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Author Kevin P White

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Does near-infrared fluorescent cholangiography with indocyanine green reduce bile duct injuries and conversions to open surgery during laparoscopic or robotic cholecystectomy? - A meta-analysis.

Fernando Dip, Emanuele Lo Menzo, Kevin P White, Raul J Rosenthal,

<h4>Background</h4>Bile duct injury and conversion-to-open-surgery rates remain unacceptably high during laparoscopic and robotic cholecystectomy. In a recently published randomized clinical trial, using near-infrared fluorescent cholangiography with indocyanine green intraoperatively markedly enhanced biliary-structure visualization. Our systematic literature review compares bile duct injury and conversion-to-open-surgery rates in patients undergoing laparoscopic or robotic ... Read more >>

Surgery (Surgery)
[2021, :]

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To mock or not: a comprehensive comparison of mock IP and DNA input for ChIP-seq.

Jinrui Xu, Michelle M Kudron, Alec Victorsen, Jiahao Gao, Haneen N Ammouri, Fabio C P Navarro, Louis Gevirtzman, Robert H Waterston, Kevin P White, Valerie Reinke, Mark Gerstein,

Chromatin immunoprecipitation (IP) followed by sequencing (ChIP-seq) is the gold standard to detect transcription-factor (TF) binding sites in the genome. Its success depends on appropriate controls removing systematic biases. The predominantly used controls, i.e. DNA input, correct for uneven sonication, but not for nonspecific interactions of the IP antibody. Another ... Read more >>

Nucleic Acids Res (Nucleic acids research)
[2020, :]

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STARRPeaker: uniform processing and accurate identification of STARR-seq active regions.

Donghoon Lee, Manman Shi, Jennifer Moran, Martha Wall, Jing Zhang, Jason Liu, Dominic Fitzgerald, Yasuhiro Kyono, Lijia Ma, Kevin P White, Mark Gerstein,

STARR-seq technology has employed progressively more complex genomic libraries and increased sequencing depths. An issue with the increased complexity and depth is that the coverage in STARR-seq experiments is non-uniform, overdispersed, and often confounded by sequencing biases, such as GC content. Furthermore, STARR-seq readout is confounded by RNA secondary structure ... Read more >>

Genome Biol (Genome biology)
[2020, 21(1):298]

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Automated microfluidic platform for dynamic and combinatorial drug screening of tumor organoids.

Brooke Schuster, Michael Junkin, Sara Saheb Kashaf, Isabel Romero-Calvo, Kori Kirby, Jonathan Matthews, Christopher R Weber, Andrey Rzhetsky, Kevin P White, Savaş Tay,

Three-dimensional (3D) cell culture technologies, such as organoids, are physiologically relevant models for basic and clinical applications. Automated microfluidics offers advantages in high-throughput and precision analysis of cells but is not yet compatible with organoids. Here, we present an automated, high-throughput, microfluidic 3D organoid culture and analysis system to facilitate ... Read more >>

Nat Commun (Nature communications)
[2020, 11(1):5271]

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Corrugated Purple-Black Plaque on the Left Cheek: Challenge.

Matthew A Pimentel, Kevin P White, Nicole M Fett,

Am J Dermatopathol (The American Journal of dermatopathology)
[2020, :]

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Retrospective Cohort: Genomic Differences Between Pigmented Spindle Cell Nevi of Reed and Reed-Like Melanomas.

Lauren S Mohan, Ayesha U Khan, Bin Zhang, Victor L Quan, Katherine Shi, Elnaz Panah, Maria Cristina Isales, Pedram Yazdan, Yongzhan Zhang, Nike Beaubier, Timothy J Taxter, Elsy V Compres, Daniel Kim, Kevin P White, Pedram Gerami,

BACKGROUND:Some melanomas closely resemble pigmented spindle cell nevi (PSCN) of Reed histologically. The distinction of these entities is important for clinical management. A recent study showed most PSCN (78%) are fusion-driven, commonly involving NTRK3 (57%). Conversely, BRAF V600E mutations are not characteristic of PSCN but are frequent in melanoma. OBJECTIVE:In ... Read more >>

Am J Dermatopathol (The American Journal of dermatopathology)
[2020, 42(9):641-647]

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Expanded encyclopaedias of DNA elements in the human and mouse genomes.

, Jill E Moore, Michael J Purcaro, Henry E Pratt, Charles B Epstein, Noam Shoresh, Jessika Adrian, Trupti Kawli, Carrie A Davis, Alexander Dobin, Rajinder Kaul, Jessica Halow, Eric L Van Nostrand, Peter Freese, David U Gorkin, Yin Shen, Yupeng He, Mark Mackiewicz, Florencia Pauli-Behn, Brian A Williams, Ali Mortazavi, Cheryl A Keller, Xiao-Ou Zhang, Shaimae I Elhajjajy, Jack Huey, Diane E Dickel, Valentina Snetkova, Xintao Wei, Xiaofeng Wang, Juan Carlos Rivera-Mulia, Joel Rozowsky, Jing Zhang, Surya B Chhetri, Jialing Zhang, Alec Victorsen, Kevin P White, Axel Visel, Gene W Yeo, Christopher B Burge, Eric Lécuyer, David M Gilbert, Job Dekker, John Rinn, Eric M Mendenhall, Joseph R Ecker, Manolis Kellis, Robert J Klein, William S Noble, Anshul Kundaje, Roderic Guigó, Peggy J Farnham, J Michael Cherry, Richard M Myers, Bing Ren, Brenton R Graveley, Mark B Gerstein, Len A Pennacchio, Michael P Snyder, Bradley E Bernstein, Barbara Wold, Ross C Hardison, Thomas R Gingeras, John A Stamatoyannopoulos, Zhiping Weng,

The human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context of their production. To better delineate these elements, phase III of the Encyclopedia of DNA Elements (ENCODE) Project has expanded analysis of the cell and tissue repertoires of RNA transcription, ... Read more >>

Nature (Nature)
[2020, 583(7818):699-710]

Cited: 13 times

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Perspectives on ENCODE.

, Michael P Snyder, Thomas R Gingeras, Jill E Moore, Zhiping Weng, Mark B Gerstein, Bing Ren, Ross C Hardison, John A Stamatoyannopoulos, Brenton R Graveley, Elise A Feingold, Michael J Pazin, Michael Pagan, Daniel A Gilchrist, Benjamin C Hitz, J Michael Cherry, Bradley E Bernstein, Eric M Mendenhall, Daniel R Zerbino, Adam Frankish, Paul Flicek, Richard M Myers,

The Encylopedia of DNA Elements (ENCODE) Project launched in 2003 with the long-term goal of developing a comprehensive map of functional elements in the human genome. These included genes, biochemical regions associated with gene regulation (for example, transcription factor binding sites, open chromatin, and histone marks) and transcript isoforms. The ... Read more >>

Nature (Nature)
[2020, 583(7818):693-698]

Cited: 3 times

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An integrative ENCODE resource for cancer genomics.

Jing Zhang, Donghoon Lee, Vineet Dhiman, Peng Jiang, Jie Xu, Patrick McGillivray, Hongbo Yang, Jason Liu, William Meyerson, Declan Clarke, Mengting Gu, Shantao Li, Shaoke Lou, Jinrui Xu, Lucas Lochovsky, Matthew Ung, Lijia Ma, Shan Yu, Qin Cao, Arif Harmanci, Koon-Kiu Yan, Anurag Sethi, Gamze Gürsoy, Michael Rutenberg Schoenberg, Joel Rozowsky, Jonathan Warrell, Prashant Emani, Yucheng T Yang, Timur Galeev, Xiangmeng Kong, Shuang Liu, Xiaotong Li, Jayanth Krishnan, Yanlin Feng, Juan Carlos Rivera-Mulia, Jessica Adrian, James R Broach, Michael Bolt, Jennifer Moran, Dominic Fitzgerald, Vishnu Dileep, Tingting Liu, Shenglin Mei, Takayo Sasaki, Claudia Trevilla-Garcia, Su Wang, Yanli Wang, Chongzhi Zang, Daifeng Wang, Robert J Klein, Michael Snyder, David M Gilbert, Kevin Yip, Chao Cheng, Feng Yue, X Shirley Liu, Kevin P White, Mark Gerstein,

ENCODE comprises thousands of functional genomics datasets, and the encyclopedia covers hundreds of cell types, providing a universal annotation for genome interpretation. However, for particular applications, it may be advantageous to use a customized annotation. Here, we develop such a custom annotation by leveraging advanced assays, such as eCLIP, Hi-C, ... Read more >>

Nat Commun (Nature communications)
[2020, 11(1):3696]

Cited: 1 time

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Bariatric surgery decreases the number of first-time hospital admissions for cancer in severely obese patients. A retrospective analysis of the National Inpatient Sample database.

Camila Ortiz Gómez, David Romero-Funes, Rene Aleman, Joel S Frieder, Juliana Henrique, David Gutierrez-Blanco, Kevin P White, Emanuele Lo Menzo, Samuel Szomstein, Raul J Rosenthal,

<h4>Background</h4>According to the U.S. Centers for Disease Control, cancers linked to overweight or obesity accounted for roughly 40% of all U.S. malignancies in 2014.<h4>Objectives</h4>The primary aim of this epidemiologic study was to assess whether bariatric surgery might have any preventative role against obesity-linked cancers among individuals with obesity.<h4>Setting</h4>Hospitals across the United ... Read more >>

Surg Obes Relat Dis (Surgery for obesity and related diseases : official journal of the American Society for Bariatric Surgery)
[2020, 16(11):1648-1654]

Cited: 0 times

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IFSO (International Federation for Surgery of Obesity and Metabolic Disorders) Consensus Conference Statement on One-Anastomosis Gastric Bypass (OAGB-MGB): Results of a Modified Delphi Study.

Almino C Ramos, Jean-Marc Chevallier, Kamal Mahawar, Wendy Brown, Lilian Kow, Kevin P White, Scott Shikora, ,

<h4>Background</h4>One-anastomosis gastric bypass (OAGB-MGB) is currently the third performed primary bariatric surgical procedure worldwide. However, the procedure is hampered by numerous controversies and there is considerable variability in surgical technique, patient selection, and pre- and postoperative care among the surgeons performing this procedure. This paper reports the results of a ... Read more >>

Obes Surg (Obesity surgery)
[2020, 30(5):1625-1634]

Cited: 1 time

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DRAMS: A tool to detect and re-align mixed-up samples for integrative studies of multi-omics data.

Yi Jiang, Gina Giase, Kay Grennan, Annie W Shieh, Yan Xia, Lide Han, Quan Wang, Qiang Wei, Rui Chen, Sihan Liu, Kevin P White, Chao Chen, Bingshan Li, Chunyu Liu,

Studies of complex disorders benefit from integrative analyses of multiple omics data. Yet, sample mix-ups frequently occur in multi-omics studies, weakening statistical power and risking false findings. Accurately aligning sample information, genotype, and corresponding omics data is critical for integrative analyses. We developed DRAMS (https://github.com/Yi-Jiang/DRAMS) to Detect and Re-Align Mixed-up ... Read more >>

PLoS Comput Biol (PLoS computational biology)
[2020, 16(4):e1007522]

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Concordance between fMRI and Wada test for memory lateralization in temporal lobe epilepsy: A meta-analysis and systematic review.

Andreu Massot-Tarrús, Kevin P White, Seyed Reza Mousavi, Susan Hayman-Abello, Brent Hayman-Abello, Seyed M Mirsattari,

<h4>Objective</h4>The Wada test (WT) is increasingly being replaced by functional magnetic resonance imaging (fMRI) to evaluate memory lateralization before temporal lobe epilepsy (TLE) surgery. We aimed to determine, via meta-analysis, agreement between the two tests and identify predictors of disagreement.<h4>Methods</h4>We performed a systematic search for studies comparing WT and fMRI ... Read more >>

Epilepsy Behav (Epilepsy & behavior : E&B)
[2020, 107:107065]

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The Drosophila MLR COMPASS complex is essential for programming cis-regulatory information and maintaining epigenetic memory during development.

Claudia B Zraly, Abdul Zakkar, John Hertenstein Perez, Jeffrey Ng, Kevin P White, Matthew Slattery, Andrew K Dingwall,

The MLR COMPASS complex monomethylates H3K4 that serves to epigenetically mark transcriptional enhancers to drive proper gene expression during animal development. Chromatin enrichment analyses of the Drosophila MLR complex reveals dynamic association with promoters and enhancers in embryos with late stage enrichments biased toward both active and poised enhancers. RNAi ... Read more >>

Nucleic Acids Res (Nucleic acids research)
[2020, 48(7):3476-3495]

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Ulcerative C2 neurocutaneous dysesthesia (trigeminal trophic syndrome in an alternative distribution).

Dylan Haynes, Christina Topham, Tamar Hajar, Alex G Ortega-Loayza, Kevin P White, Jesse J Keller,

Trigeminal trophic syndrome is an uncommon condition characterized by paresthesia, itch, and self-inflicted wounds following the trigeminal dermatome(s). Similar processes adhering to cervical nerve distributions have been reported, calling into question the specificity of trigeminal trophic syndrome for the trigeminal network. Herein, we report patient with trigeminal trophic syndrome adhering ... Read more >>

Dermatol Online J (Dermatology online journal)
[2020, 26(1):]

Cited: 0 times

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Pediatric cellular neurothekeoma: Seven cases and systematic review of the literature.

Morgan Murphrey, Austin Huy Nguyen, Kevin P White, Alfons Krol, Richard Bernert, Kevin Yarbrough,

BACKGROUND/OBJECTIVES:Neurothekeoma is a rare, benign, cutaneous neoplasm consisting of Schwann cells and perineural cells in myxoid stroma. Cellular neurothekeoma (CNT) was previously thought to represent a morphologic variant of neurothekeoma, but recent studies have shown that CNTs are unrelated to neurothekeomas and are more likely of histiocytic lineage. METHODS:Herein, we ... Read more >>

Pediatr Dermatol (Pediatric dermatology)
[2020, 37(2):320-325]

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Comparative Analyses of Vertebrate Gut Microbiomes Reveal Convergence between Birds and Bats.

Se Jin Song, Jon G Sanders, Frédéric Delsuc, Jessica Metcalf, Katherine Amato, Michael W Taylor, Florent Mazel, Holly L Lutz, Kevin Winker, Gary R Graves, Gregory Humphrey, Jack A Gilbert, Shannon J Hackett, Kevin P White, Heather R Skeen, Sarah M Kurtis, Jack Withrow, Thomas Braile, Matthew Miller, Kevin G McCracken, James M Maley, Vanessa O Ezenwa, Allison Williams, Jessica M Blanton, Valerie J McKenzie, Rob Knight,

Diet and host phylogeny drive the taxonomic and functional contents of the gut microbiome in mammals, yet it is unknown whether these patterns hold across all vertebrate lineages. Here, we assessed gut microbiomes from ∼900 vertebrate species, including 315 mammals and 491 birds, assessing contributions of diet, phylogeny, and physiology ... Read more >>

mBio (mBio)
[2020, 11(1):]

Cited: 5 times

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Management of Cutaneous T-Cell Lymphoma/Mycosis Fungoides Occurring in the Setting of Solid Organ Transplantation: Report of 2 Cases.

David B Griffin, Tamar Hajar, Eric Simpson, Kevin P White, Michi M Shinohara,

Clin Lymphoma Myeloma Leuk (Clinical lymphoma, myeloma & leukemia)
[2020, 20(2):e39-e42]

Cited: 0 times

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The Cushing reflex and the vasopressin-mediated hemodynamic response to increased intracranial pressure during acute elevations in intraabdominal pressure.

Lisandro Montorfano, Giulio Giambartolomei, David Romero Funes, Emanuele Lo Menzo, Fernando Dip, Kevin P White, Raul J Rosenthal,

BACKGROUND:Abdominal compartment syndrome has been linked to detrimental hemodynamic side effects that include increased intracranial pressure and diminished renal function, but the mechanisms behind this continue to be elucidated. In this study, we sought to investigate any direct association between acute elevations in intra-abdominal pressure and intracranial hypertension during experimentally ... Read more >>

Surgery (Surgery)
[2020, 167(2):478-483]

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The utility and challenges of histopathologic evaluation in the diagnosis of nonmalignant skin ulcers.

Phoebe Hammer, Emile Latour, Mary C Bohnett, Fatima McKenzie, Veselina B Korcheva, Stephanie Mengden, Kevin P White, Alex G Ortega-Loayza,

Histopathologic evaluation of cutaneous ulcers is indicated when the clinical diagnosis is unclear or when ulcers have not responded to standard of care. Many nonmalignant skin ulcers lack specific histologic findings on biopsy and pose a diagnostic challenge. While the usefulness of skin biopsies to diagnose underlying malignancy in ulcerated ... Read more >>

Wound Repair Regen (Wound repair and regeneration : official publication of the Wound Healing Society [and] the European Tissue Repair Society)
[2020, 28(2):219-223]

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Integrated genomic profiling expands clinical options for patients with cancer.

Nike Beaubier, Martin Bontrager, Robert Huether, Catherine Igartua, Denise Lau, Robert Tell, Alexandria M Bobe, Stephen Bush, Alan L Chang, Derick C Hoskinson, Aly A Khan, Emily Kudalkar, Benjamin D Leibowitz, Ariane Lozachmeur, Jackson Michuda, Jerod Parsons, Jason F Perera, Ameen Salahudeen, Kaanan P Shah, Timothy Taxter, Wei Zhu, Kevin P White,

Genomic analysis of paired tumor-normal samples and clinical data can be used to match patients to cancer therapies or clinical trials. We analyzed 500 patient samples across diverse tumor types using the Tempus xT platform by DNA-seq, RNA-seq and immunological biomarkers. The use of a tumor and germline dataset led ... Read more >>

Nat Biotechnol (Nature biotechnology)
[2019, 37(11):1351-1360]

Cited: 8 times

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Integrated paired-end enhancer profiling and whole-genome sequencing reveals recurrent CCNE1 and IGF2 enhancer hijacking in primary gastric adenocarcinoma.

Wen Fong Ooi, Amrita M Nargund, Kevin Junliang Lim, Shenli Zhang, Manjie Xing, Amit Mandoli, Jing Quan Lim, Shamaine Wei Ting Ho, Yu Guo, Xiaosai Yao, Suling Joyce Lin, Tannistha Nandi, Chang Xu, Xuewen Ong, Minghui Lee, Angie Lay-Keng Tan, Yue Ning Lam, Jing Xian Teo, Atsushi Kaneda, Kevin P White, Weng Khong Lim, Steven G Rozen, Bin Tean Teh, Shang Li, Anders J Skanderup, Patrick Tan,

OBJECTIVE:Genomic structural variations (SVs) causing rewiring of cis-regulatory elements remain largely unexplored in gastric cancer (GC). To identify SVs affecting enhancer elements in GC (enhancer-based SVs), we integrated epigenomic enhancer profiles revealed by paired-end H3K27ac ChIP-sequencing from primary GCs with tumour whole-genome sequencing (WGS) data (PeNChIP-seq/WGS). DESIGN:We applied PeNChIP-seq to ... Read more >>

Gut (Gut)
[2020, 69(6):1039-1052]

Cited: 2 times

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Primary cutaneous Epstein-Barr virus-positive diffuse large B-cell lymphoma (DLBCL) in a patient taking fingolimod.

Abby Wills, Guang Fan, Edward Kim, Craig Y Okada, Kevin P White, R Samuel Hopkins,

A 55-year-old man with relapsing-remitting multiple sclerosis on fingolimod presented to the dermatology clinic with skin lesions on the left temple and cheek. Histopathology showed a diffuse infiltrate of enlarged, atypical lymphocytes throughout the dermis with an overlying grenz zone and a subpopulation of scattered smaller lymphocytes and plasma cells. ... Read more >>

Dermatol Online J (Dermatology online journal)
[2019, 25(9):]

Cited: 0 times

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Metabolic Surgery Reduces the Risk of Progression From Chronic Kidney Disease to Kidney Failure.

David Romero Funes, David Gutierrez Blanco, Camila Ortiz Gómez, Joel S Frieder, Emanuele Lo Menzo, Samuel Szomstein, Kevin P White, Raul J Rosenthal,

<h4>Introduction</h4>According to the Chronic Kidney Disease Prognosis Consortium (CKD-PC), 1 in 4 patients age ≥ 65 in North America has some form of chronic kidney disease (CKD), while 3 in 100 will progress to kidney failure. The aim of this study was to evaluate whether bariatric surgery alters the progression ... Read more >>

Ann Surg (Annals of surgery)
[2019, 270(3):511-518]

Cited: 0 times

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Distinct Genomic Features in a Retrospective Cohort of Mucosal, Acral and Vulvovaginal Melanomas.

Katherine Shi, Bin Zhang, Betty Y Kong, Yongzhan Zhang, Catherine Igartua, Lauren S Mohan, Victor L Quan, Elnaz Panah, Maria Cristina Isales, Nike Beaubier, Timothy J Taxter, Kevin P White, Lihua Zou, Pedram Gerami,

<h4>Background</h4>Compared to sun-exposed melanomas, less is known regarding the pathogenesis of sun-protected melanomas. Sun-protected melanomas share many epidemiologic factors but their genetic heterogeneity is not well studied.<h4>Objective</h4>We investigated the genomic profile of acral, mucosal and vulvovaginal melanomas. We hypothesize that mucosal melanomas, recognized for their uniquely aggressive clinical behavior, have ... Read more >>

J Am Acad Dermatol (Journal of the American Academy of Dermatology)
[2019, :]

Cited: 0 times

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