Publications by Tero Aittokallio
256 publications found
Publications 2024
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Integrated drug profiling and CRISPR screening identify BCR::ABL1-independent vulnerabilities in chronic myeloid leukemia
Cell Rep Med, 5 (5), 101521
DOI 10.1016/j.xcrm.2024.101521, PubMed 38653245 -
Editorial overview-Artificial intelligence methodologies in structural biology: Bridging the gap to medical applications
Curr Opin Struct Biol, 87, 102862
DOI 10.1016/j.sbi.2024.102862, PubMed 38870638 -
A synthetic lethal dependency on casein kinase 2 in response to replication-perturbing therapeutics in RB1-deficient cancer cells
Sci Adv, 10 (21), eadj1564
DOI 10.1126/sciadv.adj1564, PubMed 38781347 -
RepurposeDrugs: an interactive web-portal and predictive platform for repurposing mono- and combination therapies
Brief Bioinform, 25 (4)
DOI 10.1093/bib/bbae328, PubMed 38980370 -
Single-cell transcriptomes identify patient-tailored therapies for selective co-inhibition of cancer clones
Nat Commun, 15 (1), 8579
DOI 10.1038/s41467-024-52980-5, PubMed 39362905 -
ScType enables fast and accurate cell type identification from spatial transcriptomics data
Bioinformatics, 40 (7)
DOI 10.1093/bioinformatics/btae426, PubMed 38936341 -
Attention-based approach to predict drug-target interactions across seven target superfamilies
Bioinformatics, 40 (8)
DOI 10.1093/bioinformatics/btae496, PubMed 39115379 -
Hyperactive STAT5 hijacks T cell receptor signaling and drives immature T cell acute lymphoblastic leukemia
J Clin Invest, 134 (8)
DOI 10.1172/JCI168536, PubMed 38618957 -
Validation guidelines for drug-target prediction methods
Expert Opin Drug Discov, 1-15 (in press)
DOI 10.1080/17460441.2024.2430955, PubMed 39568436 -
Optimizing drug combinations for T-PLL: restoring DNA damage and P53-mediated apoptotic responses
Blood, 144 (15), 1595-1610
DOI 10.1182/blood.2023022884, PubMed 38941598 -
Tutorial on survival modeling with applications to omics data
Bioinformatics, 40 (3)
DOI 10.1093/bioinformatics/btae132, PubMed 38445722
Publications 2023
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Chemogenomic library design strategies for precision oncology, applied to phenotypic profiling of glioblastoma patient cells
iScience, 26 (7), 107209
DOI 10.1016/j.isci.2023.107209, PubMed 37485377 -
Robust scoring of selective drug responses for patient-tailored therapy selection
Nat Protoc, 19 (1), 60-82
DOI 10.1038/s41596-023-00903-x, PubMed 37996540 -
PP2A-based triple-strike therapy overcomes mitochondrial apoptosis resistance in brain cancer cells
Mol Oncol, 17 (9), 1803-1820
DOI 10.1002/1878-0261.13488, PubMed 37458534 -
OSCAR: Optimal subset cardinality regression using the L0-pseudonorm with applications to prognostic modelling of prostate cancer
PLoS Comput Biol, 19 (3), e1010333
DOI 10.1371/journal.pcbi.1010333, PubMed 36897911 -
Glioblastoma and the search for non-hypothesis driven combination therapeutics in academia
Front Oncol, 12, 1075559
DOI 10.3389/fonc.2022.1075559, PubMed 36733367 -
Systematic Literature Review of Economic Evaluations of Treatment Alternatives in Chronic Lymphocytic Leukemia
BioDrugs, 37 (2), 219-233
DOI 10.1007/s40259-023-00583-9, PubMed 36795353 -
The miR-141/200c-STAT4 Axis Contributes to Leukemogenesis by Enhancing Cell Proliferation in T-PLL
Cancers (Basel), 15 (9)
DOI 10.3390/cancers15092527, PubMed 37173993 -
Breeze 2.0: an interactive web-tool for visual analysis and comparison of drug response data
Nucleic Acids Res, 51 (W1), W57-W61
DOI 10.1093/nar/gkad390, PubMed 37178002 -
Resistance to immune checkpoint therapies by tumour-induced T-cell desertification and exclusion: key mechanisms, prognostication and new therapeutic opportunities
Br J Cancer, 129 (8), 1212-1224
DOI 10.1038/s41416-023-02361-4, PubMed 37454231
Publications 2022
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What are the current challenges for machine learning in drug discovery and repurposing?
Expert Opin Drug Discov, 17 (5), 423-425
DOI 10.1080/17460441.2022.2050694, PubMed 35255749 -
Computational Pipeline for Rational Drug Combination Screening in Patient-Derived Cells
Methods Mol Biol, 2449, 327-348
DOI 10.1007/978-1-0716-2095-3_14, PubMed 35507270 -
Artificial intelligence for drug response prediction in disease models
Brief Bioinform, 23 (1)
DOI 10.1093/bib/bbab450, PubMed 34655289 -
Development of actionable targets of multi-kinase inhibitors (AToMI) screening platform to dissect kinase targets of staurosporines in glioblastoma cells
Sci Rep, 12 (1), 13796
DOI 10.1038/s41598-022-18118-7, PubMed 35963891 -
Tumor microenvironment as a metapopulation model: The effects of angiogenesis, emigration and treatment modalities
J Theor Biol, 545, 111147
DOI 10.1016/j.jtbi.2022.111147, PubMed 35489642 -
High intratumoral dihydrotestosterone is associated with antiandrogen resistance in VCaP prostate cancer xenografts in castrated mice
iScience, 25 (5), 104287
DOI 10.1016/j.isci.2022.104287, PubMed 35573198 -
Fully-automated and ultra-fast cell-type identification using specific marker combinations from single-cell transcriptomic data
Nat Commun, 13 (1), 1246
DOI 10.1038/s41467-022-28803-w, PubMed 35273156 -
SynergyFinder 3.0: an interactive analysis and consensus interpretation of multi-drug synergies across multiple samples
Nucleic Acids Res, 50 (W1), W739-W743
DOI 10.1093/nar/gkac382, PubMed 35580060 -
An immunity and pyroptosis gene-pair signature predicts overall survival in acute myeloid leukemia
Leukemia, 36 (10), 2384-2395
DOI 10.1038/s41375-022-01662-6, PubMed 35945345 -
Systematic review of computational methods for drug combination prediction
Comput Struct Biotechnol J, 20, 2807-2814
DOI 10.1016/j.csbj.2022.05.055, PubMed 35685365 -
Drug response profiles in patient-derived cancer cells across histological subtypes of ovarian cancer: real-time therapy tailoring for a patient with low-grade serous carcinoma
Br J Cancer, 128 (4), 678-690
DOI 10.1038/s41416-022-02067-z, PubMed 36476658 -
Discovery of host-directed modulators of virus infection by probing the SARS-CoV-2-host protein-protein interaction network
Brief Bioinform, 23 (6)
DOI 10.1093/bib/bbac456, PubMed 36305426 -
Evaluation of statistical approaches for association testing in noisy drug screening data
BMC Bioinformatics, 23 (1), 188
DOI 10.1186/s12859-022-04693-z, PubMed 35585485 -
Combinations of Host- and Virus-Targeting Antiviral Drugs Confer Synergistic Suppression of SARS-CoV-2
Microbiol Spectr, 10 (5), e0333122
DOI 10.1128/spectrum.03331-22, PubMed 36190406 -
Target-specific compound selectivity for multi-target drug discovery and repurposing
Front Pharmacol, 13, 1003480
DOI 10.3389/fphar.2022.1003480, PubMed 36225560 -
Functional Testing to Characterize and Stratify PI3K Inhibitor Responses in Chronic Lymphocytic Leukemia
Clin Cancer Res, 28 (20), 4444-4455
DOI 10.1158/1078-0432.CCR-22-1221, PubMed 35998013 -
Tissue-specific identification of multi-omics features for pan-cancer drug response prediction
iScience, 25 (8), 104767
DOI 10.1016/j.isci.2022.104767, PubMed 35992090 -
EnrichIntersect: an R package for custom set enrichment analysis and interactive visualization of intersecting sets
Bioinform Adv, 2 (1), vbac073
DOI 10.1093/bioadv/vbac073, PubMed 36699400
Publications 2021
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Re-defining synthetic lethality by phenotypic profiling for precision oncology
Cell Chem Biol, 28 (3), 246-256
DOI 10.1016/j.chembiol.2021.01.026, PubMed 33631125 -
Crowdsourced mapping of unexplored target space of kinase inhibitors
Nat Commun, 12 (1), 3307
DOI 10.1038/s41467-021-23165-1, PubMed 34083538 -
Characterizing the Quality of Insight by Interactions: A Case Study
IEEE Trans Vis Comput Graph, 27 (8), 3410-3424
DOI 10.1109/TVCG.2020.2977634, PubMed 32142444 -
Network-guided identification of cancer-selective combinatorial therapies in ovarian cancer
Brief Bioinform, 22 (6)
DOI 10.1093/bib/bbab272, PubMed 34343245 -
Inhibition of Arenaviruses by Combinations of Orally Available Approved Drugs
Antimicrob Agents Chemother, 65 (4)
DOI 10.1128/AAC.01146-20, PubMed 33468464 -
Erratum for Herring et al., "Inhibition of Arenaviruses by Combinations of Orally Available Approved Drugs"
Antimicrob Agents Chemother, 65 (6)
DOI 10.1128/AAC.00653-21, PubMed 34006613 -
Patient-tailored design for selective co-inhibition of leukemic cell subpopulations
Sci Adv, 7 (8)
DOI 10.1126/sciadv.abe4038, PubMed 33608276 -
Multi-modal meta-analysis of cancer cell line omics profiles identifies ECHDC1 as a novel breast tumor suppressor
Mol Syst Biol, 17 (3), e9526
DOI 10.15252/msb.20209526, PubMed 33750001 -
Implementing a Functional Precision Medicine Tumor Board for Acute Myeloid Leukemia
Cancer Discov, 12 (2), 388-401
DOI 10.1158/2159-8290.CD-21-0410, PubMed 34789538 -
Corrections: Reinstated p53 response and high anti-T-cell leukemia activity by the novel alkylating deacetylase inhibitor tinostamustine
Leukemia, 35 (1), 293
DOI 10.1038/s41375-020-01067-3, PubMed 33097839 -
Novel Small Molecule Hsp90/Cdc37 Interface Inhibitors Indirectly Target K-Ras-Signaling
Cancers (Basel), 13 (4)
DOI 10.3390/cancers13040927, PubMed 33672199 -
Artificial intelligence, machine learning, and drug repurposing in cancer
Expert Opin Drug Discov, 16 (9), 977-989
DOI 10.1080/17460441.2021.1883585, PubMed 33543671 -
Development of HDAC Inhibitors Exhibiting Therapeutic Potential in T-Cell Prolymphocytic Leukemia
J Med Chem, 64 (12), 8486-8509
DOI 10.1021/acs.jmedchem.1c00420, PubMed 34101461 -
Modeling drug combination effects via latent tensor reconstruction
Bioinformatics, 37 (Suppl_1), i93-i101
DOI 10.1093/bioinformatics/btab308, PubMed 34252952 -
Bayesian multi-source regression and monocyte-associated gene expression predict BCL-2 inhibitor resistance in acute myeloid leukemia
NPJ Precis Oncol, 5 (1), 71
DOI 10.1038/s41698-021-00209-9, PubMed 34302041 -
Drug Combinations as a First Line of Defense against Coronaviruses and Other Emerging Viruses
mBio, 12 (6), e0334721
DOI 10.1128/mbio.03347-21, PubMed 34933447 -
Drug Combinations as a First Line of Defense against Coronaviruses and Other Emerging Viruses
mBio, 12 (6), e03347-21 -
Multi-Omics Marker Analysis Enables Early Prediction of Breast Tumor Progression
Front Genet, 12, 670749
DOI 10.3389/fgene.2021.670749, PubMed 34149812
Publications 2020
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RUNX1 mutations in blast-phase chronic myeloid leukemia associate with distinct phenotypes, transcriptional profiles, and drug responses
Leukemia, 35 (4), 1087-1099
DOI 10.1038/s41375-020-01011-5, PubMed 32782381 -
Improved detection of differentially represented DNA barcodes for high-throughput clonal phenomics
Mol Syst Biol, 16 (3), e9195
DOI 10.15252/msb.20199195, PubMed 32187448 -
Integrated drug profiling and CRISPR screening identify essential pathways for CAR T-cell cytotoxicity
Blood, 135 (9), 597-609
DOI 10.1182/blood.2019002121, PubMed 31830245 -
A relational database to identify differentially expressed genes in the endometrium and endometriosis lesions
Sci Data, 7 (1), 284
DOI 10.1038/s41597-020-00623-x, PubMed 32859947 -
A normalized drug response metric improves accuracy and consistency of anticancer drug sensitivity quantification in cell-based screening
Commun Biol, 3 (1), 42
DOI 10.1038/s42003-020-0765-z, PubMed 31974521 -
SynergyFinder 2.0: visual analytics of multi-drug combination synergies
Nucleic Acids Res, 48 (W1), W488-W493
DOI 10.1093/nar/gkaa216, PubMed 32246720 -
SynergyFinder: a web application for analyzing drug combination dose-response matrix data
Bioinformatics, 36 (8), 2645
DOI 10.1093/bioinformatics/btaa102, PubMed 32118251 -
SynToxProfiler: An interactive analysis of drug combination synergy, toxicity and efficacy
PLoS Comput Biol, 16 (2), e1007604
DOI 10.1371/journal.pcbi.1007604, PubMed 32012154 -
Leveraging multi-way interactions for systematic prediction of pre-clinical drug combination effects
Nat Commun, 11 (1), 6136
DOI 10.1038/s41467-020-19950-z, PubMed 33262326 -
Phosphoproteome and drug-response effects mediated by the three protein phosphatase 2A inhibitor proteins CIP2A, SET, and PME-1
J Biol Chem, 295 (13), 4194-4211
DOI 10.1074/jbc.RA119.011265, PubMed 32071079 -
KIT pathway upregulation predicts dasatinib efficacy in acute myeloid leukemia
Leukemia, 34 (10), 2780-2784
DOI 10.1038/s41375-020-0978-7, PubMed 32678289 -
Noncanonical effector functions of the T-memory-like T-PLL cell are shaped by cooperative TCL1A and TCR signaling
Blood, 136 (24), 2786-2802
DOI 10.1182/blood.2019003348, PubMed 33301031 -
Breeze: an integrated quality control and data analysis application for high-throughput drug screening
Bioinformatics, 36 (11), 3602-3604
DOI 10.1093/bioinformatics/btaa138, PubMed 32119072 -
Multiobjective optimization identifies cancer-selective combination therapies
PLoS Comput Biol, 16 (12), e1008538
DOI 10.1371/journal.pcbi.1008538, PubMed 33370253 -
Reinstated p53 response and high anti-T-cell leukemia activity by the novel alkylating deacetylase inhibitor tinostamustine
Leukemia, 34 (9), 2513-2518
DOI 10.1038/s41375-020-0772-6, PubMed 32099034 -
UBR5 Is Coamplified with MYC in Breast Tumors and Encodes an Ubiquitin Ligase That Limits MYC-Dependent Apoptosis
Cancer Res, 80 (7), 1414-1427
DOI 10.1158/0008-5472.CAN-19-1647, PubMed 32029551 -
Interactive visual analysis of drug-target interaction networks using Drug Target Profiler, with applications to precision medicine and drug repurposing
Brief Bioinform, 21 (1), 211-220
DOI 10.1093/bib/bby119, PubMed 30566623 -
A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer
Nat Genet, 52 (4), 448-457
DOI 10.1038/s41588-020-0603-8, PubMed 32246132 -
Systematic mapping of cancer cell target dependencies using high-throughput drug screening in triple-negative breast cancer
Comput Struct Biotechnol J, 18, 3819-3832
DOI 10.1016/j.csbj.2020.11.001, PubMed 33335681
Publications 2019
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Novel Screening Method Identifies PI3Kα, mTOR, and IGF1R as Key Kinases Regulating Cardiomyocyte Survival
J Am Heart Assoc, 8 (21), e013018
DOI 10.1161/JAHA.119.013018, PubMed 31617439 -
Phenotypic Screening Combined with Machine Learning for Efficient Identification of Breast Cancer-Selective Therapeutic Targets
Cell Chem Biol, 26 (7), 970-979.e4
DOI 10.1016/j.chembiol.2019.03.011, PubMed 31056464 -
DNMT Inhibitors Increase Methylation in the Cancer Genome
Front Pharmacol, 10, 385
DOI 10.3389/fphar.2019.00385, PubMed 31068808 -
Genome-wide off-targets of drugs: risks and opportunities
Cell Biol Toxicol, 35 (6), 485-487
DOI 10.1007/s10565-019-09491-7, PubMed 31432301 -
Pharmacological reactivation of MYC-dependent apoptosis induces susceptibility to anti-PD-1 immunotherapy
Nat Commun, 10 (1), 620
DOI 10.1038/s41467-019-08541-2, PubMed 30728358 -
Publisher Correction: Pharmacological reactivation of MYC-dependent apoptosis induces susceptibility to anti-PD-1 immunotherapy
Nat Commun, 10 (1), 932
DOI 10.1038/s41467-019-08956-x, PubMed 30787321 -
Modelling of killer T-cell and cancer cell subpopulation dynamics under immuno- and chemotherapies
J Theor Biol, 488, 110136
DOI 10.1016/j.jtbi.2019.110136, PubMed 31887273 -
Genetic and functional implications of an exonic TRIM55 variant in heart failure
J Mol Cell Cardiol, 138, 222-233
DOI 10.1016/j.yjmcc.2019.12.008, PubMed 31866377 -
Prediction of drug combination effects with a minimal set of experiments
Nat Mach Intell, 1 (12), 568-577
DOI 10.1038/s42256-019-0122-4, PubMed 32368721 -
Integrated Analysis of Drug Sensitivity and Selectivity to Predict Synergistic Drug Combinations and Target Coaddictions in Cancer
Methods Mol Biol, 1888, 205-217
DOI 10.1007/978-1-4939-8891-4_12, PubMed 30519949 -
Cost-effective survival prediction for patients with advanced prostate cancer using clinical trial and real-world hospital registry datasets
Int J Med Inform, 133, 104014
DOI 10.1016/j.ijmedinf.2019.104014, PubMed 31783311 -
Chemogenomic Analysis of the Druggable Kinome and Its Application to Repositioning and Lead Identification Studies
Cell Chem Biol, 26 (11), 1608-1622.e6
DOI 10.1016/j.chembiol.2019.08.007, PubMed 31521622 -
Network pharmacology modeling identifies synergistic Aurora B and ZAK interaction in triple-negative breast cancer
NPJ Syst Biol Appl, 5, 20
DOI 10.1038/s41540-019-0098-z, PubMed 31312514 -
JAK/STAT-Activating Genomic Alterations Are a Hallmark of T-PLL
Cancers (Basel), 11 (12)
DOI 10.3390/cancers11121833, PubMed 31766351
Publications 2018
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Machine learning and feature selection for drug response prediction in precision oncology applications
Biophys Rev, 11 (1), 31-39
DOI 10.1007/s12551-018-0446-z, PubMed 30097794 -
Global proteomics profiling improves drug sensitivity prediction: results from a multi-omics, pan-cancer modeling approach
Bioinformatics, 34 (8), 1353-1362
DOI 10.1093/bioinformatics/btx766, PubMed 29186355 -
Immune cell contexture in the bone marrow tumor microenvironment impacts therapy response in CML
Leukemia, 32 (7), 1643-1656
DOI 10.1038/s41375-018-0175-0, PubMed 29925907 -
Learning with multiple pairwise kernels for drug bioactivity prediction
Bioinformatics, 34 (13), i509-i518
DOI 10.1093/bioinformatics/bty277, PubMed 29949975 -
Aggressive natural killer-cell leukemia mutational landscape and drug profiling highlight JAK-STAT signaling as therapeutic target
Nat Commun, 9 (1), 1567
DOI 10.1038/s41467-018-03987-2, PubMed 29674644 -
Methods for High-throughput Drug Combination Screening and Synergy Scoring
Methods Mol Biol, 1711, 351-398
DOI 10.1007/978-1-4939-7493-1_17, PubMed 29344898 -
Patient-Customized Drug Combination Prediction and Testing for T-cell Prolymphocytic Leukemia Patients
Cancer Res, 78 (9), 2407-2418
DOI 10.1158/0008-5472.CAN-17-3644, PubMed 29483097 -
Secreted frizzled-related protein 2 (SFRP2) expression promotes lesion proliferation via canonical WNT signaling and indicates lesion borders in extraovarian endometriosis
Hum Reprod, 33 (5), 817-831
DOI 10.1093/humrep/dey026, PubMed 29462326 -
Adrenals Contribute to Growth of Castration-Resistant VCaP Prostate Cancer Xenografts
Am J Pathol, 188 (12), 2890-2901
DOI 10.1016/j.ajpath.2018.07.029, PubMed 30273606 -
Combined ASRGL1 and p53 immunohistochemistry as an independent predictor of survival in endometrioid endometrial carcinoma
Gynecol Oncol, 149 (1), 173-180
DOI 10.1016/j.ygyno.2018.02.016, PubMed 29486992 -
Novel activities of safe-in-human broad-spectrum antiviral agents
Antiviral Res, 154, 174-182
DOI 10.1016/j.antiviral.2018.04.016, PubMed 29698664 -
PP2A inhibition is a druggable MEK inhibitor resistance mechanism in KRAS-mutant lung cancer cells
Sci Transl Med, 10 (450)
DOI 10.1126/scitranslmed.aaq1093, PubMed 30021885 -
Drug-Sensitivity Screening and Genomic Characterization of 45 HPV-Negative Head and Neck Carcinoma Cell Lines for Novel Biomarkers of Drug Efficacy
Mol Cancer Ther, 17 (9), 2060-2071
DOI 10.1158/1535-7163.MCT-17-0733, PubMed 29970484 -
ePCR: an R-package for survival and time-to-event prediction in advanced prostate cancer, applied to real-world patient cohorts
Bioinformatics, 34 (22), 3957-3959
DOI 10.1093/bioinformatics/bty477, PubMed 29912284 -
Susceptibility of low-density lipoprotein particles to aggregate depends on particle lipidome, is modifiable, and associates with future cardiovascular deaths
Eur Heart J, 39 (27), 2562-2573
DOI 10.1093/eurheartj/ehy319, PubMed 29982602 -
Drug Target Commons 2.0: a community platform for systematic analysis of drug-target interaction profiles
Database (Oxford), 2018, 1-13
DOI 10.1093/database/bay083, PubMed 30219839
Publications 2017
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Matched preclinical designs for improved translatability
Sci Transl Med, 9 (389)
DOI 10.1126/scitranslmed.aal4101, PubMed 28490671 -
Systematic identification of feature combinations for predicting drug response with Bayesian multi-view multi-task linear regression
Bioinformatics, 33 (14), i359-i368
DOI 10.1093/bioinformatics/btx266, PubMed 28881998 -
Discovery of novel drug sensitivities in T-PLL by high-throughput ex vivo drug testing and mutation profiling
Leukemia, 32 (3), 774-787
DOI 10.1038/leu.2017.252, PubMed 28804127 -
The inconvenience of data of convenience: computational research beyond post-mortem analyses
Nat Methods, 14 (10), 937-938
DOI 10.1038/nmeth.4457, PubMed 28960198 -
Antiviral Properties of Chemical Inhibitors of Cellular Anti-Apoptotic Bcl-2 Proteins
Viruses, 9 (10)
DOI 10.3390/v9100271, PubMed 28946654 -
Orphan G protein-coupled receptor GPRC5A modulates integrin β1-mediated epithelial cell adhesion
Cell Adh Migr, 11 (5-6), 434-446
DOI 10.1080/19336918.2016.1245264, PubMed 27715394 -
Whole-genome view of the consequences of a population bottleneck using 2926 genome sequences from Finland and United Kingdom
Eur J Hum Genet, 25 (4), 477-484
DOI 10.1038/ejhg.2016.205, PubMed 28145424 -
Computational-experimental approach to drug-target interaction mapping: A case study on kinase inhibitors
PLoS Comput Biol, 13 (8), e1005678
DOI 10.1371/journal.pcbi.1005678, PubMed 28787438 -
A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines
Cell Syst, 5 (5), 485-497.e3
DOI 10.1016/j.cels.2017.09.004, PubMed 28988802 -
Systematic drug sensitivity testing reveals synergistic growth inhibition by dasatinib or mTOR inhibitors with paclitaxel in ovarian granulosa cell tumor cells
Gynecol Oncol, 144 (3), 621-630
DOI 10.1016/j.ygyno.2016.12.016, PubMed 28104295 -
MediSyn: uncertainty-aware visualization of multiple biomedical datasets to support drug treatment selection
BMC Bioinformatics, 18 (Suppl 10), 393
DOI 10.1186/s12859-017-1785-7, PubMed 28929971 -
SynergyFinder: a web application for analyzing drug combination dose-response matrix data
Bioinformatics, 33 (15), 2413-2415
DOI 10.1093/bioinformatics/btx162, PubMed 28379339 -
Seed-effect modeling improves the consistency of genome-wide loss-of-function screens and identifies synthetic lethal vulnerabilities in cancer cells
Genome Med, 9 (1), 51
DOI 10.1186/s13073-017-0440-2, PubMed 28569207 -
JAK1/2 and BCL2 inhibitors synergize to counteract bone marrow stromal cell-induced protection of AML
Blood, 130 (6), 789-802
DOI 10.1182/blood-2016-02-699363, PubMed 28619982 -
Antiandrogens Reduce Intratumoral Androgen Concentrations and Induce Androgen Receptor Expression in Castration-Resistant Prostate Cancer Xenografts
Am J Pathol, 188 (1), 216-228
DOI 10.1016/j.ajpath.2017.08.036, PubMed 29126837 -
Re: Fatemeh Seyednasrollah, Mehrad Mahmoudian, Liisa Rautakorpi, et al. How Reliable are Trial-based Prognostic Models in Real-world Patients with Metastatic Castration-resistant Prostate Cancer? Eur Urol. 2017;71:838-40
Eur Urol, 72 (3), e68-e69
DOI 10.1016/j.eururo.2017.04.030, PubMed 28499620 -
Early metabolic markers identify potential targets for the prevention of type 2 diabetes
Diabetologia, 60 (9), 1740-1750
DOI 10.1007/s00125-017-4325-0, PubMed 28597074 -
Rapalogs can promote cancer cell stemness in vitro in a Galectin-1 and H-ras-dependent manner
Oncotarget, 8 (27), 44550-44566
DOI 10.18632/oncotarget.17819, PubMed 28562352 -
Improving the efficacy-safety balance of polypharmacology in multi-target drug discovery
Expert Opin Drug Discov, 13 (2), 179-192
DOI 10.1080/17460441.2018.1413089, PubMed 29233023 -
C-SPADE: a web-tool for interactive analysis and visualization of drug screening experiments through compound-specific bioactivity dendrograms
Nucleic Acids Res, 45 (W1), W495-W500
DOI 10.1093/nar/gkx384, PubMed 28472495 -
Drug Target Commons: A Community Effort to Build a Consensus Knowledge Base for Drug-Target Interactions
Cell Chem Biol, 25 (2), 224-229.e2
DOI 10.1016/j.chembiol.2017.11.009, PubMed 29276046 -
In Search of System-Wide Productivity Gains - The Role of Global Collaborations in Preclinical Translation
Clin Transl Sci, 10 (6), 423-425
DOI 10.1111/cts.12498, PubMed 28929592 -
Corrigendum to "Searching for drug synergy in complex dose-response landscapes using an interaction potency model" [Comput. Struct. Biotechnol. J. 13 (2015) 504-513]
Comput Struct Biotechnol J, 15, 387
DOI 10.1016/j.csbj.2017.07.003, PubMed 29991977
Publications 2016
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Drug response prediction by inferring pathway-response associations with kernelized Bayesian matrix factorization
Bioinformatics, 32 (17), i455-i463
DOI 10.1093/bioinformatics/btw433, PubMed 27587662 -
CIP2A Promotes T-Cell Activation and Immune Response to Listeria monocytogenes Infection
PLoS One, 11 (4), e0152996
DOI 10.1371/journal.pone.0152996, PubMed 27100879 -
Identification of selective cytotoxic and synthetic lethal drug responses in triple negative breast cancer cells
Mol Cancer, 15 (1), 34
DOI 10.1186/s12943-016-0517-3, PubMed 27165605 -
Prediction of overall survival for patients with metastatic castration-resistant prostate cancer: development of a prognostic model through a crowdsourced challenge with open clinical trial data
Lancet Oncol, 18 (1), 132-142
DOI 10.1016/S1470-2045(16)30560-5, PubMed 27864015 -
Systematic drug screening reveals specific vulnerabilities and co-resistance patterns in endocrine-resistant breast cancer
BMC Cancer, 16, 378
DOI 10.1186/s12885-016-2452-5, PubMed 27378269 -
The Hydroxysteroid (17β) Dehydrogenase Family Gene HSD17B12 Is Involved in the Prostaglandin Synthesis Pathway, the Ovarian Function, and Regulation of Fertility
Endocrinology, 157 (10), 3719-3730
DOI 10.1210/en.2016-1252, PubMed 27490311 -
Transcriptional response networks for elucidating mechanisms of action of multitargeted agents
Drug Discov Today, 21 (7), 1063-75
DOI 10.1016/j.drudis.2016.03.001, PubMed 26979547 -
Optimized design and analysis of preclinical intervention studies in vivo
Sci Rep, 6, 30723
DOI 10.1038/srep30723, PubMed 27480578 -
Enhanced sensitivity to glucocorticoids in cytarabine-resistant AML
Leukemia, 31 (5), 1187-1195
DOI 10.1038/leu.2016.314, PubMed 27833094 -
Consistency in drug response profiling
Nature, 540 (7631), E5-E6
DOI 10.1038/nature20171, PubMed 27905421 -
Cancer stem cell drugs target K-ras signaling in a stemness context
Oncogene, 35 (40), 5248-5262
DOI 10.1038/onc.2016.59, PubMed 26973241 -
Comprehensive Drug Testing of Patient-derived Conditionally Reprogrammed Cells from Castration-resistant Prostate Cancer
Eur Urol, 71 (3), 319-327
DOI 10.1016/j.eururo.2016.04.019, PubMed 27160946 -
Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis
Nat Commun, 7, 12460
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Erratum: Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis
Nat Commun, 7, 13205
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Multi-Omics Studies towards Novel Modulators of Influenza A Virus-Host Interaction
Viruses, 8 (10)
DOI 10.3390/v8100269, PubMed 27690086 -
Phosphoproteomics to Characterize Host Response During Influenza A Virus Infection of Human Macrophages
Mol Cell Proteomics, 15 (10), 3203-3219
DOI 10.1074/mcp.M116.057984, PubMed 27486199
Publications 2015
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Identification of drug candidates and repurposing opportunities through compound-target interaction networks
Expert Opin Drug Discov, 10 (12), 1333-45
DOI 10.1517/17460441.2015.1096926, PubMed 26429153 -
TIMMA-R: an R package for predicting synergistic multi-targeted drug combinations in cancer cell lines or patient-derived samples
Bioinformatics, 31 (11), 1866-8
DOI 10.1093/bioinformatics/btv067, PubMed 25638808 -
Accumulated Metabolites of Hydroxybutyric Acid Serve as Diagnostic and Prognostic Biomarkers of Ovarian High-Grade Serous Carcinomas
Cancer Res, 76 (4), 796-804
DOI 10.1158/0008-5472.CAN-15-2298, PubMed 26685161 -
Label-free quantitative phosphoproteomics with novel pairwise abundance normalization reveals synergistic RAS and CIP2A signaling
Sci Rep, 5, 13099
DOI 10.1038/srep13099, PubMed 26278961 -
Network pharmacology applications to map the unexplored target space and therapeutic potential of natural products
Nat Prod Rep, 32 (8), 1249-66
DOI 10.1039/c5np00005j, PubMed 26030402 -
Impact of normalization methods on high-throughput screening data with high hit rates and drug testing with dose-response data
Bioinformatics, 31 (23), 3815-21
DOI 10.1093/bioinformatics/btv455, PubMed 26254433 -
Relevance Rank Platform (RRP) for Functional Filtering of High Content Protein-Protein Interaction Data
Mol Cell Proteomics, 14 (12), 3274-83
DOI 10.1074/mcp.M115.050773, PubMed 26499835 -
Specific cancer-associated mutations in the switch III region of Ras increase tumorigenicity by nanocluster augmentation
Elife, 4, e08905
DOI 10.7554/eLife.08905, PubMed 26274561 -
Systematic Mapping of Kinase Addiction Combinations in Breast Cancer Cells by Integrating Drug Sensitivity and Selectivity Profiles
Chem Biol, 22 (8), 1144-55
DOI 10.1016/j.chembiol.2015.06.021, PubMed 26211361 -
What is synergy? The Saariselkä agreement revisited
Front Pharmacol, 6, 181
DOI 10.3389/fphar.2015.00181, PubMed 26388771 -
Liver lipid metabolism is altered by increased circulating estrogen to androgen ratio in male mouse
J Proteomics, 133, 66-75
DOI 10.1016/j.jprot.2015.12.009, PubMed 26691839 -
From drug response profiling to target addiction scoring in cancer cell models
Dis Model Mech, 8 (10), 1255-64
DOI 10.1242/dmm.021105, PubMed 26438695 -
Searching for Drug Synergy in Complex Dose-Response Landscapes Using an Interaction Potency Model
Comput Struct Biotechnol J, 13, 504-13
DOI 10.1016/j.csbj.2015.09.001, PubMed 26949479 -
Systematic Identification of MicroRNAs That Impact on Proliferation of Prostate Cancer Cells and Display Changed Expression in Tumor Tissue
Eur Urol, 69 (6), 1120-8
DOI 10.1016/j.eururo.2015.09.019, PubMed 26489476 -
MicroRNA-135b regulates ERα, AR and HIF1AN and affects breast and prostate cancer cell growth
Mol Oncol, 9 (7), 1287-300
DOI 10.1016/j.molonc.2015.03.001, PubMed 25907805
Publications 2014
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A community effort to assess and improve drug sensitivity prediction algorithms
Nat Biotechnol, 32 (12), 1202-12
DOI 10.1038/nbt.2877, PubMed 24880487 -
Statistical detection of quantitative protein biomarkers provides insights into signaling networks deregulated in acute myeloid leukemia
Proteomics, 14 (21-22), 2443-53
DOI 10.1002/pmic.201300460, PubMed 25211154 -
Intra-tissue steroid profiling indicates differential progesterone and testosterone metabolism in the endometrium and endometriosis lesions
J Clin Endocrinol Metab, 99 (11), E2188-97
DOI 10.1210/jc.2014-1913, PubMed 25137424 -
Castration induces up-regulation of intratumoral androgen biosynthesis and androgen receptor expression in an orthotopic VCaP human prostate cancer xenograft model
Am J Pathol, 184 (8), 2163-73
DOI 10.1016/j.ajpath.2014.04.010, PubMed 24949550 -
Regularized machine learning in the genetic prediction of complex traits
PLoS Genet, 10 (11), e1004754
DOI 10.1371/journal.pgen.1004754, PubMed 25393026 -
Toward more realistic drug-target interaction predictions
Brief Bioinform, 16 (2), 325-37
DOI 10.1093/bib/bbu010, PubMed 24723570 -
PhosFox: a bioinformatics tool for peptide-level processing of LC-MS/MS-based phosphoproteomic data
Proteome Sci, 12, 36
DOI 10.1186/1477-5956-12-36, PubMed 25028575 -
Network pharmacology strategies toward multi-target anticancer therapies: from computational models to experimental design principles
Curr Pharm Des, 20 (1), 23-36
DOI 10.2174/13816128113199990470, PubMed 23530504 -
Making sense of large-scale kinase inhibitor bioactivity data sets: a comparative and integrative analysis
J Chem Inf Model, 54 (3), 735-43
DOI 10.1021/ci400709d, PubMed 24521231 -
Ovarian endometriosis signatures established through discovery and directed mass spectrometry analysis
J Proteome Res, 13 (11), 4983-94
DOI 10.1021/pr500384n, PubMed 25099244 -
Quantitative scoring of differential drug sensitivity for individually optimized anticancer therapies
Sci Rep, 4, 5193
DOI 10.1038/srep05193, PubMed 24898935 -
Novel Lignan and stilbenoid mixture shows anticarcinogenic efficacy in preclinical PC-3M-luc2 prostate cancer model
PLoS One, 9 (4), e93764
DOI 10.1371/journal.pone.0093764, PubMed 24699425 -
Phosphoproteomics combined with quantitative 14-3-3-affinity capture identifies SIRT1 and RAI as novel regulators of cytosolic double-stranded RNA recognition pathway
Mol Cell Proteomics, 13 (10), 2604-17
DOI 10.1074/mcp.M114.038968, PubMed 24997996
Publications 2013
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Predicting drug-target interactions through integrative analysis of chemogenetic assays in yeast
Mol Biosyst, 9 (4), 768-79
DOI 10.1039/c3mb25591c, PubMed 23420501 -
Anticancer compound ABT-263 accelerates apoptosis in virus-infected cells and imbalances cytokine production and lowers survival rates of infected mice
Cell Death Dis, 4 (7), e742
DOI 10.1038/cddis.2013.267, PubMed 23887633 -
Chk1 targeting reactivates PP2A tumor suppressor activity in cancer cells
Cancer Res, 73 (22), 6757-69
DOI 10.1158/0008-5472.CAN-13-1002, PubMed 24072747 -
Genetic variants and their interactions in disease risk prediction - machine learning and network perspectives
BioData Min, 6 (1), 5
DOI 10.1186/1756-0381-6-5, PubMed 23448398 -
Individualized systems medicine strategy to tailor treatments for patients with chemorefractory acute myeloid leukemia
Cancer Discov, 3 (12), 1416-29
DOI 10.1158/2159-8290.CD-13-0350, PubMed 24056683 -
Target inhibition networks: predicting selective combinations of druggable targets to block cancer survival pathways
PLoS Comput Biol, 9 (9), e1003226
DOI 10.1371/journal.pcbi.1003226, PubMed 24068907
Publications 2012
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The rocky road to personalized medicine: computational and statistical challenges
Per Med, 9 (2), 109-114
DOI 10.2217/pme.12.1, PubMed 29758814 -
Obatoclax, saliphenylhalamide, and gemcitabine inhibit influenza a virus infection
J Biol Chem, 287 (42), 35324-35332
DOI 10.1074/jbc.M112.392142, PubMed 22910914 -
Pravastatin-induced improvement in coronary reactivity and circulating ATP and ADP levels in young adults with type 1 diabetes
Front Physiol, 3, 338
DOI 10.3389/fphys.2012.00338, PubMed 22934084 -
Improved statistical modeling of tumor growth and treatment effect in preclinical animal studies with highly heterogeneous responses in vivo
Clin Cancer Res, 18 (16), 4385-96
DOI 10.1158/1078-0432.CCR-11-3215, PubMed 22745104 -
Wrapper-based selection of genetic features in genome-wide association studies through fast matrix operations
Algorithms Mol Biol, 7 (1), 11
DOI 10.1186/1748-7188-7-11, PubMed 22551170 -
A multilevel layout algorithm for visualizing physical and genetic interaction networks, with emphasis on their modular organization
BioData Min, 5, 2
DOI 10.1186/1756-0381-5-2, PubMed 22448851
Publications 2011
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Optimized detection of transcription factor-binding sites in ChIP-seq experiments
Nucleic Acids Res, 40 (1), e1
DOI 10.1093/nar/gkr839, PubMed 22009681 -
Probabilistic analysis of probe reliability in differential gene expression studies with short oligonucleotide arrays
IEEE/ACM Trans Comput Biol Bioinform, 8 (1), 217-25
DOI 10.1109/TCBB.2009.38, PubMed 21071809 -
Quantitative subcellular proteome and secretome profiling of influenza A virus-infected human primary macrophages
PLoS Pathog, 7 (5), e1001340
DOI 10.1371/journal.ppat.1001340, PubMed 21589892 -
Quantitative maps of genetic interactions in yeast - comparative evaluation and integrative analysis
BMC Syst Biol, 5, 45
DOI 10.1186/1752-0509-5-45, PubMed 21435228 -
PolyAlign: A Versatile LC-MS Data Alignment Tool for Landmark-Selected and -Automated Use
Int J Proteomics, 2011, 450290
DOI 10.1155/2011/450290, PubMed 22084688
Publications 2010
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Mahalanobis distance screening of Arabidopsis mutants with chlorophyll fluorescence
Photosynth Res, 105 (3), 273-83
DOI 10.1007/s11120-010-9578-0, PubMed 20730565 -
Genome-wide profiling of interleukin-4 and STAT6 transcription factor regulation of human Th2 cell programming
Immunity, 32 (6), 852-62
DOI 10.1016/j.immuni.2010.06.011, PubMed 20620947 -
Early suppression of immune response pathways characterizes children with prediabetes in genome-wide gene expression profiling
J Autoimmun, 35 (1), 70-6
DOI 10.1016/j.jaut.2010.03.001, PubMed 20356713 -
Genome-wide scoring of positive and negative epistasis through decomposition of quantitative genetic interaction fitness matrices
PLoS One, 5 (7), e11611
DOI 10.1371/journal.pone.0011611, PubMed 20657656 -
Quantitative proteomics analysis of the nuclear fraction of human CD4+ cells in the early phases of IL-4-induced Th2 differentiation
Mol Cell Proteomics, 9 (9), 1937-53
DOI 10.1074/mcp.M900483-MCP200, PubMed 20467038 -
Genetic variants and their interactions in the prediction of increased pre-clinical carotid atherosclerosis: the cardiovascular risk in young Finns study
PLoS Genet, 6 (9), e1001146
DOI 10.1371/journal.pgen.1001146, PubMed 20941391
Publications 2009
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Nocturnal transcutaneous carbon dioxide tension in postmenopausal estrogen users and non-users
Menopause Int, 15 (3), 107-12
DOI 10.1258/mi.2009.009028, PubMed 19723680 -
Transcutaneous carbon dioxide profile during sleep reveals metabolic risk factors in post-menopausal females
Eur Respir J, 34 (5), 1132-9
DOI 10.1183/09031936.00017909, PubMed 19574334 -
Dealing with missing values in large-scale studies: microarray data imputation and beyond
Brief Bioinform, 11 (2), 253-64
DOI 10.1093/bib/bbp059, PubMed 19965979 -
Understanding sleep-disordered breathing through mathematical modelling
Sleep Med Rev, 13 (5), 333-43
DOI 10.1016/j.smrv.2008.09.008, PubMed 19285884 -
Genoscape: a Cytoscape plug-in to automate the retrieval and integration of gene expression data and molecular networks
Bioinformatics, 25 (19), 2617-8
DOI 10.1093/bioinformatics/btp464, PubMed 19654116 -
Optimized detection of differential expression in global profiling experiments: case studies in clinical transcriptomic and quantitative proteomic datasets
Brief Bioinform, 10 (5), 547-55
DOI 10.1093/bib/bbp033, PubMed 19549804 -
Resampling reveals sample-level differential expression in clinical genome-wide studies
OMICS, 13 (5), 381-96
DOI 10.1089/omi.2009.0027, PubMed 19663710 -
An update on clinical proteomics in Alzheimer's research
J Neurochem, 112 (6), 1386-414
DOI 10.1111/j.1471-4159.2009.06558.x, PubMed 20050976 -
Probe-level estimation improves the detection of differential splicing in Affymetrix exon array studies
Genome Biol, 10 (7), R77
DOI 10.1186/gb-2009-10-7-r77, PubMed 19607685 -
A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments
BMC Genomics, 10, 618
DOI 10.1186/1471-2164-10-618, PubMed 20017957 -
Filtering strategies for improving protein identification in high-throughput MS/MS studies
Proteomics, 9 (4), 848-60
DOI 10.1002/pmic.200800517, PubMed 19160393
Publications 2008
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Model-based prediction of sequence alignment quality
Bioinformatics, 24 (19), 2165-71
DOI 10.1093/bioinformatics/btn414, PubMed 18678587 -
Overnight variability in transcutaneous carbon dioxide predicts vascular impairment in women
Exp Physiol, 93 (7), 880-91
DOI 10.1113/expphysiol.2007.041277, PubMed 18296495 -
Reproducibility-optimized test statistic for ranking genes in microarray studies
IEEE/ACM Trans Comput Biol Bioinform, 5 (3), 423-431
DOI 10.1109/tcbb.2007.1078, PubMed 18670045 -
Predicting quantitative genetic interactions by means of sequential matrix approximation
PLoS One, 3 (9), e3284
DOI 10.1371/journal.pone.0003284, PubMed 18818762 -
Missing value imputation improves clustering and interpretation of gene expression microarray data
BMC Bioinformatics, 9, 202
DOI 10.1186/1471-2105-9-202, PubMed 18423022 -
Alignment of LC-MS images, with applications to biomarker discovery and protein identification
Proteomics, 8 (4), 650-72
DOI 10.1002/pmic.200700791, PubMed 18297649
Publications 2007
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Systematic construction of gene coexpression networks with applications to human T helper cell differentiation process
Bioinformatics, 23 (16), 2096-103
DOI 10.1093/bioinformatics/btm309, PubMed 17553854 -
Can carotid body perfusion act as a respiratory controller?
J Theor Biol, 249 (4), 737-48
DOI 10.1016/j.jtbi.2007.09.010, PubMed 17936799 -
Overnight features of transcutaneous carbon dioxide measurement as predictors of metabolic status
Artif Intell Med, 42 (1), 55-65
DOI 10.1016/j.artmed.2007.09.001, PubMed 17981017 -
Computer-assisted identification of multitrace electrophoretic patterns in differential display experiments
Electrophoresis, 28 (6), 879-93
DOI 10.1002/elps.200600424, PubMed 17309051
Publications 2006
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A statistical score for assessing the quality of multiple sequence alignments
BMC Bioinformatics, 7, 484
DOI 10.1186/1471-2105-7-484, PubMed 17081313 -
Model-based analysis of mechanisms responsible for sleep-induced carbon dioxide differences
Bull Math Biol, 68 (2), 315-41
DOI 10.1007/s11538-005-9059-3, PubMed 16794933 -
Parameter estimation of a respiratory control model from noninvasive carbon dioxide measurements during sleep
Math Med Biol, 24 (2), 225-49
DOI 10.1093/imammb/dql031, PubMed 17164471 -
Inspiratory flow shape clustering: an automated method to monitor upper airway performance during sleep
Comput Methods Programs Biomed, 85 (1), 8-18
DOI 10.1016/j.cmpb.2006.09.012, PubMed 17084481 -
Automated pattern ranking in differential display data analysis
Methods Mol Biol, 317, 111-22
DOI 10.1385/1-59259-968-0:111, PubMed 16264225 -
Graph-based methods for analysing networks in cell biology
Brief Bioinform, 7 (3), 243-55
DOI 10.1093/bib/bbl022, PubMed 16880171 -
Improving identification of differentially expressed genes by integrative analysis of Affymetrix and Illumina arrays
OMICS, 10 (3), 369-80
DOI 10.1089/omi.2006.10.369, PubMed 17069514 -
GOlorize: a Cytoscape plug-in for network visualization with Gene Ontology-based layout and coloring
Bioinformatics, 23 (3), 394-6
DOI 10.1093/bioinformatics/btl605, PubMed 17127678 -
Th1 response and cytotoxicity genes are down-regulated in cutaneous T-cell lymphoma
Clin Cancer Res, 12 (16), 4812-21
DOI 10.1158/1078-0432.CCR-06-0532, PubMed 16914566 -
Biochemical and clinical approaches in evaluating the prognosis of colon cancer
Anticancer Res, 26 (6C), 4745-51
PubMed 17214335
Publications 2005
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Non-invasive respiratory monitoring during wakefulness and sleep in pre- and postmenopausal women
Respir Physiol Neurobiol, 150 (1), 66-74
DOI 10.1016/j.resp.2005.03.012, PubMed 15927542 -
Geometrical distortions in two-dimensional gels: applicable correction methods
J Chromatogr B Analyt Technol Biomed Life Sci, 815 (1-2), 25-37
DOI 10.1016/j.jchromb.2004.07.037, PubMed 15652796 -
Integrating probe-level expression changes across generations of Affymetrix arrays
Nucleic Acids Res, 33 (22), e193
DOI 10.1093/nar/gni193, PubMed 16356924 -
A comparative evaluation of software for the analysis of liquid chromatography-tandem mass spectrometry data from isotope coded affinity tag experiments
Proteomics, 5 (11), 2748-60
DOI 10.1002/pmic.200401187, PubMed 15952233 -
A human ImmunoChip cDNA microarray provides a comprehensive tool to study immune responses
J Immunol Methods, 303 (1-2), 122-34
DOI 10.1016/j.jim.2005.06.004, PubMed 16054160 -
Quality classification of tandem mass spectrometry data
Bioinformatics, 22 (4), 400-6
DOI 10.1093/bioinformatics/bti829, PubMed 16352652 -
Medroxyprogesterone improves nocturnal breathing in postmenopausal women with chronic obstructive pulmonary disease
Respir Res, 6 (1), 28
DOI 10.1186/1465-9921-6-28, PubMed 15807890 -
Sleep quality, daytime sleepiness and fasting insulin levels in women with chronic obstructive pulmonary disease
Respir Med, 99 (7), 856-63
DOI 10.1016/j.rmed.2004.11.017, PubMed 15939247 -
Improving missing value estimation in microarray data with gene ontology
Bioinformatics, 22 (5), 566-72
DOI 10.1093/bioinformatics/btk019, PubMed 16377613
Publications 2004
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Statistical methods for identifying conserved residues in multiple sequence alignment
Stat Appl Genet Mol Biol, 3, Article28
DOI 10.2202/1544-6115.1074, PubMed 16646807
Publications 2003
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Efficient estimation of emission probabilities in profile hidden Markov models
Bioinformatics, 19 (18), 2359-68
DOI 10.1093/bioinformatics/btg328, PubMed 14668219 -
Prediction of inspiratory flow shapes during sleep with a mathematic model of upper airway forces
Sleep, 26 (7), 857-63
DOI 10.1093/sleep/26.7.857, PubMed 14655920 -
Computational strategies for analyzing data in gene expression microarray experiments
J Bioinform Comput Biol, 1 (3), 541-86
DOI 10.1142/s0219720003000319, PubMed 15290769 -
Electrophoretic signal comparison applied to mRNA differential display analysis
Biotechniques, 34 (1), 116-22
DOI 10.2144/03341rr02, PubMed 12545548 -
Identification of novel IL-4/Stat6-regulated genes in T lymphocytes
J Immunol, 171 (7), 3627-35
DOI 10.4049/jimmunol.171.7.3627, PubMed 14500660 -
Identification of novel genes regulated by IL-12, IL-4, or TGF-beta during the early polarization of CD4+ lymphocytes
J Immunol, 171 (10), 5328-36
DOI 10.4049/jimmunol.171.10.5328, PubMed 14607935 -
Kinetics and STAT4- or STAT6-mediated regulation of genes involved in lymphocyte polarization to Th1 and Th2 cells
Eur J Immunol, 33 (4), 1105-16
DOI 10.1002/eji.200323899, PubMed 12672077 -
Comparison of PDQuest and Progenesis software packages in the analysis of two-dimensional electrophoresis gels
Proteomics, 3 (10), 1936-46
DOI 10.1002/pmic.200300544, PubMed 14625856 -
Effect of medroxyprogesterone on inspiratory flow shapes during sleep in postmenopausal women
Respir Physiol Neurobiol, 134 (2), 131-43
DOI 10.1016/s1569-9048(02)00208-2, PubMed 12609480 -
State of vigilance, oestrogen replacement therapy, and lipid profile as modifiers of nocturnal movement-induced heart rate responses
Clin Physiol Funct Imaging, 23 (5), 293-9
DOI 10.1046/j.1475-097x.2003.00513.x, PubMed 12950328
Publications 2002
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Adjustment of the human respiratory system to increased upper airway resistance during sleep
Bull Math Biol, 64 (1), 3-28
DOI 10.1006/bulm.2001.0264, PubMed 11868337 -
Hierarchical grid transformation for image warping in the analysis of two-dimensional electrophoresis gels
Proteomics, 2 (11), 1504-15
DOI 10.1002/1615-9861(200211)2:11<1504::AID-PROT1504>3.0.CO;2-B, PubMed 12442250
Publications 2001
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A model of a snorer's upper airway
Math Biosci, 170 (1), 79-90
DOI 10.1016/s0025-5564(00)00062-6, PubMed 11259804 -
Automated detection of differently expressed fragments in mRNA differential display
Electrophoresis, 22 (10), 1935-45
DOI 10.1002/1522-2683(200106)22:10<1935::AID-ELPS1935>3.0.CO;2-5, PubMed 11465492 -
Analysis of inspiratory flow shapes in patients with partial upper-airway obstruction during sleep
Chest, 119 (1), 37-44
DOI 10.1378/chest.119.1.37, PubMed 11157582 -
Climacteric vasomotor symptoms do not predict nocturnal breathing abnormalities in postmenopausal women
Maturitas, 39 (1), 29-37
DOI 10.1016/s0378-5122(01)00172-4, PubMed 11451618
Publications 2000
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Detection of high-frequency respiratory movements during sleep
Comput Methods Programs Biomed, 61 (3), 171-85
DOI 10.1016/s0169-2607(99)00043-7, PubMed 10710180 -
Analysis of similarity of electrophoretic patterns in mRNA differential display
Electrophoresis, 21 (14), 2947-56
DOI 10.1002/1522-2683(20000801)21:14<2947::AID-ELPS2947>3.0.CO;2-N, PubMed 11001309
Publications 1999
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Improving the false nearest neighbors method with graphical analysis
Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics, 60 (1), 416-21
DOI 10.1103/physreve.60.416, PubMed 11969777 -
Classification of nasal inspiratory flow shapes by attributed finite automata
Comput Biomed Res, 32 (1), 34-55
DOI 10.1006/cbmr.1998.1499, PubMed 10066354