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Paper · 34552244

Biologically informed deep neural network for prostate cancer discovery.

Elmarakeby HA and 13 others. Nature, 2021. Cited by 307 papers, by iCite.

11 sourcespapers-2026-11-12-0.1.0

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ConductScience Library. Biologically informed deep neural network for prostate cancer discovery. Papers, record 34552244. Release papers-2026-11-12-0.1.0, 12 Nov 2026. https://conductscience.org/library/papers/34552244

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Paper

PubMed's record of the paper, with iCite's citation figures. No abstract is shown.

Title
Biologically informed deep neural network for prostate cancer discovery.
PubMed
Journal
Nature
PubMed
Year
2021
PubMed
Publication types
Journal Article, Research Support, N.I.H., Extramural, Research Support, Non-U.S. Gov't, Research Support, U.S. Gov't, Non-P.H.S.
PubMed
Citations, by iCite
307
iCite
Relative citation ratio, by iCite
15.4
iCite
Revised in PubMed
2026-05-22
PubMed

Authors14

The authors in the order PubMed's record lists them, with the ORCID iDs it states.

OrderAuthorForenameKindORCID iD
1Elmarakeby HAHaitham Ahttps://orcid.org/0000-0002-4315-4347
2Hwang JJustinhttps://orcid.org/0000-0003-1686-7103
3Arafeh RRand
4Crowdis JJett
5Gang SSydney
6Liu DDavid
7AlDubayan SHSaud H
8Salari KKeyan
9Kregel SSteven
10Richter CCamden

1 to 10 of 14Source PubMed

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Topics11

NLM's MeSH indexing of the paper, its major topics first.

MeSH termMajor
Deep LearningMajor topic
Prostatic NeoplasmsMajor topic
Cell Cycle Proteins
Drug Resistance, Neoplasm
Humans
Male
Proto-Oncogene Proteins
Receptor, Fibroblast Growth Factor, Type 1
Receptors, Androgen
Reproducibility of Results
Tumor Suppressor Protein p53

Source PubMed

Grants2

Each grant PubMed's record writes, matched to the NIH project NIH's grant and paper links name for this paper, and each of those links the record does not write.

Grant, as the record writes itAgencyCountryNIH projectStated bySource
U01 CA176058NCI NIH HHSUnited StatesU01CA176058PubMed and NIHNIH RePORTER
U01 CA233100NCI NIH HHSUnited StatesU01CA233100PubMed and NIHNIH RePORTER

Trials0

The trials whose ClinicalTrials.gov record lists the paper, and the trial numbers the paper's PubMed record names.

None in this release.

Comments and corrections2

PubMed's comments and corrections, NLM's own indexing: retractions first, then expressions of concern, errata and updates, and comments last.

KindPMIDTitleIn PapersSource
Comment in34,856,063Is Artificial Intelligence Ready for "Primetime" in Urology?https://conductscience.org/library/papers/34856063PubMed
Comment in35,593,059Uro-Science.https://conductscience.org/library/papers/35593059PubMed

References43

The papers the reference list in PubMed's record names, those in our copy of PubMed, in the list's order.

OrderPMIDTitleJournalYearIn PapersSource
126,000,489Integrative clinical genomics of advanced prostate cancer.Cell2015https://conductscience.org/library/papers/26000489PubMed
231,061,129Genomic correlates of clinical outcome in advanced prostate cancer.Proc Natl Acad Sci U S A2019https://conductscience.org/library/papers/31061129PubMed
329,505,029Using deep learning to model the hierarchical structure and function of a cell.Nat Methods2018https://conductscience.org/library/papers/29505029PubMed
431,080,069A White-Box Machine Learning Approach for Revealing Antibiotic Mechanisms of Action.Cell2019https://conductscience.org/library/papers/31080069PubMed
533,096,023Predicting Drug Response and Synergy Using a Deep Learning Model of Human Cancer Cells.Cancer Cell2020https://conductscience.org/library/papers/33096023PubMed
625,830,880The evolutionary history of lethal metastatic prostate cancer.Nature2015https://conductscience.org/library/papers/25830880PubMed
729,985,747Clinical and Genomic Characterization of Treatment-Emergent Small-Cell Neuroendocrine Prostate Cancer: A Multi-institutional Prospective Study.J Clin Oncol2018https://conductscience.org/library/papers/29985747PubMed
829,610,475The long tail of oncogenic drivers in prostate cancer.Nat Genet2018https://conductscience.org/library/papers/29610475PubMed
930,382,943Immunogenomic analyses associate immunological alterations with mismatch repair defects in prostate cancer.J Clin Invest2018https://conductscience.org/library/papers/30382943PubMed
1030,928,160Genomic Drivers of Poor Prognosis and Enzalutamide Resistance in Metastatic Castration-resistant Prostate Cancer.Eur Urol2019https://conductscience.org/library/papers/30928160PubMed

1 to 10 of 43

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Cited by252

The papers in our copy of PubMed whose reference list names this one, newest first. iCite, which reads more sources, counts 307 citations.

PMIDTitleJournalYearIn PapersSource
42,979,500Post-Translational Control of PD-L1 in Cancer Immunity and Immunotherapy Resistance.Immunotargets Ther2026https://conductscience.org/library/papers/42979500PubMed
42,960,345Explainable artificial intelligence in prostate and bladder cancer: A review of imaging, digital pathology, molecular profiling, and clinical data.Curr Urol2026https://conductscience.org/library/papers/42960345PubMed
42,942,329Pathway-Masked Kolmogorov-Arnold Networks Yield an Interpretable Transcriptomic Score Associated with Colorectal Cancer Progression Independently of Clinical Stage.Life (Basel)2026https://conductscience.org/library/papers/42942329PubMed
42,936,269xNNPCD identifies regulators of programmed cell death by integrating perturbation transcriptomes with cancer dependency profiles.NAR Cancer2026https://conductscience.org/library/papers/42936269PubMed
42,899,193Knowledge Graphs for Cervical Cancer Across the Care Continuum: From Vaccination and Screening to Personalized Therapy.Ther Clin Risk Manag2026https://conductscience.org/library/papers/42899193PubMed
42,889,514From inherited susceptibility to tumor state: toward a stage-aware architecture for genomic risk stratification in prostate cancer.Front Genet2026https://conductscience.org/library/papers/42889514PubMed
42,799,696ASAS-NANP SYMPOSIUM: Mathematical modeling in animal nutrition-modeling in the agriculture 4.0 era and beyond: merging mechanistic knowledge and artificial intelligence with hybrid modeling.J Anim Sci2026https://conductscience.org/library/papers/42799696PubMed
42,782,810Explicit Mechanistic Operators in Predictive Virtual Cells: Evidence, Failure Modes, and a Minimum Falsification Framework for Single-Cell Perturbation Prediction.Cells2026https://conductscience.org/library/papers/42782810PubMed
42,688,326A Knowledge-Enhanced Multimodal Framework with Genomic Reconstruction for DLBCL Drug Response Prediction.Comput Struct Biotechnol J2026https://conductscience.org/library/papers/42688326PubMed
42,680,988Using Biological Networks to Guide Biomedical Prediction.Methods Mol Biol2026https://conductscience.org/library/papers/42680988PubMed

1 to 10 of 252

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Genes18

The genes the Gene search release ties to the paper: Swiss-Prot's references first, then PubTator's text mining.

GeneNCBI Gene IDLinked byIn GenesSource
ABL125PubTator's text mininghttps://conductscience.org/library/genes/25NCBI Gene
CDK41,019PubTator's text mininghttps://conductscience.org/library/genes/1019NCBI Gene
CDK61,021PubTator's text mininghttps://conductscience.org/library/genes/1021NCBI Gene
EIF3E3,646PubTator's text mininghttps://conductscience.org/library/genes/3646NCBI Gene
FGF62,251PubTator's text mininghttps://conductscience.org/library/genes/2251NCBI Gene
FGFR12,260PubTator's text mininghttps://conductscience.org/library/genes/2260NCBI Gene
FGFR22,263PubTator's text mininghttps://conductscience.org/library/genes/2263NCBI Gene
FGFR32,261PubTator's text mininghttps://conductscience.org/library/genes/2261NCBI Gene
MDM24,193PubTator's text mininghttps://conductscience.org/library/genes/4193NCBI Gene
MDM44,194PubTator's text mininghttps://conductscience.org/library/genes/4194NCBI Gene

1 to 10 of 18

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Drugs0

The drugs whose trials, in the Pipelines release, list the paper.

None in this release.

Data0

The data bank entries PubMed's record names. Trial numbers are under Trials.

None in this release.

Data dates

The date of each source this release read.

PubMed
2026-11-06
PubMed
iCite
2026-11-05
iCite
PMC's ID file
2026-11-05
PMC's ID file
NIH RePORTER's grant and paper links
2026-11-01
NIH RePORTER's grant and paper links
Trials
2026-11-12
Gene search
2026-11-11
Pipelines
2026-09-18

Sources 11

  • ChEMBL, through Open TargetsCC BY-SA 3.0
  • ClinicalTrials.govNo license stated
  • HGNCCC0
  • iCiteCC BY 4.0
  • NCBI GenePublic domain (US government)
  • NIH RePORTER's grant and paper linksPublic domain
  • Open TargetsCC0 1.0
  • PMC's ID filePublic domain (US government)
  • PubMedNLM's terms
  • PubTator 3Public domain
  • UniProtCC BY 4.0
Each source's terms
  • ChEMBL, through Open TargetsCC BY-SA 3.0, for the parts from ChEMBL. Read on 8 Nov 2026 at https://platform-docs.opentargets.org/licence
  • ClinicalTrials.govnone stated
  • HGNCCC0: https://www.genenames.org/about/license/
  • iCiteCC BY 4.0
  • NCBI GeneNone named for the file. NCBI says information created by or for the US government on its site is in the public domain, and asks that NLM be acknowledged: https://www.ncbi.nlm.nih.gov/home/about/policies/
  • NIH RePORTER's grant and paper linksPublic domain (NIH RePORTER)
  • Open TargetsCC0 1.0. Open Targets asks that users cite its latest paper: Buniello et al. 2025, Open Targets Platform: facilitating therapeutic hypotheses building in drug discovery, Nucleic Acids Research 53(D1):D1467, PMID 39657122. Read on 8 Nov 2026 at https://platform-docs.opentargets.org/licence
  • PMC's ID fileNone named for the file. NCBI says information created by or for the US government on its site is in the public domain, and asks that NLM be acknowledged: https://www.ncbi.nlm.nih.gov/home/about/policies/
  • PubMedNLM's terms
  • PubTator 3Public domain
  • UniProtCC BY 4.0. UniProt's licence file: "All databases and documents in the UniProt FTP directory may be copied and redistributed freely, without advance permission, provided that this copyright statement is reproduced with each copy." UniProt asks that users cite its latest paper: The UniProt Consortium, UniProt: the Universal Protein Knowledgebase in 2025, Nucleic Acids Research 53:D609-D617, https://doi.org/10.1093/nar/gkae1010. Read on 9 Nov 2026 at https://www.uniprot.org/help/license

ClinicalTrials.gov's data carry an international copyright outside the United States: https://clinicaltrials.gov/about-site/terms-conditions.

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