Andrea Califano

Columbia University Irving Medical Center

Also affiliated with Chan Zuckerberg Biohub San Francisco, National Center on Addiction and Substance Abuse at Columbia University, Chan Zuckerberg Initiative (United States), DarwinHealth (United States), New York Genome Center, Comprehensive Clinical Research, Columbia University

Biochemistry, Genetics and Molecular BiologyMedicine

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 1%percentile

14.6Author DataRank

Indexed papers

4in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Why this DataRank?

An author's DataRank is the sum of the DataRanks of all 4 indexed papers attributed to them. A prolific author with many moderate-impact papers can outrank one with a single high-impact paper.

Author scores recompute whenever paper DataRanks are refreshed, so this number lags the underlying paper scores by at most one batch run.

Read the full methodology →

The highest-impact dataset this researcher has shared, ranked by DataRank — the single contribution doing the most to lift their data-sharing standing.

A promoter-level mammalian expression atlas

Nature(2014)10.1038/nature13182

Top 2%

8.9DataRank

Top 2%2192 citations

Alistair R. R. Forrest, J. Kenneth Baillie, Michiel de Hoon, Timo Lassmann, Ivan V. Kulakovskiy +262 more

Papers

Driven by 96 papers — median percentile 87. Top paper: “Single-cell protein activity analysis identifies recurrence-associated renal tumor macrophages”.

Single-cell protein activity analysis identifies recurrence-associated renal tumor macrophages

Cell(2021)10.1016/j.cell.2021.04.038

N/A

9.0DataRank · unranked

379 citations

Nivedita Chowdhury, Scott M. Haake, Casey R. Ager, Vinson Wang, Lukas Vlahos +12 more

A promoter-level mammalian expression atlas

Nature(2014)10.1038/nature13182

Top 2%

8.9DataRank

Top 2%2192 citations

Alistair R. R. Forrest, J. Kenneth Baillie, Michiel de Hoon, Timo Lassmann, Ivan V. Kulakovskiy +262 more

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

Circulation(2020)10.1161/circulationaha.120.048378

N/A

8.9DataRank · unranked

636 citations

Chenyi Xue, Benjamin J. Auerbach, Jiaxin Fan, Alexander C. Bashore, Jian Cui +17 more

Genomic and transcriptomic analysis of checkpoint blockade response in advanced non-small cell lung cancer

Nature Genetics(2023)10.1038/s41588-023-01355-5

Top 6%

4.0DataRank

Top 6%188 citations

Matthew D. Hellmann, Monica Arniella, Mark Holton, Samuel S. Freeman, Vivek Naranbhai +37 more

Tumour-selective activity of RAS-GTP inhibition in pancreatic cancer

Nature(2024)10.1038/s41586-024-07379-z

N/A

3.9DataRank · unranked

182 citations

Jingjing Jiang, Tanner C. Dalton, Álvaro Curiel‐García, A. Cole Edwards, Yingyun Wang +61 more

Network-based assessment of HDAC6 activity predicts preclinical and clinical responses to the HDAC6 inhibitor ricolinostat in breast cancer

Nature Cancer(2022)10.1038/s43018-022-00489-5

N/A

2.2DataRank · unranked

77 citations

Qingfei Pan, Codruța Chiuzan, Maika Onishi, Yuxin Li, Haiyan Tan +21 more

Anti-PD-1 immunotherapy with androgen deprivation therapy induces robust immune infiltration in metastatic castration-sensitive prostate cancer

Cancer Cell(2023)10.1016/j.ccell.2023.10.006

N/A

1.6DataRank · unranked

80 citations

Aleksandar Obradović, Matthew C. Dallos, Emerson A. Lim, Karie Runcie, Casey R. Ager +16 more

Airway basal cells show regionally distinct potential to undergo metaplastic differentiation

eLife(2022)10.7554/elife.80083

N/A

1.4DataRank · unranked

56 citations

Ying Yang, Lihao Guo, Jun Qian, Jian Ge, Débora Sinner +4 more

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

eLife(2020)10.7554/elife.52707

N/A

1.4DataRank · unranked

41 citations

Mehmet Eren Ahsen, Thomas Schaffter, Xintong Chen, Ronald Realubit, Charles Karan +4 more

A Transcriptome-Based Precision Oncology Platform for Patient–Therapy Alignment in a Diverse Set of Treatment-Resistant Malignancies

Cancer Discovery(2023)10.1158/2159-8290.cd-22-1020

Top 20%

1.0DataRank

Top 20%43 citations

Filemon S. Dela Cruz, Adina Grunn, Daniel Diolaiti, Audrey Mauguen, Allison R. Rainey +50 more

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

Nature Biomedical Engineering(2022)10.1038/s41551-022-00882-6

N/A

0.920DataRank · unranked

461 citations

Diogo Teles, Keith Yeager, Daniel Naveed Tavakol, Yimu Zhao, Alan Chramiec +21 more

Promotion of cholangiocarcinoma growth by diverse cancer-associated fibroblast subpopulations

Cancer Cell(2021)10.1016/j.ccell.2021.03.012

N/A

0.903DataRank · unranked

410 citations

Ajay Nair, Francesco Brundu, Aashreya Ravichandra, Sonakshi Bhattacharjee, Michitaka Matsuda +32 more

How to build the virtual cell with artificial intelligence: Priorities and opportunities

Cell(2024)10.1016/j.cell.2024.11.015

N/A

0.861DataRank · unranked

310 citations

Yusuf Roohani, Yanay Rosen, Ankit Gupta, Xikun Zhang, Marcel Roed +37 more

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

Nature Genetics(2012)10.1038/ng.2355

N/A

0.842DataRank · unranked

273 citations

Atul Janardhan Butte, Stephen Friend, Trey Ideker, Eric E. Schadt, Andrea Califano

Immunostimulatory Cancer-Associated Fibroblast Subpopulations Can Predict Immunotherapy Response in Head and Neck Cancer

Clinical Cancer Research(2022)10.1158/1078-0432.ccr-21-3570

N/A

0.806DataRank · unranked

215 citations

Diana Graves, Michael Korrer, Yu Wang, Sohini Roy, Abdullah Naveed +13 more

OncoLoop: A Network-Based Precision Cancer Medicine Framework

Cancer Discovery(2022)10.1158/2159-8290.cd-22-0342

N/A

0.787DataRank · unranked

37 citations

Juan Martín Arriaga, Francisca Nunes de Almeida, Min Zou, Eugene F. Douglass, Florencia Picech +19 more

A CRISPR/Cas9-Engineered ARID1A -Deficient Human Gastric Cancer Organoid Model Reveals Essential and Nonessential Modes of Oncogenic Transformation

Cancer Discovery(2021)10.1158/2159-8290.cd-20-1109

N/A

0.771DataRank · unranked

170 citations

Kevin S. Kolahi, Yuhong Du, Chiung-Ying Chang, A. Krokhotin, Ajay Nair +18 more

A modular master regulator landscape controls cancer transcriptional identity

Cell(2021)10.1016/j.cell.2020.11.045

N/A

0.749DataRank · unranked

146 citations

Àlvaro Aytés, Sunny J. Jones, Prem S. Subramaniam, Federico M. Giorgi, Eugene F. Douglass +9 more

SMARCAL1 is a dual regulator of innate immune signaling and PD-L1 expression that promotes tumor immune evasion

Cell(2024)10.1016/j.cell.2024.01.008

N/A

0.689DataRank · unranked

98 citations

Alessandro Vasciaveo, Angelo Taglialatela, Xiao Chen, Tessa M. Firestone, Allison R. Hickman +28 more

Isthmus progenitor cells contribute to homeostatic cellular turnover and support regeneration following intestinal injury

Cell(2024)10.1016/j.cell.2024.05.004

N/A

0.673DataRank · unranked

88 citations

Alessandro Vasciaveo, Yosuke Ochiai, Woosook Kim, Biyun Zheng, Luca Zanella +17 more

A Phase II Study of the Efficacy and Safety of Oral Selinexor in Recurrent Glioblastoma

Clinical Cancer Research(2021)10.1158/1078-0432.ccr-21-2225

N/A

0.644DataRank · unranked

72 citations

Patrick Y. Wen, Martin J. van den Bent, Scott R. Plotkin, Annemiek Walenkamp, Adam L. Green +13 more

A Community Challenge for Pancancer Drug Mechanism of Action Inference from Perturbational Profile Data

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.12.21.423514

Top 32%

0.625DataRank

Top 32%20 citations

Robert J. Allaway, Bence Szalai, Wenyu Wang, Tingzhong Tian, Adrià Fernández‐Torras +23 more

Systematic elucidation and pharmacological targeting of tumor-infiltrating regulatory T cell master regulators

Cancer Cell(2023)10.1016/j.ccell.2023.04.003

N/A

0.612DataRank · unranked

58 citations

Casey R. Ager, Mikko Turunen, Thomas R. Nirschl, Mohsen Khosravi‐Maharlooei, Alina C. Iuga +16 more

UHRF1 is a mediator of KRAS driven oncogenesis in lung adenocarcinoma

Nature Communications(2023)10.1038/s41467-023-39591-2

N/A

0.553DataRank · unranked

39 citations

Marta Román, Alex G. Lee, David R. Simpson, Phuong Dinh, Stanley G. Leung +7 more

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

Nature Biotechnology(2020)10.1038/s41587-020-0652-7

N/A

0.550DataRank · unranked

38 citations

David R. Simpson, Diana Murray, Evan Paull, Brennan Chu, Somnath Tagore +9 more

Tff2 defines transit-amplifying pancreatic acinar progenitors that lack regenerative potential and are protective against Kras-driven carcinogenesis

Cell stem cell(2023)10.1016/j.stem.2023.07.002

N/A

0.529DataRank · unranked

33 citations

Feijing Wu, Pasquale Laise, Takayuki Tanaka, Na Fu, Woosook Kim +23 more

Entinostat in patients with relapsed or refractory abdominal neuroendocrine tumors

The Oncologist(2024)10.1093/oncolo/oyae118

N/A

0.504DataRank · unranked

17 citations

Mengxi Zhou, Edward P. Gelmann, Lyndon Luk, Susan E. Bates, Andrea Califano +2 more

Systematic, Protein Activity-based Characterization of Single Cell State

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.05.20.445002

N/A

0.483DataRank · unranked

24 citations

Aleksandar Obradović, Jeremy Worley, Xiangtian Tan, Andrew Howe, Pasquale Laise +4 more

Validation of a non-oncogene encoded vulnerability to exportin 1 inhibition in pediatric renal tumors

Med(2022)10.1016/j.medj.2022.09.002

N/A

0.457DataRank · unranked

20 citations

Prabhjot S. Mundi, Lianna J. Marks, Chelsey Burke, Michael V. Ortiz, Daniel Diolaiti +17 more

Longitudinal Immune Profiling Reveals Unique Myeloid and T-cell Phenotypes Associated with Spontaneous Immunoediting in a Prostate Tumor Model

Cancer Immunology Research(2021)10.1158/2326-6066.cir-20-0637

N/A

0.434DataRank · unranked

17 citations

Aleksandar Obradović, Juan Martín Arriaga, Matthew G. Chaimowitz, Andrea Califano, Cory Abate‐Shen +2 more

NSD2 maintains lineage plasticity and castration-resistance in neuroendocrine prostate cancer

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.07.18.549585

N/A

0.420DataRank · unranked

8 citations

Alessandro Vasciaveo, D Karagiannis, Zhen Sun, Xiao CHEN, Fabio Socciarelli +15 more

Interrogation of genome-wide, experimentally dissected gene regulatory networks reveals mechanisms underlying dynamic cellular state control

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.06.28.449297

N/A

0.406DataRank · unranked

14 citations

Jeremy Worley, Mikko Turunen, Kelly Wong, Ester Calvo Fernández, Evan Paull +7 more

Adult enteric Dclk1-positive glial and neuronal cells reveal distinct responses to acute intestinal injury

American Journal of Physiology-Gastrointestinal and Liver Physiology(2022)10.1152/ajpgi.00244.2021

N/A

0.352DataRank · unranked

5 citations

Giovanni Valenti, Lorenzo Tomassoni, Yosuke Ochiai, Bryana Belin, Ryota Takahashi +16 more

A model for network-based identification and pharmacological targeting of aberrant, replication-permissive transcriptional programs induced by viral infection

Communications Biology(2022)10.1038/s42003-022-03663-8

N/A

0.330DataRank · unranked

8 citations

Megan L. Stanifer, Gideon Bosker, Xiaoyun Sun, Sergio Triana, Patricio Doldan +11 more

Ras-dependent activation of BMAL2 regulates hypoxic metabolism in pancreatic cancer

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.03.19.533333

N/A

0.330DataRank · unranked

8 citations

Sam R. Holmstrom, Cristina Castillo, Carmine F. Palermo, Stephen A. Sastra, Anthony Andren +21 more

Pre-clinical validation of an RNA-based precision oncology platform for patient-therapy alignment in a diverse set of human malignancies resistant to standard treatments

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.10.03.462951

N/A

0.312DataRank · unranked

7 citations

Filemon S. Dela Cruz, Adina Grunn, Daniel Diolaiti, Audrey Mauguen, Allison R. Rainey +48 more

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

Scientific Reports(2020)10.1038/s41598-020-67310-0

N/A

0.292DataRank · unranked

6 citations

Jonnell C. Small, Alessandro Vasciaveo, Kenichi Shimada, Tal Hirschhorn, Andrea Califano +2 more

Systematic Elucidation and Pharmacological Targeting of Tumor-Infiltrating Regulatory T Cell Master Regulators

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.02.22.481404

N/A

0.292DataRank · unranked

6 citations

Casey R. Ager, Mikko Turunen, Thomas R. Nirschl, Mohsen Khosravi‐Maharlooei, Christopher M. Jackson +10 more

Targeted delivery of napabucasin with radiotherapy improves outcomes in diffuse midline glioma

Neuro-Oncology(2024)10.1093/neuonc/noae215

N/A

0.292DataRank · unranked

6 citations

Xu Zhang, Genesis De Los Santos, Hong-Jian Wei, Ester Calvo Fernández, Shoufu Duan +24 more

Kinases Controlling Stability of the Oncogenic MYCN Protein

ACS Medicinal Chemistry Letters(2023)10.1021/acsmedchemlett.3c00274

N/A

0.269DataRank · unranked

5 citations

Eduard Reznik, Brygida Bisikirska, Vasiliki Polychronidou, Qian Wang, Arie Zask +4 more

Epigenetic targeting of PGBD5-dependent DNA damage in SMARCB1-deficient sarcomas

Journal of Clinical Investigation(2025)10.1172/jci179282

N/A

0.269DataRank · unranked

5 citations

Helen S. Mueller, Daniel Cameron, Phillip Demarest, Nadia Zaffaroni, Noemi Arrighetti +12 more

Network-based elucidation of colon cancer drug resistance by phosphoproteomic time-series analysis

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.02.15.528736

N/A

0.241DataRank · unranked

4 citations

Wenxue Li, Mikko Turunen, Jing He, Prem S. Subramaniam, Sergey Pampou +8 more

Integrative Network-based Association Studies: Leveraging cell regulatory models in the post-GWAS era

Nature Precedings(2011)10.1038/npre.2011.5732.1

N/A

0.241DataRank · unranked

4 citations

Stephen Friend, Trey Ideker, Atul Janardhan Butte, Eric E. Schadt, Andrea Califano

Preface: RECOMB Systems Biology, Regulatory Genomics, and DREAM 2012 Special Issue

Journal of Computational Biology(2013)10.1089/cmb.2013.008p

N/A

0.176DataRank · unranked

1 citations

Sharon L. R. Kardia, Gustavo Stolovitzky, Andrea Califano

Isthmus progenitor cells contribute to homeostatic cellular turnover and support regeneration following intestinal injury

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.04.26.489611

N/A

0.165DataRank · unranked

2 citations

Alessandro Vasciaveo, Yoshiyuki Ochiai, W. Kim, Moritz Middelhoff, Henrik Nienhüser +12 more

Single-Cell RNAseq Analysis Reveals Robust, Anti-PD-1-Mediated Increase of Immune Infiltrate in Metastatic Castration-Sensitive Prostate Cancer

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.05.06.490968

N/A

0.165DataRank · unranked

2 citations

Aleksandar Obradović, Matthew C. Dallos, Emerson A. Lim, Karie Runcie, Casey R. Ager +15 more

RECOMB/ISCB Systems Biology, Regulatory Genomics, and DREAM 2013 Special Issue

Journal of Computational Biology(2014)10.1089/cmb.2014.009p

N/A

0.165DataRank · unranked

2 citations

Sharon L. R. Kardia, Gustavo Stolovitzky, Andrea Califano

Protocol for automated graph-based clustering of single-cell RNA-seq data with application in mouse intestinal stem cells

STAR Protocols(2025)10.1016/j.xpro.2025.104000

N/A

0.165DataRank · unranked

2 citations

Luca Zanella, Yosuke Ochiai, Leonardo Golinelli, Andrea Califano, Ermanno Malagola +2 more

The carnosinase dipeptidase CNDP1 is a novel metabolic vulnerability in brain metastasis

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.03.18.644053

N/A

0.104DataRank · unranked

1 citations

Alcida Karz, Maya Navarro, Victoria Osorio-Vasquez, Olga Katsara, Adam K. Walker +21 more

Identification and validation of a non-genetically encoded vulnerability to XPO1 inhibition in malignant rhabdoid tumors – expanding patient-driven discovery beyond the N-of-1

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.10.02.462793

N/A

0.104DataRank · unranked

1 citations

Daniel Diolaiti, Prabhjot S. Mundi, Ervin S. Gaviria, Allison R. Rainey, Darrell J. Yamashiro +8 more

Identification and Targeting of Regulators of SARS-CoV-2-Host Interactions in the Airway Epithelium

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.10.11.617898

N/A

0.104DataRank · unranked

1 citations

Heeju Noh, Lorenzo Tomassoni, Danting Cao, Yizhou Zhou, Ke Xiao +8 more

Preclinical evaluation of XPO1 inhibition in Wilms tumors.

Journal of Clinical Oncology(2020)10.1200/jco.2020.38.15_suppl.3580

N/A

0.104DataRank · unranked

1 citations

Armaan Siddiquee, Daoqi You, Prabhjot S. Mundi, Lianna J. Marks, Kristina Guillan +6 more

Systematic elucidation and pharmacologic targeting of non-oncogene dependencies in imatinib-resistant gastrointestinal stromal tumor

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.10.12.681609

N/A

0DataRank · unranked

0 citations

Adina Grunn, Arsenije Kojadinovic, Charles Karan, Ronald Realubit, Cristina I. Caescu +9 more

Preface: RECOMB/ISCB Systems Biology, Regulatory Genomics, and DREAM 2014 Special Issue

Journal of Computational Biology(2015)10.1089/cmb.2015.020p

N/A

0DataRank · unranked

0 citations

Sharon L. R. Kardia, Gustavo Stolovitzky, Andrea Califano

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

Cell Systems(2020)10.1016/j.cels.2020.11.006

N/A

0DataRank · unranked

47 citations

Moritz Heusel, Isabell Bludau, Ben C. Collins, Claudia Martelli, Evan G. Williams +5 more

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

Nature Communications(2020)10.1038/s41467-020-19177-y

N/A

0DataRank · unranked

56 citations

Diane B. Ré, Virginia Le Verche, Mariano J. Alvarez, Alessandro Vasciaveo, Arnaud Jacquier +17 more

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

Cell Reports(2020)10.1016/j.celrep.2020.108474

N/A

0DataRank · unranked

35 citations

William Shin, Valentina Schiavone, Lukas Vlahos, Xiaochuan Tu, Davide Carnevali +9 more

N-quinoline-benzenesulfonamide derivatives exert potent anti-lymphoma effect by targeting NF-κB

iScience(2020)10.1016/j.isci.2020.101884

N/A

0DataRank · unranked

3 citations

Michael Mangone, Alison Rinderspacher, Shi‐Xian Deng, Luigi Scotto, Michael Markson +5 more

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

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.05.12.091256

N/A

0DataRank · unranked

19 citations

Gideon Bosker, Xiaoyun Sun, Yao Shen, Eugene F. Douglass, Charles Karan +5 more

Network-based assessment of HDAC6 activity is highly predictive of pre-clinical and clinical responses to the HDAC6 inhibitor ricolinostat

medRxiv(2020)10.1101/2020.04.23.20066928

N/A

0DataRank · unranked

5 citations

Qingfei Pan, Cody Chiuzan, Maika Onishi, Mariano J. Alvarez, Erin Honan +17 more

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

Frontiers in Bioengineering and Biotechnology(2020)10.3389/fbioe.2020.00798

N/A

0DataRank · unranked

0 citations

Paola Nicoletti, Damien Arnol, Andrea Califano, María Rodríguez Martínez, An-phi Nguyen

BACH2 inhibition reverses β cell failure in type 2 diabetes models

Journal of Clinical Investigation(2021)10.1172/jci153876

N/A

0DataRank · unranked

74 citations

Hongxu Ding, Thomas B. Farb, Alexander M. Efanov, Jiajun Sun, Julie L. Gore +6 more

HER3 Is an Actionable Target in Advanced Prostate Cancer

Cancer Research(2021)10.1158/0008-5472.can-21-3360

N/A

0DataRank · unranked

69 citations

Susana Miranda, Ruth Riisnaes, Bora Gurel, Mariantonietta D’Ambrosio, Alessandro Vasciaveo +40 more

Targeting the T-Cell Lymphoma Epigenome Induces Cell Death, Cancer Testes Antigens, Immune-Modulatory Signaling Pathways

Molecular Cancer Therapeutics(2021)10.1158/1535-7163.mct-20-0377

N/A

0DataRank · unranked

20 citations

Cristina Kinahan, Eugene F. Douglass, Changchun Deng, Maryam Safari, Beatrice Casadei +10 more

An Information Theoretic Framework for Protein Activity Measurement

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.10.02.462873

N/A

0DataRank · unranked

4 citations

Lukas Vlahos, Codruța Chiuzan, Andrea Califano, Aaron T. Griffin

Network-based identification and pharmacological targeting of host cell master regulators induced by SARS-CoV-2 infection

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.07.03.451001

N/A

0DataRank · unranked

0 citations

Megan L. Stanifer, Gideon Bosker, Xiaoyun Sun, Sergio Triana, Patricio Doldan +11 more

A community challenge for a pancancer drug mechanism of action inference from perturbational profile data

Cell Reports Medicine(2022)10.1016/j.xcrm.2021.100492

N/A

0DataRank · unranked

69 citations

Robert J. Allaway, Bence Szalai, Wenyu Wang, Tingzhong Tian, Adrià Fernández‐Torras +23 more

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

JCI Insight(2022)10.1172/jci.insight.157694

N/A

0DataRank · unranked

15 citations

Nina Suda, Junjie Yu, Changyu Zhu, Jinsook Son, Hongxu Ding +4 more

OncoLoop: A network-based precision cancer medicine framework

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.02.11.479456

N/A

0DataRank · unranked

3 citations

Min Zou, Juan Martín Arriaga, Francisca Nunes de Almeida, Eugene F. Douglass, Maho Shibata +15 more

KINOMO: A non-negative matrix factorization framework for recovering intra- and inter-tumoral heterogeneity from single-cell RNA-seq data

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.05.02.490362

N/A

0DataRank · unranked

3 citations

Yiping Wang, Jana Biermann, Raúl Rabadán, Andrea Califano, Benjamin Izar +1 more

Airway Basal Cells Show Regionally Distinct Potential to Undergo Metaplastic Differentiation

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.05.04.490677

N/A

0DataRank · unranked

2 citations

Ying Yang, Jun Qian, Jian Ge, Débora Sinner, Hongxu Ding +3 more

A Model for Network-Based Identification and Pharmacological Targeting of Aberrant, Replication-Permissive Transcriptional Programs Induced by Viral Infection

Research Square(2022)10.21203/rs.3.rs-1287631/v1

N/A

0DataRank · unranked

0 citations

Megan L. Stanifer, Gideon Bosker, Xiaoyun Sun, Sergio Triana, Patricio Doldan +11 more

Therapeutic blood-brain barrier modulation and stroke treatment by a bioengineered FZD4-selective WNT surrogate in mice

Nature Communications(2023)10.1038/s41467-023-37689-1

N/A

0DataRank · unranked

65 citations

Sung‐Jin Lee, Lukas Vlahos, Kanako Yuki, Cara C. Rada, Vincent van Unen +16 more

Tumor Explants Elucidate a Cascade of Paracrine SHH, WNT, and VEGF Signals Driving Pancreatic Cancer Angiosuppression

Cancer Discovery(2023)10.1158/2159-8290.cd-23-0240

N/A

0DataRank · unranked

22 citations

Amanda R. Decker-Farrell, Lukas Vlahos, Dafydd H. Thomas, Álvaro Curiel‐García, H. Carlo Maurer +14 more

Activating Transcription Factor 5 Promotes Neuroblastoma Metastasis by Inducing Anoikis Resistance

Cancer Research Communications(2023)10.1158/2767-9764.crc-23-0154

N/A

0DataRank · unranked

15 citations

Shuobo Boboila, Shunpei Okochi, James M. Angelastro, Angela V. Kadenhe‐Chiweshe, Gonzalo López +5 more

NaRnEA: An Information Theoretic Framework for Gene Set Analysis

Entropy(2023)10.3390/e25030542

N/A

0DataRank · unranked

7 citations

Lukas Vlahos, Codruța Chiuzan, Andrea Califano, Aaron T. Griffin

Subtype-selective prenylated isoflavonoids disrupt regulatory drivers of MYCN-amplified cancers

Cell chemical biology(2023)10.1016/j.chembiol.2023.11.007

N/A

0DataRank · unranked

7 citations

Alessandro Vasciaveo, Jonnell C. Small, Arie Zask, Eduard Reznik, Nailah Smith +7 more

“Tumor Explants Elucidate a Cascade of Paracrine SHH, WNT, and VEGF Signals Driving Pancreatic Cancer Angiosuppression”

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.03.02.529724

N/A

0DataRank · unranked

3 citations

Amanda R. Decker-Farrell, Lukas Vlahos, Dafydd Thomas, Álvaro Curiel‐García, H. Carlo Maurer +14 more

Compound Mechanism of Action and Polypharmacology can be Elucidated by Large-Scale Perturbational Profile Analysis

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.10.08.561457

N/A

0DataRank · unranked

1 citations

Tal Hirschhorn, Eugene F. Douglass, Diana Murray, Stephen J. Trudeau, Mikko Turunen +13 more

Systematic Pan-cancer Functional Inference and Validation of Hyper, Hypo and Neomorphic Mutations

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.04.29.538640

N/A

0DataRank · unranked

0 citations

Samuel C. S. Tsang, Gordon B. Mills, Andrea Califano, Somnath Tagore

Data from Activating Transcription Factor 5 Promotes Neuroblastoma Metastasis by Inducing Anoikis Resistance

(2023)10.1158/2767-9764.c.6976989.v1

N/A

0DataRank · unranked

0 citations

Shuobo Boboila, Shunpei Okochi, James M. Angelastro, Angela V. Kadenhe‐Chiweshe, Gonzalo López +5 more

Morphogenesis and regeneration share a conserved core transition cell state program that controls lung epithelial cell fate

Developmental Cell(2024)10.1016/j.devcel.2024.11.017

N/A

0DataRank · unranked

14 citations

Benjamin van Soldt, Lukas Vlahos, Yizhuo Zhou, Jun Qian, Pasquale Laise +7 more

Network-based elucidation of colon cancer drug resistance mechanisms by phosphoproteomic time-series analysis

Nature Communications(2024)10.1038/s41467-024-47957-3

N/A

0DataRank · unranked

12 citations

Wenxue Li, Mikko Turunen, Jing He, Prem S. Subramaniam, Sergey Pampou +8 more

The Wnt-dependent master regulator NKX1-2 controls mouse pre-implantation development

Stem Cell Reports(2024)10.1016/j.stemcr.2024.04.004

N/A

0DataRank · unranked

3 citations

Davide Carnevali, Xiangtian Tan, Mariano J. Alvarez, David-Emlyn Parfitt, Umberto Di Vicino +12 more

Genome-wide studies define new genetic mechanisms of IgA vasculitis

medRxiv(2024)10.1101/2024.10.10.24315041

N/A

0DataRank · unranked

5 citations

Li Zhu, Sara Monteiro-Martins, Aaron T. Griffin, Lukas Vlahos, Masashi Fujita +88 more

Reverse engineering neuron type-specific and type-orthogonal splicing-regulatory networks using single-cell transcriptomes

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.06.13.597128

N/A

0DataRank · unranked

3 citations

Melissa Campbell, Miquel Anglada-Girotto, Huijuan Feng, Andrea Califano, Edmund Au +2 more

The regulatory architecture of the primed pluripotent cell state

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.03.25.586622

N/A

0DataRank · unranked

0 citations

Mariano J. Alvarez, Hui Zhao, Napon Chirathivat, Andrea Califano, Michael M. Shen +1 more

Regulatory network analysis of Dclk1 gene expression reveals a tuft cell-ILC2 axis that inhibits pancreatic tumor progression

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.08.30.610508

N/A

0DataRank · unranked

0 citations

Pasquale Laise, Ryota Takahashi, Feijing Wu, Tuo Ruan, Alessandro Vasciaveo +11 more

Reverse engineering neuron-type-specific and type-orthogonal splicing-regulatory networks using diverse cellular transcriptomes

Cell Reports(2025)10.1016/j.celrep.2025.115898

N/A

0DataRank · unranked

4 citations

Melissa Campbell, Miquel Anglada-Girotto, Huijuan Feng, Andrea Califano, Edmund Au +2 more

The regulatory architecture of the primed pluripotent cell state

Nature Communications(2025)10.1038/s41467-025-57894-4

N/A

0DataRank · unranked

3 citations

Mariano J. Alvarez, Hui Zhao, Napon Chirathivat, Andrea Califano, Michael M. Shen +1 more

Morphogenesis and regeneration share a conserved core transition cell state program that controls lung epithelial cell fate

Developmental Cell(2025)10.1016/j.devcel.2025.08.014

N/A

0DataRank · unranked

3 citations

Benjamin van Soldt, Lukas Vlahos, Yizhuo Zhou, Jun Qian, Pasquale Laise +7 more

Lipidomic changes in persister cancer cells drive enhanced ferroptosis sensitivity

Ferroptosis and Oxidative Stress(2025)10.70401/fos.2025.0003

N/A

0DataRank · unranked

1 citations

Fereshteh Zandkarimi, Joleen M. Csuka, Qiulin Zhu, Jenny Jin, Taruna Vani Neelakantan +12 more

Regulatory network analysis of Dclk1 gene expression reveals a tuft cell-ILC2 axis that inhibits pancreatic tumor progression

Cell Reports(2025)10.1016/j.celrep.2025.115734

N/A

0DataRank · unranked

2 citations

Pasquale Laise, Feijing Wu, Ryota Takahashi, Tuo Ruan, Alessandro Vasciaveo +13 more

Identification and targeting of regulators of SARS-CoV-2–host interactions in the airway epithelium

Science Advances(2025)10.1126/sciadv.adu2079

N/A

0DataRank · unranked

1 citations

Heeju Noh, Lorenzo Tomassoni, Dianbo Cao, Yizhuo Zhou, Xiangyi Ke +8 more

Single Nuclei-Derived Molecular Subtypes of Gastrointestinal Stromal Tumors Correlate with Clinicopathologic Features and Predict Clinical Outcomes

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.04.21.647322

N/A

0DataRank · unranked

0 citations

Alexander T. Wenzel, John Y. Jun, Diwakar Guragain, Chih‐Min Tang, Mark Antkowiak +19 more

Complex Assembly and Activity States as Multifaceted Protein Attributes Explaining Phenotypic Variability

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.09.25.678633

N/A

0DataRank · unranked

0 citations

Peng Xue, Isabell Bludau, Claudia Martelli, Evan G. Williams, Ben C. Collins +4 more

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