Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: cran: Rtsne

https://packages.ecosyste.ms/registries/cran.r-project.org/packages/Rtsne

T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation
9 versions
Latest release: over 2 years ago
51 dependent packages
35,206 downloads last month

Papers Mentioning Rtsne 255

10.15252/msb.20209698
<scp>CEN</scp> ‐tools: an integrative platform to identify the contexts of essential genes
Cited by: 9
Author(s): Sumana Sharma, Cansu Dinçer, Paula Weidemüller, Gavin J. Wright, Evangelia Petsalaki
Software Mentions: 5
Published: about 4 years ago
10.1007/s00122-020-03759-x
Multi-omics-based prediction of hybrid performance in canola
Cited by: 19
Author(s): Dominic Knoch, Christian R. Werner, Rhonda C. Meyer, David Riewe, Amine Abbadi, Sophie Lücke, Rod J. Snowdon, Thomas Altmann
Software Mentions: 5
Published: almost 4 years ago
10.1016/j.stemcr.2019.04.012
Human iPSC-Derived Retinal Pigment Epithelium: A Model System for Prioritizing and Functionally Characterizing Causal Variants at AMD Risk Loci
Cited by: 31
Author(s): Erin N. Smith, Agnieszka D’Antonio‐Chronowska, William W. Greenwald, Victor Borja, Lana Ribeiro Aguiar, Robert Pogue, Hiroko Matsui, Paola Benaglio, Shyamanga Borooah, Matteo D’Antonio, Radha Ayyagari, Kelly A. Frazer
Software Mentions: 5
Published: over 5 years ago
10.1038/s41598-018-37679-0
Acidogenesis, solventogenesis, metabolic stress response and life cycle changes in Clostridium beijerinckii NRRL B-598 at the transcriptomic level
Cited by: 46
Author(s): Petra Patáková, Barbora Branská, Karel Sedlář, Maryna Vasylkivska, Katerina Jureckova, Jan Kolek, Pavlína Koščová, Ivo Provazník
Software Mentions: 5
Published: almost 6 years ago
10.3389/fgene.2021.706814
A Nomogram Integrating Ferroptosis- and Immune-Related Biomarkers for Prediction of Overall Survival in Lung Adenocarcinoma
Cited by: 2
Author(s): Mengyu Chai, Xiuchun Li, Yaxin Zhang, Yemeng Tang, Pingping Shu, Lin Jia, Ke–Qing Shi, Liangxing Wang, Xiaoying Huang
Software Mentions: 5
Published: about 3 years ago
10.7554/eLife.63642
Microbial genetic and transcriptional contributions to oxalate degradation by the gut microbiota in health and disease
Cited by: 23
Author(s): Menghan Liu, Joseph C. Devlin, Jiyuan Hu, Angelina Volkova, Thomas Battaglia, Melody Ho, John R. Asplin, Allyson L. Byrd, P’ng Loke, Huilin Li, Kelly V. Ruggles, Aristotelis Tsirigos, Martin J. Blaser, Lama Nazzal
Software Mentions: 5
Published: over 3 years ago
10.7150/jca.47698
Mass Spectrometry Imaging Differentiates Chromophobe Renal Cell Carcinoma and Renal Oncocytoma with High Accuracy
Cited by: 7
Author(s): Mark Kriegsmann, Rita Casadonte, Nadine Maurer, Christine Stoehr, Franziska Erlmeier, Holger Moch, Kerstin Junker, Christiane Zgorzelski, Wilko Weichert, Kristina Schwamborn, Sören‐Oliver Deininger, Matthias M. Gaida, Gunhild Mechtersheimer, Albrecht Stenzinger, Peter Schirmacher, Arndt Hartmann, Joerg Kriegsmann, Katharina Kriegsmann
Software Mentions: 5
Published: almost 5 years ago
10.1186/s12977-019-0494-x
Heterogeneity in HIV and cellular transcription profiles in cell line models of latent and productive infection: implications for HIV latency
Cited by: 32
Author(s): Sushama Telwatte, Sara Morón-López, Dvir Aran, Peggy Kim, Christine L. Hsieh, Sunil Kumar Joshi, Mauricio Montaño, Warner C. Greene, Atul J. Butte, Joseph K. Wong, Steven A. Yukl
Software Mentions: 5
Published: about 5 years ago
10.1038/s41598-020-68617-8
The origin of early Acheulean expansion in Europe 700 ka ago: new findings at Notarchirico (Italy)
Cited by: 34
Author(s): Marie‐Hélène Moncel, Carmen Santagata, Alison Pereira, Sébastien Nomade, Pierre Voinchet, Jean‐Jacques Bahain, Camille Daujeard, Antonio Curci, Cristina Lemorini, Bruce Hardy, Giacomo Eramo, Claudio Berto, Jean‐Paul Raynal, Marta Arzarello, Beniamino Mecozzi, Alessio Iannucci, Raffaele Sardella, Ignazio Allegretta, Emanuela Delluniversità, Roberto Terzano, Pauline Dugas, Gwenolé Jouanic, Alain Queffelec, Andrea D’Andrea, Rosario Valentini, Eleonora Minucci, Laura Carpentiero, Marcello Piperno
Software Mentions: 5
Published: over 4 years ago
10.3389/fmolb.2021.609865
Development and Validation of a Prognostic Gene Signature in Clear Cell Renal Cell Carcinoma
Cited by: 7
Author(s): Chuanchuan Zhan, Zichu Wang, Chao Xu, Xiao Huang, Junzhou Su, Bisheng Chen, Mingshan Wang, Zhihong Qi, Péter Bai
Software Mentions: 5
Published: over 3 years ago
10.1016/j.molmet.2017.02.007
Heterogeneity of hypothalamic pro-opiomelanocortin-expressing neurons revealed by single-cell RNA sequencing
Cited by: 125
Author(s): Brian Y.H. Lam, Irène Cimino, Joseph Polex-Wolf, Sara Kohnke, Debra Rimmington, Valentine P. Iyemere, Nicholas Heeley, Chiara Cossetti, Reiner Schulte, Luís R. Saraiva, Darren W. Logan, Clémence Blouet, Stephen O’Rahilly, Anthony P. Coll, Giles S.H. Yeo
Software Mentions: 5
Published: over 7 years ago
10.1007/s13238-020-00720-y
Integrative analysis of in vivo recording with single-cell RNA-seq data reveals molecular properties of light-sensitive neurons in mouse V1
Cited by: 9
Author(s): Jianwei Liu, Mengdi Wang, Le Sun, Na Pan, Changjiang Zhang, Junjing Zhang, Zhentao Zuo, Sheng He, Qian Wu, Xiaoqun Wang
Software Mentions: 5
Published: over 4 years ago
10.1186/s40478-018-0614-1
Transcriptomic and epigenetic profiling of ‘diffuse midline gliomas, H3 K27M-mutant’ discriminate two subgroups based on the type of histone H3 mutated and not supratentorial or infratentorial location
Cited by: 78
Author(s): David Castel, Cathy Philippe, Thomas Kergrohen, Martin Sill, Jane Merlevede, E. Barret, Stéphanie Puget, Christian Sainte‐Rose, Christof M. Kramm, Chris Jones, Pascale Varlet, Stefan M. Pfister, Jacques Grill, David Jones, Marie‐Anne Debily
Software Mentions: 5
Published: about 6 years ago
10.1038/s41598-020-65119-5
Multi-omic signatures identify pan-cancer classes of tumors beyond tissue of origin
Cited by: 17
Author(s): Agustín González-Reymúndez, Ana I. Vázquez
Software Mentions: 5
Published: over 4 years ago
10.3389/fncel.2020.00245
A Primer on Constructing Plasticity Phenotypes to Classify Experience-Dependent Development of the Visual Cortex
Cited by: 2
Author(s): Justin L. Balsor, Dezi Ahuja, David Jones, Kathryn Murphy
Software Mentions: 5
Published: about 4 years ago
10.3390/cancers12082257
A Global Gene Body Methylation Measure Correlates Independently with Overall Survival in Solid Cancer Types
Cited by: 1
Author(s): Dietmar Pils, Elisabeth Steindl, Anna Bachmayr-Heyda, Sabine Dekan, Stefanie Aust
Software Mentions: 5
Published: over 4 years ago
10.1186/s13059-018-1489-y
Genome organization and chromatin analysis identify transcriptional downregulation of insulin-like growth factor signaling as a hallmark of aging in developing B cells
Cited by: 25
Author(s): Hashem Koohy, Daniel J. Bolland, Louise S. Matheson, Stefan Schoenfelder, Claudia Stellato, Andrew Dimond, Csilla Várnai, Peter Chovanec, Tamara Chessa, Jérémy Denizot, Raquel Manzano García, Steven Wingett, Paula Freire-Pritchett, Takashi Nagano, Phillip T. Hawkins, Len R. Stephens, Sarah Elderkin, Mikhail Spivakov, Peter Fraser, Anne E. Corcoran, Patrick Varga‐Weisz
Software Mentions: 5
Published: about 6 years ago
10.18632/aging.203289
A innovative prognostic symbol based on neutrophil extracellular traps (NETs)-related lncRNA signature in non-small-cell lung cancer
Cited by: 13
Author(s): Fang Chen, Fen Liu, Yong Wang, Shangkun Yuan, Renfang Chen, Xiaotong Qiu, Xiaoying Qian, Xinwei Zhang, Zhehao Xiao, Qian Wang, Biqi Fu, Yong Li
Software Mentions: 5
Published: over 3 years ago
10.1186/s13059-016-1010-4
GiniClust: detecting rare cell types from single-cell gene expression data with Gini index
Cited by: 229
Author(s): Lan Jiang, Huidong Chen, Luca Pinello, Guo‐Cheng Yuan
Software Mentions: 5
Published: over 8 years ago
10.7150/ijbs.45050
A Novel Ferroptosis-related Gene Signature for Overall Survival Prediction in Patients with Hepatocellular Carcinoma
Cited by: 342
Author(s): Jie Liang, De-Shen Wang, Haocheng Lin, Xiuxing Chen, Hui Yang, Yun Zheng, Yuhong Li
Software Mentions: 5
Published: almost 5 years ago
10.3389/fcell.2021.712196
A Novel Classifier Based on Urinary Proteomics for Distinguishing Between Benign and Malignant Ovarian Tumors
Cited by: 11
Author(s): Maowei Ni, Jie Zhou, Zhihui Zhu, Jingtao Yuan, Wei‐Jiang Gong, Jun Zhu, Zhong Zheng, Huajun Zhao
Software Mentions: 5
Published: about 3 years ago
10.3389/fmicb.2020.00266
Identification of Anti-Mycobacterium and Anti-Legionella Compounds With Potential Distinctive Structural Scaffolds From an HD-PBL Using Phenotypic Screens in Amoebae Host Models
Cited by: 7
Author(s): Nabil Hanna, Sébastien Kicka, Gianpaolo Chiriano, Christopher F. Harrison, Hajer Ouertatani Sakouhi, Valentin Trofimov, Agata Kranjc, Jahn Nitschke, Marco Pagni, Pierre Cosson, Hubert Hilbi, Léonardo Scapozza, Thierry Soldati
Software Mentions: 5
Published: almost 5 years ago
10.1186/s12864-021-07722-y
Unravelling population structure heterogeneity within the genome of the malaria vector Anopheles gambiae
Cited by: 1
Author(s): Melina Campos, Luísa D P Rona, Katie Willis, George K. Christophides, Robert M. MacCallum
Software Mentions: 5
Published: over 3 years ago
10.1002/1878-0261.12616
High CD206 levels in Hodgkin lymphoma‐educated macrophages are linked to matrix‐remodeling and lymphoma dissemination
Cited by: 23
Author(s): Annekatrin Arlt, Frederike von Bonin, Thorsten Rehberg, Paula Pérez-Rubio, Julia C. Engelmann, Katharina Limm, Sarah Reinke, Christian Dullin, Xueni Sun, Rieke Specht, Markus Maulhardt, Franziska Linke, Gertrude Bunt, Wolfram Klapper, Martina Vockerodt, Jörg Wilting, Tobias Pukrop, Katja Dettmer, Wolfram Gronwald, Peter J. Oefner, Rainer Spang, Dieter Kube
Software Mentions: 5
Published: almost 5 years ago
10.1038/s41420-020-0263-6
Temporal transcriptome analysis of neuronal commitment reveals the preeminent role of the divergent lncRNA biotype and a critical candidate gene during differentiation
Cited by: 3
Author(s): Bharat Prajapati, Mahar Fatima, Mena Fatma, Priya Maddhesiya, Himali Arora, Teesta Naskar, Subhashree Devasenapathy, Pankaj Seth, Subrata Sinha
Software Mentions: 5
Published: over 4 years ago
10.1172/jci.insight.144255
Disruption of innate defense responses by endoglycosidase HPSE promotes cell survival
Cited by: 14
Author(s): Alex Agelidis, Benjamin A. Turturice, Rahul K. Suryawanshi, Tejabhiram Yadavalli, Dinesh Jaishankar, Joshua Ames, James Hopkins, Lulia Koujah, Chandrashekhar D. Patil, Satvik Hadigal, Evan J. Kyzar, Anaamika Campeau, Jacob M. Wozniak, David J. Gonzalez, Israël Vlodavsky, Jinping Li, David L. Perkins, Patricia W. Finn, Deepak Shukla
Software Mentions: 4
Published: over 3 years ago
10.1007/s00401-020-02218-7
Molecular characterization of CNS paragangliomas identifies cauda equina paragangliomas as a distinct tumor entity
Cited by: 17
Author(s): Leonille Schweizer, Felix Thierfelder, Christian Thomas, Patrick Soschinski, Abigail K Suwala, Damian Stichel, Annika K. Wefers, Lars Wessels, Martin Misch, Hee-Yeong Kim, Ruben Jödicke, Daniel Teichmann, David Kaul, Johannes Kahn, Michael Bockmayr, Martin Hasselblatt, Alexander Younsi, Andreas Unterberg, Bettina Knie, Jan Walter, Diaa Al Safatli, Sven-Axel May, Andreas Jödicke, Georgios Ntoulias, Dag Moskopp, Peter Vajkoczy, Frank L. Heppner, David Capper, Wolfgang Hartmann, Christian Hartmann, Andreas von Deimling, David Reuß, Anne Schöler, Arend Koch
Software Mentions: 4
Published: about 4 years ago
10.1002/advs.202000938
Atlas of Musculoskeletal Stem Cells with the Soft and Hard Tissue Differentiation Architecture
Cited by: 7
Author(s): Zi Yin, Junxin Lin, Ruojin Yan, Richun Liu, Mengfei Liu, Bo Zhou, Wenyan Zhou, An Chen, Yangwu Chen, Yin Hu, Chunmei Fan, Kun Zhao, Bowen Wu, Xiaohui Zou, Jin Zhang, Ahmed El-Hashash, Xiao Chen
Software Mentions: 4
Published: about 4 years ago
10.18632/aging.203352
Development and validation of prognostic model based on the analysis of autophagy-related genes in colon cancer
Cited by: 8
Author(s): Yongfeng Wang, Kaili Lin, Tianchun Xu, Liuli Wang, Liangyin Fu, Guangming Zhang, Jing Ai, Yajun Jiao, Rongrong Zhu, Xiaoyong Han, Hui Cai
Software Mentions: 4
Published: over 3 years ago
10.1186/s12864-020-07009-8
Bivalent genes that undergo transcriptional switching identify networks of key regulators of embryonic stem cell differentiation
Cited by: 6
Author(s): Ah-Jung Jeon, Greg Tucker‐Kellogg
Software Mentions: 4
Published: about 4 years ago
10.1042/BSR20210583
Identification and validation of <i>ADME</i> genes as prognosis and therapy markers for hepatocellular carcinoma patients
Cited by: 4
Author(s): Jukun Wang, Ke Han, Chao Zhang, Xin Chen, Li Yu, Linzhong Zhu, Tao Luo
Software Mentions: 4
Published: over 3 years ago
10.1038/s41416-020-0796-8
Molecular subtypes of oropharyngeal cancer show distinct immune microenvironment related with immune checkpoint blockade response
Cited by: 16
Author(s): Min Hwan Kim, Jaehwan Kim, Ji Min Lee, Jae Woo Choi, Dongmin Jung, Hojin Cho, Hyundeok Kang, Min Hee Hong, Su Jin Heo, Se Heon Kim, Eun Chang Choi, Da Hee Kim, Young Min Park, Sang Woo Kim, Sun Och Yoon, Yoon Woo Koh, Byoung Chul Cho, Hye Ryun Kim
Software Mentions: 4
Published: over 4 years ago
10.12688/wellcomeopenres.15590.1
Evolutionary analysis of the most polymorphic gene family in falciparum malaria
Cited by: 56
Author(s): Thomas D. Otto, Sammy A. Assefa, Ulrike Böhme, Mandy Sanders, Dominic Kwiatkowski, Matthew Berriman, Chris Newbold
Software Mentions: 4
Published: almost 5 years ago
10.1186/s12957-021-02244-z
Identification of a ferroptosis-related gene signature predictive model in colon cancer
Cited by: 17
Author(s): Ye Wang, Heng-bo Xia, Zhang-ming Chen, Lei Meng, Aiming Xu
Software Mentions: 4
Published: over 3 years ago
10.1002/pld3.28
Divergent leaf shapes among <i>Passiflora</i> species arise from a shared juvenile morphology
Cited by: 24
Author(s): Daniel H. Chitwood, Wagner Campos Otoni
Software Mentions: 4
Published: about 7 years ago
10.1371/journal.pone.0225899
Diversity of a cytokinin dehydrogenase gene in wild and cultivated barley
Cited by: 3
Author(s): Beata I. Czajkowska, Conor M. Finlay, Glynis Jones, Terence A. Brown
Software Mentions: 4
Published: almost 5 years ago
10.3390/cancers12051143
Differential B-Cell Receptor Signaling Requirement for Adhesion of Mantle Cell Lymphoma Cells to Stromal Cells
Cited by: 8
Author(s): Laia Sadeghi, Gustav Arvidsson, Magali Merrien, Agata M. Wasik, André Görgens, C. I. Edvard Smith, Birgitta Sander, Anthony P. H. Wright
Software Mentions: 4
Published: over 4 years ago
10.3390/cancers12020381
NASA GeneLab Platform Utilized for Biological Response to Space Radiation in Animal Models
Cited by: 16
Author(s): J. Tyson McDonald, R. Stainforth, Jack Miller, Thomas J. Cahill, Willian A. da Silveira, Komal S. Rathi, Gary Hardiman, Deanne Taylor, Sylvain V. Costes, Vinita Chauhan, Robert Meller, Afshin Beheshti
Software Mentions: 4
Published: almost 5 years ago
10.3390/cancers12071913
The LIM Protein Ajuba Augments Tumor Metastasis in Colon Cancer
Cited by: 10
Author(s): Noëlle Dommann, Daniel Sánchez-Taltavull, Linda Eggs, Fabienne Esther Birrer, Tess M. Brodie, Lilian Salm, Felix Alexander Baier, Michaela Medová, Magali Humbert, Mario P. Tschan, Guido Beldi, Daniel Candinas, Deborah Stroka
Software Mentions: 4
Published: over 4 years ago
10.1016/j.cell.2018.11.044
Genome-wide CRISPR Screens in T Helper Cells Reveal Pervasive Crosstalk between Activation and Differentiation
Cited by: 115
Author(s): Johan Henriksson, Xi Chen, Tomás Gomes, Ubaid Ullah, Kerstin B. Meyer, Ricardo J. Miragaia, Graham Dy, Jhuma Pramanik, Kosuke Yusa, Riitta Lahesmaa, Sarah A. Teichmann
Software Mentions: 4
Published: almost 6 years ago
10.1016/j.celrep.2021.108860
COX2 regulates senescence secretome composition and senescence surveillance through PGE2
Cited by: 30
Author(s): S. Goncalves, Kai Yin, Yoko Itō, Adelyne Chan, Ioana Olan, Sarah Gough, Liam Cassidy, Eva M. Serrao, Stephen Smith, Andrew Young, Masashi Narita, Matthew Hoare
Software Mentions: 4
Published: over 3 years ago
10.1038/s41422-018-0066-y
Single-cell RNA-seq reveals the diversity of trophoblast subtypes and patterns of differentiation in the human placenta
Cited by: 242
Author(s): Yawei Liu, Xiaoying Fan, Rui Wang, Xiaoyin Lu, Yan-Li Dang, Huiying Wang, Haiyan Lin, Cheng Zhu, Hao Ge, James C. Cross, Hongmei Wang
Software Mentions: 4
Published: over 6 years ago
10.1038/s41422-019-0251-7
Guiding T lymphopoiesis from pluripotent stem cells by defined transcription factors
Cited by: 39
Author(s): Rong Guo, Fang Hu, Qitong Weng, Chen Lv, Hongling Wu, Lijuan Liu, Zongcheng Li, Yang Zeng, Zhijie Bai, Mengyun Zhang, Yuting Liu, Xiaofei Liu, Chengxiang Xia, Tongjie Wang, Pingwei Zhou, Kaitao Wang, Yong Dong, Yuxuan Luo, Xiangzhong Zhang, Yuxian Guan, Geng Yang, Juan Du, Yangqiu Li, Yu Lan, Jiekai Chen, Bing Liu, Jinyong Wang
Software Mentions: 4
Published: about 5 years ago
10.1186/s12014-021-09318-w
Circulating proteins associated with allergy development in infants—an exploratory analysis
Cited by: 5
Author(s): Marit Stockfelt, Mun‐Gwan Hong, Bill Hesselmar, Ingegerd Adlerberth, Agnes E. Wold, Jochen M. Schwenk, Anna‐Carin Lundell, Anna Rudin
Software Mentions: 4
Published: over 3 years ago
10.1016/j.cub.2019.09.031
Differential Sperm Motility Mediates the Sex Ratio Drive Shaping Mouse Sex Chromosome Evolution
Cited by: 37
Author(s): Claudia Cattoni Rathje, Emma Elizabeth Philippa Johnson, Deborah Drage, Christina Patinioti, Graciela Silvestri, Nabeel A. Affara, Côme Ialy-Radio, Julie Cocquet, Benjamin M. Skinner, Peter J. I. Ellis
Software Mentions: 4
Published: about 5 years ago
10.1016/j.devcel.2020.01.023
Functional Heterogeneity within the Developing Zebrafish Epicardium
Cited by: 46
Author(s): Michael Weinberger, Filipa C. Simões, Roger Patient, Tatjana Sauka‐Spengler, Paul R. Riley
Software Mentions: 4
Published: over 4 years ago
10.1016/j.esmoop.2020.100037
Expression and prognostic significance of PDGF ligands and receptors across soft tissue sarcomas
Cited by: 6
Author(s): Mehdi Brahmi, Tom Lesluyes, Armelle Dufresne, Maud Toulmonde, Antoîne Italiano, Olivier Mir, Axel Le Cesne, Thibaud Valentin, Christine Chevreau, Sylvie Bonvalot, Nicolas Penel, Jean‐Michel Coindre, Sophie Le Guellec, François Le Loarer, Marie Karanian, Jean‐Yves Blay, Frédéric Chibon
Software Mentions: 4
Published: almost 4 years ago
10.3389/fgene.2020.614888
Integrated Analysis of Immunity- and Ferroptosis-Related Biomarker Signatures to Improve the Prognosis Prediction of Hepatocellular Carcinoma
Cited by: 41
Author(s): Xuanlong Du, Zhang Ye-wei
Software Mentions: 4
Published: almost 4 years ago
10.3389/fgene.2021.690509
Identification and Validation of a Ferroptosis-Related Long Non-coding RNA Signature for Predicting the Outcome of Lung Adenocarcinoma
Cited by: 27
Author(s): Zhiyuan Zheng, Qian Zhang, Wei Wu, Yu Xue, Shuhan Liu, Qiaoqian Chen, Lin Dong
Software Mentions: 4
Published: over 3 years ago
10.3389/fimmu.2019.02403
Adaptive Features of Natural Killer Cells in Multiple Sclerosis
Cited by: 15
Author(s): Antía Moreira, Elisenda Alari-Pahissa, Elvira Munteis, Antonio Vera, Ana Zabalza, Mireia Llop, Noelia Villarrubia, Marcel Costa‐García, Roberto Álvarez‐Lafuente, Luisa María Villar, Miguel López‐Botet, José Enrique Martínez-Rodríguez
Software Mentions: 4
Published: about 5 years ago
10.3389/fimmu.2016.00603
TGF-β Affects the Differentiation of Human GM-CSF+ CD4+ T Cells in an Activation- and Sodium-Dependent Manner
Cited by: 5
Author(s): Szabolcs Éliás, Angelika Schmidt, Venkateshan Kannan, John Andersson, Jesper Tegnér
Software Mentions: 4
Published: almost 8 years ago
10.3389/fmicb.2020.00410
Transcriptional Responses of Dictyostelium discoideum Exposed to Different Classes of Bacteria
Cited by: 9
Author(s): Otmane Lamrabet, Astrid Melotti, Frédéric Burdet, Nabil Hanna, Jackie Perrin, Jahn Nitschke, Marco Pagni, Hubert Hilbi, Thierry Soldati, Pierre Cosson
Software Mentions: 4
Published: over 4 years ago
10.3389/fmicb.2021.639913
Comparison of Microbial Communities in Colorado Potato Beetles (Leptinotarsa decemlineata Say) Collected From Different Sources in China
Cited by: 6
Author(s): Yanxue Yu, Yuhan Wang, Hongwei Li, Xiubo Yu, Wangpeng Shi, Junfeng Zhai
Software Mentions: 4
Published: over 3 years ago
10.1186/s13059-018-1416-2
Single-cell RNA-seq analysis unveils a prevalent epithelial/mesenchymal hybrid state during mouse organogenesis
Cited by: 135
Author(s): Ji Dong, Yuqiong Hu, Xiaoying Fan, Xinglong Wu, Yunuo Mao, Boqiang Hu, Hongshan Guo, Lu Wen, Fuchou Tang
Software Mentions: 4
Published: over 6 years ago
10.1186/s13073-019-0638-6
Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data
Cited by: 628
Author(s): Francesca Finotello, Clemens Mayer, Christina Plattner, Gerhard Laschober, Dietmar Rieder, Hubert Hackl, Anne Krogsdam, Zuzana Loncová, Wilfried Posch, Doris Wilflingseder, Sieghart Sopper, Marieke E. Ijsselsteijn, Thomas P. Brouwer, Douglas B. Johnson, Yaomin Xu, Yu Wang, Melinda E. Sanders, Mónica Valéria Estrada, Paula I. Ericsson-Gonzalez, Pornpimol Charoentong, Justin M. Balko, Noel F.C.C. de Miranda, Zlatko Trajanoski
Software Mentions: 4
Published: over 5 years ago
10.1080/19490976.2021.1897209
The high prevalence of <i>Clostridioides difficile</i> among nursing home elders associates with a dysbiotic microbiome
Cited by: 6
Author(s): John P. Haran, Doyle V. Ward, Shakti Bhattarai, Ethan Loew, Protiva Dutta, Amanda Higgins, Beth A. McCormick, Vanni Bucci
Software Mentions: 4
Published: almost 4 years ago
10.3390/jcm8101535
Connecting Histopathology Imaging and Proteomics in Kidney Cancer through Machine Learning
Cited by: 30
Author(s): Francisco Azuaje, Sang Yoon Kim, Daniel Hernández, Gunnar Dittmar
Software Mentions: 4
Published: about 5 years ago
10.1038/s41598-020-77433-z
High CD45 expression of CD8+ and CD4+ T cells correlates with the size of HIV-1 reservoir in blood
Cited by: 7
Author(s): Stefan Petkov, Yonas Bekele, Tadepally Lakshmikanth, Bo Hejdeman, Maurizio Zazzi, Petter Brodin, Francesca Chiodi
Software Mentions: 4
Published: almost 4 years ago
10.1038/s41598-021-86821-y
Prediction of single-cell mechanisms for disease progression in hypertrophic remodelling by a trans-omics approach
Cited by: 3
Author(s): Momoko Hamano, Seitaro Nomura, Midori Iida, Issei Komuro, Yoshihiro Yamanishi
Software Mentions: 4
Published: over 3 years ago
10.1084/jem.20201729
Yolk sac, but not hematopoietic stem cell–derived progenitors, sustain erythropoiesis throughout murine embryonic life
Cited by: 40
Author(s): Francisca Soares-da-Silva, Laina Freyer, Ramy Elsaid, Odile Burlen-Defranoux, Lorea Iturri, Odile Sismeiro, Perpétua Pinto-do-Ó, Elisa Gomez Perdiguero, Ana Cumano
Software Mentions: 4
Published: almost 4 years ago
10.3389/fpls.2018.01163
Gene Co-expression Network Analysis Suggests the Existence of Transcriptional Modules Containing a High Proportion of Transcriptionally Differentiated Homoeologs in Hexaploid Wheat
Cited by: 15
Author(s): Kotaro Takahagi, Komaki Inoue, Keiichi Mochida
Software Mentions: 3
Published: over 6 years ago
10.3389/fgene.2021.564780
Distinct Extracellular RNA Profiles in Different Plasma Components
Cited by: 8
Author(s): Jing Jia, Shangdong Yang, Jinyong Huang, Hong Zheng, Ying He, Liang Wang
Software Mentions: 3
Published: over 3 years ago
10.1186/s13059-016-0937-9
In silico lineage tracing through single cell transcriptomics identifies a neural stem cell population in planarians
Cited by: 76
Author(s): Alyssa M. Molinaro, Bret J. Pearson
Software Mentions: 3
Published: over 8 years ago
10.3390/cancers12092704
Mass Spectrometry Imaging for Reliable and Fast Classification of Non-Small Cell Lung Cancer Subtypes
Cited by: 13
Author(s): Mark Kriegsmann, Christiane Zgorzelski, Rita Casadonte, Kristina Schwamborn, Thomas Muley, Hauke Winter, Martin Eichhorn, Florian Eichhorn, Arne Warth, Sören‐Oliver Deininger, Petros Christopoulos, Michael Thomas, Thomas Longerich, Albrecht Stenzinger, Wilko Weichert, Carsten Müller‐Tidow, Jörg Kriegsmann, Peter Schirmacher, Katharina Kriegsmann
Software Mentions: 3
Published: about 4 years ago
10.3389/fonc.2021.629327
Identification and Validation of Ubiquitin-Specific Proteases as a Novel Prognostic Signature for Hepatocellular Carcinoma
Cited by: 11
Author(s): Wenkai Ni, Saiyan Bian, Mengqi Zhu, Qisheng Song, Jianping Zhang, Mingbing Xiao, Wenjie Zheng
Software Mentions: 3
Published: over 3 years ago
10.3389/fcimb.2021.637570
Whipworm-Associated Intestinal Microbiome Members Consistent Across Both Human and Mouse Hosts
Cited by: 11
Author(s): Bruce A. Rosa, Caroline Snowden, John Martin, Kerstin Fischer, Jonah Kupritz, Ethiopia Beshah, Taniawati Supali, Lincoln Gankpala, Peter U. Fischer, Joseph F. Urban, Makedonka Mitreva
Software Mentions: 3
Published: over 3 years ago
10.1186/s13059-018-1553-7
Holo-Seq: single-cell sequencing of holo-transcriptome
Cited by: 26
Author(s): Zhengyun Xiao, Cheng Guo, Jiao Yang, Ci Pan, Ran Li, Danmei Jia, Jing Zhu, Chao Wu, Min Zheng, Junling Jia
Software Mentions: 3
Published: about 6 years ago
10.3390/jcm10112450
Ideal Cardiovascular Health in Former Smokers
Cited by: 3
Author(s): Jane A. Leopold, Elliott M. Antman
Software Mentions: 3
Published: over 3 years ago
10.1093/aobpla/plaa034
Correlated evolution of leaf and root anatomic traits in Dendrobium (Orchidaceae)
Cited by: 3
Author(s): Ying Qu, Jialin Huang, Shi‐Bao Zhang
Software Mentions: 3
Published: over 4 years ago
10.1016/j.ebiom.2019.04.016
Beyond multidrug resistance: Leveraging rare variants with machine and statistical learning models in Mycobacterium tuberculosis resistance prediction
Cited by: 51
Author(s): Michael L Chen, Akshith Doddi, Jimmy Royer, Luca Freschi, Marco Schito, Matthew Ezewudo, Isaac S. Kohane, Andrew L. Beam, Farhat Mustafa
Software Mentions: 3
Published: over 5 years ago
10.1371/journal.pone.0242521
In silico analysis identifies a putative cell-of-origin for BRAF fusion-positive cerebellar pilocytic astrocytoma
Cited by: 1
Author(s): Subhi Talal Younes, Betty Herrington
Software Mentions: 3
Published: about 4 years ago
10.1038/sdata.2017.67
Single-cell transcriptome of early embryos and cultured embryonic stem cells of cynomolgus monkeys
Cited by: 40
Author(s): Tomonori Nakamura, Yukihiro Yabuta, Ikuhiro Okamoto, Kotaro Sasaki, Chizuru Iwatani, Hideaki Tsuchiya, Mitinori Saitou
Software Mentions: 3
Published: over 7 years ago
10.1038/s42003-020-01123-9
Structure and function of a malaria transmission blocking vaccine targeting Pfs230 and Pfs230-Pfs48/45 proteins
Cited by: 34
Author(s): Kavita Singh, Martin Burkhardt, Sofia Nakuchima, Raúl Herrera, Olga Muratova, Apostolos G. Gittis, Emily Kelnhofer, Karine Reiter, Margery Smelkinson, Daniel Veltri, Bruce J. Swihart, Richard L. Shimp, Vu Nguyen, Baoshan Zhang, Nicholas J. MacDonald, Patrick E. Duffy, David N. Garboczi, David L. Narum
Software Mentions: 3
Published: over 4 years ago
10.1186/s13059-020-02102-3
Splicing-accessible coding 3′UTRs control protein stability and interaction networks
Cited by: 10
Author(s): Marco Preußner, Qingsong Gao, Eliot Morrison, Olga Herdt, Florian Finkernagel, Michael Schümann, Eberhard Krause, Christian Freund, Wei Chen
Software Mentions: 3
Published: over 4 years ago
10.1186/s12885-021-08541-w
Molecular identification of an immunity- and Ferroptosis-related gene signature in non-small cell lung Cancer
Cited by: 10
Author(s): Taisheng Liu, Honglian Luo, Jinye Zhang, Xiaoshan Hu, Jian Zhang
Software Mentions: 3
Published: over 3 years ago
10.1186/s40168-018-0559-4
Daylight exposure modulates bacterial communities associated with household dust
Cited by: 55
Author(s): Ashkaan K. Fahimipour, Erica M. Hartmann, Andrew Siemens, Jeff Kline, David A. Levin, Hannah Wilson, Clarisse M. Betancourt‐Román, Glen Brown, Mark Fretz, Dale Northcutt, Kyla Siemens, Curtis Huttenhower, Jessica L. Green, Kevin Van Den Wymelenberg
Software Mentions: 3
Published: about 6 years ago
10.3390/ijerph17207613
Tooth-Level Analysis of Dental Caries in Primary Dentition in Myanmar Children
Cited by: 9
Author(s): Yasuo Nomura, Ryoko Otsuka, Wit Yee Wint, Ayako Okada, Ryo Hasegawa, Nobuhiro Hanada
Software Mentions: 3
Published: about 4 years ago
10.3389/fgene.2019.00734
A Tool for Visualization and Analysis of Single-Cell RNA-Seq Data Based on Text Mining
Cited by: 13
Author(s): Gennaro Gambardella, Diego di Bernardo
Software Mentions: 3
Published: over 5 years ago
10.1038/s41598-019-52134-4
Prediction and Analysis of Skin Cancer Progression using Genomics Profiles of Patients
Cited by: 48
Author(s): Sherry Bhalla, Harpreet Kaur, Anjali Dhall, Gajendra P. S. Raghava
Software Mentions: 3
Published: about 5 years ago
10.1038/s41598-019-55053-6
Integrative proteomics and phosphoproteomics in pulmonary arterial hypertension
Cited by: 36
Author(s): Weiling Xu, Suzy Comhair, Ruoying Chen, Bo Hu, Yuan Hou, Yadi Zhou, Lori Mavrakis, Allison J. Janocha, Ling Li, Dongmei Zhang, Belinda Willard, Kewal Asosingh, Feixiong Cheng, Serpil C. Erzurum
Software Mentions: 3
Published: almost 5 years ago
10.26508/lsa.202000867
Gene selection for optimal prediction of cell position in tissues from single-cell transcriptomics data
Cited by: 17
Author(s): Jovan Tanevski, Thin Nguyen, Buu Truong, Nikos Karaiskos, Mehmet Eren Ahsen, Xinyu Zhang, Chang Shu, Ke Xu, Xiaoyu Liang, Ying Hu, Vu Viet Hoang Pham, Xiaomei Li, Thuc Duy Le, Adi L. Tarca, Gaurav Bhatti, Roberto Romero, Nestoras Karathanasis, Phillipe Loher, Yang Chen, Zhengqing Ouyang, Disheng Mao, Yuping Zhang, Maryam Zand, Jianhua Ruan, Christoph Hafemeister, Peng Qiu, Duc Tran, Tin Nguyen, Attila Gábor, Thomas Yu, Justin Guinney, Enrico Glaab, Roland Krause, Peter Banda, Gustavo Stolovitzky, Nikolaus Rajewsky, Julio Sáez-Rodríguez, Pablo Meyer
Software Mentions: 3
Published: about 4 years ago
10.26508/lsa.201800124
Distinctive features of lincRNA gene expression suggest widespread RNA-independent functions
Cited by: 33
Author(s): Alex Tuck, Kedar Nath Natarajan, Greggory M. Rice, Jason Borawski, Fabio Mohn, Aneliya Rankova, Matyáš Flemr, Alice Wenger, Razvan Nutiu, Sarah A. Teichmann, Marc Bühler
Software Mentions: 3
Published: over 6 years ago
10.1186/s12884-019-2703-y
Nomogram for prediction of gestational diabetes mellitus in urban, Chinese, pregnant women
Cited by: 26
Author(s): Fei Guo, Yang Sm, Yong Zhang, Xi Yang, Chen Zhang, Jianxia Fan
Software Mentions: 3
Published: almost 5 years ago
10.7150/thno.44693
A lab-on-a-disc platform enables serial monitoring of individual CTCs associated with tumor progression during EGFR-targeted therapy for patients with NSCLC
Cited by: 16
Author(s): Minji Lim, Juhee Park, Alarice Lowe, Hyoung-oh Jeong, Semin Lee, Hee Chul Park, Kyusang Lee, Gwang Ha Kim, Mi‐Hyun Kim, Yoon‐Kyoung Cho
Software Mentions: 3
Published: almost 5 years ago
10.1038/s41422-018-0125-4
Integrative single-cell analysis of transcriptome, DNA methylome and chromatin accessibility in mouse oocytes
Cited by: 99
Author(s): Chan Gu, Shanling Liu, Qihong Wu, Lin Zhang, Fan Guo
Software Mentions: 3
Published: almost 6 years ago
10.1007/s00401-020-02247-2
Clear cell meningiomas are defined by a highly distinct DNA methylation profile and mutations in SMARCE1
Cited by: 27
Author(s): Philipp Sievers, Martin Sill, Christina Blume, Arnault Tauziède‐Espariat, Daniel Schrimpf, Damian Stichel, David Reuß, Helin Dogan, Christian Hartmann, Christian Mawrin, Martin Hasselblatt, Walter Stummer, Uta Schick, Jürgen Hench, Stephan Frank, Ralf Ketter, Leonille Schweizer, Jens Schittenhelm, Stéphanie Puget, Sebastian Brandner, Zane Jaunmuktane, Benno Küsters, Zied Abdullaev, Melike Pekmezci, Matija Snuderl, Miriam Ratliff, Christel Herold‐Mende, Andreas Unterberg, Kenneth Aldape, David W. Ellison, Pieter Wesseling, Guido Reifenberger, Wolfgang Wick, Arie Perry, Pascale Varlet, Stefan M. Pfister, David Jones, Andreas von Deimling, Felix Sahm
Software Mentions: 3
Published: almost 4 years ago
10.3389/fimmu.2019.01515
Meeting the Challenges of High-Dimensional Single-Cell Data Analysis in Immunology
Cited by: 57
Author(s): Subarna Palit, Claudia Heuser, Gustavo Pereira de Almeida, Fabian J. Theis, Christina E. Zielinski
Software Mentions: 3
Published: over 5 years ago
10.1038/s41598-021-93966-3
A precision medicine approach to sex-based differences in ideal cardiovascular health
Cited by: 4
Author(s): Jane A. Leopold, Elliott M. Antman
Software Mentions: 3
Published: over 3 years ago
10.3390/life10080121
Parental Selenium Nutrition Affects the One-Carbon Metabolism and the Hepatic DNA Methylation Pattern of Rainbow Trout (Oncorhynchus mykiss) in the Progeny
Cited by: 9
Author(s): Pauline Wischhusen, Takaya Saito, Cécile Héraud, Sadasivam Kaushik, Benoı̂t Fauconneau, P. Antony Jesu Prabhu, Stéphanie Fontagné-Dicharry, Kaja H. Skjærven
Software Mentions: 3
Published: over 4 years ago
10.1186/s13287-019-1376-9
Umbilical cord as a long-term source of activatable mesenchymal stromal cells for immunomodulation
Cited by: 23
Author(s): Anton Selich, Katharina Zimmermann, Michel Tenspolde, Oliver Dittrich‐Breiholz, Constantin von Kaisenberg, Axel Schambach, Michael Rothe
Software Mentions: 3
Published: about 5 years ago
10.6026/97320630016293
COVID-19, Reduced Lung Function, and Increased Psycho-emotional Stress
Cited by: 3
Author(s): Dongyuan Wu, Dorothy Ellis, Susmita Datta
Software Mentions: 3
Published: over 4 years ago
10.3389/fimmu.2021.645478
Restoration of NK Cell Cytotoxic Function With Elotuzumab and Daratumumab Promotes Elimination of Circulating Plasma Cells in Patients With SLE
Cited by: 13
Author(s): Morgane Humbel, Florence Bellanger, Natalia Fluder, Alice Horisberger, Madeleine Suffiotti, Craig Fenwick, Camillo Ribi, Denis Comte
Software Mentions: 2
Published: over 3 years ago
10.1038/s41598-021-93526-9
Transcriptome analysis discloses dysregulated genes in normal appearing tumor-adjacent thyroid tissues from patients with papillary thyroid carcinoma
Cited by: 6
Author(s): Hao He, Sandya Liyanarachchi, Wei Li, Daniel F. Comiskey, Pearlly S. Yan, Ralf Bundschuh, Altan Turkoglu, Pamela Brock, Matthew D. Ringel, Albert de la Chapelle
Software Mentions: 2
Published: over 3 years ago
10.3389/fmicb.2021.626774
Genomic Diversity and Virulence Potential of ESBL- and AmpC-β-Lactamase-Producing Escherichia coli Strains From Healthy Food Animals Across Europe
Cited by: 26
Author(s): Christa Ewers, Anno de Jong, Ellen Prenger‐Berninghoff, Farid El Garch, Ursula Leidner, Sumeet K. Tiwari, Torsten Semmler
Software Mentions: 2
Published: over 3 years ago
10.1111/eva.13288
Gene flow between island populations of the malaria mosquito, <i>Anopheles hinesorum</i> , may have contributed to the spread of divergent host preference phenotypes
Cited by: 3
Author(s): Luke Ambrose, Daniel Ortiz‐Barrientos, Robert D. Cooper, Neil F. Lobo, Thomas R. Burkot, Tanya L. Russell, Nigel W. Beebe
Software Mentions: 2
Published: over 3 years ago
10.3390/ijms22158337
Regulation Network of Colorectal-Cancer-Specific Enhancers in the Progression of Colorectal Cancer
Cited by: 3
Author(s): Bohan Chen, Yuan Ma, Jinfang Bi, Wenbin Wang, Anshun He, Guanghao Su, Zhongfang Zhao, Jiandang Shi, Lei Zhang
Software Mentions: 2
Published: over 3 years ago
10.3390/dj9020022
Improvement of the Working Environment and Daily Work-Related Tasks of Dental Hygienists Working in Private Dental Offices from the Japan Dental Hygienists’ Association Survey 2019
Cited by: 1
Author(s): Yasuo Nomura, Yuki Ohara, Yuko Yamamoto, Ayako Okada, Noriyasu Hosoya, Nobuhiro Hanada, Noriko Takei
Software Mentions: 2
Published: almost 4 years ago
10.1038/s42003-019-0657-2
Transcriptional programming and T cell receptor repertoires distinguish human lung and lymph node memory T cells
Cited by: 14
Author(s): Nathan Schoettler, Cara L. Hrusch, Kelly M. Blaine, Anne I. Sperling, Carole Ober
Software Mentions: 2
Published: about 5 years ago
10.1038/s42003-021-02676-z
High-throughput single-cell transcriptomics reveals the female germline differentiation trajectory in Arabidopsis thaliana
Cited by: 14
Author(s): Zongliu Hou, Qing Liu, Man Zhang, Lihua Zhao, Xingyue Jin, Liping Liu, Zhenxia Su, Hanyang Cai, Yuan Qin
Software Mentions: 2
Published: about 3 years ago
10.3390/cells8091069
Single-Cell Transcriptomes Reveal Characteristic Features of Mouse Hepatocytes with Liver Cholestatic Injury
Cited by: 12
Author(s): Na Chang, Lei Tian, Xiaofang Ji, Xuan Zhou, Lei Hou, Xinhao Zhao, Yang Yang, Lin Yang, Liying Li
Software Mentions: 2
Published: about 5 years ago