bioconductor: PSEA | Projects | Ecosyste.ms: Papers

10.1186/s40425-018-0422-y

33rd Annual Meeting & Pre-Conference Programs of the Society for Immunotherapy of Cancer (SITC 2018)
Cited by: 36
Author(s):
Software Mentions: 9
Published: about 6 years ago

High‐fat diet in a mouse insulin‐resistant model induces widespread rewiring of the phosphotyrosine signaling network
Cited by: 24
Author(s): Antje Dittmann, Norman J. Kennedy, Nina L Soltero, Nader Morshed, Miyeko Mana, Ömer H. Yılmaz, Roger J. Davis, Forest M. White
Software Mentions: 9
Published: over 5 years ago

10.1038/srep32976

Disease-specific classification using deconvoluted whole blood gene expression
Cited by: 17
Author(s): Li Wang, William K. Oh, Jun Zhu
Software Mentions: 8
Published: about 8 years ago

10.7554/eLife.34031

Forniceal deep brain stimulation induces gene expression and splicing changes that promote neurogenesis and plasticity
Cited by: 39
Author(s): Amy E. Pohodich, Hari Krishna Yalamanchili, Ayush T. Raman, Ying-Wooi Wan, Michael C. Gundry, Shuang Hao, Haijing Jin, Jianrong Tang, Zhandong Liu, Huda Y. Zoghbi
Software Mentions: 7
Published: over 6 years ago

10.7554/eLife.65574

KLF10 integrates circadian timing and sugar signaling to coordinate hepatic metabolism
Cited by: 16
Author(s): Anthony A Ruberto, Aline Gréchez-Cassiau, Sabrina Guérin, Luc Martin, Johana S. Revel, Mohamed Mehiri, Malayannan Subramaniam, Franck Delaunay, Michèle Teboul
Software Mentions: 5
Published: over 3 years ago

10.1186/s12859-015-0597-x

ISOpureR: an R implementation of a computational purification algorithm of mixed tumour profiles
Cited by: 30
Author(s): Catalina Anghel, Gerald Quon, Syed Haider, Francis Nguyen, Amit G. Deshwar, Quaid Morris, Paul C. Boutros
Software Mentions: 5
Published: over 9 years ago

10.1186/1471-2164-15-459

Structured RNAs and synteny regions in the pig genome
Cited by: 19
Author(s): Christian Anthon, Hakim Tafer, Jakob Hull Havgaard, Bo Thomsen, Jakob Hedegaard, Stefan E. Seemann, Sachin Pundhir, Stephanie Kehr, Sebastian Bartschat, Marie Konge Nielsen, Rasmus Oestergaard Nielsen, Merete Fredholm, Peter F. Stadler, Jan Gorodkin
Software Mentions: 5
Published: over 10 years ago

10.3390/ijms21082873

Bioinformatics Methods for Mass Spectrometry-Based Proteomics Data Analysis
Cited by: 115
Author(s): Chen Chen, Jie Hou, John J. Tanner
Software Mentions: 4
Published: over 4 years ago

10.3390/cancers12040963

Analysis of the Circadian Regulation of Cancer Hallmarks by a Cross-Platform Study of Colorectal Cancer Time-Series Data Reveals an Association with Genes Involved in Huntington’s Disease
Cited by: 14
Author(s): Müge Yalçin, Rukeia El-Athman, Koliane Ouk, Josef Priller, Angela Relógio
Software Mentions: 4
Published: over 4 years ago

10.1038/s42003-020-0804-9

Transcriptomic signatures of brain regional vulnerability to Parkinson’s disease
Cited by: 55
Author(s): Arlin Keo, Ahmed Mahfouz, Angela Ingrassia, Jean Pascal Meneboo, Céline Villenet, Eugénie Mutez, Thomas Comptdaer, Boudewijn P. F. Lelieveldt, Martin Figeac, Marie-Christine Chartier-Harlin, Wilma D. J. van de Berg, Jacobus J. van Hilten, Marcel J. T. Reinders
Software Mentions: 4
Published: over 4 years ago

10.3390/proteomes6020027

Large Scale Proteomic Data and Network-Based Systems Biology Approaches to Explore the Plant World
Cited by: 18
Author(s): Dario Di Silvestre, Andrea Bergamaschi, Edoardo Bellini, Pierluigi Mauri
Software Mentions: 3
Published: over 6 years ago

10.1038/s41598-017-17322-0

Transcriptomic profiling of the human brain reveals that altered synaptic gene expression is associated with chronological aging
Cited by: 43
Author(s): Allissa Dillman, Elisa Majounie, Jinhui Ding, J. Raphael Gibbs, Dena G. Hernandez, Sampath Arepalli, Bryan J. Traynor, Andrew B. Singleton, Dagmar Galter, Mark Cookson
Software Mentions: 3
Published: almost 7 years ago

10.7554/eLife.52981

Losing Dnmt3a dependent methylation in inhibitory neurons impairs neural function by a mechanism impacting Rett syndrome
Cited by: 37
Author(s): Laura A. Lavery, Kerstin Ure, Ying-Wooi Wan, Chongyuan Luo, Alexander J Trostle, Wei Wang, Haijing Jin, José López López, Jacinta Lucero, Mark A. Durham, Rosa Castanon, Joseph R. Nery, Zhandong Liu, Margaret A. Goodell, Joseph R. Ecker, M. Margarita Behrens, Huda Y Zoghbi
Software Mentions: 3
Published: over 4 years ago

10.1111/nyas.13188

Circadian rhythms and metabolism: from the brain to the gut and back again
Cited by: 22
Author(s): Matthew R. Cribbet, Ryan W. Logan, Mathew D. Edwards, Erin C. Hanlon, Clara Bien Peek, Jeremy J. Stubblefield, Sridhar Vasudevan, Fiona C. Ritchey, Ellen Frank
Software Mentions: 2
Published: about 8 years ago

10.1186/s12859-016-1335-8

Prioritizing biological pathways by recognizing context in time-series gene expression data
Cited by: 6
Author(s): Jusang Lee, Kyuri Jo, Sunwon Lee, Jaewoo Kang, Sun Kim
Software Mentions: 2
Published: almost 8 years ago

10.1186/1471-2164-13-610

Cell population-specific expression analysis of human cerebellum
Cited by: 44
Author(s): Aléxandre Kuhn, Abhinav Kumar, Alexandra Beilina, Allissa Dillman, Mark Cookson, Andrew B. Singleton
Software Mentions: 2
Published: almost 13 years ago

10.1186/s13024-020-00392-6

Deciphering cellular transcriptional alterations in Alzheimer’s disease brains
Cited by: 38
Author(s): Xue Wang, Mariet Allen, Shaoyu Li, Zachary Quicksall, Tulsi Patel, Troy Carnwath, Joseph S. Reddy, Minerva M. Carrasquillo, Sarah Lincoln, Thuy Nguyen, Kimberly G. Malphrus, Dennis W. Dickson, Julia E. Crook, Yan W. Asmann, Nilüfer Ertekin-Taner
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pcbi.0020131

Sampling Realistic Protein Conformations Using Local Structural Bias
Cited by: 100
Author(s): Thomas Hamelryck, John T. Kent, Anders Krogh
Software Mentions: 2
Published: about 18 years ago

10.1371/journal.pone.0122294

A Grammar Inference Approach for Predicting Kinase Specific Phosphorylation Sites
Cited by: 17
Author(s): Sriparna Datta, Soumik Mukhopadhyay
Software Mentions: 2
Published: over 9 years ago

10.3389/fnins.2014.00441

Computational deconvolution of genome wide expression data from Parkinson's and Huntington's disease brain tissues using population-specific expression analysis
Cited by: 22
Author(s): Alberto Capurro, Liviu‐Gabriel Bodea, Patrick Schaefer, Ruth Lüthi-Carter, Victoria M. Perreau
Software Mentions: 2
Published: almost 10 years ago

10.1167/iovs.62.10.22

Short-Term High Fructose Intake Impairs Diurnal Oscillations in the Murine Cornea
Cited by: 10
Author(s): Jingxin He, Xinwei Jiao, Xin Sun, Yijia Huang, Pengyang Xu, Yunxia Xue, Ting Fu, Jun Liu, Zhijie Li
Software Mentions: 2
Published: over 3 years ago

10.1016/j.isci.2021.102335

A multi-tissue multi-omics analysis reveals distinct kineztics in entrainment of diurnal transcriptomes by inverted feeding
Cited by: 27
Author(s): Haoran Xin, Fang Deng, Mingxia Zhou, Rongfeng Huang, Xiaogen Ma, He Tian, Yan Tan, Xinghua Chen, Dan Deng, Guanghou Shui, Zhihui Zhang, Min‐Dian Li
Software Mentions: 2
Published: over 3 years ago

10.1016/j.csbj.2019.01.001

Computational drug repurposing for inflammatory bowel disease using genetic information
Cited by: 19
Author(s): Liam Grenier, Pingzhao Hu
Software Mentions: 1
Published: almost 6 years ago

10.3390/cancers12092519

Definition and Independent Validation of a Proteomic-Classifier in Ovarian Cancer
Cited by: 3
Author(s): Sabine Kasimir‐Bauer, Joanna Roder, Eva Obermayr, Sven Mahner, Ignace Vergote, Liselore Loverix, Elena Ioana Braicu, Jalid Sehouli, Nicole Concin, Rainer Kimmig, Lelia Net, Heinrich Röder, Robert Zeillinger, Stefanie Aust
Software Mentions: 1
Published: about 4 years ago

10.1038/s41598-017-07199-4

PhosphoPredict: A bioinformatics tool for prediction of human kinase-specific phosphorylation substrates and sites by integrating heterogeneous feature selection
Cited by: 61
Author(s): Jiangning Song, Huilin Wang, Jiawei Wang, André Leier, Tatiana T. Marquez‐Lago, Bingjiao Yang, Ziding Zhang, Tatsuya Akutsu, Geoffrey I. Webb, Roger J. Daly
Software Mentions: 1
Published: over 7 years ago

10.1371/journal.pone.0220121

Microenvironment of ruptured cerebral aneurysms discovered using data driven analysis of gene expression
Cited by: 3
Author(s): Alexander Landry, Michael Balas, Julian Spears, Zsolt Zádor
Software Mentions: 1
Published: over 5 years ago

10.1038/s41598-018-27129-2

Analysis of the Co-existence of Long-range Transport Biomass Burning and Dust in the Subtropical West Pacific Region
Cited by: 9
Author(s): Xinyi Dong, Joshua S. Fu, Kan Huang, Neng Huei Lin, Sheng Hsiang Wang, Chia Ping Huang Yang
Software Mentions: 1
Published: over 6 years ago

10.1038/s41598-019-49470-w

Patched1 haploinsufficiency severely impacts intermediary metabolism in the skin of Ptch1+/−/ODC transgenic mice
Cited by: 1
Author(s): Changzhao Li, Bharat Mishra, Mahendra Kashyap, Zhiping Weng, Shaida A. Andrabi, Shahid Mukhtar, Arianna L. Kim, David R. Bickers, Levy Kopelovich, Mohammad Athar
Software Mentions: 1
Published: about 5 years ago

10.1128/mSystems.00693-20

Dinoroseobacter shibae Outer Membrane Vesicles Are Enriched for the Chromosome Dimer Resolution Site <i>dif</i>
Cited by: 5
Author(s): Hui Wang, Nicole Beier, Christian Boedeker, Helena Sztajer, Petra Henke, Meina Neumann‐Schaal, Johannes Mansky, Manfred Rohde, Jörg Overmann, Jörn Petersen, Frank Klawonn, Martin Kucklick, Susanne Engelmann, Jürgen Tomasch, Irene Wagner‐Döbler
Software Mentions: 1
Published: over 3 years ago

10.1186/s12859-014-0347-5

Correspondence regarding Zhong et al., BMC Bioinformatics 2013 Mar 7;14:89
Cited by: 1
Author(s): Aléxandre Kuhn
Software Mentions: 1
Published: almost 10 years ago

10.2196/mhealth.6469

A Brief Tool to Assess Image-Based Dietary Records and Guide Nutrition Counselling Among Pregnant Women: An Evaluation
Cited by: 21
Author(s): Amy M. Ashman, Claire Collins, Leanne Brown, Kym Rae, Megan E. Rollo
Software Mentions: 1
Published: about 8 years ago

10.1186/s40425-017-0219-4

Abstracts from the 4th ImmunoTherapy of Cancer Conference
Cited by: 0
Author(s): J. Ženka, V. Caisová, Ondřej Uher, P. Nedbalová, K. Kvardová, K. Masáková, G. Krejčová, L. Paďouková, I. Jochmanová, K. I. Wolf, J. Chmelař, J. Kopecký, L. Loumagne, J. Mestadier, S. D’agostino, A. Rohaut, Y. Ruffin, V. Croize, O. Lemaître, S. S. Sidhu, S. Althammer, K. Steele, M. Rebelatto, T. Tan, T. Wiestler, A. Spitzmueller, R. Korn, G. Schmidt, B. Higgs, X. Li, L. Shi, X. Jin, K. Ranade, S. Koeck, A. Amann, G. Gamerith, M. Zwierzina, E. Lorenz, H. Zwierzina, J. Kern, M. Riva, T. Baert, A. Coosemans, R. Giovannoni, E. Radaelli, W. Gsell, U. Himmelreich, M. Van Ranst, F. Xing, W. Qian, C. Dong, X. Xu, S. Guo, Q. Shi, D. Quandt, B. Seliger, C. Plett, D. C. Amberger, A. Rabe, D. Deen, Z. Stankova, A. Hirn, Y. Vokac, J. Werner, D. Krämer, A. Rank, C. Schmid, H. Schmetzer, M. Guerin, J. M. Weiss, F. Regnier, G. Renault, L. Vimeux, E. Peranzoni, V. Feuillet, M. Thoreau, T. Guilbert, A. Trautmann, N. Bercovici, D. C. Amberger, F. Doraneh-Gard, C. L. Boeck, C. Plett, C. Gunsilius, C. Kugler, J. Werner, J. Schmohl, D. Kraemer, B. Ismann, A. Rank, C. Schmid, H. M. Schmetzer, A. Markota, C. Ochs, P. May, A. Gottschlich, J. Suárez Gosálvez, C. Karches, D. Wenk, S. Endres, S. Kobold, T. Hilmenyuk, R. Klar, F. Jaschinski, G. Gamerith, F. Augustin, E. Lorenz, C. Manzl, E. Hoflehner, P. Moser, B. Zelger, S. Köck, A. Amann, J. Kern, G. Schäfer, D. Öfner, H. Maier, H. Zwierzina, S. Sopper, H. Prado-Garcia, S. Romero-Garcia, R. Sandoval-Martínez, A. Puerto-Aquino, J. Lopez-Gonzalez, U. Rumbo-Nava, R. Klar, T. Hilmenyuk, F. Jaschinski, A. Coosemans, T. Baert, Anaïs Van Hoylandt, P. Busschaert, I. Vergote, T. Baert, Anaïs Van Hoylandt, P. Busschaert, I. Vergote, A. Coosemans, J. Laengle, K. Pilatova, E. Budinska, B. Bencsikova, R. Sefr, R. Nenutil, V. Brychtova, L. Fedorova, B. Hanakova, Lenka Zdražilová-Dubská, Chris Allen, Yuan-Chieh Ku, Warren Tom, Yueming Sun, Alex Pankov, Tim Looney, Fiona Hyland, Janice Au-Young, Ann Mongan, A. Becker, J. B. L. Tan, A. Chen, K. Lawson, E. Lindsey, J. P. Powers, M. Walters, U. Schindler, S. Young, J. C. Jaen, S. Yin, Y. Chen, I. Gullo, G. Gonçalves, M. L. Pinto, M. Athelogou, Gabriela de Oliveira Almeida, R. Huss, C. Oliveira, F. Carneiro, C. Merz, J. Sykora, K. Hermann, R. Hussong, D. M. Richards, H. Fricke, O. Hill, C. Gieffers, M. P. Pinho, José Alexandre Marzagão Barbuto, Stephanie E.B. McArdle, G. Foulds, Jayakumar Vadakekolathu, Tma Abdel-Fatah, C. Johnson, S. Hood, P. Moseley, R. C. Rees, S. Y. T. Chan, A. G. Pockley, S. Rutella, C. Geppert, A. Hartmann, K. Senthil Kumar, M. Gokilavani, Sheen Wang, C. Merz, D. M. Richards, J. Sykora, M. Redondo-Müller, K. Heinonen, V. Marschall, M. Thiemann, H. Fricke, C. Gieffers, O. Hill, L. Zhang, B. Mao, Y. Jin, G. Zhai, Z. Li, Z. Wang, W. Qian, X. An, M. Qiao, J. Zhang, Q. Shi, J. Weber, H. Kluger, R. Halaban, M. Sznol, H. Roder, J. Roder, J. Grigorieva, S. Asmellash, C. Oliveira, K. Meyer, A. Steingrimsson, S. Blackmon, R. Sullivan, C. L. Boeck, D. C. Amberger, F. Doraneh-Gard, W. Sutanto, T. Guenther, J. Schmohl, F. Schuster, H. Salih, F. Babor, A. Borkhardt, H. Schmetzer, Y. Kim, I. Oh, C. Park, S. Ahn, K. Na, S. Song, Y. Choi, L. Fedorova, A. Poprach, R. Lakomy, I. Selingerova, R. Demlova, K. Pilatova, S. Kozakova, D. Valik, K. Petrakova, R. Vyzula, Lenka Zdražilová-Dubská, D. Aguilar-Cazares, M. Galicia-Velasco, C. Camacho-Mendoza, L. Islas-Vazquez, R. Chavez-Dominguez, C. Gonzalez-Gonzalez, H. Prado-Garcia, José Sullivan López‐González, S. Yang, K. D. Moynihan, M. Noh, A. Bekdemir, F. Stellacci, D. J. Irvine, B. Volz, K. Kapp, D. Oswald, B. Wittig, M. Schmidt, R. Chavez-Dominguez, D. Aguilar-Cazares, H. Prado-Garcia, L. Islas-Vazquez, José Sullivan López‐González, R. Kleef, A. Bohdjalian, D. McKee, R. W. Moss, Mesha Saeed, Sara Zalba, Reno Debets, Timo L.M. ten Hagen, S. Javed, J. Becher, F. Koch-Nolte, F. Haag, E. M. Gordon, K. K. Sankhala, N. Stumpf, W. Tseng, S. P. Chawla, N. González Suárez, Gretchen Bergado Báez, Mabel Rodríguez, A. Gutierrez Pérez, L. Chao García, Debbie Fernandez, Judith Raymond Pous, B. Sánchez Ramírez, Célia Jacoberger-Foissac, H. Saliba, C. Seguin, A. Brion, B. Frisch, S. Fournel, B. Heurtault, T. Otterhaug, M. Håkerud, A. Nedberg, V. Edwards, P. Selbo, A. Høgset, T. Jaitly, J. Dörrie, N. Schaft, S. Gross, B. Schuler-Thurner, S. Gupta, Leila Taher, G. Schuler, J. Vera, F. Rataj, F. Kraus, S. Grassmann, M. Chaloupka, S. Lesch, C. Heise, S. Endres, S. Kobold, B. M. Loureiro Cadilha, K. Dorman, C. Heise, F. Rataj, S. Endres, S. Kobold
Software Mentions: 1
Published: over 7 years ago

10.1186/1472-6807-7-2

A generalized analysis of hydrophobic and loop clusters within globular protein sequences
Cited by: 50
Author(s): Richard Eudes, Khanh Le Tuan, J. Delettré, Jean‐Paul Mornon, Isabelle Callebaut
Software Mentions: 1
Published: almost 18 years ago

10.1186/1472-6807-5-17

Protein secondary structure assignment revisited: a detailed analysis of different assignment methods
Cited by: 138
Author(s): Juliette Martin, Guillaume Letellier, Antoine Marin, Jean-François Taly, Alexandre G. de Brevern, Jean‐François Gibrat
Software Mentions: 1
Published: about 19 years ago

10.1186/1471-2199-9-71

In vivo analysis of Caenorhabditis elegans noncoding RNA promoter motifs
Cited by: 16
Author(s): Tiantian Li, Housheng He, Yunfei Wang, Haixia Zheng, Geir Skogerbø, Runsheng Chen
Software Mentions: 1
Published: almost 17 years ago

10.1186/1471-2105-14-89

Digital sorting of complex tissues for cell type-specific gene expression profiles
Cited by: 173
Author(s): Yi Zhong, Ying-Wooi Wan, Kaifang Pang, Lionel M.L. Chow, Zhandong Liu
Software Mentions: 1
Published: over 11 years ago

10.3390/ijms17030333

A New Secondary Structure Assignment Algorithm Using Cα Backbone Fragments
Cited by: 14
Author(s): Chen Cao, Guishen Wang, An Liu, Shaoping Xu, Lincong Wang, Shuxue Zou
Software Mentions: 1
Published: over 8 years ago

10.3390/ijms21030838

Mass Spectrometry-Based Multivariate Proteomic Tests for Prediction of Outcomes on Immune Checkpoint Blockade Therapy: The Modern Analytical Approach
Cited by: 8
Author(s): Julia Grigorieva, Senait Asmellash, Lelia Net, Maxim Tsypin, Heinrich Röder
Software Mentions: 1
Published: almost 5 years ago

10.3389/fnins.2014.00394

Age-related decreased inhibitory vs. excitatory gene expression in the adult autistic brain
Cited by: 16
Author(s): Louie N. van de Lagemaat, Bonnie Nijhof, DaniÃ«lle G. M. Bosch, Mahdokht Kohansal-Nodehi, Shivakumar Keerthikumar, J. Alexander Heimel
Software Mentions: 1
Published: almost 10 years ago

10.1007/s00417-021-05204-1

Needling and open filtering bleb revision after XEN-45 implantation—a retrospective outcome comparison
Cited by: 7
Author(s): Stefan H. Steiner, Hemma Resch, Barbara Kiss, Daniel Buda, Clemens Vass
Software Mentions: 1
Published: over 3 years ago

Projects: bioconductor: PSEA

Papers Mentioning PSEA 40