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: bioconductor: SIM

https://packages.ecosyste.ms/registries/bioconductor.org/packages/SIM

Integrated Analysis on two human genomic datasets
1 version
Latest release: 7 months ago
27,894 downloads total

Papers Mentioning SIM 554

10.1016/j.cell.2021.07.017
Whole-body integration of gene expression and single-cell morphology
Cited by: 59
Author(s): Hernando Vergara, Constantin Pape, Kimberly Meechan, Valentyna Zinchenko, Christel Genoud, Adrian Wanner, Kevin Nzumbi Mutemi, Benjamin Titze, Rachel Templin, Paola Bertucci, Oleg Simakov, Wiebke Dürichen, Pedro Machado, Emily L. Savage, Lothar Schermelleh, Yannick Schwab, Rainer W. Friedrich, Anna Kreshuk, Christian Tischer, Detlev Arendt
Software Mentions: 10
Published: over 2 years ago
10.1371/journal.pbio.3000528
Single-cell transcriptomics of the naked mole-rat reveals unexpected features of mammalian immunity
Cited by: 74
Author(s): Hugo G. Hilton, Nimrod D. Rubinstein, Peter Janki, Andrea Ireland, Nicholas Bernstein, Nicole L. Fong, Kevin M. Wright, Megan Smith, David Finkle, Baby Martin-McNulty, Margaret Roy, Denise M. Imai, Vladimir Jojic, Rochelle Buffenstein
Software Mentions: 10
Published: over 4 years ago
10.1186/s12859-016-1438-2
iGC—an integrated analysis package of gene expression and copy number alteration
Cited by: 13
Author(s): Yi-Pin Lai, Liang-Bo Wang, Weian Wang, Liang‐Chuan Lai, Mong‐Hsun Tsai, Tzu-Pin Lu, Eric Y. Chuang
Software Mentions: 6
Published: over 7 years ago
10.1371/journal.pmed.1003789
All-cause and cause-specific mortality during and following incarceration in Brazil: A retrospective cohort study
Cited by: 2
Author(s): Yiran E. Liu, Everton Ferreira Lemos, Crhistinne Cavalheiro Maymone Gonçalves, Roberto Dias de Oliveira, Andréa da Silva Santos, Agne Oliveira do Prado Morais, Mariana Garcia Croda, Maria de Lourdes Delgado Alves, Júlio Croda, Katharine S. Walter, Jason R Andrews
Software Mentions: 6
Published: over 2 years ago
10.3390/ijms19020357
Genotyping by Sequencing Highlights a Polygenic Resistance to Ralstonia pseudosolanacearum in Eggplant (Solanum melongena L.)
Cited by: 28
Author(s): Sylvia Salgon, Morgane Raynal, Sylvain Lebon, Jean Michel Baptiste, M. C. Daunay, Jacques Dintinger, Cyril Jourda
Software Mentions: 6
Published: over 6 years ago
10.1093/g3journal/jkab248
Harnessing multivariate, penalized regression methods for genomic prediction and QTL detection of drought-related traits in grapevine
Cited by: 5
Author(s): Charlotte Brault, Agnès Doligez, Le Cunff, Aude Coupel‐Ledru, Thierry Simonneau, Julien Chiquet, Patrice This, Timothée Flutre
Software Mentions: 6
Published: almost 3 years ago
10.15252/msb.202110272
RNA polymerase II clusters form in line with surface condensation on regulatory chromatin
Cited by: 32
Author(s): Agnieszka Pancholi, Tim Klingberg, Weichun Zhang, Roshan Prizak, Irina Mamontova, Amra Noa, Marcel Sobucki, Andrei Yu Kobitski, G. Ulrich Nienhaus, Vasily Zaburdaev, Lennart Hilbert
Software Mentions: 6
Published: over 2 years ago
10.1038/s41598-021-90335-y
Whole brain functional recordings at cellular resolution in zebrafish larvae with 3D scanning multiphoton microscopy
Cited by: 15
Author(s): Matteo Bruzzone, Enrico Chiarello, Marco Albanesi, Maria Elena Miletto Petrazzini, Aram Megighian, Claudia Lodovichi, Marco Dal Maschio
Software Mentions: 6
Published: almost 3 years ago
10.1371/journal.pgen.1009652
Powerful detection of polygenic selection and evidence of environmental adaptation in US beef cattle
Cited by: 22
Author(s): Troy N. Rowan, Harly J. Durbin, Christopher M. Seabury, Robert D. Schnabel, Jared E. Decker
Software Mentions: 6
Published: almost 3 years ago
10.1038/s41598-019-40697-1
Computational analysis of the evolutionarily conserved Missing In Metastasis/Metastasis Suppressor 1 gene predicts novel interactions, regulatory regions and transcriptional control
Cited by: 3
Author(s): Petar Petrov, Alexey V Sarapulov, Lél Eöry, Cristina Scielzo, Lydia Scarfò, Jacqueline Smith, David W. Burt, Pieta K. Mattila
Software Mentions: 6
Published: about 5 years ago
10.36834/cmej.70106
Dedicated Poster Abstracts
Cited by: 0
Author(s): Heather Hickey
Software Mentions: 5
Published: about 4 years ago
10.1186/s13059-020-02054-8
CB2 improves power of cell detection in droplet-based single-cell RNA sequencing data
Cited by: 14
Author(s): Zijian Ni, Shuyang Chen, Jared Brown, Christina Kendziorski
Software Mentions: 5
Published: almost 4 years ago
10.1038/s41598-019-55357-7
Exploring genetic architecture of grain yield and quality traits in a 16-way indica by japonica rice MAGIC global population
Cited by: 26
Author(s): Hein Zaw, Chitra Raghavan, Arnel E. Pocsedio, B. P. Mallikarjuna Swamy, Mona Liza Jubay, Rakesh Kumar Singh, Justine Bonifacio, Ramil Mauleon, Jose E. Hernandez, Merlyn S. Mendioro, Glenn B. Gregorio, Hei Leung
Software Mentions: 5
Published: over 4 years ago
10.1186/1471-2105-10-203
Integrated analysis of DNA copy number and gene expression microarray data using gene sets
Cited by: 57
Author(s): Renée X. de Menezes, Marten Boetzer, Melle Sieswerda, Gert‐Jan B. van Ommen, Judith M. Boer
Software Mentions: 5
Published: almost 15 years ago
10.1002/acm2.12678
Optimizing efficiency and safety in external beam radiotherapy using automated plan check (APC) tool and six sigma methodology
Cited by: 17
Author(s): Lukui Shi, Karl Bush, Julian Bertini, Yabo Fu, J. K. Lewis, Daniel Pham, Yong Yang, Thomas Niedermayr, Lawrie Skinner, Xing Li, Beth M. Beadle, Annie Hsu, Nataliya Kovalchuk
Software Mentions: 4
Published: almost 5 years ago
10.1186/s13012-016-0428-0
Proceedings of the 3rd Biennial Conference of the Society for Implementation Research Collaboration (SIRC) 2015: advancing efficient methodologies through community partnerships and team science
Cited by: 25
Author(s): Cara C. Lewis, Doyanne Darnell, Suzanne E. U. Kerns, Maria Monroe-DeVita, Sara J. Landes, Aaron R. Lyon, Cameo Stanick, Shannon Dorsey, Jill Locke, Brigid R. Marriott, Ajeng J. Puspitasari, Caitlin N. Dorsey, Karin S. Hendricks, Andria Pierson, Phil Fizur, Katherine Anne Comtois, Lawrence A. Palinkas, Patricia Chamberlain, Gregory A. Aarons, Amy E. Green, Mark G. Ehrhart, Elise M. Trott, Cathleen E. Willging, María E. Fernández, Nicholas H. Woolf, Shuting Liang, Natalia I. Heredia, Michelle C. Kegler, Betsy Risendal, Andrea Dwyer, Vicki Young, Dayna Campbell, Michelle Carvalho, Yvonne Kellar‐Guenther, Laura J. Damschroder, Julie C. Lowery, Sarah S. Ono, Kathleen F. Carlson, Erika Cottrell, Maya O’Neil, Travis L. Lovejoy, Joanna J. Arch, Jill Mitchell, Cara C. Lewis, Brigid R. Marriott, Kelli Scott, Jennifer Schurer Coldiron, Eric J. Bruns, Alyssa N. Hook, Benjamin C. Graham, Katelin Jordan, Rochelle F. Hanson, Angela D. Moreland, Benjamin E. Saunders, Heidi S. Resnick, Shannon Wiltsey Stirman, Cassidy A. Gutner, Jennifer M. Gamarra, Dawne Vogt, Michael K. Suvak, Jennifer Schuster Wachen, Katherine A. Dondanville, Jeffrey S. Yarvis, Jim Mintz, Alan L. Peterson, Elisa V. Borah, Brett T. Litz, Alma Molino, Stacey Young McCaughan, Patricia A. Resick, Nancy Pandhi, Nora Jacobson, Neftali Serrano, Armando del Río Hernández, Elizabeth Zeidler Schreiter, Natalie Wietfeldt, Zaher Karp, Michael D. Pullmann, Barbara A. Lucenko, Bridget Pavelle, Jacqueline A. Uomoto, Andrea Negrete, Molly Cevasco, Robert P. Franks, Christopher T. Bory, Edward J. Miech, Teresa M. Damush, Jason M. Satterfield, Derek D. Satre, Maria Wamsley, Patrick Yuan, Patricia O’Sullivan, Helen Best, Susan Velasquez, Miya L. Barnett, Lauren Brookman‐Frazee, Jennifer Regan, Nicole A. Stadnick, Alison B. Hamilton, Anna S. Lau, Scott C. Roesch, Byron J. Powell, Thomas J. Waltz, Matthew Chinman, Laura J. Damschroder, Jeffrey L. Smith, Monica M. Matthieu, Enola K. Proctor, JoAnn E. Kirchner, Craig S. Rosen, Sarah Cusworth Walker, Asia S. Bishop, Mariko Lockhart, Allison L. Rodriguez, Luisa Manfredi, Andrea Nevedal, Joel Rosenthal, Daniel M. Blonigen, Anne M. Mauricio, Thomas D. Dishion, Jenna Rudo-Stern, Justin D. Smith, Courtney Benjamin Wolk, Colleen Harker, Anne Olsen, Travis Shingledecker, Frances K. Barg, David S. Mandell, Rinad S. Beidas, Marissa C. Hansen, María P. Aranda, Isabel Torres-Vigil, Bryan Hartzler, Bradley Steinfeld, Tory Gildred, Zandrea Harlin, Fredric Shephard, Matthew Ditty, Andrea Doyle, John A. Bickel, Katharine Cristaudo, Dan Fox, Sonia Combs, David H. Lischner, Richard A. Van Dorn, Stephen Tueller, Jesse Hinde, Georgia Karuntzos, Roselyn Peterson, Lucy Berliner, Laura Murray, Yevgeny Botanov, Beverly Kikuta, Tianying Chen, Marivi Navarro-Haro, Anthony P. DuBose, Kathryn E. Korslund, Marsha M. Linehan, Elizabeth A. Karp, Sarah Edmunds, Lisa V. Ibañez, Wendy L. Stone, Jack H. Andrews, Benjamin D. Johnides, Estee M. Hausman, Kristin M. Hawley, Beth Prusaczyk, Alex Ramsey, Ana A. Baumann, Graham A. Colditz, Mimi Choy-Brown, Rosemary D. Meza, Georganna Sedlar, Leah Lucid, Nelson O. O. Zounlome, Candice M. Monson, Norman Shields, Marta Mastlej, Meredith S. H. Landy, Jeanine E. M. Lane, Natalie K. Finn, Elisa M. Torres, Carol A. Malte, Aline Lott, Andrew J. Saxon, Meredith Boyd, Jennifer Pierce, Agathe Lorthios-Guilledroit, Lucie Richard, Johanne Filiatrault, Kevin A. Hallgren, Shirley M. Crotwell, Rosa María López-Pintor Muñoz, Becky K. Gius, Benjamin O. Ladd, Barbara S. McCrady, Elizabeth G. Epstein, John D. Clapp, Danielle E. Ruderman, Melanie Barwick, Raluca Barac, Stanley Zlotkin, Laila Salim, Marnie Davidson, Alicia C. Bunger, Hillary A. Robertson, Christopher Botsko, Brandy N. Smith, Lindsay R. Trent, Melanie S. Harned, André Ivanoff, Antonio R. Garcia, Minseop Kim, Lonnie R. Snowden, John Landsverk, Annika C. Sweetland, Maria José G. Fernandes, Edilson Lima dos Santos, Cristiane S. Duarte, Afrânio Lineu Kritski, Noa Krawczyk, Caitlin Nelligan, Milton L. Wainberg, David H. Sommerfeld, Benjamin H. Chi, Echezona E. Ezeanolue, Rachel Sturke, Lydia Kline, Laura Guay, George K. Siberry, Ian M. Bennett, Rachel Gold, Johnny Mao, Diane Powers, Mindy Vredevoogd, Jürgen Unützer, Jennifer Schroeder, Lane E. Volpe, Julie Steffen, Nathaniel Jungbluth, Kelly Thompson, Eliza Segell, Pearl McGee-Vincent, Naian Liu, Robyn D. Walser, Jennifer J. Runnals, Robert Shaw, Craig S. Rosen, Janet Schmidt, Patrick S. Calhoun, Ruth Varkovitzky, Amy Drahota, Jonathan I. Martinez, Brigitte Brikho, Aubyn C. Stahmer, Anna Williamson, Ronnie M. Rubin, Matthew O. Hurford, Shawna Weaver, Arthur C. Evans, Rebecca E. Stewart, Samantha L. Matlin, Shawna Weaver, Trevor R. Hadley, Donald R. Gerke, Ericka M. Lewis, Jenna McWilliam, Jacquie Brown, Michelle Tucker, Kathleen Conte, Abigail Melvin, Freda F. Liu, Amelia Kotte, Kaitlin A. Hill, Albert C. Mah, Priya Korathu-Larson, Janelle R. Au, Sonia C. Izmirian, Scott S. Keir, Brad J. Nakamura, Charmaine K. Higa-McMillan, Brittany Rhoades Cooper, Angie Funaiole, Eleanor Dizon, Eric J. Hawkins, Hildi Hagedorn, Douglas Berger, Anissa Frank, Carol E. Achtmeyer, Anthony J. Mariano, Kate Wolitzky-Taylor, Richard A. Rawson, Richard K. Ries, Peter Roy‐Byrne, Michelle G. Craske, Dena N. Simmons, Catalina Torrente, Lori Nathanson, Grace Carroll, Kimbree Brown, Karina Ramos, Nicole Thornton, Elizabeth A. Stormshak, Daniel S. Shaw, Melvin N. Wilson, Emmy Tiderington, Bikki Tran Smith, Deborah K. Padgett, Marilyn L. Ray, Abraham Wandersman, Andrea Lamont, Gordon Hannah, Kassandra A. Alia, Lisa Saldana, Holle Schaper, Mark Campbell, Valerie B. Shapiro, B.K. Elizabeth Kim, Jennifer L. Fleming, Paul A. LeBuffe, Bryan J. Weiner, Heather M. Halko
Software Mentions: 4
Published: almost 8 years ago
10.1155/2015/738030
Current Mathematical Models for Analyzing Anti-Malarial Antibody Data with an Eye to Malaria Elimination and Eradication
Cited by: 35
Author(s): Nuno Sepúlveda, Gillian Stresman, Michael T. White, Chris Drakeley
Software Mentions: 4
Published: over 9 years ago
10.1093/gigascience/giaa035
Artifact-free whole-slide imaging with structured illumination microscopy and Bayesian image reconstruction
Cited by: 15
Author(s): Karl A. Johnson, Guy M. Hagen
Software Mentions: 4
Published: about 4 years ago
10.3390/genes10030181
ProtParCon: A Framework for Processing Molecular Data and Identifying Parallel and Convergent Amino Acid Replacements
Cited by: 4
Author(s): Fei Yuan, Hoa Nguyen, Dan Graur
Software Mentions: 4
Published: about 5 years ago
10.1038/s41396-018-0237-3
Opposing effects of final population density and stress on Escherichia coli mutation rate
Cited by: 7
Author(s): Rok Krašovec, Huw Richards, Danna R. Gifford, Roman V. Belavkin, Alastair Channon, Elizabeth Aston, Andrew J. McBain, Christopher G. Knight
Software Mentions: 4
Published: almost 6 years ago
10.1371/journal.pone.0236347
Understanding the spatial dimension of natural language by measuring the spatial semantic similarity of words through a scalable geospatial context window
Cited by: 4
Author(s): Bozhi Wang, Teng Fei, Yuhao Kang, Meng Li, Qingyun Du, Meng Han, Ning Dong
Software Mentions: 4
Published: almost 4 years ago
10.1371/journal.pgen.1008595
Super-resolution imaging of RAD51 and DMC1 in DNA repair foci reveals dynamic distribution patterns in meiotic prophase
Cited by: 22
Author(s): Johan A. Slotman, Maarten W. Paul, Fabrizia Carofiglio, H. Martijn de Gruiter, Tessa Vergroesen, Lieke Koornneef, Wiggert A. van Cappellen, Adriaan B. Houtsmuller, Willy M. Baarends
Software Mentions: 4
Published: almost 4 years ago
10.18632/oncotarget.13025
Integrative analysis of DNA copy number, DNA methylation and gene expression in multiple myeloma reveals alterations related to relapse
Cited by: 10
Author(s): Patryk Krzemiński, Luis A. Corchete, Juan Luis Garcı́a, Lucía López-Corral, Encarnación Fermiñán, Ernesto Garcı́a, Ana A. Martín, Jesús M. Hernández-Rivas, Ramón García‐Sanz, Jesús F. San Miguel, Norma C. Gutiérrez
Software Mentions: 4
Published: over 7 years ago
10.15252/msb.20209653
Single‐cell imaging of genome organization and dynamics
Cited by: 22
Author(s): Liangqi Xie, Zhe Liu
Software Mentions: 4
Published: almost 3 years ago
10.7554/eLife.18312
PDZD7-MYO7A complex identified in enriched stereocilia membranes
Cited by: 37
Author(s): Clive P. Morgan, Jocelyn F. Krey, M’hamed Grati, Bo Zhao, Shannon Fallen, Abhiraami Kannan-Sundhari, Xue Zhong Liu, Dongseok Choi, Ulrich Müller, Peter G. Barr-Gillespie
Software Mentions: 4
Published: almost 8 years ago
10.1186/s12859-015-0681-2
SIMAT: GC-SIM-MS data analysis tool
Cited by: 8
Author(s): Mohammad Ranjbar, Cristina Di Poto, Yue Joseph Wang, Habtom W. Ressom
Software Mentions: 3
Published: almost 9 years ago
10.1007/s10791-012-9187-y
#nowplaying Madonna: a large-scale evaluation on estimating similarities between music artists and between movies from microblogs
Cited by: 20
Author(s): Markus Schedl
Software Mentions: 3
Published: about 12 years ago
10.1186/s40244-014-0012-3
Towards real-time communication between in vivo neurophysiological data sources and simulator-based brain biomimetic models
Cited by: 5
Author(s): Gil Jae Lee, Andréa Matsunaga, Salvador Dura‐Bernal, Wenjie Zhang, William W. Lytton, Joseph T. Francis, J.A.B. Fortes
Software Mentions: 3
Published: over 9 years ago
10.1093/gigascience/giz073
A large interactive visual database of copy number variants discovered in taurine cattle
Cited by: 21
Author(s): Arun Kommadath, Jason R. Grant, Kirill Krivushin, Adrien M. Butty, C.F. Baes, Tara R. Carthy, D.P. Berry, Paul Stothard
Software Mentions: 3
Published: almost 5 years ago
10.3389/fpls.2020.604527
Clubroot Symptoms and Resting Spore Production in a Doubled Haploid Population of Oilseed Rape (Brassica napus) Are Controlled by Four Main QTLs
Cited by: 10
Author(s): Andrea Botero-Ramírez, Anne Laperche, Solenn Guichard, Mélanie Jubault, Antoine Gravot, Stephen E. Strelkov, Maria Manzanares-Dauleux
Software Mentions: 3
Published: over 3 years ago
10.1186/s13014-020-1461-3
Dosimetric benefit of an adaptive treatment by means of plan selection for rectal cancer patients in both short and long course radiation therapy
Cited by: 11
Author(s): Rianne de Jong, Jelle Visser, K. Crama, N. Van Wieringen, J. Wiersma, Elisabeth D. Geijsen, Arjan Bel
Software Mentions: 3
Published: over 4 years ago
10.3389/fpls.2020.01268
Comparing the Cell Dynamics of Tree-Ring Formation Observed in Microcores and as Predicted by the Vaganov–Shashkin Model
Cited by: 23
Author(s): Valentinà Buttò, Vladimir V. Shishov, Ivan Tychkov, Margarita I. Popkova, Mingzhu He, Sergio Rossi, Annie Deslauriers, Hubert Morin
Software Mentions: 3
Published: almost 4 years ago
10.1371/journal.pone.0246333
Spatial distribution of advanced stage diagnosis and mortality of breast cancer: Socioeconomic and health service offer inequalities in Brazil
Cited by: 4
Author(s): Nayara Priscila Dantas de Oliveira, Marianna de Camargo Cancela, Luciana Martins, Dyego Leandro Bezerra de Souza
Software Mentions: 3
Published: over 3 years ago
10.1371/journal.pone.0240090
Factors associated with death in patients with tuberculosis in Brazil: Competing risks analysis
Cited by: 6
Author(s): Paulo Victor de Sousa Viana, Natália Santana Paiva, Daniel Antunes Maciel Villela, Leonardo Soares Bastos, Ana Luiza Bierrenbach, Paulo Cesar Basta
Software Mentions: 3
Published: over 3 years ago
10.1371/journal.pone.0159980
Comparison of Confocal and Super-Resolution Reflectance Imaging of Metal Oxide Nanoparticles
Cited by: 32
Author(s): Emily J. Guggenheim, Abdullah O. Khan, Jeremy Pike, Lynne Chang, Iseult Lynch, Joshua Z. Rappoport
Software Mentions: 3
Published: over 7 years ago
10.1186/s41077-018-0065-6
Proceedings of the Saudi Health Simulation Conference 2018
Cited by: 0
Author(s):
Software Mentions: 3
Published: about 6 years ago
10.3389/fpls.2017.01866
Transcriptomic and Hormonal Analyses Reveal that YUC-Mediated Auxin Biogenesis Is Involved in Shoot Regeneration from Rhizome in Cymbidium
Cited by: 11
Author(s): Yang Liu, Hai-Liang Zhang, He-Rong Guo, Li Xie, Ruizhen Zeng, Xiangqian Zhang, Zhisheng Zhang
Software Mentions: 3
Published: over 6 years ago
10.3389/fdata.2019.00025
Novel Computational Approach to Predict Off-Target Interactions for Small Molecules
Cited by: 50
Author(s): Mohan Rao, Rishi Gupta, Michael J. Liguori, Mufeng Hu, Xin Huang, Srinivasa R. Mantena, Scott W. Mittelstadt, Eric A.G. Blomme, Terry R. Van Vleet
Software Mentions: 3
Published: almost 5 years ago
10.7554/eLife.42144
Muscle-specific stress fibers give rise to sarcomeres in cardiomyocytes
Cited by: 55
Author(s): Aidan M. Fenix, Abigail C. Neininger, Nilay Taneja, Karren Hyde, Mike R Visetsouk, Ryan J. Garde, Baohong Liu, Benjamin R. Nixon, Annabelle E Manalo, Jason R Becker, Scott W. Crawley, David M. Bader, Matthew J. Tyska, Qi Liu, Jennifer H. Gutzman, Dylan T. Burnette
Software Mentions: 3
Published: over 5 years ago
10.7554/eLife.56517
Inherent regulatory asymmetry emanating from network architecture in a prevalent autoregulatory motif
Cited by: 15
Author(s): Zulfikar Ali, Vinuselvi Parisutham, Sandeep Choubey, Robert C. Brewster
Software Mentions: 3
Published: almost 4 years ago
10.1186/s12199-018-0703-6
Cumulative risk effect of household dysfunction for child maltreatment after intensive intervention of the child protection system in Japan: a longitudinal analysis
Cited by: 5
Author(s): Hirotsuna Ohashi, Ichiro Wada, Yui Yamaoka, Ryoko Nakajima-Yamaguchi, Yasukazu Ogai, Nobuaki Morita
Software Mentions: 3
Published: about 6 years ago
10.1371/journal.pcbi.1006871
Determination of effective synaptic conductances using somatic voltage clamp
Cited by: 7
Author(s): Songting Li, Nan Liu, Li Yao, Xiaohui Zhang, Douglas Zhou, David Cai
Software Mentions: 3
Published: about 5 years ago
10.1186/1756-0500-5-252
Genetic mapping and identification of QTL for earliness in the globe artichoke/cultivated cardoon complex
Cited by: 38
Author(s): Ezio Portis, Davide Scaglione, Alberto Acquadro, Giovanni Mauromicale, Rosario Paolo Mauro, Steven J. Knapp, Sergio Lanteri
Software Mentions: 3
Published: almost 12 years ago
10.1002/sim.7628
Targeted maximum likelihood estimation for a binary treatment: A tutorial
Cited by: 70
Author(s): Miguel Ángel Luque-Fernandez, Michael Schomaker, Bernard Rachet, Mireille E. Schnitzer
Software Mentions: 3
Published: about 6 years ago
10.1186/s13104-015-1760-1
Structural insights into the mechanism defining substrate affinity in Arabidopsis thaliana dUTPase: the role of tryptophan 93 in ligand orientation
Cited by: 6
Author(s): Noriko Inoguchi, Kittichai Chaiseeda, Mamoru Yamanishi, Moon Ki Kim, Yunho Jang, M. Bajaj, Catherine P. Chia, Donald F. Becker, Hideaki Moriyama
Software Mentions: 3
Published: over 8 years ago
10.1186/s40478-020-00956-z
Ultrastructural and dynamic studies of the endosomal compartment in Down syndrome
Cited by: 23
Author(s): Alexandra Botté, Jeanne Lainé, Laura Xicota, Xavier Heiligenstein, G. Fontaine, Amal Kasri, Isabelle Rivals, Pollyanna Goh, Orestis Faklaris, Jack-Christophe Cossec, Étienne Morel, Anne-Sophie Rebillat, Dean Nižetić, Graça Raposo, Marie‐Claude Potier
Software Mentions: 3
Published: almost 4 years ago
10.1038/s41598-019-44994-7
Effects of Different Diets on Microbiota in The Small Intestine Mucus and Weight Regulation in Rats
Cited by: 17
Author(s): Yu Meng, Xiaojun Li, Jie Zhang, Chunlian Wang, Fanggen Lu
Software Mentions: 3
Published: almost 5 years ago
10.1371/journal.ppat.1006331
Dual role of the Toxoplasma gondii clathrin adaptor AP1 in the sorting of rhoptry and microneme proteins and in parasite division
Cited by: 37
Author(s): Kannan Venugopal, Elisabeth Werkmeister, Nicolas Barois, Jean‐Michel Saliou, Anaïs Poncet, Ludovic Huot, Fabien Sindikubwabo, Mohamed‐Ali Hakimi, Gordon Langsley, Frank Lafont, Sabrina Marion
Software Mentions: 2
Published: about 7 years ago
10.5935/abc.20150096
Mortality from Cardiovascular Diseases in the Elderly: Comparative Analysis of Two Five-year Periods
Cited by: 9
Author(s): Grasiela Piuvezam, Wilton Rodrigues Medeiros, Andressa Vellasco Brito Costa, Felipe Fonseca Emerenciano, Renata Santos, Danilo Silveira Seabra
Software Mentions: 2
Published: over 9 years ago
10.1371/journal.ppat.1008604
Pressurized DNA state inside herpes capsids—A novel antiviral target
Cited by: 19
Author(s): Alberto Brandariz-Núñez, S. Robinson, Alex Evilevitch
Software Mentions: 2
Published: almost 4 years ago
10.1186/s12919-018-0098-9
Proceedings of the 2nd BEAT-PCD conference and 3rd PCD training school: part 1
Cited by: 12
Author(s): Florian S. Halbeisen, Claire Hogg, Mikkel Christian Alanin, Zuzanna Bukowy-Bieryłło, Francisco Dası́, Julie Duncan, Amanda Friend, Myrofora Goutaki, Claire Jackson, Victoria Keenan, Amanda Harris, Robert A. Hirst, Philipp Latzin, Gemma Marsh, Kim G. Nielsen, Dominic P. Norris, Daniel Pellicer, Ana Reula, Bruna Rubbo, Nisreen Rumman, Amelia Shoemark, Woolf T. Walker, Claudia E. Kuehni, Jane S. Lucas
Software Mentions: 2
Published: about 6 years ago
10.1109/JBHI.2018.2796941
On the Accuracy and Scalability of Probabilistic Data Linkage Over the Brazilian 114 Million Cohort
Cited by: 27
Author(s): Robespierre Pita, Clícia Pinto, Samila Sena, Rosemeire Leovigildo Fiaccone, Leila Denise Alves Ferreira Amorim, Sandra Reis, Maurício L. Barreto, Spiros Denaxas, Marcos Ennes Barreto
Software Mentions: 2
Published: about 6 years ago
10.1016/j.imu.2020.100398
Towards neonatal mortality risk classification: A data-driven approach using neonatal, maternal, and social factors
Cited by: 7
Author(s): Carlos Eduardo Beluzo, Everton Silva, Luciana Correia Alves, Rodrigo Campos Bresan, Natália Martins Arruda, Ricardo Barz Sovat, Tiago Carvalho
Software Mentions: 2
Published: over 4 years ago
10.1145/3366423.3380269
Efficient Algorithms towards Network Intervention
Cited by: 1
Author(s): Hui-Ju Hung, Wang-Chien Lee, De-Nian Yang, Chih-Ya Shen, Zhen Lei, Sy‐Miin Chow
Software Mentions: 2
Published: about 4 years ago
10.1186/s12711-021-00613-6
Assessing the genetic background and genomic relatedness of red cattle populations originating from Northern Europe
Cited by: 12
Author(s): Christin Schmidtmann, Anna Amanda Schönherz, Bernt Guldbrandtsen, Jovana Marjanovic, M.P.L. Calus, Dirk Hinrichs, Georg Thaller
Software Mentions: 2
Published: about 3 years ago
10.1155/2019/9765383
Hierarchical Task-Parameterized Learning from Demonstration for Collaborative Object Movement
Cited by: 4
Author(s): Siyao Hu, Katherine J. Kuchenbecker
Software Mentions: 2
Published: over 4 years ago
10.1186/1471-2105-7-468
SNP-PHAGE – High throughput SNP discovery pipeline
Cited by: 31
Author(s): Lakshmi K. Matukumalli, John J. Grefenstette, David L. Hyten, Ik‐Young Choi, Perry B. Cregan, Curtis P. Van Tassell
Software Mentions: 2
Published: over 17 years ago
10.3390/genes12091303
Yeast as a Tool to Understand the Significance of Human Disease-Associated Gene Variants
Cited by: 10
Author(s): Tiziana Cervelli, Alvaro Galli
Software Mentions: 2
Published: over 2 years ago
10.1186/s13742-015-0090-5
A large and diverse collection of bovine genome sequences from the Canadian Cattle Genome Project
Cited by: 36
Author(s): Paul Stothard, Xiaoping Liao, Adriano S. Arantes, M. De Pauw, Colin J. Coros, Graham Plastow, Mehdi Sargolzaei, John Crowley, J. A. Basarab, F.S. Schenkel, S. S. Moore, Stephen Miller
Software Mentions: 2
Published: over 8 years ago
10.4172/2155-6148.1000218
Human μ Opioid Receptor Models with Evaluation of the Accuracy Using the Crystal Structure of the Murine μ Opioid Receptor
Cited by: 3
Author(s): Jose Manuel Perez‐Aguilar, Jeffery G. Saven, Renyu Liu
Software Mentions: 2
Published: over 12 years ago
10.1074/jbc.M115.699447
DISC1-dependent Regulation of Mitochondrial Dynamics Controls the Morphogenesis of Complex Neuronal Dendrites
Cited by: 87
Author(s): Rosalind Norkett, Souvik Modi, Nicol Birsa, Talia A. Atkin, Davor Ivankovic, Manav Pathania, Svenja V. Trossbach, Carsten Korth, Warren D. Hirst, Josef T. Kittler
Software Mentions: 2
Published: over 8 years ago
10.1534/g3.119.400061
Molecular Dissection of Quantitative Variation in Bermudagrass Hybrids (<i>Cynodon dactylon</i>x<i>transvaalensis</i>): Morphological Traits
Cited by: 4
Author(s): Sameer Khanal, Jeffrey C. Dunne, Brian M. Schwartz, Chang-Soo Kim, Susana R. Milla‐Lewis, Paul L. Raymer, W. W. Hanna, Jeevan Adhikari, Susan Auckland, Lisa K. Rainville, Andrew H. Paterson
Software Mentions: 2
Published: almost 5 years ago
10.1186/1471-2105-16-S6-S4
Computational algorithms to predict Gene Ontology annotations
Cited by: 23
Author(s): Pietro Pinoli, Davide Chicco, Marco Masseroli
Software Mentions: 2
Published: about 9 years ago
10.1534/g3.119.400068
Genetic Dissection of Resistance to the Three Fungal Plant Pathogens <i>Blumeria graminis</i>, <i>Zymoseptoria tritici</i>, and <i>Pyrenophora tritici-repentis</i> Using a Multiparental Winter Wheat Population
Cited by: 21
Author(s): Melanie Stadlmeier, Lise Nistrup Jørgensen, Beatrice Corsi, James Cockram, L. Hartl, Volker Mohler
Software Mentions: 2
Published: about 5 years ago
10.3390/antiox10091413
SVCT2 Overexpression and Ascorbic Acid Uptake Increase Cortical Neuron Differentiation, Which Is Dependent on Vitamin C Recycling between Neurons and Astrocytes
Cited by: 4
Author(s): Katterine Salazar, Francisca Espinoza, Gustavo Cerda-Gallardo, Luciano Ferrada, Rocío Magdalena, Eder Ramírez, Viviana Ulloa, Natalia Saldivia, Ninoschka Troncoso, María José Oviedo, María José Barahona, Fernando Martínez Martínez, Francisco Nualart
Software Mentions: 2
Published: over 2 years ago
10.3389/fsurg.2019.00077
Determining the Effect of External Stressors and Cognitive Distraction on Microsurgical Skills and Performance
Cited by: 9
Author(s): Shane Carr, Bronwyn Reid McDermott, Niall McInerney, Alan Hussey, Dara Byrne, Shirley Potter
Software Mentions: 2
Published: over 4 years ago
10.3389/fnsyn.2020.615059
A Picture Worth a Thousand Molecules—Integrative Technologies for Mapping Subcellular Molecular Organization and Plasticity in Developing Circuits
Cited by: 4
Author(s): Jacqueline A. Minehart, Colenso M. Speer
Software Mentions: 2
Published: over 3 years ago
10.3389/fcell.2021.660349
Coactosin Promotes F-Actin Protrusion in Growth Cones Under Cofilin-Related Signaling Pathway
Cited by: 3
Author(s): Xubin Hou, Motohiro Nozumi, Harukazu Nakamura, Michihiro Igarashi, Sayaka Sugiyama
Software Mentions: 2
Published: almost 3 years ago
10.12688/f1000research.13477.2
Badges for sharing data and code at Biostatistics: an observational study
Cited by: 13
Author(s): Anisa Rowhani-Farid, Adrian Barnett
Software Mentions: 2
Published: about 6 years ago
10.3389/fgene.2015.00167
An interpretive review of selective sweep studies in Bos taurus cattle populations: identification of unique and shared selection signals across breeds
Cited by: 56
Author(s): Beatriz Gutiérrez-Gil, Juan José Arranz, Pamela Wiener
Software Mentions: 2
Published: about 9 years ago
10.1016/j.dib.2021.107370
Hourly simulation results of building energy simulation tools using a reference office building as a case study
Cited by: 6
Author(s): Mara Magni, Fabian Ochs, Samuel de Vries, Alessandro Maccarini, Ferdinand Sigg
Software Mentions: 2
Published: over 2 years ago
10.1186/s13020-020-00369-z
Development of simultaneous interaction prediction approach (SiPA) for the expansion of interaction network of traditional Chinese medicine
Cited by: 1
Author(s): Mengjie Rui, Pang Hui, Wei Ji, Siqi Wang, Xiaoduo Yu, Lilong Wang, Chunlai Feng
Software Mentions: 2
Published: over 3 years ago
10.1242/dmm.044560
Sentinel Interaction Mapping (SIM) – A generic approach for the functional analysis of human disease gene variants using yeast
Cited by: 4
Author(s): Barry P. Young, Kathryn Post, Jesse T. Chao, Fabian Meili, Kurt Haas, Christopher Loewen
Software Mentions: 2
Published: over 4 years ago
10.3389/fimmu.2021.646159
Development of Stable Chimeric IL-15 for Trans-Presentation by the Antigen Presenting Cells
Cited by: 3
Author(s): Manoj Patidar, Naveen Yadav, Sarat K. Dalai
Software Mentions: 2
Published: about 3 years ago
10.1016/j.celrep.2021.109716
Myosin-X and talin modulate integrin activity at filopodia tips
Cited by: 25
Author(s): Mitro Miihkinen, Max L.B. Grönloh, Aleksandra Popović, Helena Vihinen, Eija Jokitalo, Benjamin T. Goult, Johanna Ivaska, Guillaume Jacquemet
Software Mentions: 2
Published: over 2 years ago
10.1007/s00216-020-03084-8
Superresolving the kidney—a practical comparison of fluorescence nanoscopy of the glomerular filtration barrier
Cited by: 7
Author(s): Lucia Cs Wunderlich, Florian Ströhl, Stefan Ströhl, Oliver Vanderpoorten, Luca Mascheroni, Clemens F. Kaminski
Software Mentions: 2
Published: over 3 years ago
10.1007/s00441-018-2793-2
Expression of trans-membrane serine protease 3 (TMPRSS3) in the human organ of Corti
Cited by: 13
Author(s): Wei Liu, Hubert Löwenheim, Peter A. Santi, Rudolf Glueckert, Anneliese Schrott‐Fischer, Helge Rask‐Andersen
Software Mentions: 2
Published: about 6 years ago
10.1371/journal.pone.0045379
BioFET-SIM Web Interface: Implementation and Two Applications
Cited by: 10
Author(s): Martin R. Hediger, Jan H. Jensen, Luca De Vico
Software Mentions: 2
Published: over 11 years ago
10.1371/journal.pone.0126141
Research on Laser Marking Speed Optimization by Using Genetic Algorithm
Cited by: 7
Author(s): Dongyun Wang, Qiwei Yu, Yu Zhang
Software Mentions: 2
Published: about 9 years ago
10.1364/BOE.403592
Method for assessing the spatiotemporal resolution of structured illumination microscopy (SIM)
Cited by: 3
Author(s): Abderrahim Boualam, Christopher J. Rowlands
Software Mentions: 2
Published: over 3 years ago
10.1371/journal.pone.0239527
Effectiveness of four antiretroviral regimens for treating people living with HIV
Cited by: 1
Author(s): Aracele Tenório de Almeida Cavalcanti, Ricardo Arraes de Alencar Ximenes, Ulysses Ramos Montarroyos, Polyana Monteiro d'Albuquerque, Rosário Antunes Fonseca, Demócrito de Barros Miranda-Filho
Software Mentions: 2
Published: over 3 years ago
10.3390/cells7080106
The Unfolded Protein Response Pathway in the Yeast Kluyveromyces lactis. A Comparative View among Yeast Species
Cited by: 22
Author(s): Mariana Hernández-Elvira, Francisco Torres-Quiroz, Abril Escamilla-Ayala, Eunice Domínguez-Martín, Ricardo Escalante, Laura Kawasaki, Laura Ongay‐Larios, Roberto Coria
Software Mentions: 2
Published: almost 6 years ago
10.3389/fpls.2021.675981
GR24, A Synthetic Strigolactone Analog, and Light Affect the Organization of Cortical Microtubules in Arabidopsis Hypocotyl Cells
Cited by: 5
Author(s): Yuliya Krasylenko, George Komis, Sofiia Hlynska, Tereza Vavrdová, Miroslav Ovečka, Tomáš Pospíšil, Jozef Šamaj
Software Mentions: 2
Published: almost 3 years ago
10.1364/BOE.414680
ML-SIM: universal reconstruction of structured illumination microscopy images using transfer learning
Cited by: 40
Author(s): Charles N. Christensen, Edward Ward, Meng Lü, Píetro Lió, Clemens F. Kaminski
Software Mentions: 2
Published: about 3 years ago
10.1016/j.cell.2020.05.051
3D Correlative Cryo-Structured Illumination Fluorescence and Soft X-ray Microscopy Elucidates Reovirus Intracellular Release Pathway
Cited by: 58
Author(s): Ilias Kounatidis, Megan L. Stanifer, Michael A. Phillips, Perrine Paul‐Gilloteaux, Xavier Heiligenstein, Hongchang Wang, Chidinma Okolo, Thomas M. Fish, Matthew C. Spink, D.I. Stuart, Ilan Davis, Steeve Boulant, Jonathan M. Grimes, Ian M. Dobbie, Maria Harkiolaki
Software Mentions: 2
Published: almost 4 years ago
10.1371/journal.pone.0249257
A graph-based cell tracking algorithm with few manually tunable parameters and automated segmentation error correction
Cited by: 11
Author(s): Katharina Löffler, Tim Scherr, Ralf Mikut
Software Mentions: 2
Published: over 2 years ago
10.26508/lsa.201900620
Quantification of cristae architecture reveals time-dependent characteristics of individual mitochondria
Cited by: 22
Author(s): Mayuko Segawa, Dane M. Wolf, Nan W. Hultgren, David S. Williams, Alexander M. van der Bliek, David B. Shackelford, Marc Liesa, Orian S. Shirihai
Software Mentions: 2
Published: almost 4 years ago
10.26508/lsa.201900564
Meiotic sex chromosome cohesion and autosomal synapsis are supported by<i>Esco2</i>
Cited by: 7
Author(s): François McNicoll, Anne Kühnel, Uddipta Biswas, Kai Hempel, Gabriela Whelan, Gregor Eichele, Rolf Jessberger
Software Mentions: 2
Published: over 4 years ago
10.1038/s42003-019-0518-z
Bioorthogonal labeling with tetrazine-dyes for super-resolution microscopy
Cited by: 89
Author(s): Gerti Beliu, Andreas Kurz, Alexander Kuhlemann, Lisa Behringer-Pliess, Mara Meub, Natalia Wolf, Jürgen Seibel, Zhen‐Dan Shi, Martin J. Schnermann, Jonathan B. Grimm, Luke D. Lavis, Sören Doose, Markus Sauer
Software Mentions: 2
Published: almost 5 years ago
10.1016/j.cub.2017.12.044
Nanoscale Dynamism of Actin Enables Secretory Function in Cytolytic Cells
Cited by: 89
Author(s): Alexandre F. Carisey, Emily M. Mace, Mezida B. Saeed, Daniel M. Davis, Jordan S. Orange
Software Mentions: 2
Published: over 6 years ago
10.3390/e23070796
Social Influence Maximization in Hypergraphs
Cited by: 11
Author(s): Alessia Antelmi, Gennaro Cordasco, Carmine Spagnuolo, Przemysław Szufel
Software Mentions: 2
Published: almost 3 years ago
10.1371/journal.pone.0252238
Excess mortality by specific causes of deaths in the city of São Paulo, Brazil, during the COVID-19 pandemic
Cited by: 15
Author(s): Gisele Aparecida Fernandes, Antônio Paulo Nassar, Gulnar Azevedo e Silva, Diego Feriani, Ivan Leonardo Avelino França e Silva, Pedro Caruso, María Paula Curado
Software Mentions: 2
Published: almost 3 years ago
10.1242/bio.019455
Insulator speckles associated with long-distance chromatin contacts
Cited by: 10
Author(s): Melanie K. Buxa, Johan A. Slotman, Martin E. van Royen, Maarten W. Paul, Adriaan B. Houtsmuller, Rainer Renkawitz
Software Mentions: 2
Published: almost 8 years ago
10.3389/fcell.2020.00195
Current and Emerging Approaches for Studying Inter-Organelle Membrane Contact Sites
Cited by: 29
Author(s): Xue Huang, Chen Jiang, Lihua Yu, Aimin Yang
Software Mentions: 2
Published: about 4 years ago
10.1371/journal.pone.0231874
The influence of the age-period-cohort effects on the temporal trend mortality from schistosomiasis in Brazil from 1980 to 2014
Cited by: 8
Author(s): Taynãna César Simões, Roberto Sena, Karina Cardoso Meira
Software Mentions: 2
Published: about 4 years ago
10.1371/journal.pone.0150320
Streptococcus pneumoniae Cell-Wall-Localized Phosphoenolpyruvate Protein Phosphotransferase Can Function as an Adhesin: Identification of Its Host Target Molecules and Evaluation of Its Potential as a Vaccine
Cited by: 14
Author(s): Yaffa Mizrachi Nebenzahl, Karin Blau, Tatyana Kushnir, Marilou Shagan, Maxim Portnoi, Avraham Cohen, Shalhevet Azriel, Itai Malka, Asad Adawi, Daniel Kafka, Shahar Dotan, Gali Guterman, Shany Troib, Tali Fishilevich, Jonathan M. Gershoni, Alex Braiman, Andrea M. Mitchell, Timothy J. Mitchell, Nurith Porat, Inna Goliand, Vered Chalifa‐Caspi, Edwin Swiatlo, Michael Tal, R. John Ellis, Natalie Elia, Ron Dagan
Software Mentions: 2
Published: about 8 years ago
10.1371/journal.pntd.0007352
The most abundant cyst wall proteins of Acanthamoeba castellanii are lectins that bind cellulose and localize to distinct structures in developing and mature cyst walls
Cited by: 17
Author(s): Pamela Magistrado-Coxen, Yousuf Aqeel, Angelo Lopez, John R. Haserick, Breeanna R. Urbanowicz, Catherine E. Costello, John Samuelson
Software Mentions: 2
Published: about 5 years ago
10.1371/journal.pgen.1004088
X Chromosome Control of Meiotic Chromosome Synapsis in Mouse Inter-Subspecific Hybrids
Cited by: 77
Author(s): Tanmoy Bhattacharyya, Radka Reifová, Soňa Gregorová, Petr Šimeček, Václav Gergelits, Martin Mistrík, Iva Martincová, Jaroslav Piálek, Jiřı́ Forejt
Software Mentions: 2
Published: over 10 years ago
10.1371/journal.pgen.1003968
Elevated Mutagenesis Does Not Explain the Increased Frequency of Antibiotic Resistant Mutants in Starved Aging Colonies
Cited by: 30
Author(s): Sophia Katz, Ruth Hershberg
Software Mentions: 2
Published: over 10 years ago
10.1371/journal.pone.0240832
Suggested deafness during hypnosis and simulation of hypnosis compared to a distraction and control condition: A study on subjective experience and cortical brain responses
Cited by: 12
Author(s): Marcel Franz, Barbara Schmidt, Holger Hecht, Ewald Naumann, Wolfgang H. R. Miltner
Software Mentions: 2
Published: over 3 years ago