Machine learning enables detection of early-stage colorectal cancer by whole-genome sequencing of plasma cell-free DNA von Wan, Nathan, Weinberg, David, Liu, Tzu-Yu, Niehaus, Katherine, Ariazi, Eric A, Delubac, Daniel, Kannan, Ajay, White, Brandon, Bailey, Mitch, Bertin, Marvin, Boley, Nathan, Bowen, Derek, Cregg, James, Drake, Adam M, Ennis, Riley, Fransen, Signe, Gafni, Erik, Hansen, Loren, Liu, Yaping, Otte, Gabriel L, Pecson, Jennifer, Rice, Brandon, Sanderson, Gabriel E, Sharma, Aarushi, St John, John, Tang, Catherina, Tzou, Abraham, Young, Leilani, Putcha, Girish, Haque, Imran S

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GenomeDISCO: a concordance score for chromosome conformation capture experiments using random walks on contact map graphs von Ursu, Oana, Boley, Nathan, Taranova, Maryna, Wang, Y X Rachel, Yardimci, Galip Gurkan, Stafford Noble, William, Kundaje, Anshul

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Selective time-dependent changes in activity and cell-specific gene expression in human postmortem brain von Dachet, Fabien, Brown, James B., Valyi-Nagy, Tibor, Narayan, Kunwar D., Serafini, Anna, Boley, Nathan, Gingeras, Thomas R., Celniker, Susan E., Mohapatra, Gayatry, Loeb, Jeffrey A.

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Evaluation of cfDNA as an early detection assay for dense tissue breast cancer von Barbirou, Mouadh, Miller, Amanda A., Gafni, Erik, Mezlini, Amel, Zidi, Asma, Boley, Nathan, Tonellato, Peter J.

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Genome-wide analysis of promoter architecture in Drosophila melanogaster von Hoskins, Roger A, Landolin, Jane M, Brown, James B, Sandler, Jeremy E, Takahashi, Hazuki, Lassmann, Timo, Yu, Charles, Booth, Benjamin W, Zhang, Dayu, Wan, Kenneth H, Yang, Li, Boley, Nathan, Andrews, Justen, Kaufman, Thomas C, Graveley, Brenton R, Bickel, Peter J, Carninci, Piero, Carlson, Joseph W, Celniker, Susan E

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Comparative analysis of the transcriptome across distant species von Gerstein, Mark B., Rozowsky, Joel, Yan, Koon-Kiu, Wang, Daifeng, Cheng, Chao, Brown, James B., Davis, Carrie A., Hillier, LaDeana, Sisu, Cristina, Li, Jingyi Jessica, Pei, Baikang, Harmanci, Arif O., Duff, Michael O., Djebali, Sarah, Alexander, Roger P., Alver, Burak H., Auerbach, Raymond, Bell, Kimberly, Bickel, Peter J., Boeck, Max E., Boley, Nathan P., Booth, Benjamin W., Cherbas, Lucy, Cherbas, Peter, Di, Chao, Dobin, Alex, Drenkow, Jorg, Ewing, Brent, Fang, Gang, Fastuca, Megan, Feingold, Elise A., Frankish, Adam, Gao, Guanjun, Good, Peter J., Guigó, Roderic, Hammonds, Ann, Harrow, Jen, Hoskins, Roger A., Howald, Cédric, Hu, Long, Huang, Haiyan, Hubbard, Tim J. P., Huynh, Chau, Jha, Sonali, Kasper, Dionna, Kato, Masaomi, Kaufman, Thomas C., Kitchen, Robert R., Ladewig, Erik, Lagarde, Julien, Lai, Eric, Leng, Jing, Lu, Zhi, MacCoss, Michael, May, Gemma, McWhirter, Rebecca, Merrihew, Gennifer, Miller, David M., Mortazavi, Ali, Murad, Rabi, Oliver, Brian, Olson, Sara, Park, Peter J., Pazin, Michael J., Perrimon, Norbert, Pervouchine, Dmitri, Reinke, Valerie, Reymond, Alexandre, Robinson, Garrett, Samsonova, Anastasia, Saunders, Gary I., Schlesinger, Felix, Sethi, Anurag, Slack, Frank J., Spencer, William C., Stoiber, Marcus H., Strasbourger, Pnina, Tanzer, Andrea, Thompson, Owen A., Wan, Kenneth H., Wang, Guilin, Wang, Huaien, Watkins, Kathie L., Wen, Jiayu, Wen, Kejia, Xue, Chenghai, Yang, Li, Yip, Kevin, Zaleski, Chris, Zhang, Yan, Zheng, Henry, Brenner, Steven E., Graveley, Brenton R., Celniker, Susan E., Gingeras, Thomas R., Waterston, Robert

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

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

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Diversity and dynamics of the Drosophila transcriptome von Brown, James B., Boley, Nathan, Eisman, Robert, May, Gemma E., Stoiber, Marcus H., Duff, Michael O., Booth, Ben W., Wen, Jiayu, Park, Soo, Suzuki, Ana Maria, Wan, Kenneth H., Yu, Charles, Zhang, Dayu, Carlson, Joseph W., Cherbas, Lucy, Eads, Brian D., Miller, David, Mockaitis, Keithanne, Roberts, Johnny, Davis, Carrie A., Frise, Erwin, Hammonds, Ann S., Olson, Sara, Shenker, Sol, Sturgill, David, Samsonova, Anastasia A., Weiszmann, Richard, Robinson, Garret, Hernandez, Juan, Andrews, Justen, Bickel, Peter J., Carninci, Piero, Cherbas, Peter, Gingeras, Thomas R., Hoskins, Roger A., Kaufman, Thomas C., Lai, Eric C., Oliver, Brian, Perrimon, Norbert, Graveley, Brenton R., Celniker, Susan E.

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The developmental transcriptome of Drosophila melanogaster von Graveley, Brenton R, Celniker, Susan E, Brooks, Angela N, Carlson, Joseph W, Duff, Michael O, Landolin, Jane M, Yang, Li, Artieri, Carlo G, van Baren, Marijke J, Boley, Nathan, Booth, Benjamin W, Brown, James B, Cherbas, Lucy, Davis, Carrie A, Dobin, Alex, Li, Renhua, Lin, Wei, Malone, John H, Mattiuzzo, Nicolas R, Miller, David, Sturgill, David, Tuch, Brian B, Zaleski, Chris, Zhang, Dayu, Blanchette, Marco, Dudoit, Sandrine, Eads, Brian, Green, Richard E, Hammonds, Ann, Jiang, Lichun, Kapranov, Phil, Langton, Laura, Perrimon, Norbert, Sandler, Jeremy E, Wan, Kenneth H, Willingham, Aarron, Zhang, Yu, Zou, Yi, Andrews, Justen, Bickel, Peter J, Brenner, Steven E, Brent, Michael R, Cherbas, Peter, Gingeras, Thomas R, Hoskins, Roger A, Kaufman, Thomas C, Oliver, Brian

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Abstract 4349: Predicting gene expression from plasma cell-free DNA using both the fragment length and fragment position von John, John A. St, Gafni, Erik, White, Brandon, Kannan, Ajay, Hansen, Loren, Jaroszewicz, Artur, Kundaje, Anshul, Boley, Nathan

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Abstract 2105: Cell-free DNA fragments inform epigenomic mechanisms for early detection of breast cancer von Gafni, Erik, Harvey, Adam, Jaroszewicz, Artur, Solari, Omid Shams, Landolin, Jane, Barbirou, Mouadh, Miller, Amanda, Tonellato, Peter J., Kundaje, Anshul, Jeffrey, Stefanie S., Curtis, Christina, Sledge, George W., Giresi, Paul, Boley, Nathan

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Comparative validation of the D. melanogaster modENCODE transcriptome annotation von Chen, Zhen-Xia, Sturgill, David, Qu, Jiaxin, Jiang, Huaiyang, Park, Soo, Boley, Nathan, Suzuki, Ana Maria, Fletcher, Anthony R, Plachetzki, David C, FitzGerald, Peter C, Artieri, Carlo G, Atallah, Joel, Barmina, Olga, Brown, James B, Blankenburg, Kerstin P, Clough, Emily, Dasgupta, Abhijit, Gubbala, Sai, Han, Yi, Jayaseelan, Joy C, Kalra, Divya, Kim, Yoo-Ah, Kovar, Christie L, Lee, Sandra L, Li, Mingmei, Malley, James D, Malone, John H, Mathew, Tittu, Mattiuzzo, Nicolas R, Munidasa, Mala, Muzny, Donna M, Ongeri, Fiona, Perales, Lora, Przytycka, Teresa M, Pu, Ling-Ling, Robinson, Garrett, Thornton, Rebecca L, Saada, Nehad, Scherer, Steven E, Smith, Harold E, Vinson, Charles, Warner, Crystal B, Worley, Kim C, Wu, Yuan-Qing, Zou, Xiaoyan, Cherbas, Peter, Kellis, Manolis, Eisen, Michael B, Piano, Fabio, Kionte, Karin, Fitch, David H, Sternberg, Paul W, Cutter, Asher D, Duff, Michael O, Hoskins, Roger A, Graveley, Brenton R, Gibbs, Richard A, Bickel, Peter J, Kopp, Artyom, Carninci, Piero, Celniker, Susan E, Oliver, Brian, Richards, Stephen

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Genome-guided transcript assembly by integrative analysis of RNA sequence data von Boley, Nathan, Stoiber, Marcus H, Booth, Benjamin W, Wan, Kenneth H, Hoskins, Roger A, Bickel, Peter J, Celniker, Susan E, Brown, James B

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

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

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Su1658 – Machine Learning Enables Detection of Early-Stage Colorectal Cancer by Whole-Genome Sequencing of Plasma Cell-Free Dna von Wan, Nathan, Weinberg, David, Liu, Tzu-yu, Niehaus, Katherine, Delubac, Daniel, Kannan, Ajay, White, Brandon, Ariazi, Eric A., Bailey, Mitch, Bertin, Marvin, Boley, Nathan, Bowen, Derek, Cregg, James, Drake, Adam, Ennis, Riley, Fransen, Signe, Gafni, Erik, Hansen, Loren, Liu, Yaping, Otte, Gabriel L., Pecson, Jennifer, Rice, Brandon, Sanderson, Gabriel E., Sharma, Aarushi, John, John St, Tang, Catherina, Tzou, Abe, Young, Leilani, Haque, Imran S., Putcha, Girish

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Navigating and mining modENCODE data von Boley, Nathan, Wan, Kenneth H., Bickel, Peter J., Celniker, Susan E.

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Genome-guided transcript assembly from integrative analysis of RNA sequence data von Boley, Nathan, Stoiber, Marcus H., Booth, Benjamin W., Wan, Kenneth H., Hoskins, Roger A., Bickel, Peter J., Celniker, Susan E., Brown, James B.

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SUBSAMPLING METHODS FOR GENOMIC INFERENCE von Bickel, Peter J., Boley, Nathan, Brown, James B., Huang, Haiyan, Zhang, Nancy R.

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