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List of works by Andrea Califano

<i>N</i>-quinoline-benzenesulfonamide derivatives exert potent anti-lymphoma effect by targeting NF-κB

scientific article published on 30 November 2020

A CLK3-HMGA2 Alternative Splicing Axis Impacts Human Hematopoietic Stem Cell Molecular Identity throughout Development.

scientific article published in April 2018

A case study of an integrative genomic and experimental therapeutic approach for rare tumors: identification of vulnerabilities in a pediatric poorly differentiated carcinoma.

scientific article published on 31 October 2016

A community computational challenge to predict the activity of pairs of compounds

scientific article

A complementary role for ELF3 and TFL1 in the regulation of flowering time by ambient temperature

scientific article published on 2 February 2009

A computational systems approach identifies synergistic specification genes that facilitate lineage conversion to prostate tissue

scientific article

A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers

scientific article

A molecular signature predictive of indolent prostate cancer

scientific article published on September 2013

A multi-organ chip with matured tissue niches linked by vascular flow

scientific article published in 2022

A precision oncology approach to the pharmacological targeting of mechanistic dependencies in neuroendocrine tumors

scientific article published on 18 June 2018

A promoter-level mammalian expression atlas

scientific article

A systems approach to drug discovery in Alzheimer's disease.

scientific article

A systems biology approach to prediction of oncogenes and molecular perturbation targets in B-cell lymphomas

scientific article

A systems biology approach to transcription factor binding site prediction

scientific article

ABC transporters and the proteasome complex are implicated in susceptibility to Stevens-Johnson syndrome and toxic epidermal necrolysis across multiple drugs

scientific article

ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context

scientific article

ARACNe-AP: gene network reverse engineering through adaptive partitioning inference of mutual information

scientific article

Accelerated parallel algorithm for gene network reverse engineering.

scientific article published on 21 September 2017

An ID2-dependent mechanism for VHL inactivation in cancer

scientific article published on 06 January 2016

An Integrated Systems Biology Approach Identifies TRIM25 as a Key Determinant of Breast Cancer Metastasis.

scientific article published in August 2017

An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma

scientific article

Assembly and interrogation of Alzheimer's disease genetic networks reveal novel regulators of progression

scientific article

B-Raf activation cooperates with PTEN loss to drive c-Myc expression in advanced prostate cancer

scientific article

BCL6 suppression of BCL2 via Miz1 and its disruption in diffuse large B cell lymphoma

scientific article published on 23 June 2009

Bone Marrow Myeloid Cells Regulate Myeloid-Biased Hematopoietic Stem Cells via a Histamine-Dependent Feedback Loop.

scientific article

CASTOR: clustering algorithm for sequence taxonomical organization and relationships

scientific article published in January 2003

CTD2 Dashboard: a searchable web interface to connect validated results from the Cancer Target Discovery and Development Network

scientific article published in January 2017

ChIP-on-chip significance analysis reveals large-scale binding and regulation by human transcription factor oncogenes

scholarly article

ChIP-on-chip significance analysis reveals ubiquitous transcription factor binding.

scientific article published on 20 November 2007

Comparative analysis of microarray normalization procedures: effects on reverse engineering gene networks

scientific article (publication date: July 2007)

Convection-enhanced delivery of etoposide is effective against murine proneural glioblastoma

scientific article

Cooperation of loss of and inflammation in prostate cancer initiation

scientific article published on 16 November 2018

Correction: Inferring Protein Modulation from Gene Expression Data Using Conditional Mutual Information

scientific article published on 15 September 2016

Correction: Novel Hybrid Phenotype Revealed in Small Cell Lung Cancer by a Transcription Factor Network Model That Can Explain Tumor Heterogeneity

scientific article published on 01 March 2019

Correlating measurements across samples improves accuracy of large-scale expression profile experiments

scientific article

Cross-Cohort Analysis Identifies a TEAD4-MYCN Positive Feedback Loop as the Core Regulatory Element of High-Risk Neuroblastoma

scientific article published on 6 March 2018

Cross-Species Single-Cell Analysis of Pancreatic Ductal Adenocarcinoma Reveals Antigen-Presenting Cancer-Associated Fibroblasts

scientific article published on 13 June 2019

Cross-species regulatory network analysis identifies a synergistic interaction between FOXM1 and CENPF that drives prostate cancer malignancy

scientific article published on May 2014

Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks.

scientific article

DIGGIT: a Bioconductor package to infer genetic variants driving cellular phenotypes

scientific article

Dclk1 Defines Quiescent Pancreatic Progenitors that Promote Injury-Induced Regeneration and Tumorigenesis

scientific article

Detection and removal of spatial bias in multiwell assays

scientific article

Dialogue on reverse-engineering assessment and methods: the DREAM of high-throughput pathway inference

scientific article published on 09 October 2007

Differentiation-state plasticity is a targetable resistance mechanism in basal-like breast cancer

scientific article published in Nature Communications

Direct ChIP-Seq significance analysis improves target prediction

scientific article published on 26 May 2015

Direct reversal of glucocorticoid resistance by AKT inhibition in acute lymphoblastic leukemia

scientific article

Discovering transcriptional regulatory regions in Drosophila by a nonalignment method for phylogenetic footprinting

scholarly article

Dissecting the interface between signaling and transcriptional regulation in human B cells

scientific article published on January 2009

Drawing networks of rejection - a systems biological approach to the identification of candidate genes in heart transplantation.

scientific article published on April 2011

Dual targeting of the Akt/mTOR signaling pathway inhibits castration-resistant prostate cancer in a genetically engineered mouse model.

scientific article

ET-57TOPOISOMERASE II IN PRONEURAL GLIOMAS, A MODULATOR OF TRANSCRIPTION AND A THERAPEUTIC TARGET.

scientific article published in November 2014

ETV4 promotes metastasis in response to activation of PI3-kinase and Ras signaling in a mouse model of advanced prostate cancer.

scientific article published on 05 August 2013

Elucidating Compound Mechanism of Action by Network Perturbation Analysis.

scientific article published on July 2015

Elucidating synergistic dependencies in lung adenocarcinoma by proteome-wide signaling-network analysis

scientific article published in PLoS ONE

Elucidation and Pharmacological Targeting of Novel Molecular Drivers of Follicular Lymphoma Progression

scientific article published on 20 November 2015

Epigenetic Regulation of ZBTB18 Promotes Glioblastoma Progression.

scientific article published on 16 May 2017

Erratum to: HDAC6 activity is a non-oncogene addiction hub for inflammatory breast cancers.

scientific article published on 19 April 2017

Erratum: Corrigendum: Structure-based prediction of protein–protein interactions on a genome-wide scale

scientific article published in Nature

Experimental microdissection enables functional harmonisation of pancreatic cancer subtypes

scientific article published on 18 January 2019

Functional characterization of somatic mutations in cancer using network-based inference of protein activity

scientific article published on 20 June 2016

Gene expression analysis of angioimmunoblastic lymphoma indicates derivation from T follicular helper cells and vascular endothelial growth factor deregulation

article

Gene expression analysis of peripheral T cell lymphoma, unspecified, reveals distinct profiles and new potential therapeutic targets

scientific article published on 15 February 2007

Gene expression analysis provides a potential rationale for revising the histological grading of follicular lymphomas

article

Gene expression analysis uncovers similarity and differences among Burkitt lymphoma subtypes.

scientific article published on 18 January 2011

Gene expression changes consistent with neuroAIDS and impaired working memory in HIV-1 transgenic rats.

scientific article

Gene expression dynamics during germinal center transit in B cells

scientific article

Gene expression profiling of hairy cell leukemia reveals a phenotype related to memory B cells with altered expression of chemokine and adhesion receptors

scientific article published on January 2004

Generation of pralatrexate resistant T-cell lymphoma lines reveals two patterns of acquired drug resistance that is overcome with epigenetic modifiers

scientific article published on 02 July 2020

Genome-Wide Discovery of Modulators of Transcriptional Interactions in Human B Lymphocytes

Genome-wide dissection of posttranscriptional and posttranslational interactions

scientific article published in January 2012

Genome-wide identification of post-translational modulators of transcription factor activity in human B cells.

scientific article published on 09 September 2009

Genomic and Phenotypic Characterization of a Broad Panel of Patient-Derived Xenografts Reflects the Diversity of Glioblastoma

scientific article published on 18 December 2019

HAUSP deubiquitinates and stabilizes N-Myc in neuroblastoma

scientific article published on 12 September 2016

HDAC6 activity is a non-oncogene addiction hub for inflammatory breast cancers

scientific article

HER3 Is an Actionable Target in Advanced Prostate Cancer

scientific article published on 09 November 2021

High-definition CpG methylation of novel genes in gastric carcinogenesis identified by next-generation sequencing.

scientific article

High-throughput validation of ceRNA regulatory networks

scientific article

Hypothalamic proteoglycan syndecan-3 is a novel cocaine addiction resilience factor

scientific article published on January 2013

Identification of Causal Genetic Drivers of Human Disease through Systems-Level Analysis of Regulatory Networks

scientific article published on 01 August 2016

Identification of Hodgkin and Reed-Sternberg cell-specific genes by gene expression profiling

scientific article

Identification of an NKX3.1-G9a-UTY transcriptional regulatory network that controls prostate differentiation

scientific article published on June 2016

Identification of causal genetic drivers of human disease through systems-level analysis of regulatory networks.

scientific article

Identification of immunotherapeutic targets by genomic profiling of rectal NET metastases.

scientific article published on 22 July 2016

Identification of neurodegenerative factors using translatome-regulatory network analysis

scientific article published on 27 July 2015

Identification of the human mature B cell miRNome

scientific article published on 14 May 2009

Identifying candidate drivers of alcohol dependence-induced excessive drinking by assembly and interrogation of brain-specific regulatory networks

scientific article published on 2 February 2015

Identifying the Potential Mechanism of Action of SNPs Associated With Breast Cancer Susceptibility With GVITamIN

scientific article published on 04 August 2020

Improving breast cancer survival analysis through competition-based multidimensional modeling

scientific article

Inferring protein modulation from gene expression data using conditional mutual information.

scientific article

Inhibition of the autocrine IL-6-JAK2-STAT3-calprotectin axis as targeted therapy for HR-/HER2+ breast cancers

scientific article

Integrated biochemical and computational approach identifies BCL6 direct target genes controlling multiple pathways in normal germinal center B cells.

scientific article

Interrogation of a context-specific transcription factor network identifies novel regulators of pluripotency

scientific article

Lessons from the DREAM2 Challenges

scientific article

Leveraging models of cell regulation and GWAS data in integrative network-based association studies

scientific article (publication date: 27 July 2012)

Lineage analysis of basal epithelial cells reveals their unexpected plasticity and supports a cell-of-origin model for prostate cancer heterogeneity

scientific article published on 24 February 2013

MEF2B mutations lead to deregulated expression of the oncogene BCL6 in diffuse large B cell lymphoma

scientific article

Management of complicated gallstones: results of an alternative approach to difficult cholecystectomies

scientific article published in October 2010

Marked gene transcript level alterations occur early during radical prostatectomy

scientific article published on 09 April 2007

Master regulators used as breast cancer metastasis classifier.

scientific article published on January 2009

Mechanism and Role of SOX2 Repression in Seminoma: Relevance to Human Germline Specification

scientific article published on 27 April 2016

Mesenchymal subtype neuroblastomas are addicted to TGF-βR2/HMGCR-driven protein geranylgeranylation

scientific article published on 01 July 2020

Molecular cancer phenotype in normal prostate tissue

scientific article

Motif-based construction of a functional map for mammalian olfactory receptors

scientific article published on 01 May 2003

Mutations of multiple genes cause deregulation of NF-kappaB in diffuse large B-cell lymphoma.

scientific article

NOTCH1 directly regulates c-MYC and activates a feed-forward-loop transcriptional network promoting leukemic cell growth

scholarly article

NSD2 is a conserved driver of metastatic prostate cancer progression

scientific article published in Nature Communications

New JBI emphasis on translational bioinformatics

Notch-mediated Ephrin signaling disrupts islet architecture and β cell function

scientific article published on 22 March 2022

Novel Hybrid Phenotype Revealed in Small Cell Lung Cancer by a Transcription Factor Network Model That Can Explain Tumor Heterogeneity.

scientific article published on 08 December 2016

Oncoprotein-specific molecular interaction maps (SigMaps) for cancer network analyses

scientific article published on 14 September 2020

PFT1, the MED25 subunit of the plant Mediator complex, promotes flowering through CONSTANS dependent and independent mechanisms in Arabidopsis.

scientific article published on 16 November 2011

PI3Kγ/δ and NOTCH1 Cross-Regulate Pathways That Define the T-cell Acute Lymphoblastic Leukemia Disease Signature.

scientific article published on 17 July 2017

PLATE-Seq for genome-wide regulatory network analysis of high-throughput screens

scientific article

Patient-Driven Discovery, Therapeutic Targeting, and Post-Clinical Validation of a Novel AKT1 Fusion-Driven Cancer

scientific article published on 15 March 2019

Pattern-based mining strategy to detect multi-locus association and gene x environment interaction

scientific article

Pharmacogenetics: ethical issues and policy options

article

Pooled shRNA screenings: computational analysis.

scientific article

Predicting Drug Response in Human Prostate Cancer from Preclinical Analysis of In Vivo Mouse Models.

scientific article

Predicting protein networks in cancer.

scientific article published in December 2014

Preface

scholarly article by Manolis Kellis published in February 2011

Preface: RECOMB Systems Biology, Regulatory Genomics, and DREAM 2011 special issue

scientific article published on 01 February 2012

Preface: RECOMB systems biology, regulatory genomics, and DREAM 2012 special issue

scientific article

Preface: RECOMB/ISCB systems biology, regulatory genomics, and DREAM 2014 Special Issue

scientific article published on 01 April 2015

Quantitative Tyrosine Phosphoproteomics of Epidermal Growth Factor Receptor (EGFR) Tyrosine Kinase Inhibitor-treated Lung Adenocarcinoma Cells Reveals Potential Novel Biomarkers of Therapeutic Response.

scientific article published on 22 March 2017

Quantitative assessment of protein activity in orphan tissues and single cells using the metaVIPER algorithm.

scientific article published on 16 April 2018

Quantitative modeling of the terminal differentiation of B cells and mechanisms of lymphomagenesis

scientific article published on 30 January 2012

RECOMB/ISCB systems biology, regulatory genomics, and DREAM 2013 special issue

scientific article published on 01 May 2014

Regulation of extra-embryonic endoderm stem cell differentiation by Nodal and Cripto signaling

scientific article

Reply to 'H-STS, L-STS and KRJ-I are not authentic GEPNET cell lines'

scientific article published on 01 October 2019

Report on EU-USA workshop: how systems biology can advance cancer research (27 October 2008)

scientific article

Report: workshop on mediastinal grey zone lymphoma

scientific article published in July 2005

Report: workshop on mediastinal grey zone lymphoma

article by Sibrand Poppema et al published 6 June 2005 in European Journal of Haematology

Resistance to neoadjuvant chemotherapy in triple-negative breast cancer mediated by a reversible drug-tolerant state

scientific article published on 01 April 2019

Reverse engineering cellular networks.

scientific article published on January 2006

Reverse engineering of TLX oncogenic transcriptional networks identifies RUNX1 as tumor suppressor in T-ALL.

scientific article published on 26 February 2012

Reverse-engineering human regulatory networks

scientific article

Rewiring makes the difference

scientific article

SECAT: Quantifying Protein Complex Dynamics across Cell States by Network-Centric Analysis of SEC-SWATH-MS Profiles

scientific article published on 01 December 2020

SJARACNe: a scalable software tool for gene network reverse engineering from big data

article

STK38 is a critical upstream regulator of MYC's oncogenic activity in human B-cell lymphoma.

scientific article

ScreenBEAM: a novel meta-analysis algorithm for functional genomics screens via Bayesian hierarchical modeling

scientific article

Single-Cell Genomics Reveals a Novel Cell State During Smooth Muscle Cell Phenotypic Switching and Potential Therapeutic Targets for Atherosclerosis in Mouse and Human

scientific article published on 23 September 2020

Striking a Balance Between Feasible and Realistic Biological Models ⬇️

scientific article published on October 5, 2011

Structure-based prediction of protein–protein interactions on a genome-wide scale

scientific article (publication date: 30 September 2012)

Survival factor NFIL3 restricts FOXO-induced gene expression in cancer

scientific article published on April 2013

Synergistic antileukemic therapies in NOTCH1-induced T-ALL.

scientific article published on 7 February 2017

Systematic elucidation of neuron-astrocyte interaction in models of amyotrophic lateral sclerosis using multi-modal integrated bioinformatics workflow

scientific article published on 04 November 2020

Systematic, network-based characterization of therapeutic target inhibitors.

scientific article published on 12 October 2017

T-cell lymphoblastic lymphoma shows differences and similarities with T-cell acute lymphoblastic leukemia by genomic and gene expression analyses

scientific article published on 30 August 2011

TMOD-18. THE PATIENT DERIVED XENOGRAFT NATIONAL RESOURCE: A COMPREHENSIVE COLLECTION OF HIGH-GRADE GLIOMA MODELS FOR PRE-CLINICAL AND TRANSLATIONAL STUDIES

The Cyni framework for network inference in Cytoscape.

scientific article published on 18 December 2014

The DLEU2/miR-15a/16-1 cluster controls B cell proliferation and its deletion leads to chronic lymphocytic leukemia

scientific article

The Host Cell ViroCheckpoint: Identification and Pharmacologic Targeting of Novel Mechanistic Determinants of Coronavirus-Mediated Hijacked Cell States

scientific article published on 18 May 2020

The Immune Landscape of Cancer

scientific article published on 4 April 2018

The Immune Landscape of Cancer

scientific article published on 01 August 2019

The Master Regulator Protein BAZ2B Can Reprogram Human Hematopoietic Lineage-Committed Progenitors into a Multipotent State

scientific article published on 01 December 2020

The N-Myc-DLL3 cascade is suppressed by the ubiquitin ligase Huwe1 to inhibit proliferation and promote neurogenesis in the developing brain.

scientific article published on August 2009

The Regulatory Machinery of Neurodegeneration in In Vitro Models of Amyotrophic Lateral Sclerosis

scientific article

The TLX1 oncogene drives aneuploidy in T cell transformation

scientific article

The challenges of systems biology. Preface

scientific article published in March 2009

The miR-424(322)/503 cluster orchestrates remodeling of the epithelium in the involuting mammary gland.

scientific article

The number of titrated microRNA species dictates ceRNA regulation.

scientific article published in May 2018

The recurrent architecture of tumour initiation, progression and drug sensitivity

scientific article published on 15 December 2016

The transcriptional network for mesenchymal transformation of brain tumours.

scientific article

The transcriptional regulatory network of proneural glioma determines the genetic alterations selected during tumor progression.

scientific article published on 03 January 2014

The transcriptomic response of cells to a drug combination is more than the sum of the responses to the monotherapies

scientific article published on 18 September 2020

The use of superelastic suture clips in laparoscopic gastric banding

scientific article published on 01 January 2008

Theory and limitations of genetic network inference from microarray data

scientific article

Toward better benchmarking: challenge-based methods assessment in cancer genomics

scientific article

Toward understanding and exploiting tumor heterogeneity

scientific article

Towards patient-based cancer therapeutics

scientific article

Tracking CD40 signaling during germinal center development

scientific article published on 26 August 2004

Transcription factor activating protein 4 is synthetically lethal and a master regulator of MYCN-amplified neuroblastoma

scientific article published on 07 June 2018

Transcriptional analysis of the B cell germinal center reaction

scientific article

Transdifferentiation as a Mechanism of Treatment Resistance in a Mouse Model of Castration-Resistant Prostate Cancer.

scientific article published on 14 April 2017

Using systems and structure biology tools to dissect cellular phenotypes

scientific article published on 10 November 2011

Verification of systems biology research in the age of collaborative competition

scientific article

ZCCHC17 is a master regulator of synaptic gene expression in Alzheimer's Disease.

scientific article published on 25 September 2017

ZFHX4 interacts with the NuRD core member CHD4 and regulates the glioblastoma tumor-initiating cell state

scientific journal article

geWorkbench: an open source platform for integrative genomics

scientific article

hARACNe: improving the accuracy of regulatory model reverse engineering via higher-order data processing inequality tests

scientific article

iTools: a framework for classification, categorization and integration of computational biology resources

scientific article published in 2008

iterClust: a statistical framework for iterative clustering analysis

scientific article published on 22 March 2018

tRNA-derived microRNA modulates proliferation and the DNA damage response and is down-regulated in B cell lymphoma.

scientific article published on 7 January 2013

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