bioconductor: ComplexHeatmap | Projects

10.1155/2021/8892479

PDZ Binding Kinase/T-LAK Cell-Derived Protein Kinase Plays an Oncogenic Role and Promotes Immune Escape in Human Tumors
Cited by: 4
Author(s): Tingting Feng, Yan Zhang, Sunbin Ling, Chenyang Xu, Yingqi Lyu, Tingting Lu, Xinyuan Liu, Ying Liu, Yiming Wan, Zhong Huang, Dan Su
Software Mentions: 8
Published: about 3 years ago

10.1371/journal.ppat.1009933

Trypanosoma brucei triggers a broad immune response in the adipose tissue
Cited by: 11
Author(s): Henrique Machado, Tiago Bizarra-Rebelo, Mariana Sequeira, Sandra Trindade, Tãnia Carvalho, Filipa Rijo‐Ferreira, Barbara Rentroia‐Pacheco, Karine Serre, Luísa M. Figueiredo
Software Mentions: 8
Published: about 3 years ago

10.1128/mSystems.00152-21

Differential Analysis of Longitudinal Methicillin-Resistant Staphylococcus aureus Colonization in Relation to Microbial Shifts in the Nasal Microbiome of Neonatal Piglets
Cited by: 2
Author(s): Shriram Patel, Abel A. Vlasblom, Koen M. Verstappen, Aldert Zomer, Ad C. Fluit, Malbert R. C. Rogers, Jaap A. Wagenaar, Marcus J. Claesson, Birgitta Duim
Software Mentions: 8
Published: about 3 years ago

10.1186/s12915-020-00863-8

Functional signatures of evolutionarily young CTCF binding sites
Cited by: 7
Author(s): Dhoyazan Azazi, Jonathan M. Mudge, Duncan T. Odom, Paul Flicek
Software Mentions: 8
Published: about 4 years ago

10.3389/fimmu.2020.00611

Human Regulatory T Cells From Umbilical Cord Blood Display Increased Repertoire Diversity and Lineage Stability Relative to Adult Peripheral Blood
Cited by: 19
Author(s): Keshav Motwani, Leeana D. Peters, Willem H Vliegen, Ahmed G Elsayed, Howard R. Seay, Maria-Cecilia Lopez, Henry V. Baker, Amanda L. Posgai, Todd M. Brusko, Daniel J. Perry, Rhonda Bacher, Joseph Larkin, Michael J. Haller
Software Mentions: 8
Published: over 4 years ago

10.1016/j.heliyon.2019.e01558

Factor Analysis for Bicluster Acquisition (FABIA) revealed vincristine-sensitive transcript pattern of canine transmissible venereal tumors
Cited by: 5
Author(s): Kaj Chokeshaiusaha, Denis Puthier, Cong Tu Nguyen, Pansawut Sudjaidee, Thanida Sananmuang
Software Mentions: 8
Published: over 5 years ago

10.1038/s41421-021-00279-w

Targeting novel LSD1-dependent ACE2 demethylation domains inhibits SARS-CoV-2 replication
Cited by: 7
Author(s): Wen Juan Tu, Robert McCuaig, Michelle Melino, Daniel J. Rawle, Thuy T. Le, Kexin Yan, Andreas Suhrbier, Rebecca L. Johnston, Lambros T. Koufariotis, Nicola Waddell, E.M. Cross, S. Tsimbalyuk, Amanda L. Bain, Elizabeth Ahern, Natasha Collinson, Simon Phipps, Jade K. Forwood, Nabila Seddiki, Sudha Rao
Software Mentions: 8
Published: over 3 years ago

10.1186/s13059-020-02155-4

Estimating the quality of eukaryotic genomes recovered from metagenomic analysis with EukCC
Cited by: 51
Author(s): Paul Saary, Alex L. Mitchell, Alex Bateman
Software Mentions: 8
Published: about 4 years ago

10.1186/s13073-020-00799-2

Single cell characterization of B-lymphoid differentiation and leukemic cell states during chemotherapy in ETV6-RUNX1-positive pediatric leukemia identifies drug-targetable transcription factor activities
Cited by: 20
Author(s): Juha Mehtonen, Susanna Teppo, Mari Lahnalampi, Aleksi Kokko, Riina Kaukonen, Laura Oksa, Maria Bouvy-Liivrand, Alena Malyukova, Artturi Mäkinen, Saara Laukkanen, Petri Mäkinen, Samuli Rounioja, Pekka Ruusuvuori, Olle Sangfelt, Riikka Lund, Tapio Lönnberg, Olli Lohi, Merja Heinäniemi
Software Mentions: 8
Published: about 4 years ago

10.1371/journal.pone.0239189

Mining GWAS and eQTL data for CF lung disease modifiers by gene expression imputation
Cited by: 8
Author(s): Hong Dang, Deepika Polineni, Rhonda G. Pace, Jaclyn R. Stonebraker, Harriet Corvol, Garry R. Cutting, Mitchell L. Drumm, Lisa J. Strug, Wanda K. O’Neal, Michael R. Knowles
Software Mentions: 8
Published: almost 4 years ago

10.1038/s41375-020-01096-y

Copy number evolution and its relationship with patient outcome—an analysis of 178 matched presentation-relapse tumor pairs from the Myeloma XI trial
Cited by: 21
Author(s): James Croft, Sidra Ellis, Amy L. Sherborne, Kim A. Sharp, Amy Price, Matthew Jenner, Mark T. Drayson, Roger G. Owen, Sally Chown, Jindriska Lindsay, Kamaraj Karunanithi, Hannah Hunter, Walter M. Gregory, Faith E. Davies, Gareth J. Morgan, Gordon Cook, Lilit Atanesyan, Suvi Savola, David A. Cairns, Graham Jackson, Richard S. Houlston, Martin Kaiser
Software Mentions: 8
Published: almost 4 years ago

10.3390/cancers12030756

Analysis of Dual Class I Histone Deacetylase and Lysine Demethylase Inhibitor Domatinostat (4SC-202) on Growth and Cellular and Genomic Landscape of Atypical Teratoid/Rhabdoid
Cited by: 23
Author(s): Mariah M. Hoffman, Jessica S. Zylla, Somshuvra Bhattacharya, Kristin Calar, Timothy W. Hartman, Ratan D. Bhardwaj, W. Keith Miskimins, Pilar de la Puente, Etienne Z. Gnimpieba, Shanta M. Messerli
Software Mentions: 8
Published: over 4 years ago

10.3389/fphys.2021.662132

Liver Transcriptome Dynamics During Hibernation Are Shaped by a Shifting Balance Between Transcription and RNA Stability
Cited by: 10
Author(s): Austin E. Gillen, Rui Fu, Kent Riemondy, Jennifer Jager, Bin Fang, Mitchell A. Lazar, Sandra L. Martin
Software Mentions: 8
Published: over 3 years ago

10.1186/s12935-020-01661-6

Intestinal region-specific Wnt signalling profiles reveal interrelation between cell identity and oncogenic pathway activity in cancer development
Cited by: 6
Author(s): R. Adam, Sanne M. van Neerven, Cayetano Pleguezuelos-Manzano, Salvatore Simmini, Nicolas Léveillé, Nina E. de Groot, Andrew N Holding, Florian Markowetz, Louis Vermeulen
Software Mentions: 8
Published: almost 4 years ago

10.1186/s12864-021-07918-2

CeTF: an R/Bioconductor package for transcription factor co-expression networks using regulatory impact factors (RIF) and partial correlation and information (PCIT) analysis
Cited by: 10
Author(s): Carlos Alberto Oliveira de Biagi, Ricardo Perecin Nociti, Danielle Barbosa Brotto, Breno Osvaldo Funicheli, Patrícia de Cássia Ruy, João Paulo Bianchi Ximenez, David Livingstone Alves Figueiredo, Wilson A. Silva
Software Mentions: 8
Published: over 3 years ago

10.1186/s13058-019-1123-2

Separation of breast cancer and organ microenvironment transcriptomes in metastases
Cited by: 33
Author(s): Mohammad A. Alzubi, Tia H. Turner, Amy L. Olex, Sahib S. Sohal, Nicholas P. Tobin, Susana Garcia Recio, Jonas Bergh, Thomas Hatschek, Joel S. Parker, Carol A. Sartorius, Charles M. Perou, Mikhail G. Dozmorov, J. Chuck Harrell
Software Mentions: 8
Published: over 5 years ago

10.1038/s41419-021-03525-x

Loss of retinoic acid receptor-related receptor alpha (Rorα) promotes the progression of UV-induced cSCC
Cited by: 6
Author(s): Guolong Zhang, Guorong Yan, Fu Zhuo, Yuhao Wu, Fei Wu, Zhe Zheng, Shiji Fang, Ying Gao, Xiao Bao, Yeqiang Liu, Xiuli Wang, Sibo Zhu
Software Mentions: 8
Published: over 3 years ago

10.3390/pathogens10050603

Altered Nasal Microbiota Composition Associated with Development of Polyserositis by Mycoplasma hyorhinis
Cited by: 9
Author(s): Miguel Blanco-Fuertes, Florencia Correa‐Fiz, Lorenzo Fraile, Marina Sibila, Virginia Aragón
Software Mentions: 7
Published: over 3 years ago

10.3390/v13061059

Comparative Analysis of Public RNA-Sequencing Data from Human Intestinal Enteroid (HIEs) Infected with Enteric RNA Viruses Identifies Universal and Virus-Specific Epithelial Responses
Cited by: 5
Author(s): Roberto J. Cieza, Jonathan L. Golob, Justin A. Colacino, Christiane E. Wobus
Software Mentions: 7
Published: over 3 years ago

10.1038/s41598-019-50485-6

Cellular reprogramming for successful CNS axon regeneration is driven by a temporally changing cast of transcription factors
Cited by: 28
Author(s): Sumona P. Dhara, Andrea Rau, Michael J. Flister, Nicole M. Recka, Michael D. Laiosa, Paul L. Auer, Ava J. Udvadia
Software Mentions: 7
Published: about 5 years ago

10.1038/s41598-019-42784-9

Transcriptomic profiles conducive to immune-mediated tumor rejection in human breast cancer skin metastases treated with Imiquimod
Cited by: 23
Author(s): Mariya Rozenblit, Wouter Hendrickx, Adriana Heguy, Luis Chiriboga, Cynthia A. Loomis, Karina Ray, Farbod Darvishian, Mikala Egeblad, Sandra Demaria, Francesco M. Marincola, Davide Bedognetti, Sylvia Adams
Software Mentions: 7
Published: over 5 years ago

10.18632/oncotarget.15993

Genome-wide DNA methylation analysis reveals molecular subtypes of pancreatic cancer
Cited by: 67
Author(s): Nitish K. Mishra, Chittibabu Guda
Software Mentions: 7
Published: over 7 years ago

10.1093/bioinformatics/btaa177

Reconstructing ribosomal genes from large scale total RNA meta-transcriptomic data
Cited by: 11
Author(s): Yaxin Xue, Anders Lanzén, Inge Jonassen
Software Mentions: 7
Published: over 4 years ago

10.3389/fmicb.2021.660719

Changes in the Community Structure of Under-Ice and Open-Water Microbiomes in Urban Lakes Exposed to Road Salts
Cited by: 14
Author(s): Isabelle B. Fournier, Connie Lovejoy, Warwick F. Vincent
Software Mentions: 7
Published: over 3 years ago

10.3390/microorganisms9061116

Environmental Conditions Modulate the Transcriptomic Response of Both Caulobacter crescentus Morphotypes to Cu Stress
Cited by: 2
Author(s): Laurens Maertens, Pauline Cherry, Françoise Tilquin, Rob Van Houdt, Jean-Yves Matroule
Software Mentions: 7
Published: over 3 years ago

10.3389/fmicb.2021.662159

Effect of Fecal Microbiota Transplantation Combined With Mediterranean Diet on Insulin Sensitivity in Subjects With Metabolic Syndrome
Cited by: 20
Author(s): Annefleur M. Koopen, Eduardo L. Almeida, Ilias Attaye, Julia J. Witjes, Elena Rampanelli, Soumia Majait, E. Marleen Kemper, Johannes H.M. Levels, Alinda W.M. Schimmel, Hilde Herrema, Torsten P. M. Scheithauer, Werner Frei, Lars Ove Dragsted, Bolette Hartmann, Jens J. Holst, Paul W. O’Toole, Albert K. Groen, Max Nieuwdorp
Software Mentions: 7
Published: over 3 years ago

10.3390/cancers13163929

Maturation State-Specific Alternative Splicing in FLT3-ITD and NPM1 Mutated AML
Cited by: 4
Author(s): Anna Wojtuszkiewicz, Inge van der Werf, Stephan Hütter, Wencke Walter, Constance Baer, Wolfgang Kern, Jeroen Janssen, Gert J. Ossenkoppele, Claudia Haferlach, Jacqueline Cloos, Torsten Haferlach
Software Mentions: 7
Published: over 3 years ago

10.1016/j.celrep.2020.107694

A Landscape of Murine Long Non-Coding RNAs Reveals the Leading Transcriptome Alterations in Adipose Tissue during Aging
Cited by: 24
Author(s): Qi Zhou, Qianfen Wan, Yuxi Jiang, Jin Liu, Qiang Li, Li Sun
Software Mentions: 7
Published: over 4 years ago

10.15252/emmm.202013180

Intraductal xenografts show lobular carcinoma cells rely on their own extracellular matrix and LOXL1
Cited by: 21
Author(s): George Sflomos, Laura Battista, Patrick Aouad, Fabio De Martino, Valentina Scabia, Athina Stravodimou, Ayyakkannu Ayyanan, Assia Ifticene‐Treboux, Philipp Bücher, Maryse Fiche, Giovanna Ambrosini, Cathrin Brisken, Rls
Software Mentions: 7
Published: over 3 years ago

10.3390/metabo9020024

Metabolic Alterations in Male-Sterile Potato as Compared to Male-Fertile
Cited by: 13
Author(s): М. Ф. Шишова, Roman Puzanskiy, О. А. Гаврилова, Shamuhommed Kurbanniazov, Kirill N. Demchenko, Vladislav V. Yemelyanov, Galina Pendinen, А. Л. Шаварда, Т. А. Гавриленко
Software Mentions: 7
Published: almost 6 years ago

10.1371/journal.pone.0258157

Dynamically expressed genes provide candidate viability biomarkers in a model coccidian
Cited by: 4
Author(s): Matthew S. Tucker, Celia O’Brien, Mark C. Jenkins, Benjamin M. Rosenthal
Software Mentions: 7
Published: about 3 years ago

10.1128/mBio.00258-20

Critical Relevance of Stochastic Effects on Low-Bacterial-Biomass 16S rRNA Gene Analysis
Cited by: 27
Author(s): John R. Erb-Downward, Nicole R. Falkowski, Jennifer D’Souza, Lisa McCloskey, Roderick A. McDonald, Christopher Brown, Kerby Shedden, Robert P. Dickson, Christine M. Freeman, Kathleen A. Stringer, Betsy Foxman, Gary B. Huffnagle, Jeffrey L. Curtis, Sara D. Adar
Software Mentions: 7
Published: over 4 years ago

10.1371/journal.pone.0239081

Diazotrophic bacteria from maize exhibit multifaceted plant growth promotion traits in multiple hosts
Cited by: 11
Author(s): Shawn M. Higdon, Tania Pozzo, Emily J. Tibbett, Colleen Chiu, Richard Jeannotte, Bart C. Weimer, A. B. Bennett
Software Mentions: 7
Published: about 4 years ago

10.18632/aging.103671

Target RNA modification for epigenetic drug repositioning in neuroblastoma: computational omics proximity between repurposing drug and disease
Cited by: 6
Author(s): Pei Ma, Lifeng Yue, Sen Zhang, Da‐Cheng Hao, Zhihong Wu, Lijia Xu, Guanhua Du, Pei‐Gen Xiao
Software Mentions: 7
Published: about 4 years ago

10.3390/jof7040253

Molecular and Environmental Triggering Factors of Pathogenicity of Fusarium oxysporum and F. solani Isolates Involved in the Coffee Corky-Root Disease
Cited by: 3
Author(s): Roberto Gamboa-Becerra, Daniel López-Lima, Luc Villain, Jean‐Christophe Breitler, Gloria Carrión, Damaris Desgarennes
Software Mentions: 7
Published: over 3 years ago

10.3389/fped.2020.623184

Timing of Newborn Blood Collection Alters Metabolic Disease Screening Performance
Cited by: 13
Author(s): Gang Peng, Yishuo Tang, Tina M. Cowan, Hongyu Zhao, Curt Scharfe
Software Mentions: 7
Published: almost 4 years ago

10.1038/s41598-021-80970-w

Breath can discriminate tuberculosis from other lower respiratory illness in children
Cited by: 19
Author(s): Carly A. Bobak, Lili Kang, Lesley Workman, Lindy Bateman, Mohammad Sharif Khan, Margaretha Prins, Lloyd May, Flavio A. Franchina, Cynthia Baard, Mark P. Nicol, Heather J. Zar, Jane E. Hill
Software Mentions: 7
Published: almost 4 years ago

10.1371/journal.pgen.1009201

Genomic and transcriptomic landscape of conjunctival melanoma
Cited by: 14
Author(s): Katarina Cisarova, Marc Folcher, Ikram El Zaoui, Rosanna Pescini Gobert, Virginie G. Peter, Béryl Royer‐Bertrand, Léonidas Zografos, Ann Schalenbourg, Michaël Nicolas, Donata Rimoldi, Serge Leyvraz, Nicolò Riggi, Alexandre Moulin, Carlo Rivolta
Software Mentions: 7
Published: almost 4 years ago

10.1038/s41598-021-94961-4

Delineating virulence of Vibrio campbellii: a predominant luminescent bacterial pathogen in Indian shrimp hatcheries
Cited by: 14
Author(s): Sujeet Kumar, Chandra Bhushan Kumar, Vidya Rajendran, Nishawlini Abishaw, P.S. Shyne Anand, S. Kannapan, Viswas Konasagara Nagaleekar, Koyadan Kizhakedath Vijayan, S.V. Alavandi
Software Mentions: 7
Published: over 3 years ago

10.3389/fncel.2020.612560

Proteomic Characterization of Human Neural Stem Cells and Their Secretome During in vitro Differentiation
Cited by: 19
Author(s): Jakub Červenka, Jiřina Tylečková, Helena Kupcová Skalníková, Kateřina Vodičková Kepková, Ievgeniia Poliakh, Ivona Valeková, Lucie Pfeiferová, Michal Kolář, Michaela Vaškovičová, Tereza Pánková, Petr Vodička
Software Mentions: 7
Published: almost 4 years ago

10.1242/dmm.049068

A mechanism linking perinatal 2,3,7,8 tetrachlorodibenzo-p-dioxin exposure to lower urinary tract dysfunction in adulthood
Cited by: 4
Author(s): Anne E. Turco, S. G. Oakes, Kimberly P. Keil Stietz, Cheryl L. Dunham, Diya B. Joseph, Thrishna S Chathurvedula, Nicholas M Girardi, Andrew J. Schneider, Joseph Gawdzik, Celeste M Sheftel, Peiqing Wang, Zunyi Wang, Dale E. Bjorling, William A. Ricke, Weiping Tang, Laura Hernández, Janet R. Keast, Adrian D. Bonev, Matthew D Grimes, Douglas W. Strand, Nathan R. Tykocki, Robyn L Tanguay, Richard E. Peterson, Chad M. Vezina
Software Mentions: 7
Published: over 3 years ago

10.3390/genes11091107

Integrated Analysis of Gene Expression, SNP, InDel, and CNV Identifies Candidate Avirulence Genes in Australian Isolates of the Wheat Leaf Rust Pathogen Puccinia triticina
Cited by: 5
Author(s): Long Song, Jing Qin Wu, Chongmei Dong, Robert Park
Software Mentions: 7
Published: about 4 years ago

10.1186/s13054-021-03503-x

Fluid proteomics of CSF and serum reveal important neuroinflammatory proteins in blood–brain barrier disruption and outcome prediction following severe traumatic brain injury: a prospective, observational study
Cited by: 26
Author(s): Caroline Lindblad, Elisa Pin, David R. Just, Faiez Al Nimer, Peter Nilsson, Bo‐Michael Bellander, Mikael Svensson, Fredrik Piehl, Eric Peter Thelin
Software Mentions: 7
Published: over 3 years ago

10.3389/fnins.2021.621121

Analysis of the Neuroproteome Associated With Cell Therapy After Intranigral Grafting in a Mouse Model of Parkinson Disease
Cited by: 1
Author(s): Hassan Dakik, Sarah Mantash, Ali Nehme, Firas Kobeissy, Masoud Zabet-Moghaddam, Parvin Mirzaei, Yehia Mechref, Afsaneh Gaillard, Laetitia Prestoz, Kazem Zibara
Software Mentions: 7
Published: over 3 years ago

10.3389/fendo.2021.672319

Adrenocortical Carcinoma Steroid Profiles: In Silico Pan-Cancer Analysis of TCGA Data Uncovers Immunotherapy Targets for Potential Improved Outcomes
Cited by: 6
Author(s): João C. D. Muzzi, Jessica Maria Magno, Milena A. Cardoso, Juliana de Moura, Mauro A. A. Castro, Bonald C. Figueiredo
Software Mentions: 7
Published: over 3 years ago

10.1038/s41598-020-63355-3

Limits in the detection of m6A changes using MeRIP/m6A-seq
Cited by: 120
Author(s): Alexa B. R. McIntyre, Nandan S. Gokhale, Leandro Cerchietti, Samie R. Jaffrey, Stacy M. Horner, Christopher E. Mason
Software Mentions: 6
Published: over 4 years ago

10.1038/s41598-019-49027-x

Association of Aggresomes with Survival Outcomes in Pediatric Medulloblastoma
Cited by: 4
Author(s): Maha Yehia, Hala Taha, Asmaa Salama, Nada Amer, Amal Mosaab, Omneya Hassanain, Amal Refaat, Dina Yassin, Ahmed Elhemaly, Soha Ahmed, Mohamed El-Beltagy, Osama Shaalan, Shahenda El‐Naggar
Software Mentions: 6
Published: about 5 years ago

10.1186/s40478-019-0681-y

A simplified approach using Taqman low-density array for medulloblastoma subgrouping
Cited by: 17
Author(s): Gustavo Alencastro Veiga Cruzeiro, Karina Bezerra Salomão, Carlos Alberto Oliveira de Biagi, Martin Baumgärtner, Dominik Sturm, Régia Caroline Peixoto Lira, Taciani de Almeida Magalhães, Mirella Baroni, Vanessa da Silva Silveira, Fabiano Pinto Saggioro, Ricardo Santos de Oliveira, Paulo Henrique dos Santos Klinger, Ana Luíza Seidinger, José Andrés Yunes, Rosane Gomes de Paula Queiróz, Sueli Mieko Oba-Shinjo, Carlos Alberto Scrideli, Suely Kazue Nagahashi Marie, Luíz Gonzaga Tone, Elvis Terci Valera
Software Mentions: 6
Published: over 5 years ago

10.1038/s41598-020-67842-5

Molecular dissection of CRC primary tumors and their matched liver metastases reveals critical role of immune microenvironment, EMT and angiogenesis in cancer metastasis
Cited by: 18
Author(s): Jiangang Liu, Yong Beom Cho, Hye Kyung Hong, Song Wu, Philip J. Ebert, Steven M. Bray, Suei Nee Wong, Jason C. Ting, John N. Calley, Catherine F. Whittington, Shripad V. Bhagwat, Christoph Reinhard, Robert A. Wild, Do‐Hyun Nam, Amit Aggarwal, Woo Yong Lee, Sheng-Bin Peng
Software Mentions: 6
Published: over 4 years ago

10.3390/jpm10040210

Association of UBE3C Variants with Reduced Kidney Function in Patients with Diabetic Kidney Disease
Cited by: 3
Author(s): Ying Chun Chen, Mei Yi Wu, Zhi Yu, Wan Hsuan Chou, Yi Ting Lai, Chih-Chin Kao, Imaniar Noor Faridah, Mai Szu Wu, Wei Chiao Chang
Software Mentions: 6
Published: about 4 years ago

10.1186/s12885-018-4848-x

Genomic analysis of DNA repair genes and androgen signaling in prostate cancer
Cited by: 53
Author(s): Kasey Jividen, Katarzyna Kedzierska, Chunsong Yang, Karol Szlachta, Aakrosh Ratan, Bryce M. Paschal
Software Mentions: 6
Published: about 6 years ago

10.3390/biology10060502

Characterization of Tumor-Associated Macrophages and the Immune Microenvironment in Limited-Stage Neuroendocrine-High and -Low Small Cell Lung Cancer
Cited by: 22
Author(s): Dávid Dóra, Christopher J. Rivard, Hui Yu, Shivaun Lueke Pickard, Viktória László, Tünde Harkó, Zsolt Megyesfalvi, Elek Dinya, Csongor Gerdán, Gábor Szegvári, Fred R. Hirsch, Balázs Döme, Zoltán Lohinai
Software Mentions: 6
Published: over 3 years ago

10.1242/bio.058222

RNA-Seq reveals changes in human placental metabolism, transport and endocrinology across the first–second trimester transition
Cited by: 15
Author(s): Malwina Prater, Russell S. Hamilton, Hong Wa Yung, Andrew Sharkey, Paul Robson, N. Erlyani Abd Hamid, Eric Jauniaux, D. Stephen Charnock-Jones, Graham J. Burton, Tereza Cindrová‐Davies
Software Mentions: 6
Published: over 3 years ago

10.3390/ijms22126307

Transcriptional Profiling Identifies Upregulation of Neuroprotective Pathways in Retinitis Pigmentosa
Cited by: 4
Author(s): Christina B. Bielmeier, Saskia Roth, Sabrina I. Schmitt, Stefaniya Boneva, Anja Schlecht, Mario Vallon, Ernst R. Tamm, Süleyman Ergün, Andreas Neueder, Barbara M. Braunger
Software Mentions: 6
Published: over 3 years ago

10.1186/s13100-019-0180-5

Transcriptome analyses of tumor-adjacent somatic tissues reveal genes co-expressed with transposable elements
Cited by: 20
Author(s): Nicky Chung, G. M. Jonaid, Sophia Quinton, Austin Ross, Corinne E. Sexton, Adrian Alberto, Cody Clymer, Daphnie Churchill, Omar Navarro Leija, Mira V. Han
Software Mentions: 6
Published: about 5 years ago

10.3389/fcvm.2021.696321

Bioinformatics and Immune Infiltration Analyses Reveal the Key Pathway and Immune Cells in the Pathogenesis of Hypertrophic Cardiomyopathy
Cited by: 11
Author(s): Xuzhe Zhang, Si Zhang, Tingting Tang, Xiang Cheng
Software Mentions: 6
Published: about 3 years ago

10.1186/s12885-020-07724-1

Correction to: Comprehensive analysis of prognostic gene signatures based on immune infiltration of ovarian cancer
Cited by: 1
Author(s): Shi-Bai Yan, Jinling Fang, Yongcai Chen, Yong Xie, Siyou Zhang, Xiaohui Zhu, Fang Fěng
Software Mentions: 6
Published: almost 4 years ago

10.1038/s41598-019-42988-z

Whole genome sequencing reveals the impact of recent artificial selection on red sea bream reared in fish farms
Cited by: 6
Author(s): Bo‐Hye Nam, DongAhn Yoo, Young‐Ok Kim, Jung Youn Park, Younhee Shin, Ga-Hee Shin, Chan-Il Park, Heebal Kim, Woori Kwak
Software Mentions: 6
Published: over 5 years ago

10.3390/cancers13112776

Evaluation of Somatic Mutations in Solid Metastatic Pan-Cancer Patients
Cited by: 8
Author(s): Moom R. Roosan, Isa Mambetsariev, Rebecca Pharaon, Jeremy Fricke, Angel Ray Baroz, Joseph Chao, Chen Chen, Mohd W. Nasser, Ramakanth Chirravuri-Venkata, Maneesh Jain, Lynette M. Smith, Susan E. Yost, Karen L. Reckamp, Raju Pillai, Leonidas Arvanitis, Michelle Afkhami, Edward W. Wang, Vincent Chung, Mihaela Cristea, Marwan Fakih, Marianna Koczywas, Erminia Massarelli, Joanne Mortimer, Yuan Yuan, Surinder K. Batra, Sumanta K. Pal, Ravi Salgia
Software Mentions: 6
Published: over 3 years ago

10.3389/fcell.2021.640476

A Comprehensive Investigation to Reveal the Relationship Between Plasmacytoid Dendritic Cells and Breast Cancer by Multiomics Data Analysis
Cited by: 8
Author(s): Sai Tian, Yan Li, Lu Fu, Zhen Zhang, Jinbo Zhang, Guofeng Meng, Weidong Zhang
Software Mentions: 6
Published: over 3 years ago

10.1073/pnas.1819788116

Genome-wide colocalization of RNA–DNA interactions and fusion RNA pairs
Cited by: 48
Author(s): Zhangming Yan, Norman Huang, Weixin Wu, Weizhong Chen, Yiqun Jiang, Jingyao Chen, Xuerui Huang, Xingzhao Wen, Jie Xu, Qiushi Jin, Kang Zhang, Zhe Chen, Shu Chien, Sheng Zhong
Software Mentions: 6
Published: almost 6 years ago

10.7554/eLife.58371

Bacterial symbiont subpopulations have different roles in a deep-sea symbiosis
Cited by: 17
Author(s): Tjorven Hinzke, Manuel Kleiner, Mareike Meister, Rabea Schlüter, Christian Hentschker, Jan Pané‐Farré, Petra Hildebrandt, Horst Felbeck, Stefan M. Sievert, Florian Bonn, Uwe Völker, Dörte Becher, Thomas Schweder, Stephanie Markert
Software Mentions: 6
Published: almost 4 years ago

10.3390/ijms21176283

Differential Profiles of Gut Microbiota and Metabolites Associated with Host Shift of Plutella xylostella
Cited by: 22
Author(s): Fei‐Ying Yang, Hafiz Sohaib Ahmed Saqib, Junhui Chen, Qian‐Qian Ruan, Liette Vasseur, Weiyi He, Minsheng You
Software Mentions: 6
Published: about 4 years ago

10.1128/mSystems.00498-19

Anoxygenic Phototrophs Span Geochemical Gradients and Diverse Morphologies in Terrestrial Geothermal Springs
Cited by: 20
Author(s): Trinity L. Hamilton, Annastacia C. Bennett, Senthil K. Murugapiran, J. R. Havig
Software Mentions: 6
Published: almost 5 years ago

10.15252/emmm.202012881

Fragmentation patterns and personalized sequencing of cell‐free DNA in urine and plasma of glioma patients
Cited by: 47
Author(s): Florent Moulière, Christopher G. Smith, Katrin Heider, Jing Su, Ymke van der Pol, Mark Thompson, James A. Morris, Jonathan C. M. Wan, Dineika Chandrananda, James Hadfield, Marta Grzelak, Irena Hudecova, Dominique‐Laurent Couturier, Wendy N. Cooper, Hui Zhao, Davina Gale, Matthew Eldridge, Colin Watts, Kevin M. Brindle, Nitzan Rosenfeld, Richard Mair
Software Mentions: 6
Published: over 3 years ago

10.12688/f1000research.17149.2

Hub genes in a pan-cancer co-expression network show potential for predicting drug responses
Cited by: 0
Author(s): Francisco Azuaje, Tony Kaoma, Céline Jeanty, Petr V. Nazarov, Arnaud Muller, Sang Yoon Kim, Gunnar Dittmar, Anna Golebiewska, Simone P. Niclou
Software Mentions: 6
Published: over 5 years ago

10.1128/mSphere.00535-21

A Comprehensive Map of Mycobacterium tuberculosis Complex Regions of Difference
Cited by: 11
Author(s): Dmitry Bespiatykh, Julia Bespyatykh, Igor Mokrousov, Egor Shitikov
Software Mentions: 6
Published: about 3 years ago

10.1186/s40168-019-0689-3

Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease
Cited by: 184
Author(s): Almut Heinken, Dmitry A. Ravcheev, Federico Baldini, Laurent Heirendt, Ronan M. T. Fleming, Ines Thiele
Software Mentions: 6
Published: over 5 years ago

10.1128/mBio.01849-21

Hofbauer Cells Spread Listeria monocytogenes among Placental Cells and Undergo Pro-Inflammatory Reprogramming while Retaining Production of Tolerogenic Factors
Cited by: 7
Author(s): Siavash Azari, Lauren J. Johnson, Amy Webb, Sophia M Kozlowski, Xiaoli Zhang, Kara M. Rood, Amal O. Amer, Stéphanie Seveau
Software Mentions: 6
Published: about 3 years ago

10.3389/fimmu.2021.632667

PD-1 Blockade Modulates Functional Activities of Exhausted-Like T Cell in Patients With Cutaneous Leishmaniasis
Cited by: 16
Author(s): Renan Garcia de Moura, Luciana Polaco Covre, Carlos Henrique Fantecelle, Vitor Alejandro Torres Gajardo, Carla Baroni Cunha, Lorenzzo Lyrio Stringari, Ashton T. Belew, Camila Batista Daniel, Sandra Ventorin von Zeidler, Carlos E. Tadokoro, Herbert Leonel de Matos Guedes, Raphael Lubiana Zanotti, David M. Mosser, Aloísio Falqueto, Arne N. Akbar, Daniel Cláudio Oliveira Gomes
Software Mentions: 6
Published: over 3 years ago

10.3390/cancers13112756

Association of Circadian Clock Gene Expression with Glioma Tumor Microenvironment and Patient Survival
Cited by: 6
Author(s): Julianie De La Cruz Minyety, Dorela Shuboni-Mulligan, Nicole Briceno, Demarrius Young, Mark R. Gilbert, Orieta Celiku, Terri S. Armstrong
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pone.0212866

Dynamic changes in lung responses after single and repeated exposures to cigarette smoke in mice
Cited by: 10
Author(s): Michelle Engle, Justine N. Monk, Corey M. Jania, Jessica R. Martin, John C. Gomez, Hong Dang, Joel S. Parker, Claire M. Doerschuk
Software Mentions: 6
Published: over 5 years ago

10.1186/s12877-019-1156-5

No effect of 25-hydroxyvitamin D supplementation on the skeletal muscle transcriptome in vitamin D deficient frail older adults
Cited by: 11
Author(s): Roland W. J. Hangelbroek, Anouk M.M. Vaes, Mark V. Boekschoten, Lex B. Verdijk, Guido Hooiveld, Luc J. C. van Loon, Lisette C. P. G. M. de Groot, Sander Kersten
Software Mentions: 6
Published: over 5 years ago

10.3389/fimmu.2020.00715

Hepatic Transcriptome Analysis Identifies Divergent Pathogen-Specific Targeting-Strategies to Modulate the Innate Immune System in Response to Intramammary Infection
Cited by: 15
Author(s): A. Heimes, J. Brodhagen, Rosemarie Weikard, Hans‐Martin Seyfert, Doreen Becker, M. Meyerholz, Wolfram Petzl, Holm Zerbe, Martina Hoedemaker, L. Rohmeier, Hans‐Joachim Schuberth, Marion Schmicke, Susanne Engelmann, Christa Kühn
Software Mentions: 6
Published: over 4 years ago

10.3389/fimmu.2021.634741

Activation of the DDR Pathway Leads to the Down-Regulation of the TGFβ Pathway and a Better Response to ICIs in Patients With Metastatic Urothelial Carcinoma
Cited by: 18
Author(s): Chaozheng Zhou, Anqi Lin, Manming Cao, Weimin Ding, Weiming Mou, Ningyi Guo, Zhenyu Chen, Jian Zhang, Peng Luo
Software Mentions: 6
Published: over 3 years ago

10.3390/genes12040549

Clinical Identification of Dysregulated Circulating microRNAs and Their Implication in Drug Response in Triple Negative Breast Cancer (TNBC) by Target Gene Network and Meta-Analysis
Cited by: 15
Author(s): Amal Qattan, Taher Al‐Tweigeri, Wafa Alkhayal, Kausar Suleman, Asma Tulbah, Suad Bin Amer
Software Mentions: 6
Published: over 3 years ago

10.1002/JLB.5MA0120-209R

Distinct and shared gene expression for human innate versus adaptive helper lymphoid cells
Cited by: 28
Author(s): Giuseppe Ercolano, Tania Wyss, Bérengère Salomé, Pedro Romero, Sara Trabanelli, Camilla Jandus
Software Mentions: 6
Published: almost 5 years ago

10.1007/s00125-019-05032-3

Clinical and genetic correlates of islet-autoimmune signatures in juvenile-onset type 1 diabetes
Cited by: 19
Author(s): Laura A. Claessens, Joris Wesselius, Menno van Lummel, Sandra Laban, Flip Mulder, Dick Mul, Tanja Nikolić, Henk‐Jan Aanstoot, Bobby P. C. Koeleman, Bart O. Roep
Software Mentions: 6
Published: about 5 years ago

10.1155/2020/8833438

Systematic Investigation of mRNA N6-Methyladenosine Machinery in Primary Prostate Cancer
Cited by: 7
Author(s): Mei Jiang, Yu‐Chuan Lu, Dongxia Duan, Hongxiang Wang, Gaoya Man, Ching Kang, Kesaier Abulimiti, Yao Li
Software Mentions: 6
Published: about 4 years ago

10.1038/s41598-021-90093-x

Prematurity alters the progenitor cell program of the upper respiratory tract of neonates
Cited by: 6
Author(s): Jessica E. Shui, Wei Wang, Helu Liu, Анна Степанова, Grace Liao, Jun Qian, Xingbin Ai, Vadim S. Ten, Jining Lü, Wellington V. Cardoso
Software Mentions: 6
Published: over 3 years ago

10.1242/dev.195883

The BMP antagonist gremlin 1 contributes to the development of cortical excitatory neurons, motor balance and fear responses
Cited by: 4
Author(s): Mari Ichinose, Nobumi Suzuki, Tongtong Wang, Hiroki Kobayashi, Laura Vrbanac, Joseph Kim Fai Ng, Josephine Wright, Tamsin R.M. Lannagan, Krystyna A. Gieniec, Martin Lewis, Ryosuke Ando, Atsushi Enomoto, Simon Koblar, Paul Q. Thomas, Daniel L. Worthley, Susan L. Woods
Software Mentions: 6
Published: over 3 years ago

10.1038/s41598-021-90735-0

Distinct microbial community along the chronic oil pollution continuum of the Persian Gulf converge with oil spill accidents
Cited by: 16
Author(s): Maryam Rezaei Somee, Seyed Mohammad Mehdi Dastgheib, Mahmoud Shavandi, Leila Ghanbari Maman, Kaveh Kavousi, Mohammad Ali Amoozegar, Maliheh Mehrshad
Software Mentions: 6
Published: over 3 years ago

10.1038/s41598-021-91214-2

Chamber-enriched gene expression profiles in failing human hearts with reduced ejection fraction
Cited by: 12
Author(s): Xin Luo, Jun Yin, Denise Dwyer, Tracy M. Yamawaki, Hong Zhou, Hongfei Ge, Chun-Ya Han, Artem Shkumatov, K. F. Snyder, Brandon Ason, Chi-Ming Li, Oliver Homann, Marina Stolina
Software Mentions: 6
Published: over 3 years ago

10.1371/journal.pgen.1008743

The genomic landscape of metastasis in treatment-naïve breast cancer models
Cited by: 16
Author(s): Christina R. Ross, Karol Szczepanek, Maxwell Lee, Howard H. Yang, Tinghu Qiu, Jack D. Sanford, Kent W. Hunter
Software Mentions: 6
Published: over 4 years ago

10.1371/journal.pbio.3001207

Pathogenic missense protein variants affect different functional pathways and proteomic features than healthy population variants
Cited by: 9
Author(s): Anna Laddach, Joseph C.F. Ng, Franca Fraternali
Software Mentions: 6
Published: over 3 years ago

10.3389/fonc.2021.592211

An Immune-Related Gene Pairs Signature Predicts Prognosis and Immune Heterogeneity in Glioblastoma
Cited by: 1
Author(s): Nijia Zhang, Ming Ge, Tao Jiang, Xiaoxia Peng, Hailang Sun, Qi Xiang, Zhewei Zou, Dapeng Li
Software Mentions: 6
Published: over 3 years ago

10.3389/fonc.2019.00692

Transcriptomic Analysis Identifies RNA Binding Proteins as Putative Regulators of Myelopoiesis and Leukemia
Cited by: 16
Author(s): Subha Saha, Krushna Chandra Murmu, Mayukh Biswas, Sohini Chakraborty, Jhinuk Basu, Swati Madhulika, Srinivasa Prasad Kolapalli, Santosh Chauhan, Amitava Sengupta, Punit Prasad
Software Mentions: 6
Published: over 5 years ago

10.1016/j.xcrm.2020.100077

Microbiota Supplementation with Bifidobacterium and Lactobacillus Modifies the Preterm Infant Gut Microbiota and Metabolome: An Observational Study
Cited by: 108
Author(s): Cristina Alcon-Giner, Matthew J. Dalby, Shabhonam Caim, Jennifer Ketskemety, Alexander Shaw, Kathleen Sim, Melissa A. Lawson, Raymond Kiu, Charlotte Leclaire, Lisa Chalklen, Magdalena Kujawska, Suparna Mitra, Fahmina Fardus‐Reid, Gusztav Belteki, Katherine McColl, Jonathan R. Swann, J. Simon Kroll, Paul Clarke, Lindsay J. Hall
Software Mentions: 6
Published: over 4 years ago

10.1186/s12864-018-5066-2

A comparative analysis of library prep approaches for sequencing low input translatome samples
Cited by: 52
Author(s): Yang Song, Béatrice Milon, Sandra Ott, Xüna Zhao, Lisa Sadzewicz, Amol C. Shetty, Erich T. Boger, Luke J. Tallon, Robert J. Morell, Anup Mahurkar, Ronna Hertzano
Software Mentions: 6
Published: about 6 years ago

10.3390/plants10061033

Metabolic Alterations in Pisum sativum Roots during Plant Growth and Arbuscular Mycorrhiza Development
Cited by: 13
Author(s): O. Y. Shtark, Roman Puzanskiy, G. S. Avdeeva, Vladislav V. Yemelyanov, А. Л. Шаварда, Daria A. Romanyuk, Marina S. Kliukova, А. А. Кирпичникова, И. А. Тихонович, Vladimir A. Zhukov, М. Ф. Шишова
Software Mentions: 6
Published: over 3 years ago

10.1016/j.cell.2021.07.023

Impaired local intrinsic immunity to SARS-CoV-2 infection in severe COVID-19
Cited by: 170
Author(s): Carly G.K. Ziegler, Vincent N. Miao, Anna H. Owings, Andrew W. Navia, Ying Tang, Joshua D. Bromley, Peter Lotfy, Meredith Sloan, Hannah Laird, Hibbard E. Williams, Micayla George, Riley S. Drake, Christian Taube, Adam Parker, Campbell B Sindel, Molly Burger, Yilianys Pride, Mohammad S Hasan, George Abraham, Michal Senitko, Tanya O. Robinson, Alex K. Shalek, Sarah C. Glover, Bruce H. Horwitz, José Ordovás-Montañés
Software Mentions: 6
Published: about 3 years ago

10.1038/s41598-021-95648-6

Four consecutive yearly point-prevalence studies in Wales indicate lack of improvement in sepsis care on the wards
Cited by: 1
Author(s): Maja Kopczynska, Harry Unwin, Richard Pugh, Ben Sharif, Thomas Chandy, Daniel Davies, Matthew E. Shield, David Purchase, Samuel C. Tilley, Arwel T Poacher, Lewis Oliva, Sam Willis, Isabelle Ray, John Ng C. Hui, Bethany Payne, Eilis Frances Wardle, Fiona Andrew, Hei Man Priscilla Chan, Jack Barrington, Jay Hale, Joanna Hawkins, Jess K. Nicholas, Lara E. Wirt, Lowri Hughes Thomas, Megan Walker, Myat P. Pan, Tallulah Ray, Umair Asim, Victoria Maidman, Zeid Atiyah, Zain M. Nasser, Zhao Xuan Tan, Laura Tan, Tamás Szakmány
Software Mentions: 6
Published: over 3 years ago

10.3389/fmolb.2021.682084

Comprehensive Molecular Analyses of a Novel Mutational Signature Classification System with Regard to Prognosis, Genomic Alterations, and Immune Landscape in Glioma
Cited by: 26
Author(s): Xinwei Han, Taoyuan Lu, Libo Wang, Long Liu, Lifeng Li, Xinwei Han
Software Mentions: 5
Published: over 3 years ago

10.1186/s12864-020-06811-8

VviERF6Ls: an expanded clade in Vitis responds transcriptionally to abiotic and biotic stresses and berry development
Cited by: 3
Author(s): Haley S. Toups, Noé Cochetel, D. J. Gray, Grant R. Cramer
Software Mentions: 5
Published: over 4 years ago

10.3390/cells9061436

Sex Chromosomes and Sex Phenotype Contribute to Biased DNA Methylation in Mouse Liver
Cited by: 14
Author(s): Qinwei Kim-Wee Zhuang, José Héctor Gálvez, Qian Xiao, Najla AlOgayil, Jeffrey Hyacinthe, Teruko Taketo, Guillaume Bourque, Anna K. Naumova
Software Mentions: 5
Published: over 4 years ago

10.1186/s12864-019-5887-7

Refinement of breast cancer molecular classification by miRNA expression profiles
Cited by: 59
Author(s): Rolf Søkilde, Helena Persson, Anna Ehinger, Anna Chiara Pirona, Mårten Fernö, Cecilia Hegardt, Christer Larsson, Niklas Loman, Martin Malmberg, Lisa Rydén, Lao H. Saal, Åke Borg, Johan Vallon-Christerson, Carlos Rovira
Software Mentions: 5
Published: over 5 years ago

10.3389/fcell.2020.580848

Adherent Intestinal Cells From Atlantic Salmon Show Phagocytic Ability and Express Macrophage-Specific Genes
Cited by: 5
Author(s): Youngjin Park, Qirui Zhang, G.F. Wiegertjes, Jorge M. O. Fernandes, Viswanath Kiron
Software Mentions: 5
Published: about 4 years ago

10.3390/cells9030665

Dysregulated Antibody, Natural Killer Cell and Immune Mediator Profiles in Autoimmune Thyroid Diseases
Cited by: 17
Author(s): Tiphaine Martin, Kristina M. Ilieva, Alessia Visconti, Michelle Beaumont, Steven Kiddle, Richard Dobson, Massimo Mangino, Ee Mun Lim, Marija Pezer, Claire J. Steves, Jordana T. Bell, Scott G. Wilson, Gordan Lauc, Mario Roederer, John P. Walsh, Tim D. Spector, Sophia N. Karagiannis
Software Mentions: 5
Published: over 4 years ago

10.3390/biology9090251

Differential Expression and miRNA–Gene Interactions in Early and Late Mild Cognitive Impairment
Cited by: 20
Author(s): Leonardo Miranda Brito, Ândrea Ribeiro-dos-Santos, Amanda Ferreira Vidal, Gilderlanio Santana de Araújo
Software Mentions: 5
Published: about 4 years ago

10.1186/s42523-021-00084-6

Probiotics mediated gut microbiota diversity shifts are associated with reduction in histopathology and shedding of Lawsonia intracellularis
Cited by: 5
Author(s): Adrian Muwonge, Anbu K. Karuppannan, Tanja Opriessnig
Software Mentions: 5
Published: over 3 years ago

Projects: bioconductor: ComplexHeatmap

Papers Mentioning ComplexHeatmap 565