Human Biology Term Papers

Research Papers

The transcriptional landscape of age in human peripheral blood

by Barbara Stranger, Peters MJ, Joehanes R, Pilling LC, Schurmann C, Conneely KN, Powell J, Reinmaa E, Sutphin GL, Zhernakova A, Schramm K, Wilson YA, Kobes S, Tukiainen T.

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PMID: 26490707

Expression Quantitative Trait Loci Information Improves Predictive Modeling of Disease Relevance of Non-Coding Genetic Variation

by Barbara Stranger, Croteau-Chonka DC, Rogers AJ, Raj T, McGeachie MJ, Qiu W, Ziniti JP, Stubbs BJ, Liang L, Martinez FD, Strunk RC, Lemanske RF, Liu AH, Carey VJ, Raby BA.

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PMID: 26474488

The microbe-mediated mechanisms affecting topsoil carbon stock in Tibetan grasslands

by Jack Gilbert, Yue H, Wang M, Wang S, Sun X, Wu L, Lin Q, Hu Y, Li X, He Z, Zhou J, Yang Y.

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PMID: 25689025

Key metabolic pathways involved in xenobiotic biotransformation and stress responses revealed by transcriptomics of the mangrove oyster Crassostrea brasiliana

by Jack Gilbert, Lüchmann KH, Clark MS, Bainy AC, Craft JA, Chipman JK, Thorne MA, Mattos JJ, Siebert MN, and Schroeder DC.

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PMID: 26186662

Circadian rhythms: A protein fold switch joins the circadian oscillator to clock output in cyanobacteria

by Michael Rust, Connie Phong, Chang YG, Cohen SE, Myers WK, Kim YI, Tseng R, Lin J, Zhang L, Boyd JS, Lee Y, Kang S, Lee D, Li S, Britt RD, Golden SS, LiWang A.

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PMID: 26113641

Using corticosteroids to reshape the gut microbiome: implications for inflammatory bowel diseases

by Jack Gilbert, Huang EY, Inoue T, Leone VA, Dalal S, Touw K, Wang Y, Musch MW, Theriault B, Higuchi K, Donovan S, Chang EB.

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PMID: 25738379

Nfkb1 is a haploinsufficient DNA damage-specific tumor suppressor

by Kevin White, Megan McNerney, Voce DJ, Schmitt AM, Uppal A, Bernal GM, Cahill KE, Wahlstrom JS, Nassiri A, Yu X, Crawley CD, Onel K, Weichselbaum RR, Yamini B

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PMID: 25043302

Metagenomes from two microbial consortia associated with Santa Barbara seep oil

by Jack Gilbert, Hawley ER, Malfatti SA, Pagani I, Huntemann M, Chen A, Foster B, Copeland A, Del Rio TG, Pati A, Jansson JR, Tringe SG, Lorenson TD, Hess M

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PMID: 24958360

Zodiac: A Comprehensive Depiction of Genetic Interactions in Cancer by Integrating TCGA Data

by Kevin White, Ian T. Foster, Yuan Ji, Zhu Y, Xu Y, Helseth DL Jr, Gulukota K, Yang S, Pesce LL, Mitra R, Müller P, Sengupta S, Guo W, Silverstein JC, Parsad N

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PMID: 25956356

Collagen degradation and MMP9 activation by Enterococcus faecalis contribute to intestinal anastomotic leak

by Jack Gilbert, Shogan BD, Belogortseva N, Luong PM, Zaborin A, Lax S, Bethel C, Ward M, Muldoon JP, Singer M, An G, Umanskiy K, Konda V, Shakhsheer B, Luo J, Klabbers R, Hancock LE, Gilbert J, Zaborina O, and Alverdy JC

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PMID: 25947163

The soil microbiome influences grapevine-associated microbiota

by Jack Gilbert, Zarraonaindia I, Owens SM, Weisenhorn P, West K, Hampton-Marcell J, Lax S, Bokulich NA, Mills DA, Martin G, Taghavi S, van der Lelie D

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PMID: 25805735

Rare occurrence of EGFRvIII deletion in head and neck squamous cell carcinoma

by Kevin White, Everett E. Vokes, Khattri A, Zuo Z, Brägelmann J, Keck MK, El Dinali M, Brown CD, Stricker T, Munagala A, Cohen EE, Lingen MW, Seiwert TY

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PMID: 25255959

A novel mechanism of inherited TBG deficiency: mutation in a liver-specific enhancer

by Kevin White, Ferrara AM, Pappa T, Fu J, Brown CD, Peterson A, Moeller LC, Wyne K, Pluzhnikov A, Trubetskoy V, Nobrega M, Weiss RE,Dumitrescu AM, Refetoff S

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PMID: 25361180

Bionimbus: a cloud for managing, analyzing and sharing large genomics datasets

by Robert Grossman, Kevin White, Allison Heath, Chaitanya Bandlamudi, Jonathan Spring, Matthew Greenway, Megan McNerney, David Hanley, Powell R, Suarez R,

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PMID: 24464852

Integrative analysis of head and neck cancer identifies two biologically distinct HPV and three non-HPV subtypes

by Kevin White, Everett E. Vokes, Keck MK, Zuo Z, Khattri A, Stricker TP, Brown CD, Imanguli M, Rieke D, Endhardt K, Fang P, Brägelmann J, DeBoer R, El-Dinali M,Aktolga S, Lei Z, Tan P, Rozen SG, Salgia R, Weichselbaum RR, Lingen MW, Story MD, Ang KK, Cohen EE, Seiwert TY

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PMID: 25492084

The complete genome sequence for putative H₂- and S-oxidizer Candidatus Sulfuricurvum sp., assembled de novo from an aquifer-derived metagenome

by Dionysios Antonopoulos, Folker Meyer, Jack Gilbert, Handley KM, Bartels D, O'Loughlin EJ, Williams KH, Trimble WL, Skinner K, Desai N, Glass EM, Paczian T, Wilke A, Kemner KM

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PMID: 24628880

Pri peptides are mediators of ecdysone for the temporal control of development

by Kevin White, Rebecca Spokony, Chanut-Delalande H, Hashimoto Y, Pelissier-Monier A, Dib A, Kondo T, Bohère J, Niimi K, Latapie Y, Inagaki S, Dubois L, Valenti P, Polesello C, Kobayashi S, Moussian B, Plaza S, Kageyama Y, Payre F

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PMID: 25344753

Transcription Factor Networks In Drosophila Melanogaster

by Kevin White, Rhee DY, Cho DY, Zhai B, Slattery M, Ma L, Mintseris J, Wong CY, White KP, Celniker SE, Przytycka TM, Gygi SP, Obar RA, Artavanis-Tsakonas S.

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PMID: 25242320

Intersection of population variation and autoimmunity genetics in human T cell activation

by Barbara Stranger, Ye CJ, Feng T, Kwon HK, Raj T, Wilson MT, Asinovski N, McCabe C, Lee MH, Frohlich I, Paik HI, Zaitlen N, Hacohen N, De Jager P, Mathis D, Regev A, Benoist C.

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PMID: 25214635

Intersection of population variation and autoimmunity genetics in human T cell activation

by Barbara Stranger, Ye CJ, Feng T, Kwon HK, Raj T, Wilson MT, Asinovski N, McCabe C, Lee MH, Frohlich I, Paik HI, Zaitlen N, Hacohen N, De Jager P, Mathis D, Regev A, Benoist C.

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PMID: 25214635

Longitudinal analysis of microbial interaction between humans and the indoor environment

by Jack Gilbert, Sean Gibbons, Lax S, Smith DP, Hampton-Marcell J, Owens SM, Handley KM, Scott NM, Larsen P, Shogan BD, Weiss S, Metcalf JL, Ursell LK,Vázquez-Baeza Y, Van Treuren W, Hasan NA, Gibson MK, Colwell R, Dantas G, Knight R

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PMID: 25170151

Comparative Analysis of Regulatory Information and Circuits Across Distant Species

by Kevin White, Boyle AP, Araya CL, Brdlik C, Cayting P, Cheng C, Cheng Y, Gardner K, Hillier LW, Janette J, Jiang L, Kasper D, Kawli T, Kheradpour P, Kundaje A, Li JJ, Ma L, Niu W, Rehm EJ, Rozowsky J, Slattery M, Spokony R, Terrell R, Vafeados D, Wang D, Weisdepp P, Wu YC, Xie D, Yan KK, Feingold EA, Good PJ, Pazin MJ, Huang H, Bickel PJ, Brenner SE, Reinke V, Waterston RH, Gerstein M, White KP, Kellis M, Snyder M.

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PMID: 25164757

Commensal Bacteria Protect Against Food Allergen Sensitization

by Dionysios Antonopoulos, Andrew T. Stefkaa, Taylor Feehleya, Prabhanshu Tripathia, Ju Qiub, Kathy McCoyc, Sarkis K. Mazmaniand, Melissa Y. Tjotae, Goo-Young Seoa, Severine Caoa, Betty R. Theriaultf, Liang Zhoub, Eugene B. Change, Yang-Xin Fua, and Cathryn R. Nagler

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Integrative and comparative genomic analysis of HPV-positive and HPV-negative head and neck squamous cell carcinomas

by Kevin White, Everett E. Vokes, Seiwert TY, Zuo Z, Keck MK, Khattri A, Pedamallu CS, Stricker T, Brown C, Pugh TJ, Stojanov P, Cho J,Lawrence MS, Getz G, Brägelmann J, DeBoer R, Weichselbaum RR, Langerman A, Portugal L, Blair E, Stenson K, Lingen MW, Cohen EE, Hammerman PS.

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PMID: 25056374

SPOP promotes tumorigenesis by acting as a key regulatory hub in kidney cancer.

by Kevin White, Li G, Ci W, Karmakar S, Chen K, Dhar R, Fan Z, Guo Z, Zhang J, Ke Y, Wang L, Zhuang M, Hu S, Li X, Zhou L, Li X, Calabrese MF, Watson ER, Prasad SM, Rinker-Schaeffer C, Eggener SE, Stricker T, Tian Y, Schulman BA, Liu J, White KP.

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PMID: 24656772

Polarization of the effects of autoimmune and neurodegenerative risk alleles in leukocytes.

by Barbara Stranger, Raj T, Rothamel K, Mostafavi S, Ye C, Lee MN, Replogle JM, Feng T, Lee M, Asinovski N, Frohlich I, Imboywa S, Von Korff A, Okada Y, Patsopoulos NA, Davis S, McCabe C, Paik HI, Srivastava GP, Raychaudhuri S, Hafler DA, Koller D, Regev A, Hacohen N, Mathis D, Benoist C, Stranger BE, De Jager PL.

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PMID: 24786080

Regulation of Gene Expression in Autoimmune Disease Loci and the Genetic Basis of Proliferation in CD4+ Effector Memory T Cells.

by Barbara Stranger, Hu X, Kim H, Raj T, Brennan PJ, Trynka G, Teslovich N, Slowikowski K, Chen WM, Onengut S, Baecher-Allan C, De Jager PL, Rich SS, Stranger BE, Brenner MB, Raychaudhuri S.

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PMID: 24968232

Expression QTL-based analyses reveal candidate causal genes and loci across five tumor types.

by Barbara Stranger, Li Q, Stram A, Chen C, Kar S, Gayther S, Pharoah P, Haiman C, Stranger B, Kraft P, Freedman ML.

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PMID: 24907074

DiseaseConnect: a comprehensive web server for mechanism-based disease-disease connections.

by Andrey Rzhetsky, Liu CC, Tseng YT, Li W, Wu CY, Mayzus I, Rzhetsky A, Sun F, Waterman M, Chen JJ, Chaudhary PM, Loscalzo J, Crandall E, Zhou XJ.

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PMID: 24895436

Diverse patterns of genomic targeting by transcriptional regulators in Drosophila melanogaster.

by Robert Grossman, Rebecca Spokony, Rob Arthur, Matt Slattery, Lijia Ma, Alec Victorsen, Jason Grundstad, Wenxuan Gao, Jennifer Moran, Edward (Jay) Rehm, Kevin White, Kheradpour P, Kundaje A, Nègre N, Crofts A, Ptashkin R, Zieba J, Ostapenko A, Suchy S, Jameel N, Kellis M.

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PMID: 24985916

Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill.

by Jack Gilbert, Mason OU, Scott NM, Gonzalez A, Robbins-Pianka A, Bælum J, Kimbrel J, Bouskill NJ, Prestat E, Borglin S, Joyner DC, Fortney JL, Jurelevicius D, Stringfellow WT, Alvarez-Cohen L, Hazen TC, Knight R, Gilbert JA, Jansson JK.

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PMID: 24451203

Human and environmental impacts on river sediment microbial communities.

by Jack Gilbert, Gibbons SM, Jones E, Bearquiver A, Blackwolf F, Roundstone W, Scott N, Hooker J, Madsen R, Coleman ML, Gilbert JA.

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PMID: 24841417

Understanding cultivar-specificity and soil determinants of the cannabis microbiome.

by Jack Gilbert, Hawley ER, Malfatti SA, Pagani I, Huntemann M, Chen A, Foster B, Copeland A, Del Rio TG, Pati A, Jansson JR, Gilbert JA, Tringe SG, Lorenson TD, Hess M.

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PMID: 24932479

Metagenomes from two microbial consortia associated with Santa Barbara seep oil.

by Jack Gilbert, Hawley ER, Malfatti SA, Pagani I, Huntemann M, Chen A, Foster B, Copeland A, Del Rio TG, Pati A, Jansson JR, Gilbert JA, Tringe SG, Lorenson TD, Hess M.

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PMID: 24958360

Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity.

by Jack Gilbert, Parfrey LW, Walters WA, Lauber CL, Clemente JC, Berg-Lyons D, Teiling C, Kodira C, Mohiuddin M, Brunelle J, Driscoll M, Fierer N, Knight R.

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PMID: 24995004

The complete genome sequence for putative H2 - and S-oxidizer Candidatus Sulfuricurvum sp., assembled de novo from an aquifer-derived metagenome.

by Dionysios Antonopoulos, Handley KM, Bartels D, O'Loughlin EJ, Williams KH, Trimble WL, Skinner K, Gilbert JA, Desai N, Glass EM, Paczian T, Wilke A, Kemner KM, Meyer F.

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PMID: 24628880

Regulation of gene expression in autoimmune disease loci and the genetic basis of proliferation in CD4+ effector memory T cells

by Barbara Stranger, Hu X, Kim H, Raj T, Brennan PJ, Trynka G, Teslovich N, Slowikowski K, Chen WM, Onengut S, Baecher-Allan C, De Jager PL, Rich SS, Brenner MB, Raychaudhuri S.

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PMID: 24968232

Disturbed subsurface microbial communities follow equivalent trajectories despite different structural starting points.

by Jack Gilbert, Handley KM, Wrighton KC, Miller CS, Wilkins MJ, Kantor RS, Thomas BC, Williams KH, Gilbert JA, Long PE, Banfield JF.

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PMID: 24674078

The Gut of Geographically Disparate Ciona intestinalis Harbors a Core Microbiota.

by Jack Gilbert, Dishaw LJ, Flores-Torres J, Lax S, Gemayel K, Leigh B, Melillo D, Mueller MG, Natale L, Zucchetti I, De Santis R, Pinto MR, Litman GW, Gilbert JA.

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PMID: 24695540

Comparison of brush and biopsy sampling methods of the ileal pouch for assessment of mucosa-associated microbiota of human subjects.

by Dionysios Antonopoulos, Huse SM, Young VB, Morrison HG, Antonopoulos DA, Kwon J, Dalal S, Arrieta R, Hubert NA, Shen L, Vineis JH, Koval JC, Sogin ML, Chang EB, Raffals LE.

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PMID: 24529162

Exercise prevents weight gain and alters the gut microbiota in a mouse model of high fat diet-induced obesity.

by Dionysios Antonopoulos, Evans CC, Lepard KJ, Kwak JW, Stancukas MC, Laskowski S, Dougherty J, Moulton L, Glawe A, Wang Y, Leone V, Antonopoulos DA, Smith D, Chang EB, Ciancio MJ.

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PMID: 24670791

Hydroxymethylation at gene regulatory regions directs stem/early progenitor cell commitment during erythropoiesis.

by Robert Grossman, Madzo J, Liu H, Rodriguez A, Vasanthakumar A, Sundaravel S, Caces DB, Looney TJ, Zhang L, Lepore JB, Macrae T, Duszynski R, Shih AH, Song CX, Yu M, Yu Y, Grossman R, Raumann B, Verma A, He C, Levine RL, Lavelle D, Lahn BT, Wickrema A, Godley LA.

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PMID: 24373966

Toward more transparent and reproducible omics studies through a common metadata checklist and data publications.

by Robert Grossman, Kolker E, Özdemir V, Martens L, Hancock W, Anderson G, Anderson N, Aynacioglu S, Baranova A, Campagna SR, Chen R, Choiniere J, Dearth SP, Feng WC, Ferguson L, Fox G, Frishman D, Grossman R, Heath A, Higdon R, Hutz MH, Janko I, Jiang L, Joshi S, Kel A, Kemnitz JW, Kohane IS, Kolker N, Lancet D, Lee E, Li W, Lisitsa A, Llerena A, Macnealy-Koch C, Marshall JC, Masuzzo P, May A, Mias G, Monroe M, Montague E, Mooney S, Nesvizhskii A, Noronha S, Omenn G, Rajasimha H, Ramamoorthy P, Sheehan J, Smarr L, Smith CV, Smith T, Snyder M, Rapole S, Srivastava S, Stanberry L, Stewart E, Toppo S, Uetz P, Verheggen K, Voy BH, Warnich L, Wilhelm SW, Yandl G.

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PMID: 24456465

CD33: increased inclusion of exon 2 implicates the Ig V-set domain in Alzheimer's disease susceptibility

by Barbara Stranger, Raj T, Ryan KJ, Replogle JM, Chibnik LB, Rosenkrantz L, Tang A, Rothamel K, Stranger BE, Bennett DA, Evans DA, De Jager PL, Bradshaw EM

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PMID: 24381305

Uncovering the Genetics of Skeletal Muscle Growth and Regeneration

Mar. 8, 2018 — To investigate the mechanism behind skeletal muscle growth and regeneration, researchers bombarded zebrafish with chemical mutagen and screened for larvae with defective skeletal muscle structure. ... read more


Mar. 8, 2018 — Deleting a single gene from mosquitoes can make them highly resistant to the malaria parasite and thus much less likely to transmit the parasite to humans, according to a new ... read more


Inherited Mutation Leads to Overproduction of Erythropoietin in Blood

Mar. 8, 2018 — A newly-discovered hereditary mutation is responsible for an increased production of erythropoietin (EPO) in the blood. This mutation causes a messenger RNA (mRNA) that is not normally involved in ... read more


Scientists Discover a Key Function of ALS-Linked Protein

Mar. 8, 2018 — The protein FUS, whose mutation or disruption causes many cases of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), works as a central component of one of the most important ... read more


Mar. 8, 2018 — Impaired transport processes in neurons contribute to diseases such as amyotrophic lateral sclerosis. Scientists have now identified key actors in these ... read more


New Way Found to Defeat HIV Latency

Mar. 8, 2018 — Researchers have found a mechanism for making HIV come out of hiding and become susceptible to anti-HIV ... read more


Link Between BRCA1 and Ewing Sarcoma

Mar. 7, 2018 — Scientists have discovered a surprising connection between a breast cancer protein, BRCA1, and a pediatric cancer called Ewing ... read more


Mar. 7, 2018 — Seizure suppression is the focus of an original research -- and they have the pictures to prove it. Their new work sheds new light on epilepsy, a chronic neurological disorder marked by recurrent, ... read more


36 New Genes Implicated in Cardiac Disease

Mar. 7, 2018 — A professor has developed a new personalized method to discover genes implicated in complex diseases. One of the ultimate goals of the research is to create personalized therapeutic drugs to reverse ... read more


Molecular Imaging Strategy for Determining Molecular Classifications of NSCLC

Mar. 7, 2018 — Recent findings suggest a novel positron emission tomography (PET) imaging approach determining epidermal growth factor receptor (EGFR) mutation status for improved lung cancer patient ... read more


When Sepsis Patients Face Brain Impairment, Is Gut Bacteria to Blame?

Mar. 7, 2018 — Halting the voyage of gut bacteria to the brain could help prevent harmful brain inflammation after a sepsis infection, a new study ... read more


More Realistic and Accurate Organs-on-Chips

Mar. 7, 2018 — In a step toward better diagnosis and treatment of digestive conditions, such as inflammatory bowel disease, scientists report that they have developed a first-of-its-kind collagen-based membrane for ... read more


Mapping a Genetic Risk

Mar. 7, 2018 — Clinicians and health researchers often look at gene mutation to predict whether a fetus is at risk for a birth defect, or a person is at risk of developing a disease, but these predictions are not ... read more


Determining the Cause of Difficult-to-Control Mitochondrial Diseases

Mar. 7, 2018 — A research group has discovered that the 'non-essential' amino acid taurine is important for protein translation in mitochondria and is involved in mitochondrial disease development. The ... read more


Mapping the Genome Jungle: Unique Animal Traits Could Offer Insight Into Human Disease

Mar. 7, 2018 — An interdisciplinary team of scientists are using animals' unique traits to pinpoint regions of the human genome that might affect ... read more


Linking Virus Sensing With Gene Expression, a Plant Immune System Course-Corrects

Mar. 6, 2018 — Researchers have identified a crucial link in the process of how plants regulate their antiviral ... read more


Mar. 6, 2018 — If you've ever wondered how strenuous exercise translates into better endurance, researchers may now have your answer. Scientists have shown that the protein ERR? (ERR gamma) helps deliver many ... read more


A New Tactic for Eczema?

Mar. 6, 2018 — Existing treatments for eczema, which affects about 17 percent of children in developed countries, are expensive or have side effects. A new study suggests a different approach to eczema, one that ... read more


Mar. 6, 2018 — Calcium ions enable cells to communicate with one another, allowing neurons to interact, muscles to contract, and the heart's muscle cells to synchronize and beat. To better understand these ... read more


Bioengineering Team's 'Circuit' Work May Benefit Gene Therapy

Mar. 6, 2018 — Researchers have designed genetic 'circuits' out of living cellular material in order to gain a better understanding of how proteins function, with the goal of making ... read more


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