A machine learning approach to integrate big data for precision medicine in acute myeloid leukemia

[1]  E. Estey,et al.  Mitoxantrone, Etoposide, and Cytarabine (MEC) Following Epigenetic Priming with Decitabine in Adults with Relapsed/Refractory Acute Myeloid Leukemia or Other High-Grade Myeloid Neoplasms: A Phase 1/2 Study , 2017, Leukemia.

[2]  E. Estey,et al.  A Phase 1/2 Study of G-CSF, Cladribine, Cytarabine, and Dose-Escalated Mitoxantrone (G-CLAM) in Adults with Newly Diagnosed Acute Myeloid Leukemia (AML) or High-Risk Myelodysplastic Syndrome (MDS) , 2016 .

[3]  Hristo S. Paskov,et al.  Multitask learning improves prediction of cancer drug sensitivity , 2016, Scientific Reports.

[4]  Benjamin A. Logsdon,et al.  Extracting a low-dimensional description of multiple gene expression datasets reveals a potential driver for tumor-associated stroma in ovarian cancer , 2016, bioRxiv.

[5]  S. Gore,et al.  Lost in translation? Ten years of development of histone deacetylase inhibitors in acute myeloid leukemia and myelodysplastic syndromes , 2016, Expert opinion on investigational drugs.

[6]  N. Chattopadhyay,et al.  Proteomic discovery of MNT as a novel interacting partner of E3 ubiquitin ligase E6AP and a key mediator of myeloid differentiation , 2015, Oncotarget.

[7]  L. Rönnstrand,et al.  Brain-Expressed X-linked (BEX) proteins in human cancers. , 2015, Biochimica et biophysica acta.

[8]  B. Wegiel,et al.  Role and Regulation of Myeloid Zinc Finger Protein 1 in Cancer , 2015, Journal of cellular biochemistry.

[9]  Marcos González,et al.  Panobinostat as part of induction and maintenance for elderly patients with newly diagnosed acute myeloid leukemia: phase Ib/II panobidara study , 2015, Haematologica.

[10]  G. Deng,et al.  Low expressions of ARS2 and CASP8AP2 predict relapse and poor prognosis in pediatric acute lymphoblastic leukemia patients treated on China CCLG-ALL 2008 protocol. , 2015, Leukemia research.

[11]  Su-In Lee,et al.  Sparse expression bases in cancer reveal tumor drivers , 2015, Nucleic acids research.

[12]  E. Estey,et al.  Mitoxantrone, Etoposide, and Cytarabine (MEC) Following Epigenetic Priming with Decitabine in Adults with Relapsed/Refractory Acute Myeloid Leukemia (AML) or High-Risk Myelodysplastic Syndrome (MDS): A Phase 1 Study , 2014 .

[13]  Nci Dream Community.  A community effort to assess and improve drug sensitivity prediction algorithms , 2014 .

[14]  Roberto Sanchez,et al.  The bromodomain: from epigenome reader to druggable target. , 2014, Biochimica et biophysica acta.

[15]  Su-In Lee,et al.  Efficient Dimensionality Reduction for High-Dimensional Network Estimation , 2014, ICML.

[16]  Jiwang Zhang,et al.  Co-inhibition of NF-κB and JNK is synergistic in TNF-expressing human AML , 2014, The Journal of experimental medicine.

[17]  R. Siebert,et al.  Germline and somatic SMARCA4 mutations characterize small cell carcinoma of the ovary, hypercalcemic type , 2014, Nature Genetics.

[18]  Zhaohui S. Qin,et al.  Therapeutic Targeting of BET Bromodomain Proteins in Castration-Resistant Prostate Cancer , 2014, Nature.

[19]  G. Crabtree,et al.  Essential role of BRG, the ATPase subunit of BAF chromatin remodeling complexes, in leukemia maintenance. , 2014, Blood.

[20]  W. Hahn,et al.  Residual Complexes Containing SMARCA2 (BRM) Underlie the Oncogenic Drive of SMARCA4 (BRG1) Mutation , 2014, Molecular and Cellular Biology.

[21]  A. Domínguez-López,et al.  Significance of CASP8AP2 and H2AFZ expression in survival and risk of relapse in children with acute lymphoblastic leukemia , 2014, Leukemia & lymphoma.

[22]  Laura M. Heiser,et al.  A community effort to assess and improve drug sensitivity prediction algorithms , 2014, Nature Biotechnology.

[23]  Benjamin Haibe-Kains,et al.  Inconsistency in large pharmacogenomic studies , 2013, Nature.

[24]  Ulrich Lehmann,et al.  Mutant IDH1 promotes leukemogenesis in vivo and can be specifically targeted in human AML. , 2013, Blood.

[25]  Benjamin J. Raphael,et al.  Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. , 2013, The New England journal of medicine.

[26]  D. Margolis,et al.  Serum 2-hydroxyglutarate levels predict isocitrate dehydrogenase mutations and clinical outcome in acute myeloid leukemia. , 2012, Blood.

[27]  Dimitris Anastassiou,et al.  Biomolecular Events in Cancer Revealed by Attractor Metagenes , 2012, PLoS Comput. Biol..

[28]  M. Konopleva,et al.  Phase II trial of vorinostat with idarubicin and cytarabine for patients with newly diagnosed acute myelogenous leukemia or myelodysplastic syndrome. , 2012, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[29]  S. Lok,et al.  Sorafenib treatment of FLT3-ITD(+) acute myeloid leukemia: favorable initial outcome and mechanisms of subsequent nonresponsiveness associated with the emergence of a D835 mutation. , 2012, Blood.

[30]  S. Ramaswamy,et al.  Systematic identification of genomic markers of drug sensitivity in cancer cells , 2012, Nature.

[31]  Adam A. Margolin,et al.  The Cancer Cell Line Encyclopedia enables predictive modeling of anticancer drug sensitivity , 2012, Nature.

[32]  Cell Lines , 1992, Spermatogenesis.

[33]  S. Lok,et al.  Sorafenib treatment of FLT 3-ITD acute myeloid leukemia : favorable initial outcome and mechanisms of subsequent nonresponsiveness associated with the emergence of a D 835 mutation , 2012 .

[34]  Joshua M. Stuart,et al.  Subtype and pathway specific responses to anticancer compounds in breast cancer , 2011, Proceedings of the National Academy of Sciences.

[35]  R. Klose,et al.  The oncometabolite 2‐hydroxyglutarate inhibits histone lysine demethylases , 2011, EMBO reports.

[36]  Bin Wang,et al.  Oncometabolite 2-hydroxyglutarate is a competitive inhibitor of α-ketoglutarate-dependent dioxygenases. , 2011, Cancer cell.

[37]  Ash A. Alizadeh,et al.  Association of a leukemic stem cell gene expression signature with clinical outcomes in acute myeloid leukemia. , 2010, JAMA.

[38]  D. Pe’er,et al.  An Integrated Approach to Uncover Drivers of Cancer , 2010, Cell.

[39]  Paul Tseng,et al.  Trace Norm Regularization: Reformulations, Algorithms, and Multi-Task Learning , 2010, SIAM J. Optim..

[40]  M. Caligiuri,et al.  Sp1/NFkappaB/HDAC/miR-29b regulatory network in KIT-driven myeloid leukemia. , 2010, Cancer cell.

[41]  Tak W. Mak,et al.  Cancer-associated metabolite 2-hydroxyglutarate accumulates in acute myelogenous leukemia with isocitrate dehydrogenase 1 and 2 mutations , 2010, The Journal of experimental medicine.

[42]  R. Marschalek,et al.  CASP8AP2 is a novel partner gene of MLL rearrangement with t(6;11)(q15;q23) in acute myeloid leukemia. , 2009, Cancer genetics and cytogenetics.

[43]  H. Drexler,et al.  Hypomethylation and expression of BEX2, IGSF4 and TIMP3 indicative of MLL translocations in Acute Myeloid Leukemia , 2009, Molecular Cancer.

[44]  Babak Shahbaba,et al.  A pluripotency signature predicts histologic transformation and influences survival in follicular lymphoma patients. , 2009, Blood.

[45]  Nir Friedman,et al.  Probabilistic Graphical Models - Principles and Techniques , 2009 .

[46]  R. Larson,et al.  Histone Deacetylase Inhibitor Romidepsin Has Differential Activity in Core Binding Factor Acute Myeloid Leukemia , 2008, Clinical Cancer Research.

[47]  B. Volkman,et al.  Heterodimer formation of the myeloid zinc finger 1 SCAN domain and association with promyelocytic leukemia nuclear bodies. , 2008, Leukemia research.

[48]  T. Robak,et al.  Cladribine combined with high doses of arabinoside cytosine, mitoxantrone, and G‐CSF (CLAG‐M) is a highly effective salvage regimen in patients with refractory and relapsed acute myeloid leukemia of the poor risk: a final report of the Polish Adult Leukemia Group , 2007, European journal of haematology.

[49]  Ethan M. Lange,et al.  Prioritized Subset Analysis: Improving Power in Genome-wide Association Studies , 2007, Human Heredity.

[50]  R. Bristow,et al.  Promyelocytic leukemia nuclear bodies behave as DNA damage sensors whose response to DNA double-strand breaks is regulated by NBS1 and the kinases ATM, Chk2, and ATR , 2006, The Journal of cell biology.

[51]  L. Wasserman,et al.  False discovery control with p-value weighting , 2006 .

[52]  Larry Wasserman,et al.  Using linkage genome scans to improve power of association in genome scans. , 2006, American journal of human genetics.

[53]  M. Henriksson,et al.  Mnt transcriptional repressor is functionally regulated during cell cycle progression , 2005, Oncogene.

[54]  H. Zou,et al.  Addendum: Regularization and variable selection via the elastic net , 2005 .

[55]  H. Zou,et al.  Regularization and variable selection via the elastic net , 2005 .

[56]  W. Hiddemann,et al.  Detailed analysis of FLT3 expression levels in acute myeloid leukemia. , 2005, Haematologica.

[57]  S. Lees-Miller,et al.  DNA damage-induced activation of ATM and ATM-dependent signaling pathways. , 2004, DNA repair.

[58]  D. Pe’er,et al.  Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data , 2003, Nature Genetics.

[59]  H. Drexler,et al.  FLT3 mutations in acute myeloid leukemia cell lines , 2003, Leukemia.

[60]  Susan J Clark,et al.  DNA methylation and gene silencing in cancer: which is the guilty party? , 2002, Oncogene.

[61]  G. Ehninger,et al.  Analysis of Flt3-activating Mutations in 979 Patients with Acute Myelogenous Leukemia: Association with Fab Subtypes and Identification of Subgroups with Poor Prognosis , 2022 .

[62]  M. Caligiuri,et al.  Absence of the wild-type allele predicts poor prognosis in adult de novo acute myeloid leukemia with normal cytogenetics and the internal tandem duplication of FLT3: a cancer and leukemia group B study. , 2001, Cancer research.

[63]  P. Pandolfi,et al.  Mzf1 controls cell proliferation and tumorigenesis. , 2001, Genes & development.

[64]  K. Cornetta,et al.  Forced over-expression of the myeloid zinc finger gene MZF-1 inhibits apoptosis and promotes oncogenesis in interleukin-3-dependent FDCP.1 cells. , 1996, Leukemia.

[65]  F. Mandelli,et al.  Mitoxantrone, etoposide, and intermediate-dose cytarabine: an effective and tolerable regimen for the treatment of refractory acute myeloid leukemia. , 1991, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.