HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies von Edge, Peter, Bafna, Vineet, Bansal, Vikas

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Exploring the landscape of focal amplifications in cancer using AmpliconArchitect von Deshpande, Viraj, Luebeck, Jens, Nguyen, Nam-Phuong D., Bakhtiari, Mehrdad, Turner, Kristen M., Schwab, Richard, Carter, Hannah, Mischel, Paul S., Bafna, Vineet

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Extrachromosomal oncogene amplification in tumour pathogenesis and evolution von Verhaak, Roel G. W., Bafna, Vineet, Mischel, Paul S.

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HapCUT: an efficient and accurate algorithm for the haplotype assembly problem von Bansal, Vikas, Bafna, Vineet

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Variable number tandem repeats mediate the expression of proximal genes von Bakhtiari, Mehrdad, Park, Jonghun, Ding, Yuan-Chun, Shleizer-Burko, Sharona, Neuhausen, Susan L., Halldórsson, Bjarni V., Stefánsson, Kári, Gymrek, Melissa, Bafna, Vineet

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Proteogenomics to discover the full coding content of genomes: A computational perspective von Castellana, Natalie, Bafna, Vineet

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Learning natural selection from the site frequency spectrum von Ronen, Roy, Udpa, Nitin, Halperin, Eran, Bafna, Vineet

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AmpliconReconstructor integrates NGS and optical mapping to resolve the complex structures of focal amplifications von Luebeck, Jens, Coruh, Ceyda, Dehkordi, Siavash R., Lange, Joshua T., Turner, Kristen M., Deshpande, Viraj, Pai, Dave A., Zhang, Chao, Rajkumar, Utkrisht, Law, Julie A., Mischel, Paul S., Bafna, Vineet

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Skmer: assembly-free and alignment-free sample identification using genome skims von Sarmashghi, Shahab, Bohmann, Kristine, P Gilbert, M Thomas, Bafna, Vineet, Mirarab, Siavash

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Estimating repeat spectra and genome length from low-coverage genome skims with RESPECT von Sarmashghi, Shahab, Balaban, Metin, Rachtman, Eleonora, Touri, Behrouz, Mirarab, Siavash, Bafna, Vineet

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Inferring gene ontologies from pairwise similarity data von Kramer, Michael, Dutkowski, Janusz, Yu, Michael, Bafna, Vineet, Ideker, Trey

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De novo somatic mutations in components of the PI3K-AKT3-mTOR pathway cause hemimegalencephaly von Lee, Jeong Ho, Huynh, My, Silhavy, Jennifer L, Kim, Sangwoo, Dixon-Salazar, Tracy, Heiberg, Andrew, Scott, Eric, Bafna, Vineet, Hill, Kiley J, Collazo, Adrienne, Funari, Vincent, Russ, Carsten, Gabriel, Stacey B, Mathern, Gary W, Gleeson, Joseph G

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Transcriptional immune suppression and up-regulation of double-stranded DNA damage and repair repertoires in ecDNA-containing tumors von Lin, Miin S, Jo, Se-Young, Luebeck, Jens, Chang, Howard Y, Wu, Sihan, Mischel, Paul S, Bafna, Vineet

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Longitudinal assessment of tumor development using cancer avatars derived from genetically engineered pluripotent stem cells von Koga, Tomoyuki, Chaim, Isaac A., Benitez, Jorge A., Markmiller, Sebastian, Parisian, Alison D., Hevner, Robert F., Turner, Kristen M., Hessenauer, Florian M., D’Antonio, Matteo, Nguyen, Nam-phuong D., Saberi, Shahram, Ma, Jianhui, Miki, Shunichiro, Boyer, Antonia D., Ravits, John, Frazer, Kelly A., Bafna, Vineet, Chen, Clark C., Mischel, Paul S., Yeo, Gene W., Furnari, Frank B.

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ViFi: accurate detection of viral integration and mRNA fusion reveals indiscriminate and unregulated transcription in proximal genomic regions in cervical cancer von Nguyen, Nam-phuong D, Deshpande, Viraj, Luebeck, Jens, Mischel, Paul S, Bafna, Vineet

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Clear: Composition of Likelihoods for Evolve and Resequence Experiments von Iranmehr, Arya, Akbari, Ali, Schlötterer, Christian, Bafna, Vineet

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Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer von Hon, Gary C, Hawkins, R David, Caballero, Otavia L, Lo, Christine, Lister, Ryan, Pelizzola, Mattia, Valsesia, Armand, Ye, Zhen, Kuan, Samantha, Edsall, Lee E, Camargo, Anamaria Aranha, Stevenson, Brian J, Ecker, Joseph R, Bafna, Vineet, Strausberg, Robert L, Simpson, Andrew J, Ren, Bing

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Ultraaccurate genome sequencing and haplotyping of single human cells von Chu, Wai Keung, Edge, Peter, Lee, Ho Suk, Bansal, Vikas, Bafna, Vineet, Huang, Xiaohua, Zhang, Kun

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Multiple mechanisms drive genomic adaptation to extreme O2 levels in Drosophila melanogaster von Iranmehr, Arya, Stobdan, Tsering, Zhou, Dan, Zhao, Huiwen, Kryazhimskiy, Sergey, Bafna, Vineet, Haddad, Gabriel G.

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algorithmic approach for breakage-fusion-bridge detection in tumor genomes von Zakov, Shay, Kinsella, Marcus, Bafna, Vineet

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