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Items: 26

1.

Uncovering the subtype-specific temporal order of cancer pathway dysregulation.

Khakabimamaghani S, Ding D, Snow O, Ester M.

PLoS Comput Biol. 2019 Nov 11;15(11):e1007451. doi: 10.1371/journal.pcbi.1007451. eCollection 2019 Nov.

2.

MOLI: multi-omics late integration with deep neural networks for drug response prediction.

Sharifi-Noghabi H, Zolotareva O, Collins CC, Ester M.

Bioinformatics. 2019 Jul 15;35(14):i501-i509. doi: 10.1093/bioinformatics/btz318.

3.

Collaborative intra-tumor heterogeneity detection.

Khakabimamaghani S, Malikic S, Tang J, Ding D, Morin R, Chindelevitch L, Ester M.

Bioinformatics. 2019 Jul 15;35(14):i379-i388. doi: 10.1093/bioinformatics/btz355.

4.

Factors that determine the loss of control when reducing therapy by steps in the treatment of moderate-severe asthma in standard clinical practice: A multicentre Spanish study.

Martínez-Moragón E, Delgado J, Mogrovejo S, Fernández-Sánchez T; en nombre del grupo de investigación STEP; Los autores quieren agradecer su colaboración a los siguientes investigadores participantes ordenados alfabéticamente, Jesús JL, Ángel MOM, Patricia PM, Miguel TT, Begoña CO, Ángel FT, Purificación GD, Wilfox JRT, Brian VA, José ZYJ, Teresa ABM, Marta FJ, Nieves HMR, Marta VA, Antonio ÁFJ, Sara AS, Rosa BGM, Estela GNM, Diego AC, Núria AS, Cristina BG, Astrid CL, David RC, Jordi JP, Alejandra LG, Olga LS, Carlos MR, Pilar MO, Xavier MG, Ester PN, Francisco PC, Karina PC, Antoni RB, Luisa ROM, Dan SB, Joan SB, Pere SM, Ana SS, Lorena SR, Joan VC, Xavier VG, Ignacio AZ, Ignacio AE, Miguel HP, Milagros IPM, Carmen JM, Adolfo LC, Amaia LL, Paula LL, Joaquina PP, Vanessa ZL, Lidia AG, Pablo GMJ, Marisa MD, Teresa PM, Tahar A, Isabel AIM, Michael AO, Aurelio AM, Ignacio GN, Diego GF, Antonio LC, Luis FP, Maria MME, Félix OP, Isabela R, Antonio RPJ, Dolores SSM, Frederic TS, Alberto LN, Pedro GB, Luis GMF, Patricia MC, Manuel ECL, Marina BA, Manuel GPJ, Vanessa GP, Francisco-Javier GB, Pilar IS, Jorge MRP, Fernando MN, Ramón NO, Carracedo SM, Juan SA, Julia TR, Santiago AE, Carlos SN, Gladis ST, Mar ERM, Fernando FLJ, Ángeles LJM, José RVM, Susana CP, Silvia DQ, Antonio NEJ, Eduardo FG, Belén HJ, Victoria MG, Lucía VV, Joaquín CS, Santonio CVJ, Alfonso ALJ, Eduardo AC, María CMJ, Dolores SVA, Patricia BM, Begoña BR, Beatriz FP, Domingo FG, Virginia SG, Adolfo VRL, Silvia LA, Francisco CG, Teresa GF, Joaquín ML, Noemí MM, Soledad AV, Darío AA, Irina B, Puerto CAMD, Remedios CC, Fernando CA, Mercedes CÁ, Belén HME, Magdalena DCR, Mar GCMD, Leticia GR, Andrés GRTJ, Eloina GM, Emma GS, Fernando GT, Aythamy HS, Lys HHP, Ruth HMM, Pedro LR, Belén LB, Ester MV, Beatriz MC, Antonio MF, Esther MG, Elena OC, Fernando PS, Yesenia PAA, Raquel PR, Natividad QR, Ángela RP, Beatriz RJ, Mercedes RR, Ana RI, Antonio RP, José SGM, Jesús TTM, Laura VF, Concepción VA, Alexandra YM, Ismael APGR, José ARAR, Manuel BMJ, Miguel BM, Gustavo LM, Ignacio GN, Francisco LL, Alfonso MP, Ezequiel OST, Alicia PG, Manuel PEC, Carmen SE, Francisco AAÁ, Consuelo ARM, Rubén AE, Roberto BM, Javier CLF, Tamara GU, Sonia HM, Alfredo RL, Raquel DQ.

Rev Clin Esp. 2019 Jul 23. pii: S0014-2565(19)30150-X. doi: 10.1016/j.rce.2019.05.004. [Epub ahead of print] English, Spanish.

PMID:
31350049
5.

Performance comparison of linear and non-linear feature selection methods for the analysis of large survey datasets.

Krakovska O, Christie G, Sixsmith A, Ester M, Moreno S.

PLoS One. 2019 Mar 21;14(3):e0213584. doi: 10.1371/journal.pone.0213584. eCollection 2019.

6.

SUBSTRA: Supervised Bayesian Patient Stratification.

Khakabimamaghani S, Kelkar YD, Grande BM, Morin RD, Ester M, Ziemek D.

Bioinformatics. 2019 Sep 15;35(18):3263-3272. doi: 10.1093/bioinformatics/btz112.

PMID:
30768166
7.

Tissue-Specific Subcellular Localization Prediction Using Multi-Label Markov Random Fields.

Zhu L, Hofestadt R, Ester M.

IEEE/ACM Trans Comput Biol Bioinform. 2019 Sep-Oct;16(5):1471-1482. doi: 10.1109/TCBB.2019.2897683. Epub 2019 Feb 5.

PMID:
30736003
8.

HUME: large-scale detection of causal genetic factors of adverse drug reactions.

Mansouri M, Yuan B, Ross CJD, Carleton BC, Ester M.

Bioinformatics. 2018 Dec 15;34(24):4274-4283. doi: 10.1093/bioinformatics/bty475.

PMID:
29931042
9.

Automation of CT-based haemorrhagic stroke assessment for improved clinical outcomes: study protocol and design.

Chinda B, Medvedev G, Siu W, Ester M, Arab A, Gu T, Moreno S, D'Arcy RCN, Song X.

BMJ Open. 2018 Apr 19;8(4):e020260. doi: 10.1136/bmjopen-2017-020260.

10.

Prognostic factors among TB and TB/DM comorbidity among patients on short course regimen within Nairobi and Kiambu counties in Kenya.

Mburu JW, Kingwara L, Ester M, Andrew N.

J Clin Tuberc Other Mycobact Dis. 2018 Apr 10;12:9-13. doi: 10.1016/j.jctube.2018.04.005. eCollection 2018 Aug.

11.

Use of classification and regression tree (CART), to identify hemoglobin A1C (HbA1C) cut-off thresholds predictive of poor tuberculosis treatment outcomes and associated risk factors.

Mburu JW, Kingwara L, Ester M, Andrew N.

J Clin Tuberc Other Mycobact Dis. 2018 Mar 13;11:10-16. doi: 10.1016/j.jctube.2018.01.002. eCollection 2018 May.

12.

SimBoost: a read-across approach for predicting drug-target binding affinities using gradient boosting machines.

He T, Heidemeyer M, Ban F, Cherkasov A, Ester M.

J Cheminform. 2017 Apr 18;9(1):24. doi: 10.1186/s13321-017-0209-z.

13.

A three-tier algorithm for guanidinoacetate methyltransferase (GAMT) deficiency newborn screening.

Sinclair GB, van Karnebeek CD, Ester M, Boyd F, Nelson T, Stockler-Ipsiroglu S, Vallance H.

Mol Genet Metab. 2016 Jul;118(3):173-7. doi: 10.1016/j.ymgme.2016.05.002. Epub 2016 May 7.

PMID:
27233226
14.

BAYESIAN BICLUSTERING FOR PATIENT STRATIFICATION.

Khakabimamaghani S, Ester M.

Pac Symp Biocomput. 2016;21:345-56.

15.

The East Jakarta Project: surveillance for highly pathogenic avian influenza A(H5N1) and seasonal influenza viruses in patients seeking care for respiratory disease, Jakarta, Indonesia, October 2011-September 2012.

Storms AD, Kusriastuti R, Misriyah S, Praptiningsih CY, Amalya M, Lafond KE, Samaan G, Triada R, Iuliano AD, Ester M, Sidjabat R, Chittenden K, Vogel R, Widdowson MA, Mahoney F, Uyeki TM.

Epidemiol Infect. 2015 Dec;143(16):3394-404. doi: 10.1017/S0950268815000771. Epub 2015 Apr 27.

PMID:
25912029
16.

A highly specialized flavin mononucleotide riboswitch responds differently to similar ligands and confers roseoflavin resistance to Streptomyces davawensis.

Pedrolli DB, Matern A, Wang J, Ester M, Siedler K, Breaker R, Mack M.

Nucleic Acids Res. 2012 Sep 1;40(17):8662-73. Epub 2012 Jun 26.

17.

Optimally discriminative subnetwork markers predict response to chemotherapy.

Dao P, Wang K, Collins C, Ester M, Lapuk A, Sahinalp SC.

Bioinformatics. 2011 Jul 1;27(13):i205-13. doi: 10.1093/bioinformatics/btr245.

18.

Module discovery by exhaustive search for densely connected, co-expressed regions in biomolecular interaction networks.

Colak R, Moser F, Chu JS, Schönhuth A, Chen N, Ester M.

PLoS One. 2010 Oct 25;5(10):e13348. doi: 10.1371/journal.pone.0013348. Erratum in: PLoS One. 2010;5(12) doi: 10.1371/annotation/ab9e87d9-f59c-4dab-aea5-a3c1116d3d85.

19.

Inferring cancer subnetwork markers using density-constrained biclustering.

Dao P, Colak R, Salari R, Moser F, Davicioni E, Schönhuth A, Ester M.

Bioinformatics. 2010 Sep 15;26(18):i625-31. doi: 10.1093/bioinformatics/btq393.

20.

PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes.

Yu NY, Wagner JR, Laird MR, Melli G, Rey S, Lo R, Dao P, Sahinalp SC, Ester M, Foster LJ, Brinkman FS.

Bioinformatics. 2010 Jul 1;26(13):1608-15. doi: 10.1093/bioinformatics/btq249. Epub 2010 May 13.

21.

Dense graphlet statistics of protein interaction and random networks.

Colak R, Hormozdiari F, Moser F, Schönhuth A, Holman J, Ester M, Sahinalp SC.

Pac Symp Biocomput. 2009:178-89.

22.

Slider--maximum use of probability information for alignment of short sequence reads and SNP detection.

Malhis N, Butterfield YS, Ester M, Jones SJ.

Bioinformatics. 2009 Jan 1;25(1):6-13. doi: 10.1093/bioinformatics/btn565. Epub 2008 Oct 30.

23.

Assessment and integration of publicly available SAGE, cDNA microarray, and oligonucleotide microarray expression data for global coexpression analyses.

Griffith OL, Pleasance ED, Fulton DL, Oveisi M, Ester M, Siddiqui AS, Jones SJ.

Genomics. 2005 Oct;86(4):476-88.

PMID:
16098712
24.

PSORTb v.2.0: expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis.

Gardy JL, Laird MR, Chen F, Rey S, Walsh CJ, Ester M, Brinkman FS.

Bioinformatics. 2005 Mar 1;21(5):617-23. Epub 2004 Oct 22.

PMID:
15501914
25.

PSORT-B: Improving protein subcellular localization prediction for Gram-negative bacteria.

Gardy JL, Spencer C, Wang K, Ester M, Tusnády GE, Simon I, Hua S, deFays K, Lambert C, Nakai K, Brinkman FS.

Nucleic Acids Res. 2003 Jul 1;31(13):3613-7.

26.

Comparison of cephalometric analysis with ethnicity in obstructive sleep apnea syndrome.

Will MJ, Ester MS, Ramirez SG, Tiner BD, McAnear JT, Epstein L.

Sleep. 1995 Dec;18(10):873-5.

PMID:
8746394

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