bioconductor: ACME | Projects | Ecosyste.ms: Papers

10.1371/journal.pcbi.1000227

Analyzing ChIP-chip Data Using Bioconductor
Cited by: 19
Author(s): Joern Toedling, Wolfgang Huber
Software Mentions: 39
Published: over 15 years ago

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data
Cited 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: about 14 years ago

10.1186/1471-2105-11-194

Starr: Simple Tiling ARRay analysis of Affymetrix ChIP-chip data
Cited by: 32
Author(s): Benedikt Zacher, Pei Fen Kuan, Achim Tresch
Software Mentions: 12
Published: about 14 years ago

10.1186/1471-2105-8-221

Ringo – an R/Bioconductor package for analyzing ChIP-chip readouts
Cited by: 156
Author(s): Joern Toedling, Oleg Sklyar, Wolfgang Huber
Software Mentions: 9
Published: almost 17 years ago

10.1038/ismej.2017.197

Microbial life on a sand grain: from bulk sediment to single grains
Cited by: 79
Author(s): David Probandt, Thilo Eickhorst, Andreas Ellrott, Rudolf Amann, Katrin Knittel
Software Mentions: 7
Published: over 6 years ago

10.1371/journal.pone.0052299

Cell-Type Specific DNA Methylation Patterns Define Human Breast Cellular Identity
Cited 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: over 11 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: almost 16 years ago

10.1186/s13059-021-02302-5

ACME dissociation: a versatile cell fixation-dissociation method for single-cell transcriptomics
Cited 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: about 3 years ago

10.1371/journal.pone.0206628

Simplified, automated methods for assessing pixel intensities of fluorescently-tagged drugs in cells
Cited by: 0
Author(s): Allan Kachelmeier, Tsering Shola, William B. Meier, Anastasiya Johnson, Meiyan Jiang, Peter S. Steyger
Software Mentions: 4
Published: over 5 years ago

10.1007/s10270-016-0519-z

Dual deep modeling: multi-level modeling with dual potencies and its formalization in F-Logic
Cited by: 18
Author(s): Bernd Neumayr, Christoph G. Schuetz, Manfred A. Jeusfeld, Michael Schrefl
Software Mentions: 4
Published: about 8 years ago

10.1186/1471-2164-13-42

An evaluation of two-channel ChIP-on-chip and DNA methylation microarray normalization strategies
Cited by: 17
Author(s): Michiel E. Adriaens, Magali Jaillard, Lars Eijssen, Claus Mayer, Chris T. Evelo
Software Mentions: 4
Published: over 12 years ago

10.1371/journal.pone.0098371

Treatment for Stable Coronary Artery Disease: A Network Meta-Analysis of Cost-Effectiveness Studies
Cited 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: almost 10 years ago

10.1038/srep46533

A New Approach to Evaluating Aberrant DNA Methylation Profiles in Hepatocellular Carcinoma as Potential Biomarkers
Cited 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: about 7 years ago

10.1002/pmic.201900335

Deep Learning in Proteomics
Cited by: 77
Author(s): Bo Wen, Wen‐Feng Zeng, Yuxing Liao, Zhiao Shi, Sara R. Savage, Wen Jiang, Bing Zhang
Software Mentions: 2
Published: over 3 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 Excision
Cited 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 2005–2014
Cited by: 7
Author(s): Christian Lycke Ellingsen, Marta Ebbing, G. Cecilie Alfsen, Stein Emil Vollset
Software Mentions: 2
Published: over 5 years ago

10.1371/journal.pone.0148379

BioSig3D: High Content Screening of Three-Dimensional Cell Culture Models
Cited by: 18
Author(s): Cemal Cagatay Bilgin, Gerald Fontenay, Qingsu Cheng, Hang Chang, Ju Han, Bahram Parvin
Software Mentions: 2
Published: about 8 years ago

10.1371/journal.pone.0038319

Microbial and Chemical Characterization of Underwater Fresh Water Springs in the Dead Sea
Cited 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: almost 12 years ago

10.3390/s20030752

Developing a Secure Low-Cost Radon Monitoring System
Cited by: 17
Author(s): Alberto Alvarellos, Marcos Gestal, Julián Dorado, Juan R. Rabuñal
Software Mentions: 2
Published: over 4 years ago

10.3390/s21041392

Fault Injection Emulation for Systems in FPGAs: Tools, Techniques and Methodology, a Tutorial
Cited 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 Domains
Cited 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: over 11 years ago

10.1186/1471-2105-14-76

BioTile, A Perl based tool for the identification of differentially enriched regions in tiling microarray data
Cited by: 3
Author(s): Jerry Guintivano, Michal Arad, Kellie L.K. Tamashiro, Todd D. Gould, Zachary Kaminsky
Software Mentions: 2
Published: about 11 years ago

10.1371/journal.pone.0203702

Investigating potential mediator between statin and coronary artery calcification
Cited by: 9
Author(s): Donghun Lee, Hyung Joon Joo, Ho Won Jung, Do Sun Lim
Software Mentions: 1
Published: over 5 years ago

10.1371/journal.pone.0064801

Genome-Wide Methylated DNA Immunoprecipitation Analysis of Patients with Polycystic Ovary Syndrome
Cited by: 37
Author(s): Haoran Shen, Lihua Qiu, Zhiqing Zhang, Yuanyuan Qin, Cong Cao, Wen Di
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0064592

Evaluating the Quality of National Mortality Statistics from Civil Registration in South Africa, 1997–2007
Cited by: 46
Author(s): Jané Joubert, Chalapati Rao, Debbie Bradshaw, Theo Vos, Alan D Lopez
Software Mentions: 1
Published: almost 11 years ago

10.3390/cancers12061660

Uncovering the Tumor Antigen Landscape: What to Know about the Discovery Process
Cited by: 22
Author(s): Sara Feola, Jacopo Chiaro, Beatriz Martins, Vincenzo Cerullo
Software Mentions: 1
Published: almost 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: almost 5 years ago

10.1140/epjc/s10052-014-3211-x

Lepton flavor violation in flavored gauge mediation
Cited by: 35
Author(s): Lorenzo Calibbi, Paride Paradisi, Robert Ziegler
Software Mentions: 1
Published: over 9 years ago

10.3389/fgene.2021.645640

Exact Probability Landscapes of Stochastic Phenotype Switching in Feed-Forward Loops: Phase Diagrams of Multimodality
Cited by: 6
Author(s): Anna Terebus, Farid Manuchehrfar, Youfang Cao, Jie Liang
Software Mentions: 1
Published: almost 3 years ago

10.3389/fgene.2019.01141

Machine Learning for Cancer Immunotherapies Based on Epitope Recognition by T Cell Receptors
Cited by: 31
Author(s): Anja Mösch, Silke Raffegerst, Manon Weis, Dolores J. Schendel, Dmitrij Frishman
Software Mentions: 1
Published: over 4 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 Merger
Cited by: 4
Author(s): Miriam Rosa, Steffen R. Giessner, Rita Guerra, Sven Waldzus, Anna-Maria Kersting, Katarina Veličković, Elizabeth Collins
Software Mentions: 1
Published: over 4 years ago

10.1186/gm346

H3K4me3 inversely correlates with DNA methylation at a large class of non-CpG-island-containing start sites
Cited 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: over 12 years ago

10.1186/s41118-018-0027-9

Mortality, morbidity and health in developed societies: a review of data sources
Cited by: 5
Author(s): Guillaume Wunsch, Catherine Gourbin
Software Mentions: 1
Published: over 6 years ago

10.1186/s12963-015-0056-y

Multiple causes of death analysis of chronic diseases: the example of diabetes
Cited by: 32
Author(s): Ugo Fedeli, Giacomo Zoppini, Carlo Alberto Goldoni, Francesco Avossa, Giuseppe Mastrangelo, Mario Saugo
Software Mentions: 1
Published: over 8 years ago

10.1186/s12963-016-0082-4

Improving the usefulness of US mortality data: new methods for reclassification of underlying cause of death
Cited by: 42
Author(s): Kyle J Foreman, Mohsen Naghavi, Majid Ezzati
Software Mentions: 1
Published: about 8 years ago

10.1073/pnas.1908158117

High-dose ascorbic acid synergizes with anti-PD1 in a lymphoma mouse model
Cited 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: over 4 years ago

10.1038/srep17232

ω-Tbo-IT1–New Inhibitor of Insect Calcium Channels Isolated from Spider Venom
Cited 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: over 8 years ago

10.3390/toxins9050154

New Disulfide-Stabilized Fold Provides Sea Anemone Peptide to Exhibit Both Antimicrobial and TRPA1 Potentiating Properties
Cited 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: about 7 years ago

10.1128/mBio.02911-19

Staphylococcus epidermidis MSCRAMM SesJ Is Encoded in Composite Islands
Cited 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: about 4 years ago

10.7554/eLife.39596

Size control of the inner ear via hydraulic feedback
Cited 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: over 4 years ago

10.4269/ajtmh.17-0389

President’s Address (November 2016): American Society of Tropical Medicine and Hygiene
Cited by: 2
Author(s): Stephen Higgs
Software Mentions: 1
Published: almost 7 years ago

10.7554/eLife.37131

Lamellar projections in the endolymphatic sac act as a relief valve to regulate inner ear pressure
Cited 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: almost 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 study
Cited 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: almost 5 years ago

10.1186/s12859-019-2720-x

3DMMS: robust 3D Membrane Morphological Segmentation of C. elegans embryo
Cited by: 14
Author(s): Jianfeng Cao, Ming Kin Wong, Zhongying Zhao, Hong Yan
Software Mentions: 1
Published: about 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 mechanism
Cited by: 8
Author(s): Yilin Ye, Jian Wang, Yunwan Xu, Yi Wang, Ying Pan, Qi Song, Xing Liu, Ji Wan
Software Mentions: 1
Published: over 3 years ago

10.1186/1471-2105-12-57

Tiling array data analysis: a multiscale approach using wavelets
Cited by: 8
Author(s): Alexander Karpikov, Joel Rozowsky, Mark Gerstein
Software Mentions: 1
Published: about 13 years ago

10.1186/1471-2164-13-728

Genomic insights of protein arginine methyltransferase Hmt1 binding reveals novel regulatory functions
Cited by: 8
Author(s): Eric J. Milliman, Zihua Hu, Michael C. Yu
Software Mentions: 1
Published: over 11 years ago

10.1186/s12879-016-1664-2

Growing burden of sepsis-related mortality in northeastern Italy: a multiple causes of death analysis
Cited by: 14
Author(s): Ugo Fedeli, Pasquale Piccinni, Elena Schievano, Mario Saugo, Giampietro Pellizzer
Software Mentions: 1
Published: almost 8 years ago

10.1186/1472-6947-12-37

Identification of pneumonia and influenza deaths using the death certificate pipeline
Cited by: 16
Author(s): Kailah Davis, Catherine J. Staes, Jeffrey Duncan, Sean Igo, Julio C. Facelli
Software Mentions: 1
Published: about 12 years ago

10.1093/bioinformatics/btab312

Predicting MHC-peptide binding affinity by differential boundary tree
Cited by: 5
Author(s): Peiyuan Feng, Jianyang Zeng, Jianzhu Ma
Software Mentions: 1
Published: almost 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 analysis
Cited 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: about 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 Strategies
Cited by: 4
Author(s): Cengiz Taşçı, Nihat Özçelik
Software Mentions: 1
Published: over 12 years ago

10.1016/j.omtm.2020.10.003

In Situ Detection of Adeno-associated Viral Vector Genomes with SABER-FISH
Cited by: 13
Author(s): Sean K. Wang, Sylvain W. Lapan, Christin M Hong, Tyler B. Krause, Constance L. Cepko
Software Mentions: 1
Published: over 3 years ago

10.3390/pharmacy8030139

Learn Today–Apply Tomorrow: The SMART Pharmacist Program
Cited by: 4
Author(s): Michael J. Rouse, Arijana Meštrović
Software Mentions: 1
Published: almost 4 years ago

10.1371/journal.pcbi.1009214

Beyond the chemical master equation: Stochastic chemical kinetics coupled with auxiliary processes
Cited by: 8
Author(s): Davin Lunz, Grégory Batt, Jakob Ruess, J. Frédéric Bonnans
Software Mentions: 1
Published: almost 3 years ago

10.1371/journal.pcbi.1002780

ACME: Automated Cell Morphology Extractor for Comprehensive Reconstruction of Cell Membranes
Cited by: 105
Author(s): Kishore Mosaliganti, Ramil R. Noche, Fengzhu Xiong, Ian A. Swinburne, Sean G. Megason
Software Mentions: 1
Published: over 11 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 Transcription
Cited 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: over 10 years ago

10.1371/journal.pgen.0020051

Genome-Wide Analysis of Menin Binding Provides Insights into MEN1 Tumorigenesis
Cited 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: about 18 years ago

10.1371/journal.pgen.1000446

Transcription Initiation Activity Sets Replication Origin Efficiency in Mammalian Cells
Cited by: 220
Author(s): Joana Sequeira-Mendes, Ramón Díaz‐Uriarte, Anwyn Apedaile, Derek Huntley, Neil Brockdorff, Marı́a Gómez
Software Mentions: 1
Published: about 15 years ago

10.1371/journal.pgen.0030136

Identification and Characterization of Cell Type–Specific and Ubiquitous Chromatin Regulatory Structures in the Human Genome
Cited 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: almost 17 years ago

10.1371/journal.pone.0007839

Gene Regulation and Epigenetic Remodeling in Murine Embryonic Stem Cells by c-Myc
Cited by: 73
Author(s): Chin Hsing Lin, Chen Wei Lin, Hisashi Tanaka, Matthew L. Fero, Robert N. Eisenman
Software Mentions: 1
Published: over 14 years ago

10.1371/journal.pone.0007722

Genetic Diversity of Arginine Catabolic Mobile Element in Staphylococcus epidermidis
Cited 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: over 14 years ago

10.1371/journal.pone.0004103

Topoisomerase IIβ Activates a Subset of Neuronal Genes that Are Repressed in AT-Rich Genomic Environment
Cited by: 54
Author(s): Kuniaki Sano, Mary Miyaji-Yamaguchi, Kimiko Tsutsui, Ken Tsutsui
Software Mentions: 1
Published: over 15 years ago

Projects: bioconductor: ACME

Papers Mentioning ACME 63