Ecosyste.ms: Papers

10.1186/s12859-016-1241-0

systemPipeR: NGS workflow and report generation environment
Cited by: 148
Author(s): Tyler W. H. Backman, Thomas Girke
Software Mentions: 19
Published: almost 8 years ago

10.1016/j.molcel.2021.05.023

Global analysis of protein-RNA interactions in SARS-CoV-2-infected cells reveals key regulators of infection
Cited by: 87
Author(s): Wael Kamel, Marko Noerenberg, Berati Cerikan, Honglin Chen, Aino I Järvelin, Mohamed Kammoun, Young Seok Lee, Shuai Ni, Manuel García-Moreno, Anna Andrejeva, Michael J. Deery, Natasha Johnson, Christopher J Neufeldt, Mirko Cortese, Michael Knight, Kathryn S. Lilley, Javier Martı̂nez, Ilan Davis, Ralf Bartenschlager, Shabaz Mohammed, Alfredo Castelló
Software Mentions: 18
Published: over 3 years ago

10.1371/journal.pone.0189789

An integrative framework to reevaluate the Neotropical catfish genus Guyanancistrus (Siluriformes: Loricariidae) with particular emphasis on the Guyanancistrus brevispinis complex
Cited by: 11
Author(s): Sonia Fisch-Muller, Jan H. Mol, Raphaël Covain
Software Mentions: 16
Published: over 6 years ago

10.1155/2016/7972351

Advancements in RNASeqGUI towards a Reproducible Analysis of RNA-Seq Experiments
Cited by: 11
Author(s): Francesco Russo, Dario Righelli, Claudia Angelini
Software Mentions: 11
Published: over 8 years ago

10.1186/s12859-021-04211-7

RNAdetector: a free user-friendly stand-alone and cloud-based system for RNA-Seq data analysis
Cited by: 6
Author(s): Alessandro La Ferlita, Salvatore Alaimo, Sebastiano Di Bella, Emanuele Martorana, Georgios I. Laliotis, Francesco Bertoni, Luciano Cascione, Philip N. Tsichlis, Alfredo Ferro, Roberta Bosotti, Alfredo Pulvirenti
Software Mentions: 10
Published: over 3 years ago

10.1186/1471-2164-16-S6-S3

RAP: RNA-Seq Analysis Pipeline, a new cloud-based NGS web application
Cited by: 54
Author(s): Mattia D’Antonio, Paolo D’Onorio De Meo, Matteo Pallocca, Ernesto Picardi, Anna Maria D’Erchia, Raffaele Calogero, Tiziana Castrignanò, Graziano Pesole
Software Mentions: 9
Published: over 9 years ago

10.1186/1471-2105-10-364

multiplierz: an extensible API based desktop environment for proteomics data analysis
Cited by: 63
Author(s): Jignesh R. Parikh, Manor Askenazi, Scott B. Ficarro, Tanya Cashorali, James T. Webber, Nathaniel C. Blank, Yi Zhang, Jarrod A. Marto
Software Mentions: 6
Published: almost 15 years ago

10.1186/s13015-014-0027-z

BicPAM: Pattern-based biclustering for biomedical data analysis
Cited by: 57
Author(s): Rui Henriques, Sara C. Madeira
Software Mentions: 5
Published: almost 10 years ago

10.1371/journal.pntd.0003284

Improvements on Restricted Insecticide Application Protocol for Control of Human and Animal African Trypanosomiasis in Eastern Uganda
Cited by: 30
Author(s): Dennis Muhanguzi, Kim Picozzi, Jan Hatendorf, Michael Thrusfield, Susan C. Welburn, John David Kabasa, Charles Waiswa
Software Mentions: 5
Published: almost 10 years ago

10.1186/s13059-019-1880-3

PIRCh-seq: functional classification of non-coding RNAs associated with distinct histone modifications
Cited by: 17
Author(s): Jingwen Fang, Qing Ma, Constance R. Chu, Beibei Huang, Lingjie Li, Pengfei Cai, Pedro J. Batista, Karen Tolentino, Jin Xu, Rui Li, Pengcheng Du, Kun Qu, Howard Y. Chang
Software Mentions: 4
Published: almost 5 years ago

10.1186/1472-6807-9-28

Improving consensus contact prediction via server correlation reduction
Cited by: 27
Author(s): Xin Gao, Dongbo Bu, Jinbo Xu, Ming Li
Software Mentions: 4
Published: over 15 years ago

10.1002/ece3.7760

Balancing selection, genetic drift, and human‐mediated introgression interplay to shape MHC (functional) diversity in Mediterranean brown trout
Cited by: 6
Author(s): Lorenzo Talarico, Silvio Marta, Anna Rita Rossi, Simone Di Crescenzo, Gerardo Petrosino, Marco Martinoli, Lorenzo Tancioni
Software Mentions: 4
Published: about 3 years ago

10.1038/s41598-020-75270-8

Raw transcriptomics data to gene specific SSRs: a validated free bioinformatics workflow for biologists
Cited by: 8
Author(s): D. N. U. Naranpanawa, C. H. W. M. R. B. Chandrasekara, P. C. G. Bandaranayake, Asitha U. Bandaranayake
Software Mentions: 4
Published: almost 4 years ago

10.1186/s12859-020-03565-8

ELIXIR-IT HPC@CINECA: high performance computing resources for the bioinformatics community
Cited by: 22
Author(s): Tiziana Castrignanò, Silvia Gioiosa, Tiziano Flati, Mirko Cestari, Ernesto Picardi, Matteo Chiara, Maddalena Fratelli, Stefano Amente, Marco Cirilli, M. A. Tangaro, Giovanni Chillemi, Graziano Pesole, Federico Zambelli
Software Mentions: 4
Published: about 4 years ago

10.1186/1471-2105-8-148

primetv: a viewer for reconciled trees
Cited by: 25
Author(s): Bengt Sennblad, Eva Schreil, Ann-Charlotte Berglund Sonnhammer, Jens Lagergren, Lars Arvestad
Software Mentions: 4
Published: over 17 years ago

10.1093/gigascience/giy125

A benchmark study of k-mer counting methods for high-throughput sequencing
Cited by: 43
Author(s): Swati Manekar, S. R. Sathe
Software Mentions: 4
Published: almost 6 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: over 8 years ago

10.1186/s12864-018-4528-x

A systematic approach to RNA-associated motif discovery
Cited by: 14
Author(s): Tian Gao, Jiang Shu, Juan Cui
Software Mentions: 3
Published: over 6 years ago

10.1002/ece3.7228

Nesting, brood rearing, and summer habitat selection by translocated greater sage‐grouse in North Dakota, USA
Cited by: 4
Author(s): Kade D. Lazenby, Peter S. Coates, Shawn T. O’Neil, Michel T. Kohl, David K. Dahlgren
Software Mentions: 3
Published: over 3 years ago

10.1186/1743-0003-5-25

Review on solving the inverse problem in EEG source analysis
Cited by: 848
Author(s): Reuben Grech, Tracey A. Cassar, Joseph Muscat, Tracey A. Camilleri, Simon G. Fabri, Michalis Zervakis, Petros Xanthopoulos, Vangelis Sakkalis, Bart Vanrumste
Software Mentions: 3
Published: almost 16 years ago

10.1111/jcmm.13238

State of the art technologies to explore long non-coding RNAs in cancer
Cited by: 57
Author(s): Saeede Salehi, Mohammad Taheri, Negar Azarpira, Abdolhossein Zare, Abbas Behzad-Behbahani
Software Mentions: 3
Published: over 7 years ago

10.1186/1471-2105-12-98

CDAO-Store: Ontology-driven Data Integration for Phylogenetic Analysis
Cited by: 20
Author(s): Brandon Chisham, Ben Wright, Hieu Giang Le, Tran Cao Son, Enrico Pontelli
Software Mentions: 3
Published: over 13 years ago

10.1186/s13059-021-02377-0

Using high-throughput multiple optical phenotyping to decipher the genetic architecture of maize drought tolerance
Cited by: 40
Author(s): Xi Wu, Hui Feng, Di Wu, Shijuan Yan, Pei Zhang, Wenbin Wang, Jun Zhang, Junli Ye, Guoxin Dai, Fan Yu, Weikun Li, Baoxing Song, Zedong Geng, Wanli Yang, Guoxin Chen, Feng Qin, William Terzaghi, Michelle C. Stitzer, Li Lin, Lizhong Xiong, Jianbing Yan, Edward S. Buckler, Wanneng Yang, Mingqiu Dai
Software Mentions: 3
Published: about 3 years ago

10.1007/s00236-015-0254-x

Compositional schedulability analysis of real-time actor-based systems
Cited by: 4
Author(s): Mohammad Mahdi Jaghoori, Frank de Boer, Delphine Longuet, Tom Chothia, Marjan Sirjani
Software Mentions: 2
Published: over 8 years ago

10.1186/1471-2105-16-S9-S1

Preface: BITS2014, the annual meeting of the Italian Society of Bioinformatics
Cited by: 0
Author(s): Angelo Facchiano, Claudia Angelini, Roberta Bosotti, Alessandro Guffanti, Anna Marabotti, Roberto Marangoni, Stefano Pascarella, Paolo Romano, Andreas Zanzoni, Manuela Helmer-Citterich
Software Mentions: 2
Published: over 9 years ago

10.1186/1471-2105-9-18

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons
Cited by: 985
Author(s): David Ellinghaus, Stefan Kurtz, Ute Willhoeft
Software Mentions: 2
Published: over 16 years ago

10.1186/1471-2105-7-398

PhyloPat: phylogenetic pattern analysis of eukaryotic genes
Cited by: 16
Author(s): Tim Hulsen, Jacob de Vlieg, Peter M.A. Groenen
Software Mentions: 2
Published: about 18 years ago

10.1186/1471-2105-12-S12-S1

Discovery of error-tolerant biclusters from noisy gene expression data
Cited by: 20
Author(s): Rohit Gupta, Navneet Rao, Vipin Kumar
Software Mentions: 2
Published: almost 13 years ago

10.1186/s12862-020-01642-3

Phylogenetic and spatial distribution of evolutionary diversification, isolation, and threat in turtles and crocodilians (non-avian archosauromorphs)
Cited by: 32
Author(s): Timothy J. Colston, Pallavi Kulkarni, Walter Jetz, R. Alexander Pyron
Software Mentions: 2
Published: about 4 years ago

10.1186/1472-6947-7-3

A UMLS-based spell checker for natural language processing in vaccine safety
Cited by: 26
Author(s): Herman D. Tolentino, Michael D. Matters, Wikke Walop, Barbara Law, Wesley Tong, Fang Liu, Paul Fontelo, Katrin Kohl, Daniel C. Payne
Software Mentions: 2
Published: over 17 years ago

10.1186/1472-6947-12-6

Recommended practices for computerized clinical decision support and knowledge management in community settings: a qualitative study
Cited by: 81
Author(s): Joan S. Ash, Dean F. Sittig, Kenneth P. Guappone, Richard H. Dykstra, Joshua E. Richardson, Adam Wright, James Carpenter, Carmit K. McMullen, Michael D. Shapiro, Arwen Bunce, Blackford Middleton
Software Mentions: 2
Published: over 12 years ago

10.1186/s13017-016-0078-1

Wells criteria for DVT is a reliable clinical tool to assess the risk of deep venous thrombosis in trauma patients
Cited by: 59
Author(s): Shrey Modi, Ryan Deisler, Karen Gozel, Patty Reicks, Eric D. Irwin, Melissa E. Brunsvold, Kaysie Banton, Greg J. Beilman
Software Mentions: 2
Published: over 8 years ago

10.3897/zookeys.1001.58447

Recognition and revision of the Phelister blairi group (Histeridae, Histerinae, Exosternini)
Cited by: 2
Author(s): Michael S. Caterino, Alexey K. Tishechkin
Software Mentions: 2
Published: almost 4 years ago

10.1371/currents.RRN1213

Hal: an Automated Pipeline for Phylogenetic Analyses of Genomic Data
Cited by: 51
Author(s): Barbara Robbertse, Ryan J. Yoder, Alexander Boyd, John Reeves, Joseph W. Spatafora
Software Mentions: 2
Published: over 13 years ago

10.1371/journal.pone.0044439

Harmony: EEG/MEG Linear Inverse Source Reconstruction in the Anatomical Basis of Spherical Harmonics
Cited by: 20
Author(s): Yury Petrov
Software Mentions: 2
Published: almost 12 years ago

10.1371/journal.pone.0096946

Genome-Wide Transcriptome Analysis Reveals that Cadmium Stress Signaling Controls the Expression of Genes in Drought Stress Signal Pathways in Rice
Cited by: 93
Author(s): Youko Oono, Takayuki Yazawa, Yoshihiro Kawahara, Hajime Kanamori, Fuminori Kobayashi, Harumi Sasaki, Satomi Mori, Jianzhong Wu, Hirokazu Handa, Takeshi Itoh, Takashi Matsumoto
Software Mentions: 2
Published: over 10 years ago

10.1371/journal.pone.0201596

Cost-minimizing team hires with participation constraint
Cited by: 0
Author(s): Hui Sun, Jianbin Huang, Ke Liu, Mengjie Wan, Yu Zhou, Chen Cao, Xiaolin Jia, Liang He
Software Mentions: 2
Published: about 6 years ago

10.12688/f1000research.13522.2

Purine-rich low complexity regions are potential RNA binding hubs in the human genome
Cited by: 6
Author(s): Ivan Antonov, Yulia A. Medvedeva
Software Mentions: 2
Published: over 5 years ago

10.3389/fnins.2020.601402

Prefrontal Asymmetry BCI Neurofeedback Datasets
Cited by: 6
Author(s): Fred Charles, Caio De Castro Martins, Marc Cavazza
Software Mentions: 2
Published: almost 4 years ago

10.3389/fpls.2016.01914

A Meta-Analysis Based Method for Prioritizing Candidate Genes Involved in a Pre-specific Function
Cited by: 12
Author(s): Jingjing Zhai, Yunjia Tang, Hao Yuan, Longteng Wang, Haoli Shang, Chuang Ma
Software Mentions: 2
Published: almost 8 years ago

10.3389/frobt.2021.577770

Exploring Co-creative Drawing Workflows
Cited by: 4
Author(s): Chipp Jansen, Elizabeth Sklar
Software Mentions: 2
Published: over 3 years ago

10.1590/S1415-47572009005000096

Clonal diversity and conservation genetics of the medicinal plant Carapichea ipecacuanha (Rubiaceae)
Cited by: 23
Author(s): Luiz Orlando de Oliveira, Bruna Afonso Venturini, Ana Aparecida Bandini Rossi, Saulo Santos Hastenreiter
Software Mentions: 2
Published: almost 15 years ago

10.1186/1939-8433-6-4

Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data
Cited by: 1,492
Author(s): Yoshihiro Kawahara, M. de la Bastide, John Hamilton, Hajime Kanamori, W. Richard McCombie, Shuai Ouyang, David C. Schwartz, Tsuyoshi Tanaka, Jianzhong Wu, Shiguo Zhou, Kevin L. Childs, Rebecca M. Davidson, Haining Lin, Lina M. Quesada‐Ocampo, Brieanne Vaillancourt, Hiroaki Sakai, Sung Shin Lee, Jungsok Kim, Hisataka Numa, Takeshi Itoh, C. Robin Buell, Takashi Matsumoto
Software Mentions: 2
Published: over 11 years ago

10.1038/s41598-019-52162-0

Structure Based Multitargeted Molecular Docking Analysis of Selected Furanocoumarins against Breast Cancer
Cited by: 78
Author(s): Reetuparna Acharya, Shinu Chacko, Pritha Bose, Antonio Lapenna, Shakti Prasad Pattanayak
Software Mentions: 2
Published: almost 5 years ago

10.3390/s141224046

A Survey of Middleware for Sensor and Network Virtualization
Cited by: 25
Author(s): Zubair Khalid, Norsheila Fisal, Mohd. Rozaini
Software Mentions: 2
Published: almost 10 years ago

10.3390/s18051556

A Personalized QoS Prediction Approach for CPS Service Recommendation Based on Reputation and Location-Aware Collaborative Filtering
Cited by: 48
Author(s): Li Kuang, Yu Long, Lan Huang, Yin Wang, Pengju Ma, Chuanbin Li, Yujia Zhu
Software Mentions: 2
Published: over 6 years ago

10.1007/s11625-017-0462-0

Applying the robust adaptation planning (RAP) framework to Ghana’s agricultural climate change adaptation regime
Cited by: 8
Author(s): Abrar Chaudhury, Philip K. Thornton, Ariella Helfgott, Chase Sova
Software Mentions: 2
Published: about 7 years ago

10.1186/s13046-017-0497-1

Che-1 sustains hypoxic response of colorectal cancer cells by affecting Hif-1α stabilization
Cited by: 24
Author(s): Tiziana Bruno, Mariacristina Valerio, Luca Casadei, Francesca De Nicola, Frauke Goeman, Matteo Pallocca, Valeria Catena, Simona Iezzi, Cristina Socolovschi, Agata Desantis, Cesare Manetti, Giovanni Blandino, Aristide Floridi, Maurizio Fanciulli
Software Mentions: 2
Published: over 7 years ago

10.1186/s13045-018-0673-6

Long non-coding RNAs in hematological malignancies: translating basic techniques into diagnostic and therapeutic strategies
Cited by: 30
Author(s): Nonthaphat Kent Wong, Chien‐Ling Huang, Rabiul Islam, Shea Ping Yip
Software Mentions: 2
Published: almost 6 years ago

10.3390/ijerph110605951

A Qualitative Process Evaluation of Classroom-Based Cognitive Behaviour Therapy to Reduce Adolescent Depression
Cited by: 18
Author(s): John Taylor, Rhiannon Phillips, Ellen Piel Cook, Lucy Georgiou, Paul Stallard, Kapil Sayal
Software Mentions: 2
Published: over 10 years ago

10.3390/ijerph110807678

Assessing Program Efficiency: A Time and Motion Study of the Mental Health Emergency Care — Rural Access Program in NSW Australia
Cited by: 19
Author(s): Emily Saurman, David Lyle, Sue Kirby, Russell Roberts
Software Mentions: 2
Published: about 10 years ago

10.7554/eLife.40037

The RNA interactome of human telomerase RNA reveals a coding-independent role for a histone mRNA in telomere homeostasis
Cited by: 12
Author(s): Roland Iványi-Nagy, Syed Moiz Ahmed, Sabrina Peter, Priya Dharshana Ramani, P.P. Ong, Oliver Dreesen, Peter Dröge
Software Mentions: 2
Published: almost 6 years ago

10.7554/eLife.23244

Prosurvival long noncoding RNA PINCR regulates a subset of p53 targets in human colorectal cancer cells by binding to Matrin 3
Cited by: 67
Author(s): Ritu Chaudhary, Berkley E. Gryder, Wendy S. Woods, Subramanian Mahadevan, Michael R. Jones, Xiao Ling Li, Lisa M. Miller Jenkins, Svetlana A. Shabalina, Min Mo, Mary Dasso, Yuan Yang, Lalage M. Wakefield, Yuelin J. Zhu, Susan M Frier, Branden S. Moriarity, Kannanganattu V. Prasanth, Pablo Pérez-Piñera, Ashish Lal
Software Mentions: 2
Published: over 7 years ago

10.3390/ijms21113828

CSI NGS Portal: An Online Platform for Automated NGS Data Analysis and Sharing
Cited by: 16
Author(s): Ömer An, Kian-Lee Tan, Ying Li, Jia Li, Chan-Shuo Wu, Bin Zhang, Leilei Chen, Henry Yang
Software Mentions: 2
Published: over 4 years ago

10.18632/oncotarget.7978

Multitargeting activity of miR-24 inhibits long-term melatonin anticancer effects
Cited by: 49
Author(s): Federica Mori, Maria Ferraiuolo, Raffaela Santoro, Andrea Sacconi, Frauke Goeman, Matteo Pallocca, Claudio Pulito, Etleva Korita, Maurizio Fanciulli, Paola Muti, Giovanni Blandino, Sabrina Strano
Software Mentions: 2
Published: over 8 years ago

10.18632/oncotarget.12060

Deptor transcriptionally regulates endoplasmic reticulum homeostasis in multiple myeloma cells
Cited by: 19
Author(s): Valeria Catena, Tiziana Bruno, Francesca De Nicola, Frauke Goeman, Matteo Pallocca, Simona Iezzi, Cristina Socolovschi, Giovanni Cigliana, Aristide Floridi, Giovanni Blandino, Maurizio Fanciulli
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0172269

DNApod: DNA polymorphism annotation database from next-generation sequence read archives
Cited by: 2
Author(s): Takako Mochizuki, Yasuhiro Tanizawa, Takatomo Fujisawa, Toshio Ohta, Naruo Nikoh, Tokurou Shimizu, Atsushi Toyoda, Asao Fujiyama, Nori Kurata, Hideki Nagasaki, Eli Kaminuma, Yasukazu Nakamura
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0170195

A Global User-Driven Model for Tile Prefetching in Web Geographical Information Systems
Cited by: 8
Author(s): Shaoming Pan, Yanwen Chong, Hang Zhang, Xicheng Tan
Software Mentions: 1
Published: over 7 years ago

10.1002/advs.202001918

Multifunctional Nanostructure RAP‐RL Rescues Alzheimer's Cognitive Deficits through Remodeling the Neurovascular Unit
Cited by: 4
Author(s): Qian Zhang, Qing Song, Xiao Gu, Mengna Zheng, Antian Wang, Gan Jiang, Meng Huang, Huan Chen, Yu Qiu, Bin Bo, Shanbao Tong, Rong Shao, Binyin Li, Gang Wang, Hao Wang, Yongbo Hu, Hongzhuan Chen, Xiaoling Gao
Software Mentions: 1
Published: almost 4 years ago

10.3390/ijerph110505541

A Qualitative Investigation of Adolescents’ Perceived Mechanisms of Change from a Universal School-Based Depression Prevention Program
Cited by: 16
Author(s): Ian M. Shochet, Roslyn Montague, Coral L. Smith, Mark R. Dadds
Software Mentions: 1
Published: over 10 years ago

10.1186/s13578-015-0050-x

Unveiling the hidden function of long non-coding RNA by identifying its major partner-protein
Cited by: 79
Author(s): Yanmin Yang, Liwei Wen, Hongliang Zhu
Software Mentions: 1
Published: almost 9 years ago

10.3390/cells10071786

GSI Treatment Preserves Protein Synthesis in C2C12 Myotubes
Cited by: 0
Author(s): Joshua R. Huot, Brian Thompson, Charlotte McMullen, Joseph Marino, Susan T. Arthur
Software Mentions: 1
Published: about 3 years ago

10.1186/s13034-015-0066-3

Parents of youth who self-injure: a review of the literature and implications for mental health professionals
Cited by: 62
Author(s): Alexis E. Arbuthnott, Stephen P. Lewis
Software Mentions: 1
Published: almost 9 years ago

10.1101/sqb.2019.84.039222

Mechanistic Dissection of RNA-Binding Proteins in Regulated Gene Expression at Chromatin Levels
Cited by: 4
Author(s): Jiayu Chen, Do Hwan Lim, Xiang‐Dong Fu
Software Mentions: 1
Published: over 5 years ago

10.1155/2012/402341

Localizing True Brain Interactions from EEG and MEG Data with Subspace Methods and Modified Beamformers
Cited by: 14
Author(s): Forooz Shahbazi Avarvand, Arne Ewald, Guido Nolte
Software Mentions: 1
Published: over 12 years ago

10.1007/s10994-013-5346-7

Using random forests to diagnose aviation turbulence
Cited by: 79
Author(s): John K. Williams
Software Mentions: 1
Published: over 11 years ago

10.3390/biom10081160

Single and Combined Methods to Specifically or Bulk-Purify RNA–Protein Complexes
Cited by: 10
Author(s): Roosje Van Ende, Sam Balzarini, Koen Geuten
Software Mentions: 1
Published: about 4 years ago

10.3390/e21030324

Efficient Algorithms for Coded Multicasting in Heterogeneous Caching Networks
Cited by: 5
Author(s): Giuseppe Vettigli, Mingyue Ji, Karthikeyan Shanmugam, Jaime Llorca, Antonia M. Tulino, Giuseppe Caire
Software Mentions: 1
Published: over 5 years ago

10.1007/s00267-017-0870-z

Transcending Landscapes: Working Across Scales and Levels in Pastoralist Rangeland Governance
Cited by: 18
Author(s): Lance W. Robinson, Enoch Ontiri, Tsegaye Alemu, Stephen S. Moiko
Software Mentions: 1
Published: over 7 years ago

10.1186/s13023-019-1139-9

RD-RAP: beyond rare disease patient registries, devising a comprehensive data and analytic framework
Cited by: 20
Author(s): M. Bellgard, Tom Snelling, James McGree
Software Mentions: 1
Published: about 5 years ago

10.3389/fgene.2021.668313

Epigenetic Regulation of the Vascular Endothelium by Angiogenic LncRNAs
Cited by: 3
Author(s): Noeline Subramaniam, Ranju Nair, Philip A. Marsden
Software Mentions: 1
Published: about 3 years ago

10.3389/fgene.2020.00186

Target of Rapamycin Regulates Genome Methylation Reprogramming to Control Plant Growth in Arabidopsis
Cited by: 19
Author(s): Tingting Zhu, Linxuan Li, Li Feng, Huijuan Mo, Maozhi Ren
Software Mentions: 1
Published: over 4 years ago

10.3389/fmicb.2019.00501

Functional Characterization of Target of Rapamycin Signaling in Verticillium dahliae
Cited by: 17
Author(s): Linxuan Li, Tingting Zhu, Yun Song, Xiumei Luo, Li Feng, Fei Zhuo, Fuguang Li, Maozhi Ren
Software Mentions: 1
Published: over 5 years ago

10.3389/fmolb.2017.00045

Probing Long Non-coding RNA-Protein Interactions
Cited by: 27
Author(s): Jasmine Barra, Eleonora Leucci
Software Mentions: 1
Published: about 7 years ago

10.3390/s19224944

Power Efficient Random Access for Massive NB-IoT Connectivity
Cited by: 13
Author(s): Mamta Agiwal, Mukesh Kumar Maheshwari, Hu Jin
Software Mentions: 1
Published: almost 5 years ago

10.3389/fphys.2019.01218

Rapid Atrial Pacing Promotes Atrial Fibrillation Substrate in Unanesthetized Instrumented Rats
Cited by: 14
Author(s): Wesam Mulla, Barak Hajaj, Sigal Elyagon, Michal Mor, Roni Gillis, Michael Murninkas, Hadar Klapper-Goldstein, Inbar Plaschkes, Vered Chalifa‐Caspi, Sharon Etzion, Yoram Etzion
Software Mentions: 1
Published: almost 5 years ago

10.1186/s40064-016-2791-3

A two-hop based adaptive routing protocol for real-time wireless sensor networks
Cited by: 5
Author(s): Sandhya Rachamalla, Anitha Sheela Kancherla
Software Mentions: 1
Published: about 8 years ago

10.3389/fpls.2017.00402

LTRtype, an Efficient Tool to Characterize Structurally Complex LTR Retrotransposons and Nested Insertions on Genomes
Cited by: 8
Author(s): Fan-Chun Zeng, Yanjie Zhao, Que-Jie Zhang, Li‐Zhi Gao
Software Mentions: 1
Published: over 7 years ago

10.3389/fpsyt.2013.00025

Genealogy of instruments for prodrome evaluation of psychosis
Cited by: 28
Author(s): Jean-Gabriel Daneault, Émmanuel Stip
Software Mentions: 1
Published: over 11 years ago

10.1007/s10488-018-0909-3

Rapid Assessment Procedure Informed Clinical Ethnography (RAPICE) in Pragmatic Clinical Trials of Mental Health Services Implementation: Methods and Applied Case Study
Cited by: 74
Author(s): Lawrence A. Palinkas, Douglas Zatzick
Software Mentions: 1
Published: almost 6 years ago

10.3389/fvets.2021.616865

Controlling Tsetse Flies and Ticks Using Insecticide Treatment of Cattle in Tororo District Uganda: Cost Benefit Analysis
Cited by: 7
Author(s): Walter Okello, Ewan T. MacLeod, Dennis Muhanguzi, Charles Waiswa, Susan C. Welburn
Software Mentions: 1
Published: over 3 years ago

10.3390/ijerph120504758

Where to Go from Here? An Exploratory Meta-Analysis of the Most Promising Approaches to Depression Prevention Programs for Children and Adolescents
Cited by: 48
Author(s): Sarah Hetrick, Georgina Cox, Sally Merry
Software Mentions: 1
Published: over 9 years ago

10.1186/s12911-015-0156-4

Multiple perspectives on clinical decision support: a qualitative study of fifteen clinical and vendor organizations
Cited by: 19
Author(s): Joan S. Ash, Dean F. Sittig, Carmit K. McMullen, Adam Wright, Arwen Bunce, Vishnu Mohan, Deborah J. Cohen, Blackford Middleton
Software Mentions: 1
Published: over 9 years ago

10.1186/s12913-015-0839-7

No longer ‘flying blind’: how access has changed emergency mental health care in rural and remote emergency departments, a qualitative study
Cited by: 32
Author(s): Emily Saurman, Sue Kirby, David Lyle
Software Mentions: 1
Published: over 9 years ago

10.1186/1471-2164-8-286

Quantitative analysis of mutation and selection pressures on base composition skews in bacterial chromosomes
Cited by: 8
Author(s): Chen Chi, Carton W. Chen
Software Mentions: 1
Published: over 17 years ago

10.1186/1471-2105-11-S3-S7

Detection of gene orthology from gene co-expression and protein interaction networks
Cited by: 18
Author(s): Fadi Towfic, Susan VanderPIas, Casey A OIiver, OIiver Couture, Christopher K TuggIe, M Heather West GreenIee, Vasant Honavar
Software Mentions: 1
Published: over 14 years ago

10.1186/s13012-020-0972-5

Adapting rapid assessment procedures for implementation research using a team-based approach to analysis: a case example of patient quality and safety interventions in the ICU
Cited by: 30
Author(s): Laura M. Holdsworth, Nadia Safaeinili, Marcy Winget, Karl Lorenz, Mary E. Lough, Steve Asch, Elizabeth Malcolm
Software Mentions: 1
Published: over 4 years ago

10.1001/jamanetworkopen.2020.28477

Assessment of Posttraumatic Stress Disorder and Educational Achievement in Sweden
Cited by: 14
Author(s): Alba Vilaplana-Pérez, Anna Sidorchuk, Ana Pérez-Vigil, Gustaf Brander, Kayoko Isoumura, Eva Hesselmark, Laura Sevilla-Cermeño, Unnur Valdimarsdóttir, Huan Song, Andreas Jangmo, Ralf Kuja‐Halkola, Brian M. D’Onofrio, Henrik Larsson, Gemma García‐Soriano, David Mataix‐Cols, Lorena Fernández de la Cruz
Software Mentions: 1
Published: almost 4 years ago

10.1002/acm2.12031

Maximizing the cost benefit of physics residency interview
Cited by: 1
Author(s): Justus Adamson, Sonja Dieterich, Yi Rong
Software Mentions: 1
Published: over 7 years ago

10.1186/1471-2105-10-S6-S3

Databases of homologous gene families for comparative genomics
Cited by: 128
Author(s): Simon Penel, Anne-Muriel Arigon, Jean-François Dufayard, Anne-Sophie Sertier, Vincent Daubin, Laurent Duret, Manolo Gouy, Guy Perrière
Software Mentions: 1
Published: over 15 years ago

10.1172/JCI93910

Circadian clock component REV-ERBα controls homeostatic regulation of pulmonary inflammation
Cited by: 139
Author(s): Marie Pariollaud, Julie Gibbs, Thomas Hopwood, Sheila Brown, Nicola Begley, Ryan Vonslow, Toryn Poolman, Baoqiang Guo, Ben Saer, D. Heulyn Jones, James P. Tellam, Stefano Bresciani, Nicholas C. O. Tomkinson, Justyna Wojno-Picon, Anthony W. J. Cooper, Dion A. Daniels, Ryan P. Trump, Daniel Grant, William J. Zuercher, Timothy M. Willson, Andrew S. MacDonald, Brian Bolognese, Patricia L. Podolin, Yolanda Sánchez, A. S. I. Loudon, David Ray
Software Mentions: 1
Published: over 6 years ago

10.1186/1939-8433-5-3

Nomenclature report on rice WRKY's - Conflict regarding gene names and its solution
Cited by: 38
Author(s): Qi Shen, Diqiu Yu, Jong Seong Jeon, Pietro Piffanelli, Pamela Abbruscato, Ze Jian Guo, Yuanji Zhang, Takeshi Itoh, Sung S. Lee, C. Robin Buell, Yasuo Nagato, Susan R. McCouch, Masahiro Yano, Guo‐Liang Wang, Kshirod K. Jena, Lizhong Xiong, Blake C. Meyers, Pankaj Jaiswal, Yukiko Yamazaki
Software Mentions: 1
Published: over 12 years ago

10.1186/1939-8433-6-14

WikiPathways for plants: a community pathway curation portal and a case study in rice and arabidopsis seed development networks
Cited by: 15
Author(s): Mamatha Hanumappa, Justin Preece, Justin Elser, Denise Nemeth, Gina Bono, Kenny Wu, Pankaj Jaiswal
Software Mentions: 1
Published: over 11 years ago

10.3390/ma14123200

Reusing Jet Grouting Waste as Filler for Road Asphalt Mixtures of Base Layers
Cited by: 13
Author(s): Francesca Russo, Rosa Veropalumbo, Salvatore Antonio Biancardo, Cristina Oreto, Fabio Scherillo, Nunzio Viscione
Software Mentions: 1
Published: over 3 years ago

10.1017/mdh.2017.77

‘From Defensive Paranoia to …Openness to Outside Scrutiny’: Prison Medical Officers in England and Wales, 1979–86
Cited by: 3
Author(s): Nicholas Duvall
Software Mentions: 1
Published: almost 7 years ago

10.3390/ma14164668

Effects of Isothermal Temperature and Soaking Time on Water Quenched Microstructure of Nickel-Based Superalloy GH3536 Semi-Solid Billets
Cited by: 1
Author(s): Guanfei Xiao, Jufu Jiang, Ying Wang, Yingze Liu, Ying Zhang, Yinfeng Tian
Software Mentions: 1
Published: about 3 years ago

10.5811/westjem.2016.12.32850

A Survey of Emergency Medicine Residents’ Use of Educational Podcasts
Cited by: 67
Author(s): Jeff Riddell, Anand Swaminathan, Monica Lee, Abdiwahab Mohamed, Rob Rogers, Salim R. Rezaie
Software Mentions: 1
Published: over 7 years ago

10.1186/s13046-019-1084-4

Poly-specific neoantigen-targeted cancer vaccines delay patient derived tumor growth
Cited by: 31
Author(s): Luigi Aurisicchio, Erika Salvatori, Lucia Lione, Silvio Bandini, Matteo Pallocca, Roberta Maggio, Maurizio Fanciulli, Francesca De Nicola, Frauke Goeman, Gennaro Ciliberto, Antonella Conforti, Laura Luberto, Fabio Palombo
Software Mentions: 1
Published: over 5 years ago

10.1186/s12284-018-0254-x

Genome-wide association study and candidate gene analysis of rice cadmium accumulation in grain in a diverse rice collection
Cited by: 67
Author(s): Junliang Zhao, Yang Wu, Shaohong Zhang, Ting Yang, Qin Liu, Jingfang Dong, Hua Fu, Xingxue Mao, Bin Liu
Software Mentions: 1
Published: almost 6 years ago

10.1186/s13071-015-0998-8

Cost analysis of options for management of African Animal Trypanosomiasis using interventions targeted at cattle in Tororo District; south-eastern Uganda
Cited by: 36
Author(s): Dennis Muhanguzi, Walter Okello, John David Kabasa, Charles Waiswa, Susan C. Welburn, Alexandra Shaw
Software Mentions: 1
Published: about 9 years ago