Maryann Martone

Maryann Martone
University of California, San Diego | UCSD · Department of Neurosciences

Ph. D.

About

371
Publications
121,353
Reads
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32,009
Citations
Additional affiliations
April 2015 - April 2018
Hypothes.is
Position
  • Managing Director
June 1990 - October 2021
University of California, San Diego
Position
  • Professor Emeritus

Publications

Publications (371)
Preprint
Full-text available
The Stimulating Peripheral Activity to Relieve Conditions (SPARC) program is a U.S. National Institutes of Health (NIH) funded effort to enhance our understanding of the neural circuitry responsible for visceral control. SPARC's mission is to identify, extract, and compile our overall existing knowledge and understanding of the autonomic nervous sy...
Article
Full-text available
Neuroscience has made significant strides over the past decade in moving from a largely closed science characterized by anemic data sharing, to a largely open science where the amount of publicly available neuroscience data has increased dramatically. While this increase is driven in significant part by large prospective data sharing studies, we ar...
Preprint
Full-text available
Traumatic brain injury (TBI) is an insult to the brain resulting from an external force and is a significant cause of morbidity and mortality in the United States. No effective clinical therapeutics currently exist for this injury. Although several therapies and procedures have been deemed successful for TBI treatment in preclinical research studie...
Article
Full-text available
Brain atlases are important reference resources for accurate anatomical description of neuroscience data. Open access, three-dimensional atlases serve as spatial frameworks for integrating experimental data and defining regions-of-interest in analytic workflows. However, naming conventions, parcellation criteria, area definitions, and underlying ma...
Article
Full-text available
Characterizing cellular diversity at different levels of biological organization and across data modalities is a prerequisite to understanding the function of cell types in the brain. Classification of neurons is also essential to manipulate cell types in controlled ways and to understand their variation and vulnerability in brain disorders. The BR...
Article
The Stimulating Peripheral Activity to Relieve Conditions (SPARC) program is a NIH-funded consortium to improve the understanding of how the autonomic nervous system (ANS) interacts with end organs and the central nervous system. A major goal of SPARC is to use this knowledge to develop the next generation of neuromodulator devices as effective dis...
Article
The December 2022 release of the SPARC Portal ( https://sparc.science ) included the first significant update to the anatomical connectivity flatmaps since the portal first launched. These flatmaps provide an interactive and visual map for the display and exploration of the autonomic nervous system of Human, rat, mouse, pig, and cat ( https://sparc...
Preprint
Full-text available
Brain atlases are important reference resources for accurate anatomical description of neuroscience data. Open access, three-dimensional atlases serve as spatial frameworks for integrating experimental data and defining regions-of-interest in analytic workflows. However, naming conventions, parcellation criteria, area definitions, and underlying ma...
Article
Full-text available
Antibodies are ubiquitous key biological research resources yet are tricky to use as they are prone to performance issues and represent a major source of variability across studies. Understanding what antibody was used in a published study is therefore necessary to repeat and/or interpret a given study. However, antibody reagents are still frequent...
Preprint
Full-text available
Characterizing cellular diversity at different levels of biological organization across data modalities is a prerequisite to understanding the function of cell types in the brain. Classification of neurons is also required to manipulate cell types in controlled ways, and to understand their variation and vulnerability in brain disorders. The BRAIN...
Article
Full-text available
The stimulating peripheral activity to relieve conditions (SPARC) program is a US National Institutes of Health-funded effort to improve our understanding of the neural circuitry of the autonomic nervous system (ANS) in support of bioelectronic medicine. As part of this effort, the SPARC project is generating multi-species, multimodal data, models,...
Article
Discovering and learning how to use fast-growing publicly available online bioinformatics and data resources can be challenging for bench scientists. The NIDDK Information Network (dkNET; https://dknet.org) is an open community resource information portal for biomedical researchers supported by the National Institute of Diabetes and Digestive and K...
Article
Full-text available
We present (i) the ApiNATOMY workflow to build knowledge models of biological connectivity, as well as (ii) the ApiNATOMY TOO map, a topological scaffold to organize and visually inspect these connectivity models in the context of a canonical architecture of body compartments. In this work, we outline the implementation of ApiNATOMY’s knowledge rep...
Article
Full-text available
Traumatic brain injury (TBI) is a major public health problem. Despite considerable research deciphering injury pathophysiology, precision therapies remain elusive. Here, we present large-scale data sharing and machine intelligence approaches to leverage TBI complexity. The Open Data Commons for TBI (ODC-TBI) is a community-centered repository emph...
Article
Full-text available
The challenge of defining and cataloging the building blocks of the brain requires a standardized approach to naming neurons and organizing knowledge about their properties. The US Brain Initiative Cell Census Network, Human Cell Atlas, Blue Brain Project, and others are generating vast amounts of data and characterizing large numbers of neurons th...
Article
Full-text available
In this perspective article, we consider the critical issue of data and other research object standardisation and, specifically, how international collaboration, and organizations such as the International Neuroinformatics Coordinating Facility (INCF) can encourage that emerging neuroscience data be Findable, Accessible, Interoperable, and Reusable...
Article
Full-text available
As neuroscience projects increase in scale and cross international borders, different ethical principles, national and international laws, regulations, and policies for data sharing must be considered. These concerns are part of what is collectively called data governance. Whereas neuroscience data transcend borders, data governance is typically co...
Article
Full-text available
Here we report the generation of a multimodal cell census and atlas of the mammalian primary motor cortex as the initial product of the BRAIN Initiative Cell Census Network (BICCN). This was achieved by coordinated large-scale analyses of single-cell transcriptomes, chromatin accessibility, DNA methylomes, spatially resolved single-cell transcripto...
Article
Full-text available
The past decade has seen accelerating movement from data protectionism in publishing toward open data sharing to improve reproducibility and translation of biomedical research. Developing data sharing infrastructures to meet these new demands remains a challenge. One model for data sharing involves simply attaching data, irrespective of its type, t...
Article
Full-text available
Increasing attention is being paid to the operation of biomedical data repositories in light of efforts to improve how scientific data is handled and made available for the long term. Multiple groups have produced recommendations for functions that biomedical repositories should support, with many using requirements of the FAIR data principles as g...
Article
Full-text available
The Data and Resource Center (DRC) of the NIH-funded SPARC program is developing databases, connectivity maps, and simulation tools for the mammalian autonomic nervous system. The experimental data and mathematical models supplied to the DRC by the SPARC consortium are curated, annotated and semantically linked via a single knowledgebase. A data po...
Article
Full-text available
Antibodies are widely used reagents to test for expression of proteins and other antigens. However, they might not always reliably produce results when they do not specifically bind to the target proteins that their providers designed them for, leading to unreliable research results. While many proposals have been developed to deal with the problem...
Article
Full-text available
A Correction to this paper has been published: https://doi.org/10.1007/s12021-021-09522-x
Preprint
Full-text available
The Data and Resource Center (DRC) of the NIH-funded SPARC program is developing databases, connectivity maps and simulation tools for the mammalian autonomic nervous system. The experimental data and mathematical models supplied to the DRC by the SPARC consortium are curated, annotated and semantically linked via a single knowledgebase. A data por...
Preprint
Full-text available
Traumatic brain injury (TBI) is a major unsolved public health problem worldwide with considerable preclinical research dedicated to recapitulating clinical TBI, deciphering the underlying pathophysiology, and developing therapeutics. However, the heterogeneity of clinical TBI and correspondingly in preclinical studies have made translation from be...
Preprint
Full-text available
The NIH Common Fund Stimulating Peripheral Activity to Relieve Conditions (SPARC) initiative is a large-scale program that seeks to accelerate the development of therapeutic devices that modulate electrical activity in nerves to improve organ function. Integral to the SPARC program are the rich anatomical and functional datasets produced by investi...
Article
Full-text available
There is great need for coordination around standards and best practices in neuroscience to support efforts to make neuroscience a data-centric discipline. Major brain initiatives launched around the world are poised to generate huge stores of neuroscience data. At the same time, neuroscience, like many domains in biomedicine, is confronting the is...
Article
Full-text available
As information and communication technology has become pervasive in our society, we are increasingly dependent on both digital data and repositories that provide access to and enable the use of such resources. Repositories must earn the trust of the communities they intend to serve and demonstrate that they are reliable and capable of appropriately...
Article
Full-text available
The reproducibility crisis is a multifaceted problem involving ingrained practices within the scientific community. Fortunately, some causes are addressed by the author's adherence to rigor and reproducibility criteria, implemented via checklists at various journals. We developed an automated tool (SciScore) that evaluates research articles based o...
Preprint
Full-text available
The challenge of defining and cataloging the building blocks of the brain requires a standardized approach to naming neurons and organizing knowledge about their properties. The US Brain Initiative Cell Census Network, Human Cell Atlas, Blue Brain Project, and others are generating vast amounts of data and characterizing large numbers of neurons th...
Preprint
Motivation: Antibodies are widely used reagents to test for expression of proteins. However, they might not always reliably produce results when they do not specifically bind to the target proteins that their providers designed them for, leading to unreliable research results. While many proposals have been developed to deal with the problem of ant...
Article
Transparency of information on the effectiveness of research resources such as cell lines and antibodies is critical for enhancing scientific rigor and reproducibility. Horbach et al. showed that 32,755 published articles have used misidentified cell lines, and the problem keeps growing as more than half a million studies cite these papers [1] . Tr...
Article
This special issue is intended to inform the scientific computing community about recent advances and the current state of the art in software and data citation. Initial work has been done elsewhere to define standards and principles for software and data citation, and the basic required infrastructure is now in place. The challenge now is to adopt...
Preprint
Full-text available
The reproducibility crisis in science is a multifaceted problem involving practices and incentives, both in the laboratory and in publication. Fortunately, some of the root causes are known and can be addressed by scientists and authors alike. After careful consideration of the available literature, the National Institutes of Health identified seve...
Article
Full-text available
The Research Resource Identifier was introduced in 2014 to better identify biomedical research resources and track their use across the literature, including key digital resources like databases and software. Authors include an RRID after the first mention of any resource used. Here we provide an overview of RRIDs and analyze their use for digital...
Article
Over the last 5 years multiple stakeholders in the field of spinal cord injury (SCI) research have initiated efforts to promote publications standards and to enable sharing of experimental data. In 2016 NIH/NINDS hosted representatives from the SCI community to streamline these efforts and to discuss the future of data sharing in the field accordin...
Article
The NIDDK Information Network (dkNET; https://dknet.org) is an open community resource portal for basic and clinical investigators in diabetes, digestive, endocrine, metabolic, kidney, and urologic diseases [1]. dkNET provides access to a collection of diverse research resources, including data, information, materials, organisms, tools, funding opp...
Article
Full-text available
This article presents a practical roadmap for scholarly data repositories to implement data citation in accordance with the Joint Declaration of Data Citation Principles (Data Citation Synthesis Group, 2014), a synopsis and harmonization of the recommendations of major science policy bodies. The roadmap was developed by the Repositories Early Adopt...
Article
The use of problematic resources such as contaminated or misidentified cell lines and cross‐reactive antibodies lead to reproducibility problems. Research has shown that about twenty percent of published studies use contaminated cell lines [1]. Many factors, including the ability to easily retrieve alert information, result in the continued use of...
Article
Full-text available
There has been a recent major upsurge in the concerns about reproducibility in many areas of science. Within the neuroimaging domain, one approach is to promote reproducibility is to target the re-executability of the publication. The information supporting such re-executability can enable the detailed examination of how an initial finding generali...
Article
Full-text available
The use of misidentified and contaminated cell lines continues to be a problem in biomedical research. Research Resource Identifiers (RRIDs) should reduce the prevalence of misidentified and contaminated cell lines in the literature by alerting researchers to cell lines that are on the list of problematic cell lines, which is maintained by the Inte...
Data
Data on number of misidentified cell lines per year.
Data
Curator-SciScore-disagreement - the false negatives (33 papers) found by the curator.
Data
Data on problematic cell lines for all journals.
Data
List of problematic cell lines extracted from Cellosaurus Version 25 (March 2018).
Preprint
There is great need for coordination around standards and best practices in neuroscience to support efforts to make neuroscience a data-centric discipline. Major brain initiatives launched around the world are poised to generate huge stores of neuroscience data. At the same time, neuroscience, like many domains in biomedicine, is confronting the is...
Preprint
There has been a recent major upsurge in the concerns about reproducibility in many areas of science. Within the neuroimaging domain, one approach is to promote reproducibility is to target the re-executability of the publication. The information supporting such re-executability can enable the detailed examination of how an initial finding generali...
Article
Full-text available
Progress in basic and clinical research is slowed when researchers fail to provide a complete and accurate report of how a study was designed, executed, and the results analyzed. Publishing rigorous scientific research involves a full description of the methods, materials, procedures, and outcomes. Investigators may fail to provide a complete descr...
Article
Full-text available
Progress in basic and clinical research is slowed when researchers fail to provide a complete and accurate report of how a study was designed, executed, and the results analyzed. Publishing rigorous scientific research involves a full description of the methods, materials, procedures, and outcomes. Investigators may fail to provide a complete descr...
Article
Full-text available
Progress in basic and clinical research is slowed when researchers fail to provide a complete and accurate report of how a study was designed, executed, and the results analyzed. Publishing rigorous scientific research involves a full description of the methods, materials, procedures, and outcomes. Investigators may fail to provide a complete descr...
Article
Full-text available
This article presents a practical roadmap for scholarly publishers to implement data citation in accordance with the Joint Declaration of Data Citation Principles (JDDCP), a synopsis and harmonization of the recommendations of major science policy bodies. It was developed by the Publishers Early Adopters Expert Group as part of the Data Citation Im...
Article
The NIDDK Information Network (dknet.org) is a portal for basic and clinical investigators that makes it easier to discover, obtain, and reuse scientific research resources. Here we demonstrate how dkNET can connect researchers to resources for obesity research. A search for “obesity” returns 264,498 results (Table 1), including physical resources...
Article
Reproducibility was assessed in the scientific literature and the field of immunology did not fare well, as described in Vasilevsky et al 2013. Antibodies and constructs used in immunological publications could not be identified in more than 50% of the cases studied. Similarly, in publications describing the recognition of immune epitopes by the ad...
Preprint
Full-text available
Progress in basic and clinical research falters when researchers fail to provide a complete and accurate report of how a study was designed, executed and results analyzed. Publishing rigorous scientific research involves a full description of the methods, materials, procedures and outcomes. Investigators may fail to provide a complete description o...
Preprint
Progress in basic and clinical research falters when researchers fail to provide a complete and accurate report of how a study was designed, executed and results analyzed. Publishing rigorous scientific research involves a full description of the methods, materials, procedures and outcomes. Investigators may fail to provide a complete description o...
Preprint
In order to increase the replicability of scientific work, the scientific community has called for practices designed to increase the transparency of research (McNutt, 2014; Nosek et al., 2015). The validity of a scientific claim depends not on the reputation of those making the claim, the venue in which the claim is made, or the novelty of the res...
Preprint
Full-text available
Most biomedical data repositories issue locally-unique accessions numbers, but do not provide globally unique, machine-resolvable, persistent identifiers for their datasets, as required by publishers wishing to implement data citation in accordance with widely accepted principles. Local accessions may however be prefixed with a namespace identifier...
Article
Full-text available
Routine data sharing, defined here as the publication of the primary data and any supporting materials required to interpret the data acquired as part of a research study, is still in its infancy in psychology, as in many domains. Nevertheless, with increased scrutiny on reproducibility and more funder mandates requiring sharing of data, the issues...
Preprint
Full-text available
Digital repositories bring direct impact and influence on the research community and society but measuring their value using formal metrics remains challenging. their value. It is challenging to define a single perfect metric that covers all quality aspects. Here, we distinguish here between impact and influence and discuss measures and mentions as...
Preprint
Full-text available
Digital repositories bring direct impact and influence on the research community and society but measuring their value using formal metrics remains challenging. their value. It is challenging to define a single perfect metric that covers all quality aspects. Here, we distinguish here between impact and influence and discuss measures and mentions as...