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: ACME
https://packages.ecosyste.ms/registries/bioconductor.org/packages/ACME
Algorithms for Calculating Microarray Enrichment (ACME)
1 version
Latest release: about 1 year ago
1 dependent package
39,245 downloads total
Papers Mentioning ACME 63
10.1371/journal.pcbi.1000227
Analyzing ChIP-chip Data Using BioconductorCited by: 19
Author(s): Joern Toedling, Wolfgang Huber
Software Mentions: 39
Published: almost 16 years ago
10.1186/1471-2105-11-237
ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip dataCited by: 868
Author(s): Lihua Julie Zhu, Claude Gazin, Nathan D. Lawson, Hervé Pagès, Simon Lin, David S. Lapointe, Michael R. Green
Software Mentions: 16
Published: over 14 years ago
10.1186/1471-2105-11-194
Starr: Simple Tiling ARRay analysis of Affymetrix ChIP-chip dataCited by: 32
Author(s): Benedikt Zacher, Pei Fen Kuan, Achim Tresch
Software Mentions: 12
Published: over 14 years ago
10.1186/1471-2105-8-221
Ringo – an R/Bioconductor package for analyzing ChIP-chip readoutsCited by: 156
Author(s): Joern Toedling, Oleg Sklyar, Wolfgang Huber
Software Mentions: 9
Published: over 17 years ago
10.1038/ismej.2017.197
Microbial life on a sand grain: from bulk sediment to single grainsCited by: 79
Author(s): David Probandt, Thilo Eickhorst, Andreas Ellrott, Rudolf Amann, Katrin Knittel
Software Mentions: 7
Published: almost 7 years ago
10.1371/journal.pone.0052299
Cell-Type Specific DNA Methylation Patterns Define Human Breast Cellular IdentityCited by: 22
Author(s): Petr Novák, Martha R. Stampfer, José L. Muñoz-Rodríguez, James C. Garbe, Mathias Ehrich, Bernard W. Futscher, Taylor J. Jensen
Software Mentions: 6
Published: almost 12 years ago
10.1186/1471-2342-8-10
Internet Image Viewer (iiV)Cited by: 9
Author(s): Joel T. Lee, Kristin Munch, John V. Carlis, José V. Pardo
Software Mentions: 6
Published: over 16 years ago
10.1186/s13059-021-02302-5
ACME dissociation: a versatile cell fixation-dissociation method for single-cell transcriptomicsCited by: 31
Author(s): Helena García-Castro, Nathan J. Kenny, Marta Iglesias, Patricia Álvarez‐Campos, Vincent Mason, Anamaria Elek, Anna Schönauer, Victoria A. Sleight, Jakke Neiro, A. Aziz Aboobaker, Jon Permanyer, Manuel Irimia, Arnau Sebé-Pedrós, Jordi Solana
Software Mentions: 5
Published: over 3 years ago
10.1371/journal.pone.0206628
Simplified, automated methods for assessing pixel intensities of fluorescently-tagged drugs in cellsCited by: 0
Author(s): Allan Kachelmeier, Tsering Shola, William B. Meier, Anastasiya Johnson, Meiyan Jiang, Peter S. Steyger
Software Mentions: 4
Published: about 6 years ago
10.1007/s10270-016-0519-z
Dual deep modeling: multi-level modeling with dual potencies and its formalization in F-LogicCited by: 18
Author(s): Bernd Neumayr, Christoph G. Schuetz, Manfred A. Jeusfeld, Michael Schrefl
Software Mentions: 4
Published: over 8 years ago
10.1186/1471-2164-13-42
An evaluation of two-channel ChIP-on-chip and DNA methylation microarray normalization strategiesCited by: 17
Author(s): Michiel E. Adriaens, Magali Jaillard, Lars Eijssen, Claus Mayer, Chris T. Evelo
Software Mentions: 4
Published: almost 13 years ago
10.1371/journal.pone.0098371
Treatment for Stable Coronary Artery Disease: A Network Meta-Analysis of Cost-Effectiveness StudiesCited by: 22
Author(s): Thibaut Caruba, Sandrine Katsahian, Catherine Schramm, Anaïs Charles-Nelson, Pierre Durieux, Dominique Bégué, Yves Juillière, Olivier Dubourg, Nicolás Danchin, Brigitte Sabatier
Software Mentions: 3
Published: over 10 years ago
10.1038/srep46533
A New Approach to Evaluating Aberrant DNA Methylation Profiles in Hepatocellular Carcinoma as Potential BiomarkersCited by: 7
Author(s): Yuan Yang, Lan‐Juan Zhao, Bo Huang, Guoqing Hou, Beibei Zhou, Jin Qian, Shengxian Yuan, Huasheng Xiao, Minghui Li, Weiping Zhou
Software Mentions: 3
Published: over 7 years ago
10.1002/pmic.201900335
Deep Learning in ProteomicsCited by: 77
Author(s): Bo Wen, Wen‐Feng Zeng, Yuxing Liao, Zhiao Shi, Sara R. Savage, Wen Jiang, Bing Zhang
Software Mentions: 2
Published: about 4 years ago
10.3389/fmicb.2020.00166
Genomic Stability of Composite SCCmec ACME and COMER-Like Genetic Elements in Staphylococcus epidermidis Correlates With Rate of ExcisionCited by: 7
Author(s): Nada Almebairik, Roxana Zamudio, Corinne Ironside, Chaitanya Joshi, Joseph D. Ralph, Adam P. Roberts, Ian M. Gould, Julie A. Morrissey, Karolin Hijazi, Marco R. Oggioni
Software Mentions: 2
Published: over 4 years ago
10.1186/s12963-018-0176-2
Injury death certificates without specification of the circumstances leading to the fatal injury – the Norwegian Cause of Death Registry 2005–2014Cited by: 7
Author(s): Christian Lycke Ellingsen, Marta Ebbing, G. Cecilie Alfsen, Stein Emil Vollset
Software Mentions: 2
Published: almost 6 years ago
10.1371/journal.pone.0148379
BioSig3D: High Content Screening of Three-Dimensional Cell Culture ModelsCited by: 18
Author(s): Cemal Cagatay Bilgin, Gerald Fontenay, Qingsu Cheng, Hang Chang, Ju Han, Bahram Parvin
Software Mentions: 2
Published: over 8 years ago
10.1371/journal.pone.0038319
Microbial and Chemical Characterization of Underwater Fresh Water Springs in the Dead SeaCited by: 136
Author(s): Danny Ionescu, Christian Siebert, Lùbos Polerecký, Yaniv Y. Munwes, Christian Lott, Stefan Häusler, Mina Bižić-Ionescu, Christian Quast, Jörg Peplies, Frank Oliver Glöckner, Alban Ramette, Tino Rödiger, Thorsten Dittmar, Aharon Oren, Stefan Geyer, Hans‐Joachim Stärk, Martin Sauter, Tobias Licha, Jonathan B. Laronne, Dirk de Beer
Software Mentions: 2
Published: over 12 years ago
10.3390/s20030752
Developing a Secure Low-Cost Radon Monitoring SystemCited by: 17
Author(s): Alberto Alvarellos, Marcos Gestal, Julián Dorado, Juan R. Rabuñal
Software Mentions: 2
Published: almost 5 years ago
10.3390/s21041392
Fault Injection Emulation for Systems in FPGAs: Tools, Techniques and Methodology, a TutorialCited by: 5
Author(s): O. Ruano, Francisco García-Herrero, Luis Alberto Aranda, Alfonso Sánchez‐Macian, Luis-Felipe Rodríguez, Juan Antonio Maestro
Software Mentions: 2
Published: over 3 years ago
10.1371/journal.pone.0047157
Distinct Distribution of Ectopically Expressed Histone Variants H2A.Bbd and MacroH2A in Open and Closed Chromatin DomainsCited by: 19
Author(s): E. S. Ioudinkova, Ana Barat, Andrey Pichugin, Eva Markovà, Ilya Sklyar, Iryna Pirozhkova, Chloé Robin, Marc Lipinski, Vasily Ogryzko, Yegor S. Vassetzky, Sergey V. Razin
Software Mentions: 2
Published: about 12 years ago
10.1186/1471-2105-14-76
BioTile, A Perl based tool for the identification of differentially enriched regions in tiling microarray dataCited by: 3
Author(s): Jerry Guintivano, Michal Arad, Kellie L.K. Tamashiro, Todd D. Gould, Zachary Kaminsky
Software Mentions: 2
Published: over 11 years ago
10.1371/journal.pone.0203702
Investigating potential mediator between statin and coronary artery calcificationCited by: 9
Author(s): Donghun Lee, Hyung Joon Joo, Ho Won Jung, Do Sun Lim
Software Mentions: 1
Published: about 6 years ago
10.1371/journal.pone.0064801
Genome-Wide Methylated DNA Immunoprecipitation Analysis of Patients with Polycystic Ovary SyndromeCited by: 37
Author(s): Haoran Shen, Lihua Qiu, Zhiqing Zhang, Yuanyuan Qin, Cong Cao, Wen Di
Software Mentions: 1
Published: over 11 years ago
10.1371/journal.pone.0064592
Evaluating the Quality of National Mortality Statistics from Civil Registration in South Africa, 1997–2007Cited by: 46
Author(s): Jané Joubert, Chalapati Rao, Debbie Bradshaw, Theo Vos, Alan D Lopez
Software Mentions: 1
Published: over 11 years ago
10.3390/cancers12061660
Uncovering the Tumor Antigen Landscape: What to Know about the Discovery ProcessCited by: 22
Author(s): Sara Feola, Jacopo Chiaro, Beatriz Martins, Vincenzo Cerullo
Software Mentions: 1
Published: over 4 years ago
10.1007/s00392-019-01490-2
When and how do patients with cardiac amyloidosis die?Cited by: 32
Author(s): Felicitas Escher, M. Senoner, Jakob Doerler, Marc-Michael Zaruba, Moritz Messner, Christine Mussner-Seeber, Micaela Ebert, Christian Ensinger, A. Mair, Alexander Kroiss, Hanno Ulmer, Stephanie Schneiderbauer-Porod, Christian Ebner, Gerhard Poelzl
Software Mentions: 1
Published: over 5 years ago
10.1140/epjc/s10052-014-3211-x
Lepton flavor violation in flavored gauge mediationCited by: 35
Author(s): Lorenzo Calibbi, Paride Paradisi, Robert Ziegler
Software Mentions: 1
Published: almost 10 years ago
10.3389/fgene.2021.645640
Exact Probability Landscapes of Stochastic Phenotype Switching in Feed-Forward Loops: Phase Diagrams of MultimodalityCited by: 6
Author(s): Anna Terebus, Farid Manuchehrfar, Youfang Cao, Jie Liang
Software Mentions: 1
Published: over 3 years ago
10.3389/fgene.2019.01141
Machine Learning for Cancer Immunotherapies Based on Epitope Recognition by T Cell ReceptorsCited by: 31
Author(s): Anja Mösch, Silke Raffegerst, Manon Weis, Dolores J. Schendel, Dmitrij Frishman
Software Mentions: 1
Published: almost 5 years ago
10.3389/fpsyg.2019.02772
They (Don’t) Need Us: Functional Indispensability Impacts Perceptions of Representativeness and Commitment When Lower-Status Groups Go Through an Intergroup MergerCited by: 4
Author(s): Miriam Rosa, Steffen R. Giessner, Rita Guerra, Sven Waldzus, Anna-Maria Kersting, Katarina Veličković, Elizabeth Collins
Software Mentions: 1
Published: almost 5 years ago
10.1186/gm346
H3K4me3 inversely correlates with DNA methylation at a large class of non-CpG-island-containing start sitesCited by: 44
Author(s): Dheepa Balasubramanian, Batool Akhtar-Zaidi, Lingyun Song, Cynthia F. Bartels, Marty L Veigl, Lydia Beard, Lois Myeroff, Kishore Guda, James Lutterbaugh, Joseph E. Willis, Gregory E. Crawford, Sanford D. Markowitz, Peter C. Scacheri
Software Mentions: 1
Published: almost 13 years ago
10.1186/s41118-018-0027-9
Mortality, morbidity and health in developed societies: a review of data sourcesCited by: 5
Author(s): Guillaume Wunsch, Catherine Gourbin
Software Mentions: 1
Published: almost 7 years ago
10.1186/s12963-015-0056-y
Multiple causes of death analysis of chronic diseases: the example of diabetesCited by: 32
Author(s): Ugo Fedeli, Giacomo Zoppini, Carlo Alberto Goldoni, Francesco Avossa, Giuseppe Mastrangelo, Mario Saugo
Software Mentions: 1
Published: about 9 years ago
10.1186/s12963-016-0082-4
Improving the usefulness of US mortality data: new methods for reclassification of underlying cause of deathCited by: 42
Author(s): Kyle J Foreman, Mohsen Naghavi, Majid Ezzati
Software Mentions: 1
Published: over 8 years ago
10.1073/pnas.1908158117
High-dose ascorbic acid synergizes with anti-PD1 in a lymphoma mouse modelCited by: 84
Author(s): Rebecca A. Luchtel, Tushar D. Bhagat, Kith Pradhan, William R. Jacobs, Mark Levine, Amit Verma, Niraj Shenoy
Software Mentions: 1
Published: almost 5 years ago
10.1038/srep17232
ω-Tbo-IT1–New Inhibitor of Insect Calcium Channels Isolated from Spider VenomCited by: 7
Author(s): Alexander Mikov, И. М. Федорова, Natalia N. Potapieva, Ekaterina E. Maleeva, Yaroslav A. Andreev, Aleksey V. Zaitsev, Kira K. Kim, Eduard V. Bocharov, Timur N. Bozin, Dmitry A. Altukhov, А.В. Липкин, Sergey A. Kozlov, Denis B. Tikhonov, Eugene V. Grishin
Software Mentions: 1
Published: almost 9 years ago
10.3390/toxins9050154
New Disulfide-Stabilized Fold Provides Sea Anemone Peptide to Exhibit Both Antimicrobial and TRPA1 Potentiating PropertiesCited by: 38
Author(s): Yulia A. Logashina, Runar Gjerp Solstad, Konstantin S. Mineev, Yuliya V. Korolkova, И. В. Мошарова, Igor A. Dyachenko, В. А. Паликов, Yu. A. Palikova, А. Н. Мурашев, Alexander S. Arseniev, Sergey A. Kozlov, Klara Stensvåg, Tor Haug, Yaroslav A. Andreev
Software Mentions: 1
Published: over 7 years ago
10.1128/mBio.02911-19
Staphylococcus epidermidis MSCRAMM SesJ Is Encoded in Composite IslandsCited by: 8
Author(s): Srishtee Arora, Xiqi Li, Andrew Hillhouse, Kranti Konganti, Sara V. Little, Sara D. Lawhon, David W. Threadgill, Samuel A. Shelburne, Magnus Höök
Software Mentions: 1
Published: over 4 years ago
10.7554/eLife.39596
Size control of the inner ear via hydraulic feedbackCited by: 42
Author(s): Kishore Mosaliganti, Ian A. Swinburne, Chon U Chan, Nikolaus Obholzer, Amelia A. Green, Shreyas Tanksale, L. Mahadevan, Sean G. Megason
Software Mentions: 1
Published: about 5 years ago
10.4269/ajtmh.17-0389
President’s Address (November 2016): American Society of Tropical Medicine and HygieneCited by: 2
Author(s): Stephen Higgs
Software Mentions: 1
Published: over 7 years ago
10.7554/eLife.37131
Lamellar projections in the endolymphatic sac act as a relief valve to regulate inner ear pressureCited by: 22
Author(s): Ian A. Swinburne, Kishore Mosaliganti, Srigokul Upadhyayula, Tsung Li Liu, David G. C. Hildebrand, Tony Tsai, Anzhi Chen, Ebaa Al-Obeidi, Anna K. Fass, Samir Malhotra, Florian Engert, Jeff W. Lichtman, Tomas Kirchhausen, Eric Betzig, Sean G. Megason
Software Mentions: 1
Published: over 6 years ago
10.1186/s13075-019-1945-4
Survival and death causes of patients with giant cell arteritis in Western Norway 1972–2012: a retrospective cohort studyCited by: 16
Author(s): Lene Kristin Brekke, Bjørg‐Tilde Svanes Fevang, Andreas P. Diamantopoulos, Jörg Aßmus, Elisabet Langseth Esperø, Clara Gram Gjesdal
Software Mentions: 1
Published: over 5 years ago
10.1186/s12859-019-2720-x
3DMMS: robust 3D Membrane Morphological Segmentation of C. elegans embryoCited by: 14
Author(s): Jianfeng Cao, Ming Kin Wong, Zhongying Zhao, Hong Yan
Software Mentions: 1
Published: over 5 years ago
10.1186/s12859-020-03946-z
MATHLA: a robust framework for HLA-peptide binding prediction integrating bidirectional LSTM and multiple head attention mechanismCited by: 8
Author(s): Yilin Ye, Jian Wang, Yunwan Xu, Yi Wang, Ying Pan, Qi Song, Xing Liu, Ji Wan
Software Mentions: 1
Published: almost 4 years ago
10.1186/1471-2105-12-57
Tiling array data analysis: a multiscale approach using waveletsCited by: 8
Author(s): Alexander Karpikov, Joel Rozowsky, Mark Gerstein
Software Mentions: 1
Published: over 13 years ago
10.1186/1471-2164-13-728
Genomic insights of protein arginine methyltransferase Hmt1 binding reveals novel regulatory functionsCited by: 8
Author(s): Eric J. Milliman, Zihua Hu, Michael C. Yu
Software Mentions: 1
Published: almost 12 years ago
10.1186/s12879-016-1664-2
Growing burden of sepsis-related mortality in northeastern Italy: a multiple causes of death analysisCited by: 14
Author(s): Ugo Fedeli, Pasquale Piccinni, Elena Schievano, Mario Saugo, Giampietro Pellizzer
Software Mentions: 1
Published: over 8 years ago
10.1186/1472-6947-12-37
Identification of pneumonia and influenza deaths using the death certificate pipelineCited by: 16
Author(s): Kailah Davis, Catherine J. Staes, Jeffrey Duncan, Sean Igo, Julio C. Facelli
Software Mentions: 1
Published: over 12 years ago
10.1093/bioinformatics/btab312
Predicting MHC-peptide binding affinity by differential boundary treeCited by: 5
Author(s): Peiyuan Feng, Jianyang Zeng, Jianzhu Ma
Software Mentions: 1
Published: over 3 years ago
10.1016/j.lanepe.2021.100071
Prevalence of mental disorders, suicidal ideation and suicides in the general population before and during the COVID-19 pandemic in Norway: A population-based repeated cross-sectional analysisCited by: 59
Author(s): Ann Kristin Knudsen, Kim Stene‐Larsen, Kristin Gustavson, Matthew Hotopf, Ronald C. Kessler, Steinar Krokstad, Jens Christoffer Skogen, Simon Øverland, Anne Reneflot
Software Mentions: 1
Published: over 3 years ago
10.4274/MIRT.33
An Overview on Coronary Heart Disease (A Comparative Evaluation of Turkey and Europe) and Cost-effectiveness of Diagnostic StrategiesCited by: 4
Author(s): Cengiz Taşçı, Nihat Özçelik
Software Mentions: 1
Published: almost 13 years ago
10.1016/j.omtm.2020.10.003
In Situ Detection of Adeno-associated Viral Vector Genomes with SABER-FISHCited by: 13
Author(s): Sean K. Wang, Sylvain W. Lapan, Christin M Hong, Tyler B. Krause, Constance L. Cepko
Software Mentions: 1
Published: almost 4 years ago
10.3390/pharmacy8030139
Learn Today–Apply Tomorrow: The SMART Pharmacist ProgramCited by: 4
Author(s): Michael J. Rouse, Arijana Meštrović
Software Mentions: 1
Published: over 4 years ago
10.1371/journal.pcbi.1009214
Beyond the chemical master equation: Stochastic chemical kinetics coupled with auxiliary processesCited by: 8
Author(s): Davin Lunz, Grégory Batt, Jakob Ruess, J. Frédéric Bonnans
Software Mentions: 1
Published: over 3 years ago
10.1371/journal.pcbi.1002780
ACME: Automated Cell Morphology Extractor for Comprehensive Reconstruction of Cell MembranesCited by: 105
Author(s): Kishore Mosaliganti, Ramil R. Noche, Fengzhu Xiong, Ian A. Swinburne, Sean G. Megason
Software Mentions: 1
Published: almost 12 years ago
10.1371/journal.pgen.1003969
Deletion of a Conserved cis-Element in the Ifng Locus Highlights the Role of Acute Histone Acetylation in Modulating Inducible Gene TranscriptionCited by: 24
Author(s): Anand Balasubramani, Colleen J. Winstead, Henrietta Turner, Karen M. Janowski, Stacey N. Harbour, Yoichiro Shibata, Gregory E. Crawford, Robin D. Hatton, Casey T. Weaver
Software Mentions: 1
Published: almost 11 years ago
10.1371/journal.pgen.0020051
Genome-Wide Analysis of Menin Binding Provides Insights into MEN1 TumorigenesisCited by: 192
Author(s): Peter C. Scacheri, Sean Davis, Duncan T. Odom, Gregory E. Crawford, Stacie Perkins, Mohamad J. Halawi, Sunita K. Agarwal, Stephen J. Marx, Allen M. Spiegel, Paul S. Meltzer, Francis S. Collins
Software Mentions: 1
Published: over 18 years ago
10.1371/journal.pgen.1000446
Transcription Initiation Activity Sets Replication Origin Efficiency in Mammalian CellsCited by: 220
Author(s): Joana Sequeira-Mendes, Ramón Díaz‐Uriarte, Anwyn Apedaile, Derek Huntley, Neil Brockdorff, Marı́a Gómez
Software Mentions: 1
Published: over 15 years ago
10.1371/journal.pgen.0030136
Identification and Characterization of Cell Type–Specific and Ubiquitous Chromatin Regulatory Structures in the Human GenomeCited by: 207
Author(s): Hualin Simon Xi, Hennady P. Shulha, Jane M. Lin, Teresa R. Vales, Yutao Fu, David M. Bodine, Ronald D.G. McKay, Josh G. Chenoweth, Paul J. Tesar, Terrence S. Furey, Bing Ren, Zhiping Weng, Gregory E. Crawford
Software Mentions: 1
Published: about 17 years ago
10.1371/journal.pone.0007839
Gene Regulation and Epigenetic Remodeling in Murine Embryonic Stem Cells by c-MycCited by: 73
Author(s): Chin Hsing Lin, Chen Wei Lin, Hisashi Tanaka, Matthew L. Fero, Robert N. Eisenman
Software Mentions: 1
Published: almost 15 years ago
10.1371/journal.pone.0007722
Genetic Diversity of Arginine Catabolic Mobile Element in Staphylococcus epidermidisCited by: 98
Author(s): Maria Miragaia, Hermı́nia de Lencastre, Françoise Perdreau-Remington, Henry F. Chambers, Julie Higashi, Paul M. Sullam, Jessica Lin, Kester I. Wong, Katherine A. King, Michael Otto, George F. Sensabaugh, Binh An Diep
Software Mentions: 1
Published: about 15 years ago
10.1371/journal.pone.0004103
Topoisomerase IIβ Activates a Subset of Neuronal Genes that Are Repressed in AT-Rich Genomic EnvironmentCited by: 54
Author(s): Kuniaki Sano, Mary Miyaji-Yamaguchi, Kimiko Tsutsui, Ken Tsutsui
Software Mentions: 1
Published: almost 16 years ago