony, Darmstadt, Gary L, DiGiulio, Daniel B, Druzin, Maurice L, Ganio, Edward, Gaudilliere, Brice, Gaudilliere, Dyani, Ghaemi, Mohammad Sajjad, Gibbs, Ronald, Han, Xiaoyuan, Lee-McMullen, Brittany, Lehallier, Benoit, Lewis, David B, Maric, Ivana, Mcilwain, David, McNeil, Leslie, Ngo, Thuy TM, Nolan, Garry, Partovi Nia, Vahid, Quaintance, Cecele, Quake, Stephen R, Relman, David A, Robaczewska, Anna, Rosenberg-Hasson, Yael, Shaw, Gary M, Sirota, Marina, Snyder, Michael P, Stanley, Natalie, Stevenson, David K, Tanada, Athena, Tibshirani, Robert, Tingle, Martha, Tsai, Amy, Winn, Virginia D, Wise, Paul, Wong, Ronald J, Wyss-Coray, Tony   +42 more
core   +3 more sources

Potential therapeutic targeting of BKCa channels in glioblastoma treatment

Molecular Oncology, EarlyView.
This review summarizes current insights into the role of BKCa and mitoBKCa channels in glioblastoma biology, their potential classification as oncochannels, and the emerging pharmacological strategies targeting these channels, emphasizing the translational challenges in developing BKCa‐directed therapies for glioblastoma treatment.
Kamila Maliszewska‐Olejniczak, Karolina Pytlak, Sandra Jaworowska, Bogusz Kulawiak, Piotr Bednarczyk   +4 more
wiley   +1 more source

MNMST: topology of cell networks leverages identification of spatial domains from spatial transcriptomics data

Genome Biology
Advances in spatial transcriptomics provide an unprecedented opportunity to reveal the structure and function of biology systems. However, current algorithms fail to address the heterogeneity and interpretability of spatial transcriptomics data. Here, we
Yu Wang, Zaiyi Liu, Xiaoke Ma
doaj   +1 more source

Nezara viridula (Hemiptera: Pentatomidae) transcriptomic analysis and neuropeptidomics [PDF]

, 2018
Stinkbugs (Hemiptera: Pentatomidae) are of major economic importance as pest of crops. Among the species composing the stinkbug complex, Nezara viridula is one of the most abundant in Brazil, Argentina and the Southern USA. However, this species has been
Catalano, María Inés, Esponda Behrens, Natalia Irene, Lavore, Andres Esteban, Ons, Sheila, Palacio, Victorio Gabriel, Pérez Gianmarco, Lucila Maité, Rivera Pomar, Rolando   +6 more
core   +2 more sources