pypi: CellProfiler | Projects | Ecosyste.ms: Papers

10.18632/oncotarget.11038

Role of the immune system in the peritoneal tumor spread of high grade serous ovarian cancer
Cited by: 33
Author(s): Katharina Auer, Anna Bachmayr-Heyda, Nyamdelger Sukhbaatar, Stefanie Aust, Klaus G. Schmetterer, Samuel M. Meier, Christopher Gerner, Christoph Grimm, Reinhard Horvat, Dietmar Pils
Software Mentions: 4
Published: about 10 years ago

10.1371/journal.pone.0218230

Atoh8 acts as a regulator of chondrocyte proliferation and differentiation in endochondral bones
Cited by: 10
Author(s): Nadine Schroeder, Manuela Wuelling, Daniel Hoffmann, Beate Brand‐Saberi, Andrea Vortkamp
Software Mentions: 4
Published: about 7 years ago

10.1093/bioinformatics/btw390

CellProfiler Analyst: interactive data exploration, analysis and classification of large biological image sets
Cited by: 106
Author(s): David Dao, Adam Fraser, Jia‐Jang Hung, Vebjorn Ljosa, Shantanu Singh, Anne E. Carpenter
Software Mentions: 4
Published: over 10 years ago

10.7554/eLife.35786

Human axial progenitors generate trunk neural crest cells in vitro
Cited by: 70
Author(s): Thomas J.R. Frith, Ilaria Granata, Matthew Wind, Erin Stout, Oliver Thompson, Katrin Neumann, Dylan Stavish, Paul R. Heath, Daniel Ortmann, James Hackland, Konstantinos Anastassiadis, Mina Gouti, James Briscoe, Valerie Wilson, Stuart L. Johnson, Marysia Placzek, Mario Rosario Guarracino, Peter W. Andrews, Anestis Tsakiridis
Software Mentions: 4
Published: about 8 years ago

10.1186/s13014-021-01853-y

Complete response to neoadjuvant chemoradiotherapy in rectal cancer is associated with RAS/AKT mutations and high tumour mutational burden
Cited by: 4
Author(s): Joanne Stockton, Louise Tee, Celina M. Whalley, Jonathan James, Mark Dilworth, Rachel Wheat, Thomas Nieto, Ian Geh, João D. Barros-Silva, Andrew D Beggs
Software Mentions: 4
Published: about 5 years ago

10.1242/bio.052936

A fully automated deep learning pipeline for high-throughput colony segmentation and classification
Cited by: 4
Author(s): Sarah H. Carl, Lea Duempelmann, Yukiko Shimada, Marc Bühler
Software Mentions: 4
Published: over 6 years ago

10.1093/bioinformatics/btab178

PRISM: recovering cell-type-specific expression profiles from individual composite RNA-seq samples
Cited by: 13
Author(s): Antti Häkkinen, Kaiyang Zhang, Amjad Alkodsi, Noora Andersson, Erdoğan Pekcan Erkan, Jun Dai, Katja Kaipio, Tarja Lamminen, Naziha Mansuri, Kaisa Huhtinen, Anna Vähärautio, Olli Carpén, Johanna Hynninen, Sakari Hietanen, Rainer Lehtonen, Sampsa Hautaniemi
Software Mentions: 4
Published: over 5 years ago

10.1038/s41598-020-64623-y

Comparative analysis of MACROD1, MACROD2 and TARG1 expression, localisation and interactome
Cited by: 20
Author(s): Roko Žaja, Gülcan Aydin, Barbara E. Lippok, Regina Feederle, Bernhard Lüscher, Karla L. H. Feijs
Software Mentions: 4
Published: over 6 years ago

10.1038/s41598-020-78081-z

Adaptive selection drives TRPP3 loss-of-function in an Ethiopian population
Cited by: 0
Author(s): Sandra M. Walsh, Mercè Izquierdo-Serra, Sandra Acosta, Albert Edo, María C. Estévez Lloret, Roser Moret, Elena Bosch, Baldo Oliva, Jaume Bertranpetit, José M. Fernández-Fernández
Software Mentions: 4
Published: almost 6 years ago

10.3389/fonc.2021.636451

Integrative Analysis of Histopathological Images and Genomic Data in Colon Adenocarcinoma
Cited by: 7
Author(s): Hui Li, Linyan Chen, Hao Zeng, Qimeng Liao, Jianrui Ji, Xuelei Ma
Software Mentions: 4
Published: about 5 years ago

10.1186/s12859-019-2880-8

Cell segmentation methods for label-free contrast microscopy: review and comprehensive comparison
Cited by: 126
Author(s): Pavel Kopel, Jan Balvan, Josef Jaroš, Florian Jug, Radim Kolář, Michal Masařík, Jaromír Gumulec
Software Mentions: 4
Published: over 7 years ago

10.1371/journal.pgen.1008680

Postglacial migration shaped the genomic diversity and global distribution of the wild ancestor of lager-brewing hybrids
Cited by: 24
Author(s): Quinn K. Langdon, David Peris, Juan Ignacio Eizaguirre, Dana A. Opulente, Kelly V. Buh, Kayla Sylvester, Martin Jarzyna, María Esther Rodríguez, Christian A. Lopes, Diego Libkind, Chris Todd Hittinger
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pcbi.1007348

Learning unsupervised feature representations for single cell microscopy images with paired cell inpainting
Cited by: 64
Author(s): Alex X. Lu, Oren Kraus, Sam Cooper, Alan M. Moses
Software Mentions: 4
Published: about 7 years ago

10.1038/s41598-018-20856-6

A cleavage product of Polycystin-1 is a mitochondrial matrix protein that affects mitochondria morphology and function when heterologously expressed
Cited by: 68
Author(s): Cheng-Chao Lin, Mahiro Kurashige, Yi Liu, Takeshi Terabayashi, Yu Ishimoto, Tanchun Wang, Vineet Choudhary, Ryan P. Hobbs, Li-Ka Liu, Ping-Hsien Lee, Patricia Outeda, Fang Zhou, Nicholas P. Restifo, Terry Watnick, Haruna Kawano, Shigeo Horie, William A. Prinz, Hong Xu, Luís F. Menezes, Gregory G. Germino
Software Mentions: 4
Published: over 8 years ago

10.7554/eLife.40162

Motion sensing superpixels (MOSES) is a systematic computational framework to quantify and discover cellular motion phenotypes
Cited by: 8
Author(s): Felix Zhou, Carlos Ruiz‐Puig, Richard Owen, Michael J. White, Jens Rittscher, Xin Lü
Software Mentions: 4
Published: over 7 years ago

10.1038/s41598-019-54493-4

Impact of Q-Griffithsin anti-HIV microbicide gel in non-human primates: In situ analyses of epithelial and immune cell markers in rectal mucosa
Cited by: 17
Author(s): Gökçe Günaydın, Gabriella Edfeldt, David Garber, Muhammad Asghar, Laura Noël‐Romas, Adam Burgener, Carolina Wählby, Lin Wang, Lisa C. Rohan, Patricia C. Guenthner, James Mitchell, Nobuyuki Matoba, Janet M. McNicholl, Kenneth E. Palmer, Annelie Tjernlund, Kristina Broliden
Software Mentions: 4
Published: almost 7 years ago

10.1038/s41597-019-0051-4

Characterization of CA-MRSA TCH1516 exposed to nafcillin in bacteriological and physiological media
Cited by: 14
Author(s): Saugat Poudel, Hannah Tsunemoto, Michael J. Meehan, Richard Szubin, Connor A. Olson, Anne Lamsa, Yara Seif, Nicholas Dillon, Alison Vrbanac, Joseph Sugie, Samira Dahesh, Jonathan M. Monk, Pieter C. Dorrestein, Joseph Pogliano, Rob Knight, Victor Nizet, Bernhard Ø. Palsson, Adam M. Feist
Software Mentions: 4
Published: over 7 years ago

10.1038/s41597-021-00933-8

Cric searchable image database as a public platform for conventional pap smear cytology data
Cited by: 19
Author(s): Mariana T. Rezende, Raniere Silva, Fagner de O. Bernardo, Alessandra Hermógenes Gomes Tobias, Paulo H. C. Oliveira, Tales Mota Machado, Caio S. Costa, Fátima N. S. de Medeiros, Daniela Ushizima, Cláudia Martins Carneiro, Andrea Gomes Campos Bianchi
Software Mentions: 4
Published: over 5 years ago

10.1007/s00204-018-2178-z

Dynamic imaging of adaptive stress response pathway activation for prediction of drug induced liver injury
Cited by: 45
Author(s): Steven Wink, Steven Hiemstra, Suzanna Huppelschoten, Janna E. Klip, Bob van de Water
Software Mentions: 4
Published: over 8 years ago

10.7554/eLife.56969

Drosophila PDGF/VEGF signaling from muscles to hepatocyte-like cells protects against obesity
Cited by: 22
Author(s): Arpan C. Ghosh, Sudhir Gopal Tattikota, Yifang Liu, Aram Comjean, Yanhui Hu, Víctor Barrera, Shannan Ho Sui, Norbert Perrimon
Software Mentions: 4
Published: almost 6 years ago

10.7554/eLife.55911

Histone deacetylase knockouts modify transcription, CAG instability and nuclear pathology in Huntington disease mice
Cited by: 4
Author(s): Marina Kovalenko, Serkan Erdin, Marissa A Andrew, Jason St. Claire, Melissa Shaughnessey, Leroy Hubert, João Luís Neto, Alexei Stortchevoi, Daniel M. Fass, Ricardo Mouro Pinto, Stephen J. Haggarty, John H. Wilson, Michael E. Talkowski, Vanessa C. Wheeler
Software Mentions: 4
Published: about 6 years ago

10.7554/eLife.59780

On the objectivity, reliability, and validity of deep learning enabled bioimage analyses
Cited by: 25
Author(s): Dennis Segebarth, Matthias Griebel, Nikolai Stein, Cora R. von Collenberg, Corinna Martin, Dominik Fiedler, Lucas B. Comeras, Anupam Sah, Victoria Schoeffler, Teresa M. Lüffe, Alexander Dürr, Rohini Gupta, Manju Sasi, Christina Lillesaar, Maren D. Lange, Ramon Tasan, Nicolas Singewald, Hans‐Christian Pape, Christoph M. Flath, Robert Blum
Software Mentions: 4
Published: almost 6 years ago

10.1038/s42003-021-02166-2

Spatially visualized single-cell pathology of highly multiplexed protein profiles in health and disease
Cited by: 5
Author(s): Mayar Allam, Thomas Hu, Shuangyi Cai, Krishnan Laxminarayanan, Robert B. Hughley, Ahmet F. Coşkun
Software Mentions: 4
Published: over 5 years ago

10.1093/molbev/msaa172

Gene Loss Predictably Drives Evolutionary Adaptation
Cited by: 49
Author(s): Jana Helsen, Karin Voordeckers, Laura Vanderwaeren, Toon Santermans, Maria Tsontaki, Kevin J. Verstrepen, Rob Jelier
Software Mentions: 4
Published: about 6 years ago

10.1016/j.cell.2013.03.012

Exit from Pluripotency Is Gated by Intracellular Redistribution of the bHLH Transcription Factor Tfe3
Cited by: 288
Author(s): Joerg Betschinger, Jennifer Nichols, Sabine Dietmann, Philip Corrin, Patrick J. Paddison, Austin Smith
Software Mentions: 4
Published: over 13 years ago

10.1172/jci.insight.146883

Highly multiplexed 2-dimensional imaging mass cytometry analysis of HBV-infected liver
Cited by: 14
Author(s): Daniel Traum, Yue J. Wang, Kathleen B. Schwarz, Jonathan Schug, David Wong, Harry L.A. Janssen, Norah A. Terrault, Mandana Khalili, Abdus S. Wahed, Karen F. Murray, Phillip Rosenthal, Simon C. Ling, Norberto Rodriguez‐Baez, Richard K. Sterling, Daryl Lau, Timothy M. Block, Michael D. Feldman, Elizabeth E. Furth, William M. Lee, David E. Kleiner, Anna S. Lok, Klaus H. Kaestner, Kyong Mi Chang
Software Mentions: 4
Published: over 5 years ago

10.1093/gigascience/giaa041

Community standards for open cell migration data
Cited by: 11
Author(s): Alejandra González-Beltrán, Paola Masuzzo, Christophe Ampè, Gert-Jan Bakker, Sébastien Besson, Robert H. Eibl, Peter Friedl, Matthias Gunzer, Mark Kittisopikul, Sylvia E. Le Dévédec, Simone Leo, Josh Moore, Yael Paran, Jaime Prilusky, Philippe Rocca-Serra, Philippe Roudot, Marc Schuster, Gwendolien Sergeant, Staffan Strömblad, Jason R. Swedlow, Merijn van Erp, Marleen Van Troys, Assaf Zaritsky, Susanna Assunta Sansone, Lennart Martens
Software Mentions: 4
Published: over 6 years ago

10.1186/s40170-021-00257-6

High-resolution spatiotemporal pHe and pO2 imaging in head and neck and oesophageal carcinoma cells
Cited by: 2
Author(s): Alexandra Blancke Soares, Robert J. Meier, Gregor Liebsch, Sabina Schwenk‐Zieger, Martin E. Kirmaier, Sebastian Theurich, Magdalena Widmann, Martin Canis, Olivier Gires, Frank Haubner
Software Mentions: 4
Published: over 5 years ago

10.1093/gigascience/giab018

Rapid development of cloud-native intelligent data pipelines for scientific data streams using the HASTE Toolkit
Cited by: 2
Author(s): Ben Blamey, Salman Toor, Martin Dahlö, Håkan Wieslander, Philip J. Harrison, Ida‐Maria Sintorn, Alan Sabirsh, Carolina Wählby, Ola Spjuth, Andreas Hellander
Software Mentions: 4
Published: over 5 years ago

10.1016/j.jbc.2021.101049

Fused in sarcoma regulates DNA replication timing and kinetics
Cited by: 5
Author(s): Weiyan Jia, Sang Hwa Kim, Mark Scalf, Peter Tonzi, Robert Millikin, William Guns, Lu Liu, Adam S. Mastrocola, Lloyd M. Smith, Tony T. Huang, Randal S. Tibbetts
Software Mentions: 4
Published: about 5 years ago

10.1007/s00018-017-2695-6

Downregulation of p53 drives autophagy during human trophoblast differentiation
Cited by: 23
Author(s): Martin Gauster, Sabine Maninger, Monika Siwetz, Alexander Deutsch, Amin El‐Heliebi, Dagmar Kolb-Lenz, Ursula Hiden, Gernot Desoyé, Florian Herse, Andreas Prokesch
Software Mentions: 4
Published: almost 9 years ago

10.1534/genetics.117.300077

RNA Interference (RNAi) Screening inDrosophila
Cited by: 86
Author(s): Florian Heigwer, Fillip Port, Michael Boutros
Software Mentions: 4
Published: over 8 years ago

10.1101/2021.06.06.446826

Evolution of enhanced innate immune evasion by the SARS-CoV-2 B.1.1.7 UK variant
Cited by: 84
Author(s): Lucy Thorne, Mehdi Bouhaddou, Ann-Kathrin Reuschl, Lorena Zuliani-Alvarez, Benjamin J. Polacco, Adrian Pelin, Jyoti Batra, Matt Whelan, Manisha R. Ummadi, Ajda Roic, Jane Turner, Kirsten Obernier, Hannes Braberg, Margaret Soucheray, Alicia Richards, Kuei‐Ho Chen, Bhavya Harjai, Danish Memon, Myra Hosmillo, Joseph Hiatt, Aminu S. Jahun, Ian Goodfellow, Mahdad Noursadeghi, Jacqueline M. Fabius, Kevan M. Shokat, Natalia Jura, Kliment A. Verba, Pedro Beltrão, Danielle L. Swaney, Adolfo Garcı́a-Sastre, Clare Jolly, Greg J. Towers, Nevan J. Krogan
Software Mentions: 4
Published: over 5 years ago

10.1186/1746-1596-8-34

CognitionMaster: an object-based image analysis framework
Cited by: 41
Author(s): Stephan Wienert, Daniel Heim, Manato Kotani, Bjoern Lindequist, Albrecht Stenzinger, Masaru Ishii, Peter Hufnagl, Michael Beil, Manfred Dietel, Carsten Denkert, Frederick Klauschen
Software Mentions: 4
Published: over 13 years ago

10.1111/mmi.14417

BactMAP: An R package for integrating, analyzing and visualizing bacterial microscopy data
Cited by: 23
Author(s): Renske van Raaphorst, Morten Kjos, Jan‐Willem Veening
Software Mentions: 4
Published: almost 7 years ago

10.12688/wellcomeopenres.15232.2

Genome-wide CRISPR screening identifies new regulators of glycoprotein secretion
Cited by: 2
Author(s): Stephanie Popa, Julien Villeneuve, Sarah E. Stewart, Esther Perez Garcia, Anna Petrunkina Harrison, Kévin Moreau
Software Mentions: 4
Published: over 6 years ago

10.1016/j.molcel.2021.04.028

Unrestrained poly-ADP-ribosylation provides insights into chromatin regulation and human disease
Cited by: 46
Author(s): Evgeniia Prokhorova, Thomas Agnew, Anne R. Wondisford, Michael Tellier, Nicole Kaminski, Danique Beijer, James Holder, Joséphine Groslambert, Marcin Suskiewicz, Kang Zhu, Julia M Reber, Sarah C. Krassnig, Luca Palazzo, Shona Murphy, Michael L. Nielsen, Aswin Mangerich, Dragana Ahel, Jonathan Baets, Roderick J. O’Sullivan, Ivan Ahel
Software Mentions: 4
Published: over 5 years ago

10.15252/msb.20178064

Large‐scale image‐based profiling of single‐cell phenotypes in arrayed CRISPR‐Cas9 gene perturbation screens
Cited by: 55
Author(s): Reinoud E. A. de Groot, Joel Lüthi, Helen Lindsay, René Holtackers, Lucas Pelkmans
Software Mentions: 3
Published: almost 9 years ago

10.7554/eLife.52370

Cortical RORβ is required for layer 4 transcriptional identity and barrel integrity
Cited by: 14
Author(s): Erin Clark, Michael Rutlin, Lucia Capano, Samuel Aviles, Jordan R Saadon, Praveen Taneja, Qiyu Zhang, James B. Bullis, Timothy Lauer, Emma Myers, Anton Schulmann, Douglas Forrest, Sacha B. Nelson
Software Mentions: 3
Published: about 6 years ago

10.7554/eLife.30054

Inducible and reversible phenotypes in a novel mouse model of Friedreich’s Ataxia
Cited by: 59
Author(s): Vijayendran Chandran, Kun Gao, Vivek Swarup, Revital Versano, Hongmei Dong, Maria C. Jordan, Daniel H. Geschwind
Software Mentions: 3
Published: almost 9 years ago

10.15252/msb.20209798

A quantitative analysis of the interplay of environment, neighborhood, and cell state in 3D spheroids
Cited by: 15
Author(s): Vito Riccardo Tomaso Zanotelli, Matthias Leutenegger, Xiao-Kang Lun, Fanny Georgi, Natalie de Souza, Bernd Bodenmiller
Software Mentions: 3
Published: almost 6 years ago

10.15252/msb.202010026

CODEX, a neural network approach to explore signaling dynamics landscapes
Cited by: 10
Author(s): Marc‐Antoine Jacques, Maciej Dobrzyński, Paolo Armando Gagliardi, Raphael Sznitman, Olivier Pertz
Software Mentions: 3
Published: over 5 years ago

10.15252/msb.202010135

The circadian oscillator analysed at the single‐transcript level
Cited by: 6
Author(s): Nicholas E. Phillips, Alice Hugues, Jake Yeung, Eric Durandau, Damien Nicolas, Félix Naef
Software Mentions: 3
Published: over 5 years ago

10.7554/eLife.69795

A zebrafish screen reveals Renin-angiotensin system inhibitors as neuroprotective via mitochondrial restoration in dopamine neurons
Cited by: 18
Author(s): Ghahyun J. Kim, Han Mo, Harrison Liu, Zhihao Wu, Steven Chen, Jiashun Zheng, Xiang Zhao, Daryl Nucum, James Shortland, Longping Peng, Mannuel Elepano, Benjamin C. Tang, Steven H. Olson, Nick A. Paras, Hao Li, Adam R. Renslo, Michelle R. Arkin, Bo Huang, Bingwei Lu, Marina Sirota, Su Guo
Software Mentions: 3
Published: about 5 years ago

10.7554/eLife.70560

Processing of the ribosomal ubiquitin-like fusion protein FUBI-eS30/FAU is required for 40S maturation and depends on USP36
Cited by: 5
Author(s): Jasmin van den Heuvel, Caroline Ashiono, Ludovic Gillet, Kerstin Dörner, Emanuel Wyler, Ivo Zemp, Ulrike Kutay
Software Mentions: 3
Published: about 5 years ago

10.15252/msb.20178007

Antisense transcription‐dependent chromatin signature modulates sense transcript dynamics
Cited by: 38
Author(s): Tom Brown, Françoise S. Howe, Struan C. Murray, M Wouters, P. Lorenz, Emily A. Seward, Scott Rata, Andrew Angel, Jane Mellor
Software Mentions: 3
Published: over 8 years ago

10.7554/eLife.22693

The vacuolar-ATPase complex and assembly factors, TMEM199 and CCDC115, control HIF1α prolyl hydroxylation by regulating cellular iron levels
Cited by: 77
Author(s): A. J. Miles, Stephen P. Burr, GL Grice, James A. Nathan
Software Mentions: 3
Published: over 9 years ago

10.7554/eLife.43668

Mutationally-activated PI3’-kinase-α promotes de-differentiation of lung tumors initiated by the BRAFV600E oncoprotein kinase
Cited by: 17
Author(s): J. Edward Van Veen, Michael T. Scherzer, Julia Boshuizen, Mollee Chu, Annie Liu, Allison Landman, Shon Green, Christy L. Trejo, Martin McMahon
Software Mentions: 3
Published: about 7 years ago

10.7554/eLife.07759

Progerin reduces LAP2α-telomere association in Hutchinson-Gilford progeria
Cited by: 89
Author(s): Alexandre Chojnowski, P.P. Ong, Esther Wong, John Lim, Rafidah Mutalif, Raju Navasankari, Bamaprasad Dutta, Henry Yang, Yi Y. Liow, Siu Kwan Sze, Thomas Boudier, Alan Colman, Brian Burke, Colin L. Stewart, Oliver Dreesen
Software Mentions: 3
Published: about 11 years ago

10.7554/eLife.47293

tec-1 kinase negatively regulates regenerative neurogenesis in planarians
Cited by: 9
Author(s): Alexander Karge, Nicolle A. Bonar, Scott T. Wood, Christian P. Petersen
Software Mentions: 3
Published: over 6 years ago

10.15252/msb.202010188

SARS‐CoV‐2 infection remodels the host protein thermal stability landscape
Cited by: 15
Author(s): Joel Selkrig, Megan L. Stanifer, André Mateus, Karin Mitosch, Iñigo Barrio-Hernandez, Mandy Rettel, Heeyoung Kim, Carlos G.P. Voogdt, Philipp Walch, Carmon Kee, Nils Kurzawa, Frank Stein, Clement M Potel, Anna Jarząb, Bernhard Küster, Ralf Bartenschlager, Steeve Boulant, Pedro Beltrão, Athanasios Typas, Mikhail M. Savitski
Software Mentions: 3
Published: over 5 years ago

10.7554/eLife.39234

Transition between fermentation and respiration determines history-dependent behavior in fluctuating carbon sources
Cited by: 38
Author(s): Bram Cerulus, Abbas Jariani, Gemma Perez-Samper, Lieselotte Vermeersch, Julian Pietsch, Matthew M. Crane, Aaron M. New, Brigida Gallone, Miguel Roncoroni, Maria C. Dzialo, Sander K. Govers, Jhana O. Hendrickx, Eva Galle, Maarten Coomans, Pieter Berden, Sara Verbandt, Peter S. Swain, Kevin J. Verstrepen
Software Mentions: 3
Published: almost 8 years ago

10.1016/j.celrep.2019.03.108

PAD2-Mediated Citrullination Contributes to Efficient Oligodendrocyte Differentiation and Myelination
Cited by: 53
Author(s): Ana Mendanha Falcão, Mandy Meijer, Antonella Scaglione, Puneet Rinwa, Eneritz Agirre, Jialiang Liang, Sara C. Buch-Larsen, Abeer Heskol, Rebecca Frawley, Michael Klingener, Manuel Varas-Godoy, Alexandre A.S.F. Raposo, Patrik Ernfors, Diogo S. Castro, Michael L. Nielsen, Patrizia Casaccia, Gonçalo Castelo‐Branco
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.ppat.1009838

Probing the spatiotemporal patterns of HBV multiplication reveals novel features of its subcellular processes
Cited by: 10
Author(s): Lei Yue, Chang Li, Mingzhu Xu, Min Wu, Jiahui Ding, Jiangxia Liu, Xiaonan Zhang, Zhenghong Yuan
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.ppat.1002957

De novo GTP Biosynthesis Is Critical for Virulence of the Fungal Pathogen Cryptococcus neoformans
Cited by: 53
Author(s): Carl A. Morrow, Eugene Valkov, Anna Stamp, Eve W. L. Chow, I. Russel Lee, Ania Wronski, Simon J. Williams, Jennifer Hill, Julianne T. Djordjevic, Ulrike Kappler, Boštjan Kobe, James S. Fraser
Software Mentions: 3
Published: almost 14 years ago

10.15252/embj.201489282

Aberrant methylation of t<scp>RNA</scp>s links cellular stress to neuro‐developmental disorders
Cited by: 426
Author(s): Sandra Blanco, Sabine Dietmann, Joana V. Flores, Shobbir Hussain, Claudia Kutter, Peter Humphreys, Margus Lukk, Patrick Lombard, Lucas Treps, Martyna Popis, Stefanie Kellner, Sabine M. Hölter, Lillian Garrett, Wolfgang Wurst, Lore Becker, Thomas Klopstock, Helmut Fuchs, Valérie Gailus‐Durner, Martin Hrabé de Angelis, Ragnhildur Thóra Káradóttir, Mark Helm, Jernej Ule, Joseph G. Gleeson, Duncan T. Odom, Michaela Frye
Software Mentions: 3
Published: about 12 years ago

10.1534/g3.116.033654

Accurate Classification of Protein Subcellular Localization from High-Throughput Microscopy Images Using Deep Learning
Cited by: 112
Author(s): Tanel Pärnamaa, Leopold Parts
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.ppat.1007601

RNAi-based small molecule repositioning reveals clinically approved urea-based kinase inhibitors as broadly active antivirals
Cited by: 25
Author(s): Markus Lesch, Madlen Luckner, Michaël Meyer, Friderike Weege, Isabella Gravenstein, Martin Raftery, Christian Sieben, Laura Martin-Sancho, Aki Imai-Matsushima, Robert-William Welke, Rebecca Frise, William Barclay, Günther Schönrich, Andreas Herrmann, Thomas Meyer, Alexander Karlas
Software Mentions: 3
Published: over 7 years ago

10.1111/imm.13341

Modified recombinant human IgG1‐Fc is superior to natural intravenous immunoglobulin at inhibiting immune‐mediated demyelination
Cited by: 1
Author(s): Christine Baksmeier, Patricia A. Blundell, Julia Steckel, Verena Schultz, Quan Gu, Ana da Silva Filipe, Alain Kohl, Chris Linnington, Dongli Lu, Anne Dell, Stuart M. Haslam, Jiabin Wang, Dan Czajkowsky, Norbert Goebels, Richard J. Pleass
Software Mentions: 3
Published: over 5 years ago

10.1038/s41419-021-03408-1

SCA-1 micro-heterogeneity in the fate decision of dystrophic fibro/adipogenic progenitors
Cited by: 13
Author(s): Giulio Giuliani, Simone Vumbaca, Claudia Fuoco, Cesare Gargioli, Ezio Giorda, Giorgia Massacci, Alessandro Palma, Alessio Reggio, Federica Riccio, Marco Rosina, Maria Vinci, Luisa Castagnoli, Gianni Cesareni
Software Mentions: 3
Published: over 5 years ago

10.1074/mcp.RA120.002102

Changes in the Oligodendrocyte Progenitor Cell Proteome with Ageing
Cited by: 46
Author(s): Alerie Guzman de la Fuente, Rayner M L Queiroz, Tanay Ghosh, Christopher E McMurran, Juan F. Cubillos, Dwight E. Bergles, Denise Fitzgerald, Clare A. Jones, Kathryn S. Lilley, Colin P. Glover, R. J. M. Franklin
Software Mentions: 3
Published: about 6 years ago

10.1016/j.gpb.2020.11.003

Computational Screening of Phase-separating Proteins
Cited by: 27
Author(s): Boyan Shen, Zhaoming Chen, Chunyu Yu, Taoyu Chen, Minglei Shi, Tingting Li
Software Mentions: 3
Published: over 5 years ago

10.1093/gigascience/giaa156

Identifying the effect of vancomycin on health care–associated methicillin-resistant Staphylococcus aureus strains using bacteriological and physiological media
Cited by: 4
Author(s): Abhishek Rajput, Saugat Poudel, Hannah Tsunemoto, Michael J. Meehan, Richard Szubin, Connor A. Olson, Yara Seif, Anne Lamsa, Nicholas Dillon, Alison Vrbanac, Joseph Sugie, Samira Dahesh, Jonathan M. Monk, Pieter C. Dorrestein, Rob Knight, Joe Pogliano, Victor Nizet, Adam M. Feist, Bernhard Ø. Palsson
Software Mentions: 3
Published: almost 6 years ago

10.1083/jcb.201702099

BAIAP3, a C2 domain–containing Munc13 protein, controls the fate of dense-core vesicles in neuroendocrine cells
Cited by: 44
Author(s): Xingmin Zhang, Shan Jiang, Kelly A. Mitok, Lingjun Li, Alan D. Attie, Thomas F.J. Martin
Software Mentions: 3
Published: over 9 years ago

10.1186/s12964-019-0336-4

Autocrine motility factor promotes endometrial cancer progression by targeting GPER-1
Cited by: 22
Author(s): Yiran Li, Yuanhui Jia, Yiding Bian, Huan Tong, Junjie Qu, Kai Wang, Xiaoping Wan
Software Mentions: 3
Published: over 7 years ago

10.3389/fpls.2020.615922

Hazelnut Pollen Phenotyping Using Label-Free Impedance Flow Cytometry
Cited by: 9
Author(s): Lorenzo Ascari, V. Cristofori, Federico Macrì, Roberto Botta, Cristian Silvestri, Tommaso De Gregorio, Eloy Suarez Huerta, Marco Di Berardino, Silvan Kaufmann, Consolata Siniscalco
Software Mentions: 3
Published: almost 6 years ago

10.1083/jcb.202011078

Cysteine cross-linking in native membranes establishes the transmembrane architecture of Ire1
Cited by: 6
Author(s): Kristina Väth, Carsten Mattes, John F. Reinhard, Roberto Covino, Heike Stumpf, Gerhard Hummer, Robert Ernst
Software Mentions: 3
Published: over 5 years ago

10.1007/s00018-020-03682-w

Semaphorin 7A restricts serotonergic innervation and ensures recovery after spinal cord injury
Cited by: 10
Author(s): Kristina Loy, Julie Fourneau, Ning Meng, Carmen K. Denecke, Giuseppe Locatelli, Florence M. Bareyre
Software Mentions: 3
Published: almost 6 years ago

10.26508/lsa.202000660

Metabolic reprogramming of fibro/adipogenic progenitors facilitates muscle regeneration
Cited by: 34
Author(s): Alessio Reggio, Marco Rosina, Natalie Krahmer, Alessandro Palma, Lucia Lisa Petrilli, Giuliano Maiolatesi, Giorgia Massacci, Illari Salvatori, Cristiana Valle, Stefano Testa, Cesare Gargioli, Claudia Fuoco, Luisa Castagnoli, Gianni Cesareni
Software Mentions: 3
Published: over 6 years ago

10.1016/j.jbc.2021.100295

The cytoprotective protein MANF promotes neuronal survival independently from its role as a GRP78 cofactor
Cited by: 27
Author(s): Ave Eesmaa, Li-Ying Yu, Helka Göös, Kristofer Nõges, Vera Kovaleva, Maarit Hellman, Richard Zimmermann, Martin Jung, Perttu Permi, Markku Varjosalo, Päivi Lindholm, Märt Saarma
Software Mentions: 3
Published: almost 6 years ago

10.1080/19490976.2021.1911534

Intestinal microbiota drives cholestasis-induced specific hepatic gene expression patterns
Cited by: 13
Author(s): Oriol Juanola, Mohsin Hassan, Pranav Kumar, Bahtiyar Yılmaz, Irene Keller, Cédric Simillion, Cornelius Engelmann, Frank Tacke, Jean‐François Dufour, Andrea De Gottardi, Sheida Moghadamrad
Software Mentions: 3
Published: almost 6 years ago

10.1073/pnas.1921055117

ASY1 acts as a dosage-dependent antagonist of telomere-led recombination and mediates crossover interference in Arabidopsis
Cited by: 54
Author(s): Christophe Lambing, Pallas Kuo, Andrew J. Tock, Stephanie D. Topp, Ian Henderson
Software Mentions: 3
Published: over 6 years ago

10.1242/dev.199616

Deep learning for bioimage analysis in developmental biology
Cited by: 24
Author(s): Adrien Hallou, Hannah Yevick, Bianca Dumitrascu, Virginie Uhlmann
Software Mentions: 3
Published: about 5 years ago

10.1371/journal.ppat.1009687

The endogenous cellular protease inhibitor SPINT2 controls SARS-CoV-2 viral infection and is associated to disease severity
Cited by: 4
Author(s): Carlos Ramirez Alvarez, Carmon Kee, Ashwini Kumar Sharma, Leonie Thomas, Florian I. Schmidt, Megan L. Stanifer, Steeve Boulant, Carl Herrmann
Software Mentions: 3
Published: over 5 years ago

10.26508/lsa.201900437

Fibro-adipogenic progenitors of dystrophic mice are insensitive to NOTCH regulation of adipogenesis
Cited by: 35
Author(s): Milica Marinković, Claudia Fuoco, Francesca Sacco, Andrea Cerquone Perpetuini, Giulio Giuliani, Elisa Micarelli, Theodora Pavlidou, Lucia Lisa Petrilli, Alessio Reggio, Federica Riccio, Filomena Spada, Simone Vumbaca, Alessandro Zuccotti, Luisa Castagnoli, Matthias Mann, Cesare Gargioli, Gianni Cesareni
Software Mentions: 3
Published: over 7 years ago

10.1038/s42003-021-02517-z

Comprehensive in situ mapping of human cortical transcriptomic cell types
Cited by: 11
Author(s): Christoffer Mattsson Langseth, Daniel Gyllborg, Jeremy A. Miller, Jennie Close, Brian Long, Ed Lein, Markus M. Hilscher, Mats Nilsson
Software Mentions: 3
Published: about 5 years ago

10.1155/2021/9975423

Hyperion Image Analysis Depicts a Preliminary Landscape of Tumor Immune Microenvironment in OSCC with Lymph Node Metastasis
Cited by: 7
Author(s): Shang Xie, Mengjie Zhang, Xiaofeng Shan, Vicky Yau, Jianyun Zhang, Wei Wang, Yongpan Yan, Zhigang Cai
Software Mentions: 3
Published: over 5 years ago

10.1016/j.ccell.2018.11.018

The ERBB-STAT3 Axis Drives Tasmanian Devil Facial Tumor Disease
Cited by: 40
Author(s): Lindsay Kosack, Bettina Wingelhofer, Alexandra Popa, Anna Orlova, Benedikt Agerer, Bojan Vilagos, Peter Marynen, Katja Parapatics, Alexander Lercher, Anna Ringler, Johanna Klughammer, Mark J. Smyth, Kseniya Khamina, Hatoon Baazim, Elvin D. de Araujo, David A. Rosa, Jisung Park, Gary Tin, Siawash Ahmar, Patrick T. Gunning, Christoph Bock, Hannah V. Siddle, Gregory M. Woods, Stefan Kubicek, Elizabeth P. Murchison, Keiryn L. Bennett, Richard Moriggl, Andréas Bergthaler
Software Mentions: 3
Published: almost 8 years ago

10.1101/2021.08.11.455959

Multiplexed detection of SARS-CoV-2 genomic and subgenomic RNA using in situ hybridization
Cited by: 3
Author(s): Kofi Acheampong, Dylan L. Schaff, Benjamin Emert, Jonathan I. Lake, Sam Reffsin, Emily Shea, Courtney E Comar, Leslie A. Litzky, Nigar Khurram, Rebecca L. Linn, Michael D. Feldman, Susan R. Weiss, Kathleen T. Montone, Sara Cherry, Sydney M. Shaffer
Software Mentions: 3
Published: about 5 years ago

10.1128/mBio.01569-16

The Antiviral Mechanism of an Influenza A Virus Nucleoprotein-Specific Single-Domain Antibody Fragment
Cited by: 24
Author(s): Leo Hanke, Kevin E. Knockenhauer, R. Camille Brewer, Eline van Diest, Florian I. Schmidt, Thomas Schwartz, Hidde L. Ploegh
Software Mentions: 3
Published: almost 10 years ago

10.1177/2472555218820805

Evaluation of Machine Learning Classifiers to Predict Compound Mechanism of Action When Transferred across Distinct Cell Lines
Cited by: 12
Author(s): Scott J. Warchal, John C. Dawson, Neil O. Carragher
Software Mentions: 3
Published: over 7 years ago

10.1186/s13014-015-0453-1

The Focinator - a new open-source tool for high-throughput foci evaluation of DNA damage
Cited by: 44
Author(s): Sebastian Oeck, Nathalie M. Malewicz, Sebastian Hurst, Justine Rudner, Verena Jendrossek
Software Mentions: 3
Published: about 11 years ago

10.1177/2472555218818053

Unbiased Phenotype Detection Using Negative Controls
Cited by: 2
Author(s): Antje Janosch, Carolin Kaffka, Marc Bickle
Software Mentions: 3
Published: over 7 years ago

10.1186/1471-2164-15-1162

Simultaneous analysis of large-scale RNAi screens for pathogen entry
Cited by: 37
Author(s): Pauli Rämö, Anna Drewek, Cécile Arrieumerlou, Niko Beerenwinkel, Houchaïma Ben-Tekaya, Bettina Cardel, Alain Casanova, Raquel Conde-Álvarez, Pascale Cossart, Gábor Csúcs, Simone Eicher, Mario Emmenlauer, Urs F. Greber, Wolf‐Dietrich Hardt, Ari Helenius, Christoph Kasper, Andreas M. Kaufmann, Saskia Kreibich, Andreas Kühbacher, Péter Z. Kunszt, Shyan Huey Low, Jason Mercer, Daria Mudrak, Simone Muntwiler, Lucas Pelkmans, Javier Pizarro‐Cerdá, Michael Podvinec, Eva Pujadas, Bernd Rinn, Vincent Rouilly, Fabian Schmich, Juliane Siebourg‐Polster, Berend Snijder, Michael Stebler, Gabriel Studer, Ewa Szczurek, Matthias C. Truttmann, Christian von Mering, Andreas Vonderheit, Artur Yakimovich, Peter Bühlmann, Christoph Dehio
Software Mentions: 3
Published: almost 12 years ago

10.1186/s12902-019-0442-8

CRISPR-Cas9-mediated knockout of SPRY2 in human hepatocytes leads to increased glucose uptake and lipid droplet accumulation
Cited by: 5
Author(s): Naomi L. Cook, Milos Pjanic, Andrew Emmerich, Abhiram Rao, Susanne Hetty, Joshua Knowles, Thomas Quertermous, Casimiro Castillejo-López, Erik Ingelsson
Software Mentions: 3
Published: almost 7 years ago

10.1186/s40478-021-01148-z

TDP-43 proteinopathy alters the ribosome association of multiple mRNAs including the glypican Dally-like protein (Dlp)/GPC6
Cited by: 10
Author(s): Erik M. Lehmkuhl, Suvithanandhini Loganathan, Eric Alsop, Alexander D. Blythe, Tina Kovalik, Nicholas P. Mortimore, Dianne Barrameda, Chuol Kueth, Randall J. Eck, Bhavani Bagevalu Siddegowda, Archi Joardar, Hannah E. Ball, Maria E. Macias, Robert Bowser, Kendall Van Keuren‐Jensen, Daniela C. Zarnescu
Software Mentions: 3
Published: over 5 years ago

10.3389/fonc.2019.01144

Quantitative Spatial Analysis of Metabolic Heterogeneity Across in vivo and in vitro Tumor Models
Cited by: 18
Author(s): Tiffany M. Heaster, Bennett A. Landman, Melissa C. Skala
Software Mentions: 3
Published: almost 7 years ago

10.3389/fonc.2021.620989

Characterization of the Tumor Immune Microenvironment in Lung Squamous Cell Carcinoma Using Imaging Mass Cytometry
Cited by: 17
Author(s): Ran Li, Ying Lin, Yu Wang, Shaoyuan Wang, Yang Yang, Xinlin Mu, Yu‐Sheng Chen, Zhancheng Gao
Software Mentions: 3
Published: over 5 years ago

10.3389/fonc.2021.636057

A Multi-Omics Analysis of Metastatic Melanoma Identifies a Germinal Center-Like Tumor Microenvironment in HLA-DR-Positive Tumor Areas
Cited by: 6
Author(s): Laura Gadeyne, Yannick Van Herck, Giorgia Milli, Zeynep Kalender Atak, Maddalena M. Bolognesi, Jasper Wouters, Lukas Marcelis, Angeliki Minia, Vaia Pliaka, Jan Roznac, Leonidas G. Alexopoulos, Giorgio Cattoretti, Oliver Bechter, Joost van den Oord, Frederik De Smet, Asier Antoranz, Francesca Maria Bosisio
Software Mentions: 3
Published: over 5 years ago

10.3389/fmicb.2020.00548

Genomic and Phenotypic Analyses of Acinetobacter baumannii Isolates From Three Tertiary Care Hospitals in Thailand
Cited by: 24
Author(s): Jessica Loraine, Eva Heinz, Rosesathorn Soontarach, Grace A. Blackwell, Richard A. Stabler, Supayang Piyawan Voravuthikunchai, Potjanee Srimanote, Pattarachai Kiratisin, Nicholas R. Thomson, Peter W. Taylor
Software Mentions: 3
Published: over 6 years ago

10.1186/1472-6750-7-66

High content image analysis for human H4 neuroglioma cells exposed to CuO nanoparticles
Cited by: 44
Author(s): Fuhai Li, Xiaobo Zhou, Jinmin Zhu, Jinwen Ma, Xudong Huang, Stephen T.C. Wong
Software Mentions: 3
Published: almost 19 years ago

10.1371/journal.pone.0215337

FluoroCellTrack: An algorithm for automated analysis of high-throughput droplet microfluidic data
Cited by: 22
Author(s): Manibarathi Vaithiyanathan, Nora Safa, Adam T. Melvin
Software Mentions: 3
Published: over 7 years ago

10.18632/oncotarget.12298

Case-specific potentiation of glioblastoma drugs by pterostilbene
Cited by: 16
Author(s): Linnéa Schmidt, Sathishkumar Baskaran, Patrik Johansson, Narendra Padhan, Damian J. Matuszewski, Lydia C. Green, Ludmila Elfineh, Shimei Wee, Maria Häggblad, Ulf Märtens, Bengt Westermark, Karin Forsberg-Nilsson, Lene Uhrbom, Lena Claesson‐Welsh, Michael Andäng, Ida‐Maria Sintorn, Bo Lundgren, Ingrid Lönnstedt, Cecilia Krona, Sven Nelander
Software Mentions: 3
Published: about 10 years ago

10.3389/fimmu.2019.00094

Sialyllactose and Galactooligosaccharides Promote Epithelial Barrier Functioning and Distinctly Modulate Microbiota Composition and Short Chain Fatty Acid Production In Vitro
Cited by: 70
Author(s): Olaf Perdijk, Peter van Baarlen, Marcela M. Fernandez-Gutierrez, Frank Schuren, Sylvia Brugman, H.F.J. Savelkoul, Michiel Kleerebezem, R. J. Joost van Neerven
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pbio.2005086

Cell-nonautonomous local and systemic responses to cell arrest enable long-bone catch-up growth in developing mice
Cited by: 35
Author(s): Alberto Roselló-Díez, Linda Madisen, Sébastien Bastide, Hongkui Zeng, Alexandra L. Joyner
Software Mentions: 3
Published: over 8 years ago

10.1007/s00497-020-00398-6

Quantitative methods in microscopy to assess pollen viability in different plant taxa
Cited by: 9
Author(s): Lorenzo Ascari, Cristina Novara, Virginia Dusio, Ludovica Oddi, Consolata Siniscalco
Software Mentions: 3
Published: almost 6 years ago

10.15252/emmm.202012574

Cooperation of LIM domain‐binding 2 (LDB2) with EGR in the pathogenesis of schizophrenia
Cited by: 2
Author(s): Tetsuo Ohnishi, Yuji Kiyama, Fumiko Arima-Yoshida, Mitsutaka Kadota, Tomoe Ichikawa, Kazuyuki Yamada, Akïharu Watanabe, Hideki Ohba, Kaori Tanaka, Akihiro Nakaya, Yasue Horiuchi, Yoshimi Iwayama, Manabu Toyoshima, Itone Ogawa, Chie Shimamoto-Mitsuyama, Motoko Maekawa, Shabeesh Balan, Makoto Arai, Mitsuhiro Miyashita, Kazuya Toriumi, Yayoi Nozaki, Rumi Kurokawa, Kazuhiro Suzuki, Akane Yoshikawa, Tomoko Toyota, Toshihiko Hosoya, Hiroyuki Okuno, Haruhiko Bito, Masanari Itokawa, Shigehiro Kuraku, Toshiya Manabe, Takeo Yoshikawa
Software Mentions: 3
Published: over 5 years ago

10.1371/journal.pone.0237972

Interactive machine learning for fast and robust cell profiling
Cited by: 1
Author(s): Lisa Laux, Marie F.A. Cutiongco, Nikolaj Gadegaard, Bjørn Sand Jensen
Software Mentions: 3
Published: about 6 years ago

10.1371/journal.pbio.3000580

12-h clock regulation of genetic information flow by XBP1s
Cited by: 34
Author(s): Yinghong Pan, Heather Ballance, Huan Meng, Naomi Gonzalez, Sam-Moon Kim, Leymaan Abdurehman, Brian York, Xi Chen, Yisrael Schnytzer, Oren Levy, Clifford C. Dacso, Colleen A. McClung, Bert W. O’Malley, Silvia Liu, Bokai Zhu
Software Mentions: 3
Published: over 6 years ago

10.3390/cancers13184600

Role of Artificial Intelligence in the Early Diagnosis of Oral Cancer. A Scoping Review
Cited by: 37
Author(s): María García-Pola, Eduardo Pons-Fuster, Carlota Suárez-Fernández, Juan M. Seoane-Romero, Amparo Romero-Méndez, Pı́a López-Jornet
Software Mentions: 3
Published: about 5 years ago

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