Gene losses in the common vampire bat illuminate molecular adaptations to blood feeding

Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm

(2021) Haoyu Cheng et al.   NATURE METHODS

Twelve years of SAMtools and BCFtools

(2021) Petr Danecek et al.   GigaScience

Non-kin adoption in the common vampire bat

(2021) Imran Razik et al.   Royal Society Open Science

Surveying the Vampire Bat (Desmodus rotundus) Serum Proteome: A Resource for Identifying Immunological Proteins and Detecting Pathogens

(2021) Benjamin A. Neely et al.   JOURNAL OF PROTEOME RESEARCH

Exocrine pancreas proteases regulate β-cell proliferation in zebrafish ciliopathy models and in murine systems

(2021) Timothy L. Hostelley et al.   Biology Open

Allosteric Modulation of NMDARs Reverses Patients' Autoantibody Effects in Mice

(2021) Marija Radosevic et al.   Neurology-Neuroimmunology & Neuroinflammation

Zinc induces iron egress from intestinal Caco-2 cells via induction of Hephaestin: A role for PI3K in intestinal iron absorption

(2020) Palsa Kondaiah et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

SciPy 1.0: fundamental algorithms for scientific computing in Python

(2020) Pauli Virtanen et al.   NATURE METHODS

Host Defense Peptide RNase 7 Is Down-regulated in the Skin of Diabetic Patients with or without Chronic Ulcers, and its Expression is Altered with Metformin

(2020) Adrian Rodríguez-Carlos et al.   ARCHIVES OF MEDICAL RESEARCH

Molecular adaptation and convergent evolution of frugivory in Old World and neotropical fruit bats

(2020) Kai Wang et al.   MOLECULAR ECOLOGY

Six reference-quality genomes reveal evolution of bat adaptations

(2020) David Jebb et al.   NATURE

Loss of chymotrypsin-like protease (CTRL) alters intrapancreatic protease activation but not pancreatitis severity in mice

(2020) Dóra Mosztbacher et al.   Scientific Reports

Genomic consequences of dietary diversification and parallel evolution due to nectarivory in leaf-nosed bats

(2020) Yocelyn T Gutiérrez-Guerrero et al.   GigaScience

Calcium signaling and secretory granule pool dynamics underlie biphasic insulin secretion and its amplification: experiments and modeling

(2019) Morten Gram Pedersen et al.   AMERICAN JOURNAL OF PHYSIOLOGY-ENDOCRINOLOGY AND METABOLISM

Evaluating the usefulness of alignment filtering methods to reduce the impact of errors on evolutionary inferences

(2019) Arnaud Di Franco et al.   BMC EVOLUTIONARY BIOLOGY

Convergent gene losses illuminate metabolic and physiological changes in herbivores and carnivores

(2019) Nikolai Hecker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Healthy Human Blood Microbiome: Fact or Fiction?

(2019) Diego J. Castillo et al.   Frontiers in Cellular and Infection Microbiology

Cooler: scalable storage for Hi-C data and other genomically labeled arrays

(2019) Nezar Abdennur et al.   BIOINFORMATICS

Evidence that Evolution of the Diabetes Susceptibility Gene SLC30A8 that Encodes the Zinc Transporter ZnT8 Drives Variations in Pancreatic Islet Zinc Content in Multiple Species

(2019) Karin J. Bosma et al.   JOURNAL OF MOLECULAR EVOLUTION

Gene expression across mammalian organ development

(2019) Margarida Cardoso-Moreira et al.   NATURE

Integrating Hi-C links with assembly graphs for chromosome-scale assembly

(2019) Jay Ghurye et al.   PLoS Computational Biology

Genes lost during the transition from land to water in cetaceans highlight genomic changes associated with aquatic adaptations

(2019) Matthias Huelsmann et al.   Science Advances

Ligand-binding properties and catalytic activity of the purified human 24-hydroxycholesterol 7α-hydroxylase, CYP39A1

(2019) I.P. Grabovec et al.   JOURNAL OF STEROID BIOCHEMISTRY AND MOLECULAR BIOLOGY

The Antimicrobial and Immunomodulatory Function of RNase 7 in Skin

(2019) Franziska Rademacher et al.   Frontiers in Immunology

RepeatFiller newly identifies megabases of aligning repetitive sequences and improves annotations of conserved non-exonic elements

(2019) Ekaterina Osipova et al.   GigaScience

Vampire Bats that Cooperate in the Lab Maintain Their Social Networks in the Wild

(2019) Simon P. Ripperger et al.   CURRENT BIOLOGY

Iron storage disease (hemochromatosis) and hepcidin response to iron load in two species of pteropodid fruit bats relative to the common vampire bat

(2018) Iga M. Stasiak et al.   JOURNAL OF COMPARATIVE PHYSIOLOGY B-BIOCHEMICAL SYSTEMIC AND ENVIRONMENTAL PHYSIOLOGY

A genomics approach reveals insights into the importance of gene losses for mammalian adaptations

(2018) Virag Sharma et al.   Nature Communications

Hologenomic adaptations underlying the evolution of sanguivory in the common vampire bat

(2018) M. Lisandra Zepeda Mendoza et al.   Nature Ecology & Evolution

MACSE v2: Toolkit for the Alignment of Coding Sequences Accounting for Frameshifts and Stop Codons

(2018) Vincent Ranwez et al.   MOLECULAR BIOLOGY AND EVOLUTION

Colour vision variation in leaf-nosed bats (Phyllostomidae): Links to cave roosting and dietary specialization

(2018) Kelly Kries et al.   MOLECULAR ECOLOGY

Using non-invasive metagenomics to characterize viral communities from wildlife

(2018) Laura M. Bergner et al.   Molecular Ecology Resources

A universal SNP and small-indel variant caller using deep neural networks

(2018) Ryan Poplin et al.   NATURE BIOTECHNOLOGY

Retention and losses of ultraviolet-sensitive visual pigments in bats

(2018) Longfei Li et al.   Scientific Reports

Integrated whole genome microarray analysis and immunohistochemical assay identifies COL11A1, GJB2 and CTRL as predictive biomarkers for pancreatic cancer

(2018) Defeng Sun et al.   Cancer Cell International

Loss of enzymes in the bile acid synthesis pathway explains differences in bile composition among mammals

(2018) Virag Sharma et al.   Genome Biology and Evolution

As Blind as a Bat? Opsin Phylogenetics Illuminates the Evolution of Color Vision in Bats

(2018) Bruno F Simões et al.   MOLECULAR BIOLOGY AND EVOLUTION

Alteration of tumor suppressor BMP5 in sporadic colorectal cancer: a genomic and transcriptomic profiling based study

(2018) Erfei Chen et al.   Molecular Cancer

Multifactorial processes underlie parallel opsin loss in neotropical bats

(2018) Alexa Sadier et al.   eLife

Preferential enhancement of GluN2B-containing native NMDA receptors by the endogenous modulator 24S-hydroxycholesterol in hippocampal neurons

(2018) Xiaofei Wei et al.   NEUROPHARMACOLOGY

Hepatic protein phosphatase 1 regulatory subunit 3B (Ppp1r3b) promotes hepatic glycogen synthesis and thereby regulates fasting energy homeostasis

(2017) Minal B. Mehta et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Their loss is our gain: regressive evolution in vertebrates provides genomic models for uncovering human disease loci

(2017) Christopher A Emerling et al.   JOURNAL OF MEDICAL GENETICS

Ablation of PPP1R3G reduces glycogen deposition and mitigates high-fat diet induced obesity

(2017) Yongxian Zhang et al.   MOLECULAR AND CELLULAR ENDOCRINOLOGY

Regulation of hepatic glucose metabolism in health and disease

(2017) Max C. Petersen et al.   Nature Reviews Endocrinology

Cholesterol-metabolizing enzyme cytochrome P450 46A1 as a pharmacologic target for Alzheimer's disease

(2017) Natalia Mast et al.   NEUROPHARMACOLOGY

Increased alignment sensitivity improves the usage of genome alignments for comparative gene annotation

(2017) Virag Sharma et al.   NUCLEIC ACIDS RESEARCH

Common vampire bat contact calls attract past food-sharing partners

(2016) Gerald G. Carter et al.   ANIMAL BEHAVIOUR

Insulin and the phosphatidylinositol 3-kinase signaling pathway regulate Ribonuclease 7 expression in the human urinary tract

(2016) Tad E. Eichler et al.   KIDNEY INTERNATIONAL

Evolution by gene loss

(2016) Ricard Albalat et al.   NATURE REVIEWS GENETICS

Coding exon-structure aware realigner (CESAR) utilizes genome alignments for accurate comparative gene annotation

(2016) Virag Sharma et al.   NUCLEIC ACIDS RESEARCH

SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation

(2016) Wei Shen et al.   PLoS One

Targeted Ablation of thePde6hGene in Mice Reveals Cross-species Differences in Cone and Rod Phototransduction Protein Isoform Inventory

(2015) Christina Brennenstuhl et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The evolution of bat nucleic acid-sensing Toll-like receptors

(2015) Marina Escalera-Zamudio et al.   MOLECULAR ECOLOGY

Dual effects of the non-esterified fatty acid receptor ‘GPR40’ for human health

(2015) Tetsumori Yamashima   PROGRESS IN LIPID RESEARCH

Human steroid and oxysterol 7α-hydroxylase CYP7B1: substrate specificity, azole binding and misfolding of clinically relevant mutants

(2014) Aleksei V. Yantsevich et al.   FEBS Journal

RELAX: Detecting Relaxed Selection in a Phylogenetic Framework

(2014) Joel O. Wertheim et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genetic, anatomic, and clinical determinants of human serum sterol and vitamin D levels

(2014) A. R. Stiles et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Epithelial Cell Shedding and Barrier Function

(2014) J. M. Williams et al.   VETERINARY PATHOLOGY

The Major Brain Cholesterol Metabolite 24(S)-Hydroxycholesterol Is a Potent Allosteric Modulator of N-Methyl-D-Aspartate Receptors

(2013) S. M. Paul et al.   JOURNAL OF NEUROSCIENCE

Dracula's children: Molecular evolution of vampire bat venom

(2013) Dolyce H.W. Low et al.   Journal of Proteomics

Is It Possible to Improve Memory Function by Upregulation of the Cholesterol 24S-Hydroxylase (CYP46A1) in the Brain?

(2013) Silvia Maioli et al.   PLoS One

The fatty acid receptor FFA1/GPR40 a decade later: how much do we know?

(2013) Arturo D. Mancini et al.   TRENDS IN ENDOCRINOLOGY AND METABOLISM

A Nonsense Mutation in PDE6H Causes Autosomal-Recessive Incomplete Achromatopsia

(2012) Susanne Kohl et al.   AMERICAN JOURNAL OF HUMAN GENETICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Increased Intestinal Lipid Absorption Caused by Ire1β Deficiency Contributes to Hyperlipidemia and Atherosclerosis in Apolipoprotein E–Deficient Mice

(2012) Jahangir Iqbal et al.   CIRCULATION RESEARCH

Reduced insulin secretion and glucose intolerance are involved in the fasting susceptibility of common vampire bats

(2012) Mariella B. Freitas et al.   GENERAL AND COMPARATIVE ENDOCRINOLOGY

Hearing in American leaf-nosed bats. IV: The Common vampire bat, Desmodus rotundus

(2012) Rickye S. Heffner et al.   HEARING RESEARCH

The Physiological Effects of Deleting the Mouse Slc30a8 Gene Encoding Zinc Transporter-8 Are Influenced by Gender and Genetic Background

(2012) Lynley D. Pound et al.   PLoS One

Ganglion-specific splicing of TRPV1 underlies infrared sensation in vampire bats

(2011) Elena O. Gracheva et al.   NATURE

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

A Critical Role for GluN2B-Containing NMDA Receptors in Cortical Development and Function

(2011) Chih-Chieh Wang et al.   NEURON

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Decreased catalytic activity and altered activation properties of PDE6C mutants associated with autosomal recessive achromatopsia

(2010) Tanja Grau et al.   HUMAN MOLECULAR GENETICS

Towards a knowledge-based Human Protein Atlas

(2010) Mathias Uhlen et al.   NATURE BIOTECHNOLOGY

Cholesterol 24-Hydroxylase: An Enzyme of Cholesterol Turnover in the Brain

(2009) David W. Russell et al.   Annual Review of Biochemistry

Deletion of the mouseSlc30a8gene encoding zinc transporter-8 results in impaired insulin secretion

(2009) Lynley D. Pound et al.   BIOCHEMICAL JOURNAL

Insulin Storage and Glucose Homeostasis in Mice Null for the Granule Zinc Transporter ZnT8 and Studies of the Type 2 Diabetes-Associated Variants

(2009) T. J. Nicolson et al.   DIABETES

G-protein-coupled receptor 40 (GPR40) expression and its regulation in human pancreatic islets: The role of type 2 diabetes and fatty acids

(2009) S. Del Guerra et al.   NUTRITION METABOLISM AND CARDIOVASCULAR DISEASES

A homologous genetic basis of the murine cpfl1 mutant and human achromatopsia linked to mutations in the PDE6C gene

(2009) B. Chang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Emerging functional roles of cathepsin E

(2008) Nousheen Zaidi et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

IRE1β Inhibits Chylomicron Production by Selectively Degrading MTP mRNA

(2008) Jahangir Iqbal et al.   Cell Metabolism

Lack of FFAR1/GPR40 Does Not Protect Mice From High-Fat Diet-Induced Metabolic Disease

(2008) H. Lan et al.   DIABETES

Gpr40 Is Expressed in Enteroendocrine Cells and Mediates Free Fatty Acid Stimulation of Incretin Secretion

(2008) S. Edfalk et al.   DIABETES

Loss of genes implicated in gastric function during platypus evolution

(2008) Gonzalo R Ordoñez et al.   GENOME BIOLOGY