Evidence map›Paper›PMID 27565351›Full record

ArticleCell2016

Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics.

Karthik Shekhar, Sylvain W Lapan, Irene E Whitney, Nicholas M Tran, Evan Z Macosko, Monika Kowalczyk, Xian Adiconis, Joshua Z Levin, James Nemesh, Melissa Goldman and 4 more

Open access · bronzeAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 683 papers.

0numbers the graph read from it
0cells of the map it votes in
683citing papers in PubMed
80.6field-weighted citation impact, top 1% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

683 citing papers in PubMed, 1,283 citations in OpenAlex.

  1. Article
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  6. Approaching a connectome of the human foveal retina.Proceedings of the National Academy of Sciences of the United States of America · 2026
    Article
  7. Article
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  9. Protocadherin 9 Promotes Cell Survival of Different Bipolar Cell Types in the Developing Mouse Retina.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2026
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623 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

14 authors at 3 institutions in 1 country.

Karthik ShekharBroad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
Sylvain W LapanDepartment of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
Irene E WhitneyCenter for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02130, USA.
Nicholas M TranCenter for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02130, USA.
Evan Z MacoskoDepartment of Genetics, Harvard Medical School, Boston, MA 02115, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
Monika KowalczykBroad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
Xian AdiconisBroad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
Joshua Z LevinBroad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
James NemeshDepartment of Genetics, Harvard Medical School, Boston, MA 02115, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
Melissa GoldmanDepartment of Genetics, Harvard Medical School, Boston, MA 02115, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
Steven A McCarrollDepartment of Genetics, Harvard Medical School, Boston, MA 02115, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
Constance L CepkoDepartment of Genetics, Harvard Medical School, Boston, MA 02115, USA; Department of Ophthalmology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA. Electronic address: cepko@genetics.med.harvard.edu.
Aviv RegevBroad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Department of Biology and Koch Institute, MIT, Cambridge, MA 02139, USA. Electronic address: aregev@broadinstitute.org.
Joshua R SanesCenter for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02130, USA. Electronic address: sanesj@mcb.harvard.edu.
Broad Institute · USHarvard University · USHoward Hughes Medical Institute · US

Funding

Comprehensive Classification Of Neuronal Subtypes By Single Cell TranscriptomicsU01MH105960 · NIMH · HARVARD UNIVERSITY · PI REGEV, AVIV, SANES, JOSHUA R · 2014 to 2016
$4.5M
Fostering Research Mentorship & Training during Psychiatry Residency SupplementR25MH094612 · NIMH · MASSACHUSETTS GENERAL HOSPITAL · PI FAVA, MAURIZIO, GREENFIELD, SHELLY F. · 2011 to 2022
$2.3M
Transcriptional Control of Retinal Bipolar Neuron DiversificationF32EY024833 · NEI · HARVARD MEDICAL SCHOOL · PI LAPAN, SYLVAIN · 2014 to 2015
$106k
NEI NIH HHS F32 EY024833NIMH NIH HHS R25 MH094612NIMH NIH HHS U01 MH105960
6 · The paper itself

Abstract

Patterns of gene expression can be used to characterize and classify neuronal types. It is challenging, however, to generate taxonomies that fulfill the essential criteria of being comprehensive, harmonizing with conventional classification schemes, and lacking superfluous subdivisions of genuine types. To address these challenges, we used massively parallel single-cell RNA profiling and optimized computational methods on a heterogeneous class of neurons, mouse retinal bipolar cells (BCs). From a population of ∼25,000 BCs, we derived a molecular classification that identified 15 types, including all types observed previously and two novel types, one of which has a non-canonical morphology and position. We validated the classification scheme and identified dozens of novel markers using methods that match molecular expression to cell morphology. This work provides a systematic methodology for achieving comprehensive molecular classification of neurons, identifies novel neuronal types, and uncovers transcriptional differences that distinguish types within a class.

Indexed as

TranscriptomeAmacrine CellsAnimalsCluster AnalysisFemaleGenetic MarkersMaleMiceMice, Inbred StrainsMice, TransgenicRetinal Bipolar CellsSequence Analysis, RNASingle-Cell AnalysisTranscription, GeneticGenetic Markers

Identifiers

PMID27565351
PMCPMC5003425
OpenAlexW2510746232

What OpenQuestion holds

Textmetadata
LicenceTDM
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.