A proximity proteomics pipeline with improved reproducibility and throughput von Zhong, Xiaofang, Li, Qiongyu, Polacco, Benjamin J, Patil, Trupti, Marley, Aaron, Foussard, Helene, Khare, Prachi, Vartak, Rasika, Xu, Jiewei, DiBerto, Jeffrey F, Roth, Bryan L, Eckhardt, Manon, von Zastrow, Mark, Krogan, Nevan J, Hüttenhain, Ruth

Volltext

Malaria exposure remodels the plasma proteome of Ghanaian children von Mohammed, Aisha M, Olwal, Charles Ochieng', Fossati, Andrea, Nyakoe, Nancy K, Fabius, Jacqueline M, Gordon, Martin, Polacco, Benjamin J, Swaney, Danielle L, Awandare, Gordon A, Krogan, Nevan J, Bouhaddou, Mehdi, Bediako, Yaw

Volltext

Automated discovery of 3D motifs for protein function annotation von Polacco, Benjamin J., Babbitt, Patricia C.

Volltext

Signaling Modulation Mediated by Ligand Water Interactions with the Sodium Site at μOR von Ople, Rohini S., Ramos-Gonzalez, Nokomis, Li, Qiongyu, Sobecks, Briana L., Aydin, Deniz, Powers, Alexander S., Faouzi, Abdelfattah, Polacco, Benjamin J., Bernhard, Sarah M., Appourchaux, Kevin, Sribhashyam, Sashrik, Eans, Shainnel O., Tsai, Bowen A., Dror, Ron O., Varga, Balazs R., Wang, Haoqing, Hüttenhain, Ruth, McLaughlin, Jay P., Majumdar, Susruta

Volltext

De novo protein identification in mammalian sperm using in situ cryoelectron tomography and AlphaFold2 docking von Chen, Zhen, Shiozaki, Momoko, Haas, Kelsey M, Skinner, Will M, Zhao, Shumei, Guo, Caiying, Polacco, Benjamin J, Yu, Zhiheng, Krogan, Nevan J, Lishko, Polina V, Kaake, Robyn M, Vale, Ronald D, Agard, David A

Volltext

Profiling the proximal proteome of the activated μ-opioid receptor von Polacco, Benjamin J., Lobingier, Braden T., Blythe, Emily E., Abreu, Nohely, Khare, Prachi, Howard, Matthew K., Gonzalez-Hernandez, Alberto J., Xu, Jiewei, Li, Qiongyu, Novy, Brandon, Naing, Zun Zar Chi, Shoichet, Brian K., Coyote-Maestas, Willow, Levitz, Joshua, Krogan, Nevan J., Von Zastrow, Mark, Hüttenhain, Ruth

Volltext

Impact of SARS-CoV-2 ORF6 and its variant polymorphisms on host responses and viral pathogenesis von Kehrer, Thomas, Cupic, Anastasija, Ye, Chengjin, Yildiz, Soner, Bouhaddou, Mehdi, Crossland, Nicholas A., Barrall, Erika A., Cohen, Phillip, Tseng, Anna, Çağatay, Tolga, Rathnasinghe, Raveen, Flores, Daniel, Jangra, Sonia, Alam, Fahmida, Mena, Ignacio, Aslam, Sadaf, Saqi, Anjali, Rutkowska, Magdalena, Ummadi, Manisha R., Pisanelli, Giuseppe, Richardson, R. Blake, Veit, Ethan C., Fabius, Jacqueline M., Soucheray, Margaret, Polacco, Benjamin J., Ak, Baran, Marin, Arturo, Evans, Matthew J., Swaney, Danielle L., Gonzalez-Reiche, Ana S., Sordillo, Emilia M., van Bakel, Harm, Simon, Viviana, Zuliani-Alvarez, Lorena, Fontoura, Beatriz M.A., Rosenberg, Brad R., Krogan, Nevan J., Martinez-Sobrido, Luis, García-Sastre, Adolfo, Miorin, Lisa

Volltext

Brahma safeguards canalization of cardiac mesoderm differentiation von Hota, Swetansu K., Rao, Kavitha S., Blair, Andrew P., Khalilimeybodi, Ali, Hu, Kevin M., Thomas, Reuben, So, Kevin, Kameswaran, Vasumathi, Xu, Jiewei, Polacco, Benjamin J., Desai, Ravi V., Chatterjee, Nilanjana, Hsu, Austin, Muncie, Jonathon M., Blotnick, Aaron M., Winchester, Sarah A. B., Weinberger, Leor S., Hüttenhain, Ruth, Kathiriya, Irfan S., Krogan, Nevan J., Saucerman, Jeffrey J., Bruneau, Benoit G.

Volltext

Protein Interaction Map of APOBEC3 Enzyme Family Reveals Deamination-Independent Role in Cellular Function von Jang, Gwendolyn M., Annan Sudarsan, Arun Kumar, Shayeganmehr, Arzhang, Prando Munhoz, Erika, Lao, Reanna, Gaba, Amit, Granadillo Rodríguez, Milaid, Love, Robin P., Polacco, Benjamin J., Zhou, Yuan, Krogan, Nevan J., Kaake, Robyn M., Chelico, Linda

Volltext

Data-Independent Acquisition Protease-Multiplexing Enables Increased Proteome Sequence Coverage Across Multiple Fragmentation Modes von Richards, Alicia L, Chen, Kuei-Ho, Wilburn, Damien B, Stevenson, Erica, Polacco, Benjamin J, Searle, Brian C, Swaney, Danielle L

Volltext

A global view of structure–function relationships in the tautomerase superfamily von Davidson, Rebecca, Baas, Bert-Jan, Akiva, Eyal, Holliday, Gemma L., Polacco, Benjamin J., LeVieux, Jake A., Pullara, Collin R., Zhang, Yan Jessie, Whitman, Christian P., Babbitt, Patricia C.

Volltext

Quantitative Proteomic Analysis Reveals apoE4-Dependent Phosphorylation of the Actin-Regulating Protein VASP von Cakir, Zeynep, Lord, Samuel J., Zhou, Yuan, Jang, Gwendolyn M., Polacco, Benjamin J., Eckhardt, Manon, Jimenez-Morales, David, Newton, Billy W., Orr, Adam L., Johnson, Jeffrey R., da Cruz, Alexandre, Mullins, R. Dyche, Krogan, Nevan J., Mahley, Robert W., Swaney, Danielle L.

Volltext

A strategy for large-scale comparison of evolutionary- and reaction-based classifications of enzyme function von Holliday, Gemma L, Brown, Shoshana D, Mischel, David, Polacco, Benjamin J, Babbitt, Patricia C

Volltext

Organic and inorganic mercurials have distinct effects on cellular thiols, metal homeostasis, and Fe-binding proteins in Escherichia coli von LaVoie, Stephen P., Mapolelo, Daphne T., Cowart, Darin M., Polacco, Benjamin J., Johnson, Michael K., Scott, Robert A., Miller, Susan M., Summers, Anne O.

Volltext

Discovering Mercury Protein Modifications in Whole Proteomes Using Natural Isotope Distributions Observed in Liquid Chromatography-Tandem Mass Spectrometry von Polacco, Benjamin J., Purvine, Samuel O., Zink, Erika M., LaVoie, Stephen P., Lipton, Mary S., Summers, Anne O., Miller, Susan M.

Volltext

The Global Phosphorylation Landscape of SARS-CoV-2 Infection von Bouhaddou, Mehdi, Memon, Danish, Meyer, Bjoern, White, Kris M., Rezelj, Veronica V., Correa Marrero, Miguel, Polacco, Benjamin J., Melnyk, James E., Ulferts, Svenja, Kaake, Robyn M., Batra, Jyoti, Richards, Alicia L., Stevenson, Erica, Gordon, David E., Rojc, Ajda, Obernier, Kirsten, Fabius, Jacqueline M., Soucheray, Margaret, Miorin, Lisa, Moreno, Elena, Koh, Cassandra, Tran, Quang Dinh, Hardy, Alexandra, Robinot, Rémy, Vallet, Thomas, Nilsson-Payant, Benjamin E., Hernandez-Armenta, Claudia, Dunham, Alistair, Weigang, Sebastian, Knerr, Julian, Modak, Maya, Quintero, Diego, Zhou, Yuan, Dugourd, Aurelien, Valdeolivas, Alberto, Patil, Trupti, Li, Qiongyu, Hüttenhain, Ruth, Cakir, Merve, Muralidharan, Monita, Kim, Minkyu, Jang, Gwendolyn, Tutuncuoglu, Beril, Hiatt, Joseph, Guo, Jeffrey Z., Xu, Jiewei, Bouhaddou, Sophia, Mathy, Christopher J.P., Gaulton, Anna, Manners, Emma J., Félix, Eloy, Shi, Ying, Goff, Marisa, Lim, Jean K., McBride, Timothy, O’Neal, Michael C., Cai, Yiming, Chang, Jason C.J., Broadhurst, David J., Klippsten, Saker, De wit, Emmie, Leach, Andrew R., Kortemme, Tanja, Shoichet, Brian, Ott, Melanie, Saez-Rodriguez, Julio, tenOever, Benjamin R., Mullins, R. Dyche, Fischer, Elizabeth R., Kochs, Georg, Grosse, Robert, García-Sastre, Adolfo, Vignuzzi, Marco, Johnson, Jeffery R., Shokat, Kevan M., Swaney, Danielle L., Beltrao, Pedro, Krogan, Nevan J.

Volltext

A SARS-CoV-2 protein interaction map reveals targets for drug repurposing von Gordon, David E, Jang, Gwendolyn M, Bouhaddou, Mehdi, Xu, Jiewei, Obernier, Kirsten, White, Kris M, O'Meara, Matthew J, Rezelj, Veronica V, Guo, Jeffrey Z, Swaney, Danielle L, Tummino, Tia A, Hüttenhain, Ruth, Kaake, Robyn M, Richards, Alicia L, Tutuncuoglu, Beril, Foussard, Helene, Batra, Jyoti, Haas, Kelsey, Modak, Maya, Kim, Minkyu, Haas, Paige, Polacco, Benjamin J, Braberg, Hannes, Fabius, Jacqueline M, Eckhardt, Manon, Soucheray, Margaret, Bennett, Melanie J, Cakir, Merve, McGregor, Michael J, Li, Qiongyu, Meyer, Bjoern, Roesch, Ferdinand, Vallet, Thomas, Mac Kain, Alice, Miorin, Lisa, Moreno, Elena, Naing, Zun Zar Chi, Zhou, Yuan, Peng, Shiming, Shi, Ying, Zhang, Ziyang, Shen, Wenqi, Kirby, Ilsa T, Melnyk, James E, Chorba, John S, Lou, Kevin, Dai, Shizhong A, Barrio-Hernandez, Inigo, Memon, Danish, Hernandez-Armenta, Claudia, Lyu, Jiankun, Mathy, Christopher J P, Perica, Tina, Pilla, Kala Bharath, Ganesan, Sai J, Saltzberg, Daniel J, Rakesh, Ramachandran, Liu, Xi, Rosenthal, Sara B, Calviello, Lorenzo, Venkataramanan, Srivats, Liboy-Lugo, Jose, Lin, Yizhu, Huang, Xi-Ping, Liu, YongFeng, Wankowicz, Stephanie A, Bohn, Markus, Safari, Maliheh, Ugur, Fatima S, Koh, Cassandra, Savar, Nastaran Sadat, Tran, Quang Dinh, Shengjuler, Djoshkun, Fletcher, Sabrina J, O'Neal, Michael C, Cai, Yiming, Chang, Jason C J, Broadhurst, David J, Klippsten, Saker, Sharp, Phillip P, Wenzell, Nicole A, Kuzuoglu-Ozturk, Duygu, Wang, Hao-Yuan, Trenker, Raphael, Young, Janet M, Cavero, Devin A, Hiatt, Joseph, Roth, Theodore L, Rathore, Ujjwal, Subramanian, Advait, Noack, Julia, Hubert, Mathieu, Stroud, Robert M, Frankel, Alan D, Rosenberg, Oren S, Verba, Kliment A, Agard, David A, Ott, Melanie, Emerman, Michael, Jura, Natalia

Volltext

Superfamily active site templates von Meng, Elaine C., Polacco, Benjamin J., Babbitt, Patricia C.

Volltext

SARS-CoV-2 variants evolve convergent strategies to remodel the host response von Bouhaddou, Mehdi, Reuschl, Ann-Kathrin, Polacco, Benjamin J., Thorne, Lucy G., Ummadi, Manisha R., Ye, Chengjin, Rosales, Romel, Pelin, Adrian, Batra, Jyoti, Jang, Gwendolyn M., Xu, Jiewei, Moen, Jack M., Richards, Alicia L., Zhou, Yuan, Harjai, Bhavya, Stevenson, Erica, Rojc, Ajda, Ragazzini, Roberta, Whelan, Matthew V.X., Furnon, Wilhelm, De Lorenzo, Giuditta, Cowton, Vanessa, Syed, Abdullah M., Ciling, Alison, Deutsch, Noa, Pirak, Daniel, Dowgier, Giulia, Mesner, Dejan, Turner, Jane L., McGovern, Briana L., Rodriguez, M. Luis, Leiva-Rebollo, Rocio, Dunham, Alistair S., Zhong, Xiaofang, Eckhardt, Manon, Fossati, Andrea, Liotta, Nicholas F., Kehrer, Thomas, Cupic, Anastasija, Rutkowska, Magdalena, Mena, Ignacio, Aslam, Sadaf, Hoffert, Alyssa, Foussard, Helene, Olwal, Charles Ochieng’, Huang, Weiqing, Zwaka, Thomas, Pham, John, Lyons, Molly, Donohue, Laura, Griffin, Aliesha, Nugent, Rebecca, Holden, Kevin, Deans, Robert, Aviles, Pablo, Lopez-Martin, Jose A., Jimeno, Jose M., Obernier, Kirsten, Fabius, Jacqueline M., Soucheray, Margaret, Hüttenhain, Ruth, Jungreis, Irwin, Kellis, Manolis, Echeverria, Ignacia, Verba, Kliment, Bonfanti, Paola, Beltrao, Pedro, Sharan, Roded, Doudna, Jennifer A., Martinez-Sobrido, Luis, Patel, Arvind H., Palmarini, Massimo, Miorin, Lisa, White, Kris, Swaney, Danielle L., Garcia-Sastre, Adolfo, Jolly, Clare, Zuliani-Alvarez, Lorena, Towers, Greg J., Krogan, Nevan J.

Volltext

De novo protein identification in mammalian sperm using in situ cryo-electron tomography and AlphaFold2 docking von Chen, Zhen, Shiozaki, Momoko, Haas, Kelsey M., Skinner, Will M., Zhao, Shumei, Guo, Caiying, Polacco, Benjamin J., Yu, Zhiheng, Krogan, Nevan J., Lishko, Polina V., Kaake, Robyn M., Vale, Ronald D., Agard, David A.

Volltext